WorldWideScience

Sample records for current molecular taxonomy

  1. Current status of the genetics and molecular taxonomy of Echinococcus species.

    Science.gov (United States)

    McManus, D P

    2013-11-01

    The taxonomy of Echinococcus has long been controversial. Based mainly on differences in morphology and host-parasite specificity characteristics, 16 species and 13 subspecies were originally described. Subsequently, most of these taxa were regarded as synonyms for Echinococcus granulosus and only 4 valid species were recognised: E. granulosus; E. multilocularis; E. oligarthrus and E. vogeli. But, over the past 50 years, laboratory and field observations have revealed considerable phenotypic variability between isolates of Echinococcus, particularly those of E. granulosus, which include differences in: morphology in both larval and adult stages, development in vitro and in vivo, host infectivity and specificity, chemical composition, metabolism, proteins and enzymes, pathogenicity and antigenicity. The application of molecular tools has revealed differences in nucleic acid sequences that reflect this phenotypic variation and the genetic and phenotypic characteristics complement the previous observations made by the descriptive parasitologists many years ago. The fact that some of these variants or strains are poorly or not infective to humans has resulted in a reappraisal of the public health significance of Echinococcus in areas where such variants occur. A revised taxonomy for species in the Echinococcus genus has been proposed that is generally accepted, and is based on the new molecular data and the biological and epidemiological characteristics of host-adapted species and strains.

  2. Clinical and Laboratory Features of the Nocardia spp. Based on Current Molecular Taxonomy

    Science.gov (United States)

    Brown-Elliott, Barbara A.; Brown, June M.; Conville, Patricia S.; Wallace, Richard J.

    2006-01-01

    The recent explosion of newly described species of Nocardia results from the impact in the last decade of newer molecular technology, including PCR restriction enzyme analysis and 16S rRNA sequencing. These molecular techniques have revolutionized the identification of the nocardiae by providing rapid and accurate identification of recognized nocardiae and, at the same time, revealing new species and a number of yet-to-be-described species. There are currently more than 30 species of nocardiae of human clinical significance, with the majority of isolates being N. nova complex, N. abscessus, N. transvalensis complex, N. farcinica, N. asteroides type VI (N. cyriacigeorgica), and N. brasiliensis. These species cause a wide variety of diseases and have variable drug susceptibilities. Accurate identification often requires referral to a reference laboratory with molecular capabilities, as many newer species are genetically distinct from established species yet have few or no distinguishing phenotypic characteristics. Correct identification is important in deciding the clinical relevance of a species and in the clinical management and treatment of patients with nocardial disease. This review characterizes the currently known pathogenic species of Nocardia, including clinical disease, drug susceptibility, and methods of identification. PMID:16614249

  3. Current and pending taxonomy of the Pasteurellaceae

    DEFF Research Database (Denmark)

    Angen, Øystein

    Since the family Pasteurellaceae was established in 1981 the taxonomy of this group of bacteria has undergone significant changes. 16S DNA sequencing showed in the early 1990-ties, that the three original genera were genetically heterogeneous. Presently, the family consists of 13 genetically cohe...

  4. A critique of current methods in nematode taxonomy | Abebe ...

    African Journals Online (AJOL)

    In the past few decades, there have been efforts to integrate molecular methods and digital 3D image-capturing technology in nematode taxonomy, the former to enhance the accuracy of identification of such a taxonomically challenging group and the latter to communicate morphological data. While the employment of ...

  5. Current taxonomy of phages infecting lactic acid bacteria

    Directory of Open Access Journals (Sweden)

    Jennifer eMahony

    2014-01-01

    Full Text Available Phages infecting lactic acid bacteria have been the focus of significant research attention over the past three decades. Through the isolation and characterization of hundreds of phage isolates, it has been possible to classify phages of the dairy starter and adjunct bacteria Lactococus lactis, Streptococcus thermophilus, Leuconostoc spp. and Lactobacillus spp. Among these, phages of L. lactis have been most thoroughly scrutinized and serve as an excellent model system to address issues that arise when attempting taxonomic classification of phages infecting other LAB species. Here, we present an overview of the current taxonomy of phages infecting LAB genera of industrial significance, the methods employed in these taxonomic efforts and how these may be employed for the taxonomy of phages of currently underrepresented and emerging phage species.

  6. Canine babesiosis: from molecular taxonomy to control

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    Irwin Peter J

    2009-03-01

    Full Text Available Abstract Canine babesiosis is a clinically significant emerging vector-borne disease caused by protozoan haemoparasites. This review article considers recent literature pertaining to the taxonomic classification of Babesia and Theileria species affecting dogs and the geographical distribution of these parasites. The diagnosis of canine babesiosis by traditional, molecular and serological methods is reviewed, together with recent advances in our understanding of the pathophysiology of piroplasmosis, and of the treatment and prevention of this disease.

  7. Questioning current practice in brown bear, Ursus arctos, conservation in Europe that undervalues taxonomy

    Energy Technology Data Exchange (ETDEWEB)

    Gippoliti, S.

    2016-07-01

    The present paper highlights problems associated with the currently–accepted taxonomy of brown bear, Ursus arctos, and their consequences for conservation at the European level. The enormous morphological variability within Ursus arctos is not acknowledged in current taxonomy and conservation practice. Seven major clades are recognized in Ursus arctos by molecular researchers, and although Western Europe maintains most of the populations belonging to the relict Clade 1 brown bear lineage, no reference to this is made in current conservation policy. Furthermore, the tiny population of Apennine brown bears, characterized by unique skull morphology, is not even recognized as a distinct ESU (evolutionari significant unit) by current European legislation, nor is it included in the IUCN Red List. This may have serious consequences as brown bear conservation in Western Europe has been mainly based on restocking and reintroduction programs. (Author)

  8. A Systems Approach to Refine Disease Taxonomy by Integrating Phenotypic and Molecular Networks

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    Xuezhong Zhou

    2018-05-01

    Full Text Available The International Classification of Diseases (ICD relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles. With statistical validations from phenotype-genotype associations and interactome networks, we demonstrate that NCD improves disease specificity owing to its overlapping categories and polyhierarchical structure. Furthermore, NCD captures the molecular diversity of diseases and defines clearer boundaries in terms of both phenotypic similarity and molecular associations, establishing a rational strategy to reform disease taxonomy. Keywords: Disease taxonomy, Network medicine, Disease phenotypes, Molecular profiles, Precision medicine

  9. Taxonomy and biology of proteocephalidean cestodes: current state and perspectives

    Czech Academy of Sciences Publication Activity Database

    Scholz, Tomáš; de Chambrier, A.

    2003-01-01

    Roč. 40, č. 2 (2003), s. 65-75 ISSN 0440-6605 R&D Projects: GA ČR GA524/01/1314 Institutional research plan: CEZ:AV0Z6022909 Keywords : Proteocephalidea * taxonomy * phylogeny Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 0.474, year: 2003

  10. Advances in molecular identification, taxonomy, genetic variation and diagnosis of Toxocara spp.

    Science.gov (United States)

    Chen, Jia; Zhou, Dong-Hui; Nisbet, Alasdair J; Xu, Min-Jun; Huang, Si-Yang; Li, Ming-Wei; Wang, Chun-Ren; Zhu, Xing-Quan

    2012-10-01

    The genus Toxocara contains parasitic nematodes of human and animal health significance, such as Toxocara canis, Toxocara cati and Toxocara vitulorum. T. canis and T. cati are among the most prevalent parasites of dogs and cats with a worldwide distribution. Human infection with T. canis and T. cati, which can cause a number of clinical manifestations such as visceral larva migrans (VLMs), ocular larva migrans (OLMs), eosinophilic meningoencephalitis (EME), covert toxocariasis (CT) and neurotoxocariasis, is considered the most prevalent neglected helminthiasis in industrialized countries. The accurate identification Toxocara spp. and their unequivocal differentiation from each other and from other ascaridoid nematodes causing VLMs and OLMs has important implications for studying their taxonomy, epidemiology, population genetics, diagnosis and control. Due to the limitations of traditional (morphological) approaches for identification and diagnosis of Toxocara spp., PCR-based techniques utilizing a range of genetic markers in the nuclear and mitochondrial genomes have been developed as useful alternative approaches because of their high sensitivity, specificity, rapidity and utility. In this article, we summarize the current state of knowledge and advances in molecular identification, taxonomy, genetic variation and diagnosis of Toxocara spp. with prospects for further studies. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution History

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    N.L.P Indi Dharmayanti

    2011-03-01

    Full Text Available Phylogenetic is described as taxonomy classification of an organism based on its evolution history namely its phylogeny and as a part of systematic science that has objective to determine phylogeny of organism according to its characteristic. Phylogenetic analysis from amino acid and protein usually became important area in sequence analysis. Phylogenetic analysis can be used to follow the rapid change of a species such as virus. The phylogenetic evolution tree is a two dimensional of a species graphic that shows relationship among organisms or particularly among their gene sequences. The sequence separation are referred as taxa (singular taxon that is defined as phylogenetically distinct units on the tree. The tree consists of outer branches or leaves that represents taxa and nodes and branch represent correlation among taxa. When the nucleotide sequence from two different organism are similar, they were inferred to be descended from common ancestor. There were three methods which were used in phylogenetic, namely (1 Maximum parsimony, (2 Distance, and (3 Maximum likehoood. Those methods generally are applied to construct the evolutionary tree or the best tree for determine sequence variation in group. Every method is usually used for different analysis and data.

  12. Susceptibility profiles of Nocardia isolates based on current taxonomy.

    Science.gov (United States)

    Schlaberg, Robert; Fisher, Mark A; Hanson, Kimberley E

    2014-01-01

    The genus Nocardia has undergone rapid taxonomic expansion in recent years, and an increasing number of species are recognized as human pathogens. Many established species have predictable antimicrobial susceptibility profiles, but sufficient information is often not available for recently described organisms. Additionally, the effectiveness of sulfonamides as first-line drugs for Nocardia has recently been questioned. This led us to review antimicrobial susceptibility patterns for a large number of molecularly identified clinical isolates. Susceptibility results were available for 1,299 isolates representing 39 different species or complexes, including 11 that were newly described, during a 6-year study period. All tested isolates were susceptible to linezolid. Resistance to trimethoprim-sulfamethoxazole (TMP-SMX) was rare (2%) except among Nocardia pseudobrasiliensis (31%) strains and strains of the N. transvalensis complex (19%). Imipenem susceptibility varied for N. cyriacigeorgica and N. farcinica, as did ceftriaxone susceptibility of the N. nova complex. Resistance to more than one of the most commonly used drugs (amikacin, ceftriaxone, TMP-SMX, and imipenem) was highest for N. pseudobrasiliensis (100%), N. transvalensis complex (83%), N. farcinica (68%), N. puris (57%), N. brasiliensis (51%), N. aobensis (50%), and N. amikacinitolerans (43%). Thus, while antimicrobial resistance can often be predicted, susceptibility testing should still be considered when combination therapy is warranted, for less well characterized species or those with variable susceptibility profiles, and for patients with TMP-SMX intolerance.

  13. Taxonomy of Campylobacter, Arcobacter, Helicobacter and related bacteria: current status, future prospects and immediate concerns

    DEFF Research Database (Denmark)

    On, Stephen L.W.

    2001-01-01

    systematics, there remain a number of important issues concerning the classification of various campylobacterial taxa that require careful consideration. Ultimately, these issues are relevant to many working in the field of applied microbiology, including clinicians, veterinarians, epidemiologists...... and taxonomists. The purpose of this article is briefly to review the major developments in the taxonomy of Campylobacter from its inception to the present day; summarize the most recent changes in the field; analyse current topical issues of special relevance to applied microbiologists, including identification...

  14. Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy.

    Science.gov (United States)

    Durand, J-D; Shen, K-N; Chen, W-J; Jamandre, B W; Blel, H; Diop, K; Nirchio, M; Garcia de León, F J; Whitfield, A K; Chang, C-W; Borsa, P

    2012-07-01

    The family Mugilidae comprises mainly coastal marine species that are widely distributed in all tropical, subtropical and temperate seas. Mugilid species are generally considered to be ecologically important and they are a major food resource for human populations in certain parts of the world. The taxonomy and systematics of the Mugilidae are still much debated and based primarily on morphological characters. In this study, we provide the first comprehensive molecular systematic account of the Mugilidae using phylogenetic analyses of nucleotide sequence variation at three mitochondrial loci (16S rRNA, cytochrome oxidase I, and cytochrome b) for 257 individuals from 55 currently recognized species. The study covers all 20 mugilid genera currently recognized as being valid. The family comprises seven major lineages that radiated early on from the ancestor to all current forms. All genera that were represented by two species or more, except Cestraeus, turned out to be paraphyletic or polyphyletic. Thus, the present phylogenetic results generally disagree with the current taxonomy at the genus level and imply that the anatomical characters used for the systematics of the Mugilidae may be poorly informative phylogenetically. The present results should provide a sound basis for a taxonomic revision of the mugilid genera. A proportion of the species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) appear to consist of cryptic species, thus warranting further taxonomic and genetic work at the infra-generic level. Copyright © 2012 Elsevier Inc. All rights reserved.

  15. Taxonomy and molecular epidemiology of Echinococcus granulosus sensu lato.

    Science.gov (United States)

    Romig, T; Ebi, D; Wassermann, M

    2015-10-30

    Echinococcus granulosus, formerly regarded as a single species with a high genotypic and phenotypic diversity, is now recognised as an assemblage of cryptic species, which differ considerably in morphology, development, host specificity (including infectivity/pathogenicity for humans) and other aspects. This diversity is reflected in the mitochondrial and nuclear genomes and has led to the construction of phylogenetic trees and hypotheses on the origin and geographic dispersal of various taxa. Based on phenotypic characters and gene sequences, E. granulosus (sensu lato) has by now been subdivided into E. granulosus sensu stricto (including the formerly identified genotypic variants G1-3), Echinococcus felidis (the former 'lion strain'), Echinococcus equinus (the 'horse strain', genotype G4), Echinococcus ortleppi (the 'cattle strain', genotype G5) and Echinococcus canadensis. The latter species, as recognised here, shows the highest diversity and is composed of the 'camel strain', genotype G6, the 'pig strain', genotype G7, and two 'cervid strains', genotypes G8 and G10. There is debate whether the closely related G6 and G7 should be placed in a separate species, but more morphological and biological data are needed to support or reject this view. In this classification, the application of rules for zoological nomenclature led to the resurrection of old species names, which had before been synonymised with E. granulosus. This nomenclatural subdivision of the agents of cystic echinococcosis (CE) may appear inconvenient for practical applications, especially because molecular tools are needed for identification of the cyst stage, and because retrospective data on 'E. granulosus' are now difficult to interpret without examination of voucher specimens. However, the increased awareness for the diversity of CE agents - now emphasised by species names rather than genotype numbers - has led to a large number of recent studies on this issue and a rapid increase of knowledge

  16. Orobanche caryophyllacea Sm. (Orobanchaceae in Poland: current distribution, taxonomy, plant communities and hosts

    Directory of Open Access Journals (Sweden)

    Renata Piwowarczyk

    2014-09-01

    Full Text Available The paper presents the current distribution of Orobanche caryophyllacea Sm. in Poland based on a critical revision of herbarium and literature data as well as the results of my field studies. The majority of localities are in south and south-eastern Poland: Małopolska Upland, Lublin Upland, Roztocze, Przemyśl Foothills, Pieniny Mts, rarely in the valleys of the Lower Vistula and Oder rivers or Wolin island. The distribution map in Poland is included. The taxonomy, biology and ecology of the species are discussed.

  17. Orobanche flava (Orobanchaceae in Poland: current distribution, taxonomy, hosts and plant communities

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    Piwowarczyk Renata

    2014-06-01

    Full Text Available Orobanche flava is a species of Central European mountain ranges, mainly the Alps and Carpathian Mts. The paper presents the current distribution of O. flava in Poland based on a critical revision of herbarium and literature data as well as results of field investigations conducted between 1999 and 2014. The distribution of species is centered in southern Poland, mainly in the Carpathian Mts., and, sporadically, in the Sudeten Mts. The distribution of O. flava in Poland is mapped. The taxonomy, biology, and ecology are also discussed.

  18. Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics.

    Science.gov (United States)

    Vitecek, Simon; Kučinić, Mladen; Previšić, Ana; Živić, Ivana; Stojanović, Katarina; Keresztes, Lujza; Bálint, Miklós; Hoppeler, Felicitas; Waringer, Johann; Graf, Wolfram; Pauls, Steffen U

    2017-06-06

    Taxonomy offers precise species identification and delimitation and thus provides basic information for biological research, e.g. through assessment of species richness. The importance of molecular taxonomy, i.e., the identification and delimitation of taxa based on molecular markers, has increased in the past decade. Recently developed exploratory tools now allow estimating species-level diversity in multi-locus molecular datasets. Here we use molecular species delimitation tools that either quantify differences in intra- and interspecific variability of loci, or divergence times within and between species, or perform coalescent species tree inference to estimate species-level entities in molecular genetic datasets. We benchmark results from these methods against 14 morphologically readily differentiable species of a well-defined subgroup of the diverse Drusinae subfamily (Trichoptera, Limnephilidae). Using a 3798 bp (6 loci) molecular data set we aim to corroborate a geographically isolated new species by integrating comparative morphological studies and molecular taxonomy. Our results indicate that only multi-locus species delimitation provides taxonomically relevant information. The data further corroborate the new species Drusus zivici sp. nov. We provide differential diagnostic characters and describe the male, female and larva of this new species and discuss diversity patterns of Drusinae in the Balkans. We further discuss potential and significance of molecular species delimitation. Finally we argue that enhancing collaborative integrative taxonomy will accelerate assessment of global diversity and completion of reference libraries for applied fields, e.g., conservation and biomonitoring.

  19. A molecular phylogeny of the Australian huntsman spiders (Sparassidae, Deleninae): implications for taxonomy and social behaviour.

    Science.gov (United States)

    Agnarsson, Ingi; Rayor, Linda S

    2013-12-01

    Huntsman spiders (Sparassidae) are a diverse group with a worldwide distribution, yet are poorly known both taxonomically and phylogenetically. They are particularly diverse in Australia where an endemic lineage, Deleninae, has diversified to form nearly 100 species. One unusual species, Delena cancerides, has been believed to be the sole group-living sparassid. Unlike all of the other subsocial and social spiders which are capture-web based or live in silken tunnels, D. cancerides are non-web building spiders that live in large matrilineal colonies of a single adult female and her offspring from multiple clutches of under the bark of dead trees. Here we report the discovery of two additional prolonged subsocial sparassid species, currently in Eodelena but here formally proposed as a synonomy of Delena (new synonoymy), Delena (Eodelena) lapidicola and D. (E.) melanochelis. We briefly describe their social demographics, behavior, and habitat use. In order to understand the evolutionary relationships among these species, and thus origin of sociality and other traits in this group, we also offer the first molecular phylogeny of Deleninae and relatives. We employ model based phylogenetic analyses on two mtDNA and three nuDNA loci using maximum likelihood and Bayesian methods, including both 'classical' concatenation approach as well as coalescent-based analysis of species trees from gene trees. Our results support the hypothesis that the delenine huntsman spiders are a monophyletic Australian radiation, approximately 23 million year old, and indicate that the current ten genera should be merged to six genera in four clades. Our findings are inconsistent with some relatively recent changes in the taxonomy of Deleninae. The three known group-living delenine species are related and likely represent a single origin of sociality with a single reversal to solitary life-styles. Our results provide strong support for the classical Isopeda, but not for the recent splitting of

  20. Taxonomy of Fungi Causing Mucormycosis and Entomophthoramycosis (Zygomycosis) and Nomenclature of the Disease: Molecular Mycologic Perspectives

    Science.gov (United States)

    2012-01-01

    Molecular phylogenetic analysis confirmed the phylum Zygomycota to be polyphyletic, and the taxa conventionally classified in Zygomycota are now distributed among the new phylum Glomeromycota and 4 subphyla incertae sedis (uncertain placement). Because the nomenclature of the disease zygomycosis was based on the phylum Zygomycota (Zygomycetes) in which the etiologic agents had been classified, the new classification profoundly affects the name of the disease. Zygomycosis was originally described as a convenient and inclusive name for 2 clinicopathologically different diseases, mucormycosis caused by members of Mucorales and entomophthoramycosis caused by species in the order Entomophthorales of Zygomycota. Without revision of original definition, the name “zygomycosis,” however, has more often been used as a synonym only for mucormycosis. This article reviews the progress and changes in taxonomy and nomenclature of Zygomycota and the disease zygomycosis. The article also reiterates the reasons why the classic names “mucormycosis” and “entomophthoramycosis” are more appropriate than “zygomycosis.” PMID:22247451

  1. Taxonomy, phylogeny and molecular epidemiology of Echinococcus multilocularis: From fundamental knowledge to health ecology.

    Science.gov (United States)

    Knapp, Jenny; Gottstein, Bruno; Saarma, Urmas; Millon, Laurence

    2015-10-30

    Alveolar echinococcosis, caused by the tapeworm Echinococcus multilocularis, is one of the most severe parasitic diseases in humans and represents one of the 17 neglected diseases prioritised by the World Health Organisation (WHO) in 2012. Considering the major medical and veterinary importance of this parasite, the phylogeny of the genus Echinococcus is of considerable importance; yet, despite numerous efforts with both mitochondrial and nuclear data, it has remained unresolved. The genus is clearly complex, and this is one of the reasons for the incomplete understanding of its taxonomy. Although taxonomic studies have recognised E. multilocularis as a separate entity from the Echinococcus granulosus complex and other members of the genus, it would be premature to draw firm conclusions about the taxonomy of the genus before the phylogeny of the whole genus is fully resolved. The recent sequencing of E. multilocularis and E. granulosus genomes opens new possibilities for performing in-depth phylogenetic analyses. In addition, whole genome data provide the possibility of inferring phylogenies based on a large number of functional genes, i.e. genes that trace the evolutionary history of adaptation in E. multilocularis and other members of the genus. Moreover, genomic data open new avenues for studying the molecular epidemiology of E. multilocularis: genotyping studies with larger panels of genetic markers allow the genetic diversity and spatial dynamics of parasites to be evaluated with greater precision. There is an urgent need for international coordination of genotyping of E. multilocularis isolates from animals and human patients. This could be fundamental for a better understanding of the transmission of alveolar echinococcosis and for designing efficient healthcare strategies. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Towards a molecular taxonomy for protists: benefits, risks, and applications in plankton ecology.

    Science.gov (United States)

    Caron, David A

    2013-01-01

    The increasing use of genetic information for the development of methods to study the diversity, distributions, and activities of protists in nature has spawned a new generation of powerful tools. For ecologists, one lure of these approaches lies in the potential for DNA sequences to provide the only immediately obvious means of normalizing the diverse criteria that presently exist for identifying and counting protists. A single, molecular taxonomy would allow studies of diversity across a broad range of species, as well as the detection and quantification of particular species of interest within complex, natural assemblages; goals that are not feasible using traditional methods. However, these advantages are not without their potential pitfalls and problems. Conflicts involving the species concept, disagreements over the true (physiological/ecological) meaning of genetic diversity, and a perceived threat by some that sequence information will displace knowledge regarding the morphologies, functions and physiologies of protistan taxa, have created debate and doubt regarding the efficacy and appropriateness of some genetic approaches. These concerns need continued discussion and eventual resolution as we move toward the irresistible attraction, and potentially enormous benefits, of the application of genetic approaches to protistan ecology. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.

  3. Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?

    Science.gov (United States)

    Viscogliosi, E.; Edgcomb, V. P.; Gerbod, D.; Noel, C.; Delgado-Viscogliosi, P.; Sogin, M. L. (Principal Investigator)

    1999-01-01

    The Parabasala are a primitive group of protists divided into two classes: the trichomonads and the hypermastigids. Until recently, phylogeny and taxonomy of parabasalids were mainly based on the comparative analysis of morphological characters primarily linked to the development of their cytoskeleton. Recent use of molecular markers, such as small subunit (SSU) rRNA has led to now insights into the systematics of the Parabasala and other groups of prolists. An updated phylogeny based on SSU rRNA is provided and compared to that inferred from ultrastructural data. The SSU rRNA phylogeny contradicts the dogma equating simple characters with pumitive characters. Hypermastigids, possessing a hyperdeveloped cytoskeleton, exhibit the most basal emergence in the parabasalid lineage. Other observations emerge from the SSU rRNA analysis, such as the secondary loss of some cytoskeleton structures in all representatives of the Monocercomonadidae, the existence of secondarily free living taxa (reversibility of parasitism) and the evidence against the co-evolution of the endobiotic parabasalids and their animal hosts. According to phylogenies based on SSU rRNA, all the trichomonad families are not monophyletic groups, putting into question the validity of current taxonomic assignments. The precise branching order of some taxa remains unclear, but this issue can possibly be addressed by the molecular analysis of additional parabasalids. The goal of such additional analyses would be to propose, in a near future, a revision of the taxonomy of this group of protists that takes into account both molecular and morphological data.

  4. Molecular taxonomy of scopulariopsis-like fungi with description of new clinical and environmental species

    NARCIS (Netherlands)

    Jagielski, Tomasz; Sandoval-Denis, Marcelo; Yu, Jin; Yao, Limin; Bakuła, Zofia; Kalita, Joanna; Skóra, Magdalena; Krzyściak, Paweł; de Hoog, G Sybren; Guarro, Josep; Gené, Josepa

    The taxonomy of scopulariopsis-like fungi, comprising numerous human opportunistic species, has recently been reassessed with delineation of the genera Microascus, Pithoascus, Pseudoscopulariopsis, and Scopulariopsis, using morphological data and multilocus sequence analysis based on four loci (ITS,

  5. My home is my bazaar - A taxonomy and classification of current wireless home network protocols

    DEFF Research Database (Denmark)

    Torbensen, Rune; Hansen, Klaus Marius; Hjorth, Theis Solberg

    2011-01-01

    to considerable challenges for developers and integrators in understanding and choosing between the available wireless technologies. To further increase technology adoption and improve business risk assessments, it is necessary to determine the important properties of the technologies in order to compare them......, cost, security, etc. Third, a classification based on the taxonomy and the collected data is presented. In the final discussion, we identify a number of key aspects that could be important technology criteria for future development of home automation protocols....

  6. Taxonomy of Cyrtochilum-alliance (Orchidaceae) in the light of molecular and morphological data

    Czech Academy of Sciences Publication Activity Database

    Szlachetko, D. L.; Kolanowska, Marta; Naczk, A.; Gorniak, M.; Dudek, M.; Rutkowski, P.; Chiron, G.

    2017-01-01

    Roč. 58, JAN (2017), č. článku 8. ISSN 1999-3110 Institutional support: RVO:86652079 Keywords : ribosomal-rna genes * hybrid speciation * chloroplast dna * allopolyploid speciation * reconstructing patterns * phylogenetic inference * reticulate evolution * concerted evolution * horizontal transfer * sequence alignment * Cyrtochilum * Monophyly * New combinations * New species * Oncidiinae * Paraphyly * Taxonomy Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 1.452, year: 2016

  7. The Taxonomy for Learning, Teaching and Assessing: Current Practices at Polytechnics in Bangladesh and its Effects in Developing Students' Competences

    Directory of Open Access Journals (Sweden)

    Faruque A. Haolader

    2015-09-01

    Full Text Available Polytechnics in Bangladesh endeavour to produce quality graduates for national and international job markets. The quality of graduates depends on several factors. This study examines the implementation process of the polytechnic curriculum with the objectives of determining the current level of practices in learn-ing/teaching material design, in delivering curriculum content, in assessing students and its effect on students' competence development. Data was collected through observation, opinion survey and competence test. Qualitative and quantitative methodologies were used for data interpretation and analysis in this descriptive type of research study. Findings revealed that the learning materials are mainly theory oriented and mostly cover those contents usually common in exams. About half of teachers are aware of the taxonomy for learning, teaching and assessing, but they rarely put importance on it. In the classroom, teachers spend only a little time for delivering content at the level of apply/analyse. However, a significant number of tasks performed in labs are practical and occupation relevant and can be classified at higher levels of the taxonomy. In student assessment, the test-items assess mainly theoretical knowledge at the level of remember. The effect of these practices is reflected in demonstrating student performance in a competence test. The study concludes with some recommendations.

  8. Molecular imaging: current status and emerging strategies

    International Nuclear Information System (INIS)

    Pysz, M.A.; Gambhir, S.S.; Willmann, J.K.

    2010-01-01

    In vivo molecular imaging has a great potential to impact medicine by detecting diseases in early stages (screening), identifying extent of disease, selecting disease- and patient-specific treatment (personalized medicine), applying a directed or targeted therapy, and measuring molecular-specific effects of treatment. Current clinical molecular imaging approaches primarily use positron-emission tomography (PET) or single photon-emission computed tomography (SPECT)-based techniques. In ongoing preclinical research, novel molecular targets of different diseases are identified and, sophisticated and multifunctional contrast agents for imaging these molecular targets are developed along with new technologies and instrumentation for multi-modality molecular imaging. Contrast-enhanced molecular ultrasound (US) with molecularly-targeted contrast microbubbles is explored as a clinically translatable molecular imaging strategy for screening, diagnosing, and monitoring diseases at the molecular level. Optical imaging with fluorescent molecular probes and US imaging with molecularly-targeted microbubbles are attractive strategies as they provide real-time imaging, are relatively inexpensive, produce images with high spatial resolution, and do not involve exposure to ionizing irradiation. Raman spectroscopy/microscopy has emerged as a molecular optical imaging strategy for ultrasensitive detection of multiple biomolecules/biochemicals with both in vivo and ex vivo versatility. Photoacoustic imaging is a hybrid of optical and US techniques involving optically-excitable molecularly-targeted contrast agents and quantitative detection of resulting oscillatory contrast agent movement with US. Current preclinical findings and advances in instrumentation, such as endoscopes and microcatheters, suggest that these molecular imaging methods have numerous potential clinical applications and will be translated into clinical use in the near future.

  9. Speciation in Indo-Pacific swiftlets (Aves: Apodidae): integrating molecular and phenotypic data for a new provisional taxonomy of the Collocalia esculenta complex.

    Science.gov (United States)

    Rheindt, Frank E; Christidis, Les; Norman, Janette A; Eaton, James A; Sadanandan, Keren R; Schodde, Richard

    2017-04-07

    White-bellied swiftlets of the Collocalia esculenta complex constitute a radiation of colony-breeding swifts distributed throughout the tropical Indo-Pacific region. Resolution of their taxonomy is challenging due to their morphological uniformity. To analyze the evolutionary history of this complex, we combine new biometric measurements and results from plumage assessment of museum specimens with novel as well as previously published molecular data. Together, this body of information constitutes the largest systematic dataset for white-bellied swiftlets yet compiled, drawn from 809 individuals belonging to 32 taxa for which new molecular, biometric, and/or plumage data are presented. We propose changing the classification of white-bellied swiftlets, for which two species are currently recognized, to elevate eight regional forms to species level, and we also describe two new subspecies. The ten taxa we recommend recognizing at the species level are: Collocalia linchi (Java to Lombok, Sumatran hills), C. dodgei (montane Borneo), C. natalis (Christmas Island), C. affinis (Greater Sundas, including the Thai-Malay Peninsula and Andaman-Nicobar Islands), C. marginata (Philippines), C. isonota (Philippines), C. sumbawae (west Lesser Sundas), C. neglecta (east Lesser Sundas), C. esculenta (Sulawesi, Moluccas, New Guinea, Bismarck Archipelago, Solomon Islands), and C. uropygialis (Vanuatu, New Caledonia). Future molecular and morphological work is needed to resolve questions of speciation and population affinities in the Philippines, Christmas Island, Wallacea and central Melanesia, and to shed light on historic diversification and patterns of gene flow in the complex.

  10. Taxonomy Icon Data: [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Phaeodactylum tricornutum Phaeodactylum_tricornutum_L.png Phaeodactylum_tricornutum..._NL.png Phaeodactylum_tricornutum_S.png Phaeodactylum_tricornutum_NS.png http://biosciencedbc.jp/taxonomy_ic...on/icon.cgi?i=Phaeodactylum+tricornutum&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Phaeodactylum+tricorn...utum&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Phaeodactylum+tricorn...utum&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Phaeodactylum+tricornutum&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=213 ...

  11. Kinetics of current formation in molecular diode

    International Nuclear Information System (INIS)

    Petrov, Eh.G.; Leonov, V.A.; Shevchenko, E.V.

    2012-01-01

    Based on the kinetic theory of election transfer in low-dimensional molecular systems, the formation of transient and stationary currents in a system 'electrode l-molecule-electrode 2' (molecular diode) is studied for different regimes of charge transmission. In the framework of the HOMO-LUMO molecular model, a situation is considered where the current formation is initiated either by molecule photoexcitation or by change of interelectrode voltage bias. It is found that the distant (tunnel) inelastic electron transfer plays a crucial role in changing molecular electronic states and, as a result, in generating transmission channels for hopping (sequential) and distant (direct) current components. The effect of inelastic tunneling is especially pronounced in the condition of resonant electron transmission.

  12. Revision of the genus Dinotoperla Tillyard, 1921 (Plecoptera: Gripopterygidae) using morphological characters and molecular data: Establishes two new genera, three new species and updates the larval taxonomy.

    Science.gov (United States)

    Mynott, Julia H; Suter, Phillip J; Theischinger, Gunther

    2017-01-23

    The larval taxonomy of Australian stoneflies (Plecoptera) shows a large disparity in knowledge when compared to the adult taxonomy with many species having undescribed larval forms. The importance of stoneflies as an indicator group for monitoring aquatic ecosystems means knowledge of the larval taxonomy and the ability to identify species is essential. This study combined morphology and mitochondrial gene sequences to associate the adult and larval life-stages for species of Dinotoperla Tillyard. Morphological identification of adult males was recognised for 17 of the 35 Dinotoperla species and combining molecular data with morphology confirmed eight new adult-larval life stage associations. Further, molecular data supported the larval taxonomy for five morphospecies which remain unassociated. The combination of molecular and morphological methods enabled the larval morphology to be reassessed for the genus Dinotoperla and this has led to the establishment of two new genera, Odontoperla, gen. nov. and Oedemaperla, gen. nov., and the new species Dinotoperla aryballoi, sp. nov, D. tasmaniensis, sp. nov. and Oedemaperla shackletoni, sp. nov. as well as the new or updated descriptions of the larvae of 31 species and a comprehensive dichotomous key to these larvae.

  13. Taxonomy Icon Data: [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Amborella trichopoda Amborella_trichopoda_L.png Amborella_trichopoda_NL.png Amborella..._trichopoda_S.png Amborella_trichopoda_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Amborella+t...richopoda&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Amborella+trichopoda&t=NL http://biosciencedb...c.jp/taxonomy_icon/icon.cgi?i=Amborella+trichopoda&t=S http://biosciencedbc.jp/ta...xonomy_icon/icon.cgi?i=Amborella+trichopoda&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=13 ...

  14. Evolutionary and geographical history of the Leishmania donovani complex with a revision of current taxonomy

    Czech Academy of Sciences Publication Activity Database

    Lukeš, Julius; Mauricio, I. L.; Schönian, G.; Dujardin, J.-C.; Soteriadou, K.; Dedet, J.-P.; Kuhls, K.; QuispeTintaya, K. W.; Jirků, Milan; Chocholová, Eva; Haralambous, C.; Pratlong, F.; Oborník, Miroslav; Horák, Aleš; Ayala, F. J.; Miles, M. A.

    2007-01-01

    Roč. 104, č. 22 (2007), s. 9375-9380 ISSN 0027-8424 R&D Projects: GA MŠk 2B06129; GA MŠk LC07032 Grant - others:EU(EU) QLK2-CT-2001-01810 Institutional research plan: CEZ:AV0Z60220518 Source of funding: R - rámcový projekt EK Keywords : leishmaniasis * parasitic protozoa * phylogeny * population genetics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.598, year: 2007

  15. Current state of molecular imaging research

    International Nuclear Information System (INIS)

    Grimm, J.; Wunder, A.

    2005-01-01

    The recent years have seen significant advances in both molecular biology, allowing the identification of genes and pathways related to disease, and imaging technologies that allow for improved spatial and temporal resolution, enhanced sensitivity, better depth penetration, improved image processing, and beneficial combinations of different imaging modalities. These advances have led to a paradigm shift in the scope of diagnostic imaging. The traditional role of radiological diagnostic imaging is to define gross anatomy and structure in order to detect pathological abnormalities. Available contrast agents are mostly non-specific and can be used to image physiological processes such as changes in blood volume, flow, and perfusion but not to demonstrate pathological alterations at molecular levels. However, alterations at the anatomical-morphological level are relatively late manifestations of underlying molecular changes. Using molecular probes or markers that bind specifically to molecular targets allows for the non-invasive visualization and quantitation of biological processes such as gene expression, apoptosis, or angiogenesis at the molecular level within intact living organisms. This rapidly evolving, multidisciplinary approach, referred to as molecular imaging, promises to enable early diagnosis, can provide improved classification of stage and severity of disease, an objective assessment of treatment efficacy, and a reliable prognosis. Furthermore, molecular imaging is an important tool for the evaluation of physiological and pathophysiological processes, and for the development of new therapies. This article comprises a review of current technologies of molecular imaging, describes the development of contrast agents and various imaging modalities, new applications in specific disease models, and potential future developments. (orig.)

  16. Molecular taxonomy provides new insights into anopheles species of the neotropical arribalzagia series.

    Directory of Open Access Journals (Sweden)

    Giovan F Gómez

    Full Text Available Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I (COI and nuclear internal transcribed spacer 2 (ITS2 sequences were used to evaluate initial identification and to investigate phylogenetic relationships of seven Anopheles morphospecies of the Arribalzagia Series from Colombia. Phylogenetic trees recovered highly supported clades for An. punctimaculas.s., An. calderoni, An. malefactor s.l., An. neomaculipalpus, An. apicimacula s.l., An. mattogrossensis and An. peryassui. This study provides the first molecular confirmation of An. malefactorfrom Colombia and discovered conflicting patterns of divergence for the molecular markers among specimens from northeast and northern Colombia suggesting the presence of two previously unrecognized Molecular Operational Taxonomic Units (MOTUs. Furthermore, two highly differentiated An. apicimacula MOTUs previously found in Panama were detected. Overall, the combined molecular dataset facilitated the detection of known and new Colombian evolutionary lineages, and constitutes the baseline for future research on their bionomics, ecology and potential role as malaria vectors.

  17. Molecular taxonomy of the two Leishmania vectors Lutzomyia umbratilis and Lutzomyia anduzei (Diptera: Psychodidae) from the Brazilian Amazon.

    Science.gov (United States)

    Scarpassa, Vera Margarete; Alencar, Ronildo Baiatone

    2013-09-11

    Lutzomyia umbratilis (a probable species complex) is the main vector of Leishmania guyanensis in the northern region of Brazil. Lutzomyia anduzei has been implicated as a secondary vector of this parasite. These species are closely related and exhibit high morphological similarity in the adult stage; therefore, they have been wrongly identified, both in the past and in the present. This shows the need for employing integrated taxonomy. With the aim of gathering information on the molecular taxonomy and evolutionary relationships of these two vectors, 118 sequences of 663 base pairs (barcode region of the mitochondrial DNA cytochrome oxidase I - COI) were generated from 72 L. umbratilis and 46 L. anduzei individuals captured, respectively, in six and five localities of the Brazilian Amazon. The efficiency of the barcode region to differentiate the L. umbratilis lineages I and II was also evaluated. The data were analyzed using the pairwise genetic distances matrix and the Neighbor-Joining (NJ) tree, both based on the Kimura Two Parameter (K2P) evolutionary model. The analyses resulted in 67 haplotypes: 32 for L. umbratilis and 35 for L. anduzei. The mean intra-specific genetic distance was 0.008 (0.002 to 0.010 for L. umbratilis; 0.008 to 0.014 for L. anduzei), whereas the mean interspecific genetic distance was 0.044 (0.041 to 0.046), supporting the barcoding gap. Between the L. umbratilis lineages I and II, it was 0.009 to 0.010. The NJ tree analysis strongly supported monophyletic clades for both L. umbratilis and L. anduzei, whereas the L. umbratilis lineages I and II formed two poorly supported monophyletic subclades. The barcode region clearly separated the two species and may therefore constitute a valuable tool in the identification of the sand fly vectors of Leishmania in endemic leishmaniasis areas. However, the barcode region had not enough power to separate the two lineages of L. umbratilis, likely reflecting incipient species that have not yet reached

  18. The impact of culture collections on molecular identification, taxonomy, and solving real problems

    Science.gov (United States)

    Among the fungi, Fusarium has stood out as a major focus for culture collection resource development over the last century. This has facilitated unprecedented molecular taxonomic advancements, which in turn has led to problem solving in plant pathology, mycotoxicology, medical mycology, and basic re...

  19. Advances in taxonomy of genus phoma: polyphyletic nature and role of phenotypic traits and molecular systematics.

    Science.gov (United States)

    Rai, Mahendra Kumar; Tiwari, Vaibhav V; Irinyi, László; Kövics, György János

    2014-06-01

    Phoma is a highly polyphyletic genus with its unclear species boundaries. The conventional system of identification is functional but it has its limitations. Besides morphological studies, chemotaxonomy, secondary metabolite and protein profiling have been assessed for the classification and identification of these fungi. Molecular datasets have provided a better outlook towards the phylogenetic and evolutionary trends of Phoma. Molecular markers such as ITS-rDNA, tubulin, actin, translation elongation factor have been widely used by the taxonomists to demarcate species. However, outcomes gained up till now represent preliminary step towards the study of Phoma systematics and a combined approach would be beneficial in the understanding of this polyphyletic group members. Lately, on the base of molecular phylogeny of the type species of the seven Phoma sections a new teleomorph family, Didymellaceae has been established, besides the Phaeosphaeriaceae related to sect. Paraphoma anamorphs, and the Leptosphaeriaceae to sect. Heterospora anamorphs. The estimated ratio is about 70 % of the recognized Phoma-like species can be associated with the Didymellaceae ascomycetous family.

  20. Gregory Bateson's relevance to current molecular biology

    DEFF Research Database (Denmark)

    Bruni, Luis Emilio

    2008-01-01

    in a developmental pathway. Being a central figure in the development of cybernetic theory he collaborated with a range of researchers from the life sciences who were innovating their own disciplines by introducing cybernetic concepts in their particular fields and disciplines. In the light of this, it should...... not come as a surprise today to realize how the general ideas that he was postulating for the study of communication systems in biology fit so well with the astonishing findings of current molecular biology, for example in the field of cellular signal transduction networks. I guess this is the case due...

  1. Tumor taxonomy for the developmental lineage classification of neoplasms

    International Nuclear Information System (INIS)

    Berman, Jules J

    2004-01-01

    The new 'Developmental lineage classification of neoplasms' was described in a prior publication. The classification is simple (the entire hierarchy is described with just 39 classifiers), comprehensive (providing a place for every tumor of man), and consistent with recent attempts to characterize tumors by cytogenetic and molecular features. A taxonomy is a list of the instances that populate a classification. The taxonomy of neoplasia attempts to list every known term for every known tumor of man. The taxonomy provides each concept with a unique code and groups synonymous terms under the same concept. A Perl script validated successive drafts of the taxonomy ensuring that: 1) each term occurs only once in the taxonomy; 2) each term occurs in only one tumor class; 3) each concept code occurs in one and only one hierarchical position in the classification; and 4) the file containing the classification and taxonomy is a well-formed XML (eXtensible Markup Language) document. The taxonomy currently contains 122,632 different terms encompassing 5,376 neoplasm concepts. Each concept has, on average, 23 synonyms. The taxonomy populates 'The developmental lineage classification of neoplasms,' and is available as an XML file, currently 9+ Megabytes in length. A representation of the classification/taxonomy listing each term followed by its code, followed by its full ancestry, is available as a flat-file, 19+ Megabytes in length. The taxonomy is the largest nomenclature of neoplasms, with more than twice the number of neoplasm names found in other medical nomenclatures, including the 2004 version of the Unified Medical Language System, the Systematized Nomenclature of Medicine Clinical Terminology, the National Cancer Institute's Thesaurus, and the International Classification of Diseases Oncolology version. This manuscript describes a comprehensive taxonomy of neoplasia that collects synonymous terms under a unique code number and assigns each

  2. Overview of the taxonomy of zooxanthellate Scleractinia.

    Science.gov (United States)

    Veron, John

    2013-11-01

    Coral taxonomy has entered a historical phase where nomenclatorial uncertainty is rapidly increasing. The fundamental cause is mandatory adherence to historical monographs that lack essential information of all sorts, and also to type specimens, if they exist at all, that are commonly unrecognizable fragments or are uncharacteristic of the species they are believed to represent. Historical problems, including incorrect subsequent type species designations, also create uncertainty for many well-established genera. The advent of in situ studies in the 1970s revealed these issues; now molecular technology is again changing the taxonomic landscape. The competing methodologies involved must be seen in context if they are to avoid becoming an additional basis for continuing nomenclatorial instability. To prevent this happening, the International Commission on Zoological Nomenclature (ICZN) will need to focus on rules that consolidate well-established nomenclature and allow for the designation of new type specimens that are unambiguous, and which include both skeletal material and soft tissue for molecular study. Taxonomic and biogeographic findings have now become linked, with molecular methodologies providing the capacity to re-visit past taxonomic decisions, and to extend both taxonomy and biogeography into the realm of evolutionary theory. It is proposed that most species will ultimately be seen as operational taxonomic units that are human rather than natural constructs, which in consequence will always have fuzzy morphological, genetic, and distribution boundaries. The pathway ahead calls for the integration of morphological and molecular taxonomies, and for website delivery of information that crosses current discipline boundaries.

  3. TAXONOMY AND GENETIC RELATIONSHIPS OF PANGASIIDAE, ASIAN CATFISHES, BASED ON MORPHOLOGICAL AND MOLECULAR ANALYSES

    Directory of Open Access Journals (Sweden)

    Rudhy Gustiano

    2007-12-01

    Full Text Available Pangasiids are economically important riverine catfishes generally residing in freshwater from the Indian subcontinent to the Indonesian Archipelago. The systematics of this family are still poorly known. Consequently, lack of such basic information impedes the understanding of the biology of the Pangasiids and the study of their aquaculture potential as well as improvement of seed production and growth performance. The objectives of the present study are to clarify phylogeny of this family based on a biometric analysis and molecular evidence using 12S ribosomal mtDNA on the total of 1070 specimens. The study revealed that 28 species are recognised as valid in Pangasiidae. Four genera are also recognized as Helicophagus Bleeker 1858, Pangasianodon Chevey 1930, Pteropangasius Fowler 1937, and Pangasius Valenciennes 1840 instead of two as reported by previous workers. The phylogenetic analysis demonstrated the recognised genera, and genetic relationships among taxa. Overall, trees from the different analyses show similar topologies and confirm the hypothesis derived from geological history, palaeontology, and similar models in other taxa of fishes from the same area. The oldest genus may already have existed when the Asian mainland was still connected to the islands in the southern part about 20 million years ago.

  4. Integrative taxonomy of ciliates: Assessment of molecular phylogenetic content and morphological homology testing.

    Science.gov (United States)

    Vďačný, Peter

    2017-10-01

    The very diverse and comparatively complex morphology of ciliates has given rise to numerous taxonomic concepts. However, the information content of the utilized molecular markers has seldom been explored prior to phylogenetic analyses and taxonomic decisions. Likewise, robust testing of morphological homology statements and the apomorphic nature of diagnostic characters of ciliate taxa is rarely carried out. Four phylogenetic techniques that may help address these issues are reviewed. (1) Split spectrum analysis serves to determine the exact number and quality of nucleotide positions supporting individual nodes in phylogenetic trees and to discern long-branch artifacts that cause spurious phylogenies. (2) Network analysis can depict all possible evolutionary trajectories inferable from the dataset and locate and measure the conflict between them. (3) A priori likelihood mapping tests the suitability of data for reconstruction of a well resolved tree, visualizes the tree-likeness of quartets, and assesses the support of an internal branch of a given tree topology. (4) Reconstruction of ancestral morphologies can be applied for analyzing homology and apomorphy statements without circular reasoning. Since these phylogenetic tools are rarely used, their principles and interpretation are introduced and exemplified using various groups of ciliates. Finally, environmental sequencing data are discussed in this light. Copyright © 2017 The Author. Published by Elsevier GmbH.. All rights reserved.

  5. Molecular Cancer Prevention: Current Status & Future Directions

    Science.gov (United States)

    Maresso, Karen Colbert; Tsai, Kenneth Y.; Brown, Powel H.; Szabo, Eva; Lippman, Scott; Hawk, Ernest

    2016-01-01

    The heterogeneity and complexity of advanced cancers strongly supports the rationale for an enhanced focus on molecular prevention as a priority strategy to reduce the burden of cancer. Molecular prevention encompasses traditional chemopreventive agents as well as vaccinations and therapeutic approaches to cancer-predisposing conditions. Despite challenges to the field, we now have refined insights into cancer etiology and early pathogenesis; successful risk assessment and new risk models; agents with broad preventive efficacy (e.g., aspirin) in common chronic diseases, including cancer; and a successful track record of more than 10 agents approved by the FDA for the treatment of precancerous lesions or cancer risk reduction. The development of molecular preventive agents does not differ significantly from the development of therapies for advanced cancers, yet has unique challenges and special considerations given that it most often involves healthy or asymptomatic individuals. Agents, biomarkers, cohorts, overall design, and endpoints are key determinants of molecular preventive trials, as with therapeutic trials, although distinctions exist for each within the preventive setting. Progress in the development and evolution of molecular preventive agents has been steadier in some organ systems, such as breast and skin, than in others. In order for molecular prevention to be fully realized as an effective strategy, a number of challenges to the field must be addressed. Here we provide a brief overview of the context for and special considerations of molecular prevention along with a discussion of the results of major randomized controlled trials. PMID:26284997

  6. Light-driven molecular current switch

    Czech Academy of Sciences Publication Activity Database

    Nešpůrek, Stanislav; Toman, Petr; Sworakowski, J.; Lipinski, J.

    2002-01-01

    Roč. 2, č. 4 (2002), s. 299-304 ISSN 1567-1739. [Multilateral Symposium between the Korean Academy of Science and Technology and the Foreign Academies. Seoul, 08.05.2002-10.05.2002] R&D Projects: GA AV ČR IAA1050901 Grant - others:GA-(PL) 4T09A 13222 Institutional research plan: CEZ:AV0Z4050913 Keywords : molecular switch * molecular electronics * charge transport Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.117, year: 2002

  7. Asteroid taxonomy

    International Nuclear Information System (INIS)

    Tholen, D.J.

    1989-01-01

    The spectral reflectivity of asteroid surfaces over the wavelength range of 0.3 to 1.1 μm can be used to classify these objects onto several broad groups with similar spectral characteristics. The three most recently developed taxonomies group the asteroids into 9, 11 or 14 different classes, depending on the technique used to perform the analysis. The distribution of the taxonomic classes shows that darker and redder objects become more dominant at larger heliocentric distances, while the rare asteroid types are found more frequently among the small objects of the planet-crossing population

  8. Taxonomy Icon Data: honey bee [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available honey bee Apis mellifera Arthropoda Apis_mellifera_L.png Apis_mellifera_NL.png Apis_mellife...ra_S.png Apis_mellifera_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Apis+mellifera&t=L h...ttp://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Apis+mellifera&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Apis+mellife...ra&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Apis+mellifera&t=NS ...

  9. Taxonomy Icon Data: thale cress [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available thale cress Arabidopsis thaliana Arabidopsis_thaliana_L.png Arabidopsis_thaliana_NL.png Arabidopsis_thal...iana_S.png Arabidopsis_thaliana_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Arabidopsis+thal...iana&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Arabidopsis+thaliana&t=NL http://...biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Arabidopsis+thaliana&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Arabidopsis+thaliana&t=NS ...

  10. Taxonomy Icon Data: sorghum [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available sorghum Sorghum bicolor Sorghum_bicolor_L.png Sorghum_bicolor_NL.png Sorghum_bicolor_S.png Sorg...hum_bicolor_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Sorghum+bicolor&t=L http://b...iosciencedbc.jp/taxonomy_icon/icon.cgi?i=Sorghum+bicolor&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Sorg...hum+bicolor&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Sorghum+bicolor&t=NS ...

  11. Taxonomy Icon Data: fission yeast [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available fission yeast Schizosaccharomyces pombe Schizosaccharomyces_pombe_L.png Schizosaccharomyce...s_pombe_NL.png Schizosaccharomyces_pombe_S.png Schizosaccharomyces_pombe_NS.png http://biosciencedbc....jp/taxonomy_icon/icon.cgi?i=Schizosaccharomyces+pombe&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Schizosaccharomyce...s+pombe&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Schizosaccharomyce...s+pombe&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Schizosaccharomyces+pombe&t=NS

  12. Taxonomy Icon Data: potato [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available potato Solanum tuberosum Solanum_tuberosum_L.png Solanum_tuberosum_NL.png Solanum_tuber...osum_S.png Solanum_tuberosum_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Solanum+tuberosum&t...=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Solanum+tuberosum&t=NL http://biosciencedbc.jp/taxonomy_...icon/icon.cgi?i=Solanum+tuberosum&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Solanum+tuberosum&t=NS ...

  13. Taxonomy Icon Data: Lotus corniculatus [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Lotus corniculatus Lotus corniculatus Lotus_corniculatus_L.png Lotus_corniculatus_NL.png Lotus_corn...iculatus_S.png Lotus_corniculatus_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lotus+corn...iculatus&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lotus+corniculatus&t=NL http://bioscie...ncedbc.jp/taxonomy_icon/icon.cgi?i=Lotus+corniculatus&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lotus+corniculatus&t=NS ...

  14. Taxonomy Icon Data: barrel medic [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available barrel medic Medicago truncatula Medicago_truncatula_L.png Medicago_truncatula_NL.png Medi...cago_truncatula_S.png Medicago_truncatula_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Medi...cago+truncatula&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Medicago+truncatula&t=NL http://biosci...encedbc.jp/taxonomy_icon/icon.cgi?i=Medicago+truncatula&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Medicago+truncatula&t=NS ...

  15. Taxonomy Icon Data: fruit fly [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available fruit fly Drosophila melanogaster Arthropoda Drosophila_melanogaster_L.png Drosophila_mela...nogaster_NL.png Drosophila_melanogaster_S.png Drosophila_melanogaster_NS.png http://biosciencedbc.jp/...taxonomy_icon/icon.cgi?i=Drosophila+melanogaster&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Drosophila+mela...nogaster&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Drosophila+mela...nogaster&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Drosophila+melanogaster&t=NS ...

  16. Taxonomy Icon Data: Lotus japonicus [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Lotus japonicus Lotus japonicus Lotus_japonicus_L.png Lotus_japonicus_NL.png Lotus_japonicus_S.png Lotus_jap...onicus_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lotus+japonicus&t=L ...http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lotus+japonicus&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lotus+jap...onicus&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lotus+japonicus&t=NS ...

  17. Taxonomy Icon Data: Japanese Ratsnake [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Japanese Ratsnake Elaphe climacophora Chordata/Vertebrata/Reptilia/etc Elaphe_climacophora_L.png Elaphe_clim...acophora_NL.png Elaphe_climacophora_S.png Elaphe_climacophora_NS.png http://bioscie...ncedbc.jp/taxonomy_icon/icon.cgi?i=Elaphe+climacophora&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Elaphe+clima...cophora&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Elaphe+clima...cophora&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Elaphe+climacophora&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=3 ...

  18. Taxonomy Icon Data: Trypanosoma brucei [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Trypanosoma brucei Trypanosoma brucei Trypanosoma_brucei_L.png Trypanosoma_brucei_NL.png Trypanoso...ma_brucei_S.png Trypanosoma_brucei_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Trypanoso...ma+brucei&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Trypanosoma+brucei&t=NL http://bioscie...ncedbc.jp/taxonomy_icon/icon.cgi?i=Trypanosoma+brucei&t=S http://biosciencedbc.jp.../taxonomy_icon/icon.cgi?i=Trypanosoma+brucei&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=121 ...

  19. Taxonomy Icon Data: Schistosoma japonicum [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Schistosoma japonicum Schistosoma japonicum Platyhelminthes Schistosoma_japonicum_L.png Schistoso...ma_japonicum_NL.png Schistosoma_japonicum_S.png Schistosoma_japonicum_NS.png http://bioscience...dbc.jp/taxonomy_icon/icon.cgi?i=Schistosoma+japonicum&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Schistoso...ma+japonicum&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Schistoso...ma+japonicum&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Schistosoma+japonicum&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=132 ...

  20. Taxonomy Icon Data: Toxoplasma gondii [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Toxoplasma gondii Toxoplasma gondii Toxoplasma_gondii_L.png Toxoplasma_gondii_NL.png Toxoplasma..._gondii_S.png Toxoplasma_gondii_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Toxoplasma...+gondii&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Toxoplasma+gondii&t=NL http://biosciencedbc.j...p/taxonomy_icon/icon.cgi?i=Toxoplasma+gondii&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Toxoplas...ma+gondii&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=113 ...

  1. Taxonomy Icon Data: Anopheles stephensi [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Anopheles stephensi Anopheles stephensi Arthropoda Anopheles_stephensi_L.png Anopheles_stephen...si_NL.png Anopheles_stephensi_S.png Anopheles_stephensi_NS.png http://biosciencedbc.jp/taxonomy_i...con/icon.cgi?i=Anopheles+stephensi&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Anopheles+stephensi&...t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Anopheles+stephensi&t=S htt...p://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Anopheles+stephensi&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=149 ...

  2. Taxonomy Icon Data: Planaria [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Planaria Dugesia japonica Platyhelminthes Dugesia_japonica_L.png Dugesia_japonica_NL.png Dugesia_jap...onica_S.png Dugesia_japonica_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Dugesia+jap...onica&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Dugesia+japonica&t=NL http://biosciencedbc.j...p/taxonomy_icon/icon.cgi?i=Dugesia+japonica&t=S http://biosciencedbc.jp/taxonomy_...icon/icon.cgi?i=Dugesia+japonica&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=124 ...

  3. The integrative future of taxonomy

    Directory of Open Access Journals (Sweden)

    Vences Miguel

    2010-05-01

    Full Text Available Abstract Background Taxonomy is the biological discipline that identifies, describes, classifies and names extant and extinct species and other taxa. Nowadays, species taxonomy is confronted with the challenge to fully incorporate new theory, methods and data from disciplines that study the origin, limits and evolution of species. Results Integrative taxonomy has been proposed as a framework to bring together these conceptual and methodological developments. Here we review perspectives for an integrative taxonomy that directly bear on what species are, how they can be discovered, and how much diversity is on Earth. Conclusions We conclude that taxonomy needs to be pluralistic to improve species discovery and description, and to develop novel protocols to produce the much-needed inventory of life in a reasonable time. To cope with the large number of candidate species revealed by molecular studies of eukaryotes, we propose a classification scheme for those units that will facilitate the subsequent assembly of data sets for the formal description of new species under the Linnaean system, and will ultimately integrate the activities of taxonomists and molecular biologists.

  4. Transient currents in a molecular photo-diode

    OpenAIRE

    Petrov, E. G.; Leonov, V. O.; May, V.; Hänggi, P.

    2012-01-01

    Light-induced charge transmission through a molecular junction (molecular diode) is studied in the framework of a HOMO-LUMO model and in using a kinetic description. Expressions are presented for the sequential (hopping) and direct (tunneling) transient current components together with kinetic equations governing the time-dependent populations of the neutral and charged molecular states which participate in the current formation. Resonant and off-resonant charge transmission processes are ana...

  5. Molecular phylogeny of the higher and lower taxonomy of the Fusarium genus and differences in the evolutionary histories of multiple genes

    Science.gov (United States)

    2011-01-01

    Background Species of the Fusarium genus are important fungi which is associated with health hazards in human and animals. The taxonomy of this genus has been a subject of controversy for many years. Although many researchers have applied molecular phylogenetic analysis to examine the taxonomy of Fusarium species, their phylogenetic relationships remain unclear only few comprehensive phylogenetic analyses of the Fusarium genus and a lack of suitable nucleotides and amino acid substitution rates. A previous stugy with whole genome comparison among Fusairum species revealed the possibility that each gene in Fusarium genomes has a unique evolutionary history, and such gene may bring difficulty to the reconstruction of phylogenetic tree of Fusarium. There is a need not only to check substitution rates of genes but also to perform the exact evaluation of each gene-evolution. Results We performed phylogenetic analyses based on the nucleotide sequences of the rDNA cluster region (rDNA cluster), and the β-tubulin gene (β-tub), the elongation factor 1α gene (EF-1α), and the aminoadipate reductase gene (lys2). Although incongruence of the tree topologies between lys2 and the other genes was detected, all genes supported the classification of Fusarium species into 7 major clades, I to VII. To obtain a reliable phylogeny for Fusarium species, we excluded the lys2 sequences from our dataset, and re-constructed a maximum likelihood (ML) tree based on the combined data of the rDNA cluster, β-tub, and EF-1α. Our ML tree indicated some interesting relationships in the higher and lower taxa of Fusarium species and related genera. Moreover, we observed a novel evolutionary history of lys2. We suggest that the unique tree topologies of lys2 are not due to an analytical artefact, but due to differences in the evolutionary history of genomes caused by positive selection of particular lineages. Conclusion This study showed the reliable species tree of the higher and lower taxonomy

  6. Bad taxonomy can kill : molecular reevaluation of Unio mancus Lamarck, 1819 (Bivalvia : Unionidae and its accepted subspecies

    Directory of Open Access Journals (Sweden)

    Prie V.

    2012-07-01

    Full Text Available The conservation status of European unionid species rests on the scientific knowledge of the 1980s, before the current revival of taxonomic reappraisals based on molecular characters. The taxonomic status of Unio mancus Lamarck, 1819, superficially similar to Unio pictorum (Linnaeus, 1758 and often synonymized with it, is re-evaluated based on a random sample of major French drainages and a systematic sample of historical type localities. We confirm the validity of U. mancus as a distinct species occurring in France and Spain, where it is structured into three geographical units here ranked as subspecies: U. m. mancus [Atlantic drainages, eastern Pyrenees, Spanish Mediterranean drainages], U. m. turtonii Payraudeau, 1826 [coastal drainages East of the Rhône and Corsica] and U. m. requienii Michaud, 1831 [Seine, Saône-Rhône, and coastal drainages West of the Rhône]. Many populations of Unio mancus have been extirpated during the 20th century and the remaining populations continue to be under pressure; U. mancus satisfies the criteria to be listed as «Endangered» in the IUCN Red List.

  7. Molecular ultrasound imaging: current status and future directions

    International Nuclear Information System (INIS)

    Deshpande, N.; Needles, A.; Willmann, J.K.

    2010-01-01

    Targeted contrast-enhanced ultrasound (molecular ultrasound) is an emerging imaging strategy that combines ultrasound technology with novel molecularly-targeted ultrasound contrast agents for assessing biological processes at the molecular level. Molecular ultrasound contrast agents are nano- or micro-sized particles that are targeted to specific molecular markers by adding high-affinity binding ligands onto the surface of the particles. Following intravenous administration, these targeted ultrasound contrast agents accumulate at tissue sites overexpressing specific molecular markers, thereby enhancing the ultrasound imaging signal. High spatial and temporal resolution, real-time imaging, non-invasiveness, relatively low costs, lack of ionising irradiation and wide availability of ultrasound systems are advantages compared to other molecular imaging modalities. In this article we review current concepts and future directions of molecular ultrasound imaging, including different classes of molecular ultrasound contrast agents, ongoing technical developments of pre-clinical and clinical ultrasound systems, the potential of molecular ultrasound for imaging different diseases at the molecular level, and the translation of molecular ultrasound into the clinic.

  8. Taxonomy Icon Data: coelacanth [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available coelacanth Latimeria chalumnae Chordata/Vertebrata/Pisciformes Latimeria_chalumnae_L.png Latime...ria_chalumnae_NL.png Latimeria_chalumnae_S.png Latimeria_chalumnae_NS.png http://biosciencedbc.j...p/taxonomy_icon/icon.cgi?i=Latimeria+chalumnae&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Latimeri...a+chalumnae&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Latimeria+chalu...mnae&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Latimeria+chalumnae&t=NS ...

  9. Taxonomy Icon Data: mandrill [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available mandrill Mandrillus sphinx Chordata/Vertebrata/Mammalia/Theria/Eutheria/Primate Mandrillus_sphinx..._L.png Mandrillus_sphinx_NL.png Mandrillus_sphinx_S.png Mandrillus_sphinx_NS.png http://biosci...encedbc.jp/taxonomy_icon/icon.cgi?i=Mandrillus+sphinx&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Mandrillus+sphinx...&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Mandrillus+sphinx...&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Mandrillus+sphinx&t=NS ...

  10. Taxonomy Icon Data: sperm whale [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available sperm whale Physeter macrocephalus Chordata/Vertebrata/Mammalia/Theria/Eutheria/Cetacea Physeter_macrocephal...us_L.png Physeter_macrocephalus_NL.png Physeter_macrocephalus_S.png Physeter_macrocephal...us_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Physeter+macrocephalus&t=L http://bioscience...dbc.jp/taxonomy_icon/icon.cgi?i=Physeter+macrocephalus&t=NL http://biosciencedbc....jp/taxonomy_icon/icon.cgi?i=Physeter+macrocephalus&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Physeter+macrocephalus&t=NS ...

  11. Taxonomy Icon Data: Oryzias javanicus [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Oryzias javanicus Oryzias javanicus Chordata/Vertebrata/Pisciformes Oryzias_javanicus_L.png Oryzias_java...nicus_NL.png Oryzias_javanicus_S.png Oryzias_javanicus_NS.png http://biosciencedbc.jp/t...axonomy_icon/icon.cgi?i=Oryzias+javanicus&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Oryzias+javan...icus&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Oryzias+javanicus&t=S ...http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Oryzias+javanicus&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=77 ...

  12. Taxonomy Icon Data: Asiatic elephant [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Asiatic elephant Elephas maximus Chordata/Vertebrata/Mammalia/Theria/Eutheria/etc. Elephas_maxim...us_L.png Elephas_maximus_NL.png Elephas_maximus_S.png Elephas_maximus_NS.png http://bioscienced...bc.jp/taxonomy_icon/icon.cgi?i=Elephas+maximus&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Elephas+maxim...us&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Elephas+maximus&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Elephas+maximus&t=NS ...

  13. Taxonomy Icon Data: Asiatic tapir [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Asiatic tapir Tapirus indicus Chordata/Vertebrata/Mammalia/Theria/Eutheria/etc. Tapirus_indicus_L.png Tapi...rus_indicus_NL.png Tapirus_indicus_S.png Tapirus_indicus_NS.png http://biosciencedbc....jp/taxonomy_icon/icon.cgi?i=Tapirus+indicus&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Tapirus+ind...icus&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Tapirus+indicus&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Tapirus+indicus&t=NS ...

  14. Taxonomy Icon Data: okapi [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available okapi Okapia johnstoni Chordata/Vertebrata/Mammalia/Theria/Eutheria/Artiodactyla Okapi...a_johnstoni_L.png Okapia_johnstoni_NL.png Okapia_johnstoni_S.png Okapia_johnstoni_NS.png http://bioscienc...edbc.jp/taxonomy_icon/icon.cgi?i=Okapia+johnstoni&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Okapi...a+johnstoni&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Okapia+johnston...i&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Okapia+johnstoni&t=NS ...

  15. Taxonomy Icon Data: fathead minnow [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available fathead minnow Pimephales promelas Chordata/Vertebrata/Pisciformes Pimephales_promela...s_L.png Pimephales_promelas_NL.png Pimephales_promelas_S.png Pimephales_promelas_NS.png http://bioscienced...bc.jp/taxonomy_icon/icon.cgi?i=Pimephales+promelas&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Pimephales+promela...s&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Pimephales+promela...s&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Pimephales+promelas&t=NS ...

  16. Taxonomy Icon Data: giant panda [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available giant panda Ailuropoda melanoleuca Chordata/Vertebrata/Mammalia/Theria/Eutheria/Carnivora Ailuropoda_mela...noleuca_L.png Ailuropoda_melanoleuca_NL.png Ailuropoda_melanoleuca_S.png Ailuropoda_mela...noleuca_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Ailuropoda+melanoleuca&t=L http://bioscien...cedbc.jp/taxonomy_icon/icon.cgi?i=Ailuropoda+melanoleuca&t=NL http://biosciencedb...c.jp/taxonomy_icon/icon.cgi?i=Ailuropoda+melanoleuca&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Ailuropoda+melanoleuca&t=NS ...

  17. Taxonomy Icon Data: Guinea baboon [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Guinea baboon Papio papio Chordata/Vertebrata/Mammalia/Theria/Eutheria/Primate Papio_papio_L.png Papio_papi...o_NL.png Papio_papio_S.png Papio_papio_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Papio+papi...o&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Papio+papio&t=NL http://bioscien...cedbc.jp/taxonomy_icon/icon.cgi?i=Papio+papio&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Papio+papio&t=NS ...

  18. Taxonomy Icon Data: white shark [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available white shark Carcharodon carcharias Chordata/Vertebrata/Pisciformes Carcharodon_carcharias_L.png Carcharo...don_carcharias_NL.png Carcharodon_carcharias_S.png Carcharodon_carcharias_NS.png http:/.../biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Carcharodon+carcharias&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Carcharo...don+carcharias&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Carcharo...don+carcharias&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Carcharodon+carcharias&t=NS ...

  19. [Molecular imaging; current status and future prospects in USA].

    Science.gov (United States)

    Kobayashi, Hisataka

    2007-02-01

    The goal of this review is to introduce the definition, current status, and future prospects of the molecular imaging, which has recently been a hot topic in medicine and the biological science in USA. In vivo imaging methods to visualize the molecular events and functions in organs or animals/humans are overviewed and discussed especially in combinations of imaging modalities (machines) and contrast agents(chemicals) used in the molecular imaging. Next, the close relationship between the molecular imaging and the nanotechnology, an important part of nanomedicine, is stressed from the aspect of united multidisciplinary sciences such as physics, chemistry, biology, and medicine.

  20. Taxonomies of Educational Objective Domain

    OpenAIRE

    Eman Ghanem Nayef; Nik Rosila Nik Yaacob; Hairul Nizam Ismail

    2013-01-01

    This paper highlights an effort to study the educational objective domain taxonomies including Bloom’s taxonomy, Lorin Anderson’s taxonomy, and Wilson’s taxonomy. In this study a comparison among these three taxonomies have been done. Results show that Bloom’s taxonomy is more suitable as an analysis tool to Educational Objective domain.

  1. Current-driven dynamics in molecular-scale devices

    International Nuclear Information System (INIS)

    Seideman, Tamar

    2003-01-01

    We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)

  2. Controlling charge current through a DNA based molecular transistor

    Energy Technology Data Exchange (ETDEWEB)

    Behnia, S., E-mail: s.behnia@sci.uut.ac.ir; Fathizadeh, S.; Ziaei, J.

    2017-01-05

    Molecular electronics is complementary to silicon-based electronics and may induce electronic functions which are difficult to obtain with conventional technology. We have considered a DNA based molecular transistor and study its transport properties. The appropriate DNA sequence as a central chain in molecular transistor and the functional interval for applied voltages is obtained. I–V characteristic diagram shows the rectifier behavior as well as the negative differential resistance phenomenon of DNA transistor. We have observed the nearly periodic behavior in the current flowing through DNA. It is reported that there is a critical gate voltage for each applied bias which above it, the electrical current is always positive. - Highlights: • Modeling a DNA based molecular transistor and studying its transport properties. • Choosing the appropriate DNA sequence using the quantum chaos tools. • Choosing the functional interval for voltages via the inverse participation ratio tool. • Detecting the rectifier and negative differential resistance behavior of DNA.

  3. Taxonomy Icon Data: moss [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available moss Physcomitrella patens subsp. patens. Physcomitrella_patens_subsp_patens_L.png Physcomitrella_patens..._subsp_patens_NL.png Physcomitrella_patens_subsp_patens_S.png Physcomitrella_patens_subsp_patens..._NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Physcomitrella+patens+subsp%2e+patens%2e&t...=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Physcomitrella+patens+subsp%2e+patens...%2e&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Physcomitrella+patens+subsp%2e+patens%2e&t

  4. Taxonomy Icon Data: Arabian camel [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Arabian camel Camelus dromedarius Chordata/Vertebrata/Mammalia/Theria/Eutheria/Artiodactyla Camel...us_dromedarius_L.png Camelus_dromedarius_NL.png Camelus_dromedarius_S.png Camelus_dromedarius_...NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Camelus+dromedarius&t=L http://biosciencedbc.jp/taxo...nomy_icon/icon.cgi?i=Camelus+dromedarius&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Camel...us+dromedarius&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Camelus+dromedarius&t=NS ...

  5. Taxonomy Icon Data: Japanese serow [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Japanese serow Capricornis crispus Chordata/Vertebrata/Mammalia/Theria/Eutheria/Artiodactyla Capricorn...is_crispus_L.png Capricornis_crispus_NL.png Capricornis_crispus_S.png Capricornis_crispus..._NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Capricornis+crispus&t=L http://biosciencedbc.jp/tax...onomy_icon/icon.cgi?i=Capricornis+crispus&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Capricorn...is+crispus&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Capricornis+crispus&t=NS ...

  6. Taxonomy Icon Data: dog [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available dog Canis lupus familiaris Chordata/Vertebrata/Mammalia/Theria/Eutheria/Carnivora Canis_lupus..._familiaris_L.png Canis_lupus_familiaris_NL.png Canis_lupus_familiaris_S.png Canis_lupus_familiari...s_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Canis+lupus+familiaris&t=L http://biosciencedbc.jp.../taxonomy_icon/icon.cgi?i=Canis+lupus+familiaris&t=NL http://biosciencedbc.jp/tax...onomy_icon/icon.cgi?i=Canis+lupus+familiaris&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Canis+lupus+familiaris&t=NS ...

  7. Taxonomy Icon Data: llama [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available llama Lama glama Chordata/Vertebrata/Mammalia/Theria/Eutheria/Artiodactyla Lama_glama_L.png Lama_glama_NL.png Lama_glama_S.png Lama_glama..._NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lama+glam...a&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lama+glama&t=NL http://biosciencedbc.jp/t...axonomy_icon/icon.cgi?i=Lama+glama&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Lama+glama&t=NS ...

  8. Interface tuning of current-induced cooling in molecular circuits

    Czech Academy of Sciences Publication Activity Database

    Foti, Giuseppe; Vázquez, Héctor

    2017-01-01

    Roč. 121, č. 2 (2017), s. 1082-1088 ISSN 1932-7447 R&D Projects: GA ČR GA15-19672S Institutional support: RVO:68378271 Keywords : current-induced heating and cooling * molecular junction * Carbene Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 4.536, year: 2016

  9. Molecular studies of Callithrix pygmaea (Primates, Platyrrhini based on transferrin intronic and ND1 regions: implications for taxonomy and conservation

    Directory of Open Access Journals (Sweden)

    Tagliaro Claudia Helena

    2000-01-01

    Full Text Available Traditional classifications of Platyrrhini monkeys, based mainly on morphological features, are being contested by recent molecular data. The subfamily Callitrichinae (Platyrrhini, Primates consists of a diverse group of species, many of them considered endangered. Our analysis of two DNA regions, a mtDNA gene (ND1 and a nuclear gene (intronic regions of the transferrin gene, suggests that Callithrix pygmaea may have sufficient variability to justify the existence of subspecies or even separate species. Phylogenetic dendrograms based on the ND1 region show that this species is more closely related to Amazonian than to Atlantic forest marmosets. These results reopen the discussion about diversity and conservation programs based exclusively on traditional classifications.

  10. Morphology and molecular taxonomy of Evlachovaea-like fungi, and the status of this unusual conidial genus.

    Science.gov (United States)

    Humber, Richard A; Rocha, Luiz F N; Inglis, Peter W; Kipnis, André; Luz, Christian

    2013-01-01

    The entomopathogenic anamorphic genus Evlachovaea was described to differ from other fungi in forming its conidia obliquely to the axis of the conidiogenous cell and with successive conidia having alternate orientations with a zipper- or chevron-like arrangement resulting in flat, ribbon-like chains. Morphological and molecular studies of six Evlachovaea-like isolates baited from Central Brazilian soils using Triatoma infestans (a vector of Chagas disease) and of other entomopathogens with Evlachovaea-like conidiogenesis led to a re-evaluation of the status of this little known fungal genus. The Brazilian isolates formed two distinct groups based on gene sequences for both the internal transcribed spacer (ITS) and translation elongation factor (EF-1α) genes, morphology, and growth patterns; both groups also differed from the type species, Evlachovaea kintrischica. More detailed studies of these fungi indicated that the alternatingly oblique orientations of forming conidia are neither a stable nor invariant character (even on single phialides). Furthermore, the molecular cladistic analysis unambiguously placed the Evlachovaea isolates firmly within the genus Isaria (Hypocreales: Cordycipitaceae). The ITS sequences of E. kintrischica were very similar or even identical to those of Isaria amoenerosea and Isaria cateniobliqua, thereby suggesting that E. kintrischica is a synonym of one of these species, and that the genus Evlachovaea must be treated as a later synonym of Isaria, which must now be recognized to include several highly divergent modes of conidiogenesis. These taxonomic findings are discussed in the context of dramatic changes recently imposed on the nomenclatural standards used to determine the correct names of all pleomorphic fungi. Published by Elsevier Ltd.

  11. THE CURRENT METHODS FOR MOLECULAR DIAGNOSTICS OF FISH DISEASES (REVIEW

    Directory of Open Access Journals (Sweden)

    O. Zaloilo

    2016-06-01

    Full Text Available Purpose. The methods of molecular diagnostic (MMD gradually become widespread in modern fish farming. MMD contain a wide variety of specific approaches, each of which has distinct limits of their possible applications and is characterized by individual peculiarities in practical performance. In addition to high sensitivity and the possibility of rapid diagnostics, the main advantage of molecular methods is to determine the uncultivated infectious agents. DNA amplification allows identifying pathogenic microorganisms at very small quantities even in the minimum sample volume. Molecular methods of diagnostic enable the determination of infection in latent or acute phases. These methods allow showing the differences between pathogens with similar antigenic structures. The current literature data on this subject usually show a methodology in the narrow context of the tasks or practical results obtained through such approaches. Thus, a synthesis of existing information on the mechanisms of action and the limits of the typical problems of basic methods of molecular diagnostics are an urgent task of fish breeding. In particular, the following description will more effectively choose one or several approaches to identify pathogens in fish. Findings. This paper reviews the basic molecular methods that are used in the world's aquaculture for diagnosis of various diseases in commercial fish species. Originality. This work is a generalization of data on the principles and mechanisms for the implementation of diagnostics based on modern molecular techniques. For each of the mentioned approaches, the most promising areas of application were shown. The information is provided in the form of a comparative analysis of each methodology, indicating positive and negative practical aspects. Practical value. The current review of modern methods of molecular diagnostic in aquaculture is focused on practical application. Generalizing and analytical information can be

  12. Characters in Arctostaphylos taxonomy

    Science.gov (United States)

    Keeley, Jon E.; Parker, V. Thomas; Vasey, Michael C.

    2017-01-01

    There is value in understanding the past and how it has affected the present. Science focuses on empirical findings, and we know that our prior experiences and those of our predecessors play important roles in determining how we interpret the present. We learn from accomplishments and foibles of predecessors and appreciate the real life experiences we have gone through. In our studies of the genus Arctostaphylos Adans. we have been struck by the fascinating stories surrounding taxonomists who have played roles in the development of our current understanding of the group. In addition to providing insights, they sometimes provide humor and lessons on the value of competition versus collaboration. We offer this history of the humans that forged the taxonomy behind Arctostaphylos classification in this light.

  13. New Molecular Targets of Anticancer Therapy - Current Status and Perspectives.

    Science.gov (United States)

    Zajac, Marianna; Muszalska, Izabela; Jelinska, Anna

    2016-01-01

    Molecularly targeted anticancer therapy involves the use of drugs or other substances affecting specific molecular targets that play a part in the development, progression and spread of a given neoplasm. By contrast, the majority of classical chemotherapeutics act on all rapidly proliferating cells, both healthy and cancerous ones. Target anticancer drugs are designed to achieve a particular aim and they usually act cytostatically, not cytotoxically like classical chemotherapeutics. At present, more than 300 biological molecular targets have been identified. The proteins involved in cellular metabolism include (among others) receptor proteins, signal transduction proteins, mRNA thread matrix synthesis proteins participating in neoplastic transformation, cell cycle control proteins, functional and structural proteins. The receptor proteins that are targeted by currently used anticancer drugs comprise the epithelial growth factor receptor (EGFR), platelet-derived growth factor receptor (PDGFR) and vascular endothelial growth factor receptor(VEGFR). Target anticancer drugs may affect extracellular receptor domains (antibodies) or intracellular receptor domains (tyrosine kinase inhibitors). The blocking of the mRNA thread containing information about the structure of oncogenes (signal transduction proteins) is another molecular target of anticancer drugs. That type of treatment, referred to as antisense therapy, is in clinical trials. When the synthesis of genetic material is disturbed, in most cases the passage to the next cycle phase is blocked. The key proteins responsible for the blockage are cyclines and cycline- dependent kinases (CDK). Clinical trials are focused on natural and synthetic substances capable of blocking various CDKs. The paper discusses the molecular targets and chemical structure of target anticancer drugs that have been approved for and currently applied in antineoplastic therapy together with indications and contraindications for their

  14. Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.

    Science.gov (United States)

    Brabec, Jan; Kostadinova, Aneta; Scholz, Tomáš; Littlewood, D Timothy J

    2015-06-19

    The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology. Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared. We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida. Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and

  15. Current Molecular Targeted Therapies for Bone and Soft Tissue Sarcomas

    Directory of Open Access Journals (Sweden)

    Kenji Nakano

    2018-03-01

    Full Text Available Systemic treatment options for bone and soft tissue sarcomas remained unchanged until the 2000s. These cancers presented challenges in new drug development partly because of their rarity and heterogeneity. Many new molecular targeting drugs have been tried in the 2010s, and some were approved for bone and soft tissue sarcoma. As one of the first molecular targeted drugs approved for solid malignant tumors, imatinib’s approval as a treatment for gastrointestinal stromal tumors (GISTs has been a great achievement. Following imatinib, other tyrosine kinase inhibitors (TKIs have been approved for GISTs such as sunitinib and regorafenib, and pazopanib was approved for non-GIST soft tissue sarcomas. Olaratumab, the monoclonal antibody that targets platelet-derived growth factor receptor (PDGFR-α, was shown to extend the overall survival of soft tissue sarcoma patients and was approved in 2016 in the U.S. as a breakthrough therapy. For bone tumors, new drugs are limited to denosumab, a receptor activator of nuclear factor κB ligand (RANKL inhibitor, for treating giant cell tumors of bone. In this review, we explain and summarize the current molecular targeting therapies approved and in development for bone and soft tissue sarcomas.

  16. Current Molecular Imaging Positron Emitting Radiotracers in Oncology

    International Nuclear Information System (INIS)

    Zhu, Aizhi; Shim, Hyunsuk

    2011-01-01

    Molecular imaging is one of the fastest growing areas of medical imaging. Positron emission tomography has been widely used in the clinical management of patients with cancer. Nuclear imaging provides biological information at the cellular, subcellular, and molecular level in living subjects with noninvasive procedures. In particular, PET imaging takes advantage of traditional diagnostic imaging techniques and introduces positron emitting probes to determine the expression of indicative molecular targets at different stages of cancer. 18F fluorodeoxyglucose ( 18F FDG), the only FDA approved oncological PET tracer, has been widely utilized in cancer diagnosis, staging, restaging, and even monitoring response to therapy; however, 18F FDG is not a tumor specific PET tracer. Over the last decade, many promising tumor specific PET tracer. Over the last decade, many promising tumor specific PET tracers have been developed and evaluated in preclinical and clinical studies. This review provides an overview of the current non 18F FDG PET tracers in oncology that have been developed based on tumor characteristics such as increased metabolism, hyperproliferation, angiogenesis, hypoxia, apoptosis, and tumor specific antigens and surface receptors

  17. Current's Fluctuations through Molecular Wires Composed of Thiophene Rings.

    Science.gov (United States)

    Ojeda Silva, Judith Helena; Cortés Peñaranda, Juan Camilo; Gómez Castaño, Jovanny A; Duque, Carlos Alberto

    2018-04-11

    We study theoretically the electronic transport and quantum fluctuations in single-molecule systems using thiophene rings as integrated elementary functions, as well as the dependence of these properties with the increase of the coupled rings, i.e., as a quantum wire. In order to analyze the current flow through these molecular systems, the thiophene rings are considered to be connected to metal contacts, which, in general terms, will be related to the application of voltages (bias voltages or gate voltages) to generate non-equilibrium behavior between the contacts. Due to the nonlinear behavior that is generated when said voltages are applied, it is possible to observe quantum fluctuations in the transport properties of these molecular wires. For the calculation of the transport properties, we applied a tight-binding approach using the Landauer-Büttiker formalism and the Fischer-Lee relationship, by means of a semi-analytic Green's function method within a real-space renormalization (decimation procedure). Our results showed an excellent agreement with results using a tight-binding model with a minimal number of parameters reported so far for these molecular systems.

  18. EPA Web Taxonomy

    Data.gov (United States)

    U.S. Environmental Protection Agency — EPA's Web Taxonomy is a faceted hierarchical vocabulary used to tag web pages with terms from a controlled vocabulary. Tagging enables search and discovery of EPA's...

  19. Manifestations of electric currents in interstellar molecular clouds

    International Nuclear Information System (INIS)

    Carlqvist, P.; Gahm, G.F.

    1991-12-01

    We draw the attention to filamentary structures in molecular clouds and point out the existence of subfilaments of sinusoidal shape and also of helix-like structures. For two dark clouds, the Lynds 204 complex and the Sandqvist 187-188 complex (The Norma 'sword') we make a detailed study of such shapes and in addition we find the possible existence of helices wound around the main filaments. All these features are highly reminiscent of morphologies encountered in solar ascending prominences and in experiments in plasma physics and suggest the existence of electric currents and magnetic fields in these clouds. On the basis of a generalization of the Bennett pinch model, we derive the magnitudes of the currents expected to flow in the filaments. Values of column densities, magnetic field strengths, and direction of the fields are derived from observations. Magnetic fields with both toroidal and axial components are considered. This study shows that axial currents of the order of a few times 10 13 A are necessary for the clouds to be in equilibrium. The corresponding mean current densities are very small and even at the very low values of the fractional abundance of electrons encountered in these clouds, the mean electron velocities are of the order of 10 -2 -10 -5 m s -1 , much lower than the thermal velocities in the clouds. We suggest that helical structures may evolve as a result of various instabilities in the pinched clouds. We also call the attention to the kink intability in connection with the sinusoidal shapes. The existence of electromagnetically controlled features in the interstellar clouds can be tested by further observations. (au)

  20. Overestimation of molecular and modelling methods and underestimation of traditional taxonomy leads to real problems in assessing and handling of the world's biodiversity.

    Science.gov (United States)

    Löbl, Ivan

    2014-02-27

    Since the 1992 Rio Convention on Biological Diversity, the earth's biodiversity is a matter of constant public interest, but the community of scientists who describe and delimit species in mega-diverse animal groups, i.e. the bulk of global biodiversity, faces ever-increasing impediments. The problems are rooted in poor understanding of specificity of taxonomy, and overestimation of quantitative approaches and modern technology. A high proportion of the animal species still remains to be discovered and studied, so a more balanced approach to the situation is needed.

  1. Current Progress of Nanomaterials in Molecularly Imprinted Electrochemical Sensing.

    Science.gov (United States)

    Zhong, Chunju; Yang, Bin; Jiang, Xinxin; Li, Jianping

    2018-01-02

    Nanomaterials have received much attention during the past decade because of their excellent optical, electronic, and catalytic properties. Nanomaterials possess high chemical reactivity, also high surface energy. Thus, provide a stable immobilization platform for biomolecules, while preserving their reactivity. Due to the conductive and catalytic properties, nanomaterials can also enhance the sensitivity of molecularly imprinted electrochemical sensors by amplifying the electrode surface, increasing the electron transfer, and catalyzing the electrochemical reactions. Molecularly imprinted polymers that contain specific molecular recognition sites can be designed for a particular target analyte. Incorporating nanomaterials into molecularly imprinted polymers is important because nanomaterials can improve the response signal, increase the sensitivity, and decrease the detection limit of the sensors. This study describes the classification of nanomaterials in molecularly imprinted polymers, their analytical properties, and their applications in the electrochemical sensors. The progress of the research on nanomaterials in molecularly imprinted polymers and the application of nanomaterials in molecularly imprinted polymers is also reviewed.

  2. Teaching Taxonomy: How Many Kingdoms?

    Science.gov (United States)

    Case, Emily

    2008-01-01

    Taxonomy, the identification, naming, and classification of living things, is an indispensable unit in any biology curriculum and indeed, an integral part of biological science. Taxonomy catalogues life's diversity and is an essential tool for communication. Textbook discussions of taxonomy range anywhere from three to eight domains of kingdoms.…

  3. Taxonomy Icon Data: Old world swallowtail [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Old world swallowtail Papilio machaon Arthropoda Papilio_machaon_L.png Papilio_machaon_NL.png Papilio_machao...n_S.png Papilio_machaon_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Papilio+machao...n&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Papilio+machaon&t=NL http://biosciencedbc....jp/taxonomy_icon/icon.cgi?i=Papilio+machaon&t=S http://biosciencedbc.jp/taxonomy_...icon/icon.cgi?i=Papilio+machaon&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=47 ...

  4. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    BACKGROUND: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of...

  5. Comment: 61 [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available .png Taxonomy icon (c) Database Center for Life Science licensed under CC Attribution2.1 Japan イメージを差し替えました(添付は旧イメージ) ttamura 2009/04/21 12:50:03 ...

  6. Company Taxonomy development

    DEFF Research Database (Denmark)

    Lund, Haakon; Ørnager, Susanne

    2016-01-01

    analyses of search log-files from WFP intranet portal (WFPgo) from September to November 2013, the results were applied and a suggested taxonomy tested at workshops conducted for the staff in headquarters. Findings – The results reveal an organization with a high demand for easier access to information...

  7. Comment: 215 [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available 215.png Taxonomy icon (c) Database Center for Life Science licensed under CC Attribution2.1 Japan アイコン:電子顕微鏡バージョン bando 2010/02/15 15:30:03 2010/02/15 15:30:03 ...

  8. Classification and taxonomy of vegetable macergens

    Directory of Open Access Journals (Sweden)

    Bukola Rhoda Aremu

    2015-11-01

    Full Text Available Macergens are bacteria capable of releasing pectic enzymes (pectolytic bacteria. These enzymatic actions result in the separation of plant tissues leading to total plant destruction. This can be attributed to soft rot diseases in vegetables. These macergens primarily belong to the genus Erwinia and to a range of opportunistic pathogens namely: the Xanthomonas spp, Pseudomonas spp., Clostridium spp., Cytophaga spp. and Bacillus spp. They consist of taxa that displayed considerable heterogeneity and intermingled with members of other genera belonging to the Enterobacteriaceae. They have been classified based on phenotypic, chemotaxonomic and genotypic which obviously not necessary in the taxonomy of all bacterial genera for defining bacterial species and describing new ones These taxonomic markers have been used traditionally as a simple technique for identification of bacterial isolates. The most important fields of taxonomy are supposed to be based on clear, reliable and worldwide applicable criteria. Hence, this review clarifies the taxonomy of the macergens to the species level and revealed that their taxonomy is beyond complete. For discovery of additional species, further research with the use modern molecular methods like phylogenomics need to be done. This can precisely define classification of macergens resulting in occasional, but significant changes in previous taxonomic schemes of these macergens.

  9. Current and future molecular diagnostics for ocular infectious diseases.

    Science.gov (United States)

    Doan, Thuy; Pinsky, Benjamin A

    2016-11-01

    Confirmation of ocular infections can pose great challenges to the clinician. A fundamental limitation is the small amounts of specimen that can be obtained from the eye. Molecular diagnostics can circumvent this limitation and have been shown to be more sensitive than conventional culture. The purpose of this review is to describe new molecular methods and to discuss the applications of next-generation sequencing-based approaches in the diagnosis of ocular infections. Efforts have focused on improving the sensitivity of pathogen detection using molecular methods. This review describes a new molecular target for Toxoplasma gondii-directed polymerase chain reaction assays. Molecular diagnostics for Chlamydia trachomatis and Acanthamoeba species are also discussed. Finally, we describe a hypothesis-free approach, metagenomic deep sequencing, which can detect DNA and RNA pathogens from a single specimen in one test. In some cases, this method can provide the geographic location and timing of the infection. Pathogen-directed PCRs have been powerful tools in the diagnosis of ocular infections for over 20 years. The use of next-generation sequencing-based approaches, when available, will further improve sensitivity of detection with the potential to improve patient care.

  10. Molecular simulation of ionic liquids: current status and future opportunities

    International Nuclear Information System (INIS)

    Maginn, E J

    2009-01-01

    Ionic liquids are salts that are liquid near ambient conditions. Interest in these unusual compounds has exploded in the last decade, both at the academic and commercial level. Molecular simulations based on classical potentials have played an important role in helping researchers understand how condensed phase properties of these materials are linked to chemical structure and composition. Simulations have also predicted many properties and unexpected phenomena that have subsequently been confirmed experimentally. The beneficial impact molecular simulations have had on this field is due in large part to excellent timing. Just when computing power and simulation methods matured to the point where complex fluids could be studied in great detail, a new class of materials virtually unknown to experimentalists came on the scene and demanded attention. This topical review explores some of the history of ionic liquid molecular simulations, and then gives examples of the recent use of molecular dynamics and Monte Carlo simulation in understanding the structure of ionic liquids, the sorption of small molecules in ionic liquids, the nature of ionic liquids in the vapor phase and the dynamics of ionic liquids. This review concludes with a discussion of some of the outstanding problems facing the ionic liquid modeling community and how condensed phase molecular simulation experts not presently working on ionic liquids might help advance the field. (topical review)

  11. Taxonomy of Payments

    DEFF Research Database (Denmark)

    Hedman, Jonas; Tan, Felix B.; Holst, Jacques

    2017-01-01

    that impact payers’ choice of payment instruments. Design/methodology/approach: Through in-depth interviews using the repertory grid technique, the authors explored 15 payers’ perceptions of six payment instruments, including coins, banknotes, debit cards, credit cards, mobile payments, and online banking....... The approach draws heavily on organizational systematics to better understand payers’ choice of payment instruments. Findings: A four-category taxonomy of payments was developed. The authors refer to the taxonomy as the 4Ps: the purchase, the payer, the payment instrument, and the physical technology...... or checks. Research limitations/implications: The findings suggest that payers view payment instruments in a much broader sense, including context, control, or cultural beliefs. Consequently, the authors suggest that researchers try to understand the essence of an innovation before assuming any economic...

  12. Taxonomy Icon Data: aye-aye [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available aye-aye Daubentonia madagascariensis Chordata/Vertebrata/Mammalia/Theria/Eutheria/Primate Daubentonia_madaga...scariensis_L.png Daubentonia_madagascariensis_NL.png Daubentonia_madagascariensis_S.png Daubentonia_madagasc...ariensis_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Daubentonia+madagascar...iensis&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Daubentonia+madagascar...iensis&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Daubentonia+madagascariensis&t=S http://bi

  13. Comment: 219 [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Japanese medaka Oryzias latipes Oryzias_latipes_L.png 219.png Taxonomy icon (c) Database Center for Life Sci...ence licensed under CC Attribution2.1 Japan アイコン:メダカ HNI-Ⅱ系統バージョン bando 2010/02/15 15:31:07 2010/02/16 09:53:27 ...

  14. Taxonomy Icon Data: Diplazium tomitaroanum Masam [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Diplazium tomitaroanum Masam Diplazium tomitaroanum Masam Diplazium_tomitaroanum_Masam_L.png Diplazium_tomit...aroanum_Masam_NL.png Diplazium_tomitaroanum_Masam_S.png Diplazium_tomitaroanum_Masa...m_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Diplazium+tomitaroanum+Masam&t=L http://bioscience...dbc.jp/taxonomy_icon/icon.cgi?i=Diplazium+tomitaroanum+Masam&t=NL http://bioscien...cedbc.jp/taxonomy_icon/icon.cgi?i=Diplazium+tomitaroanum+Masam&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Diplazium+tomitaroanum+Masam&t=NS ...

  15. Taxonomy Icon Data: Javan tree shrew [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Javan tree shrew Tupaia javanica Chordata/Vertebrata/Mammalia/Theria/Eutheria/etc. Tupaia_java...nica_L.png Tupaia_javanica_NL.png Tupaia_javanica_S.png Tupaia_javanica_NS.png http://bioscienced...bc.jp/taxonomy_icon/icon.cgi?i=Tupaia+javanica&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Tupaia+java...nica&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Tupaia+javanica&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Tupaia+javanica&t=NS ...

  16. Taxonomy Icon Data: Japanese Bush Warbler [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Japanese Bush Warbler Cettia diphone Chordata/Vertebrata/Aves Cettia_diphone_L.png Cettia_diphone..._NL.png Cettia_diphone_S.png Cettia_diphone_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Cettia+diphone...&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Cettia+diphone&t=NL http://bioscie...ncedbc.jp/taxonomy_icon/icon.cgi?i=Cettia+diphone&t=S http://biosciencedbc.jp/tax...onomy_icon/icon.cgi?i=Cettia+diphone&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=26 ...

  17. Taxonomy Icon Data: Ptychodera flava Eschscholtz (Acorn worm) [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Ptychodera flava Eschscholtz (Acorn worm) Ptychodera flava Hemichordata Ptychodera_flava_L.png Ptycho...dera_flava_NL.png Ptychodera_flava_S.png Ptychodera_flava_NS.png http://biosciencedbc.jp/t...axonomy_icon/icon.cgi?i=Ptychodera+flava&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Ptychodera+fla...va&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Ptychodera+flava&t=S htt...p://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Ptychodera+flava&t=NS http://togodb.biosciencedbc.jp/togodb/view/taxonomy_icon_comment_en?species_id=161 ...

  18. Taxonomy Icon Data: wild Bactrian camel [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available wild Bactrian camel Camelus ferus Chordata/Vertebrata/Mammalia/Theria/Eutheria/Artiodactyla Camel...us_ferus_L.png Camelus_ferus_NL.png Camelus_ferus_S.png Camelus_ferus_NS.png http://bioscience...dbc.jp/taxonomy_icon/icon.cgi?i=Camelus+ferus&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Camelus+f...erus&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Camelus+ferus&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Camelus+ferus&t=NS ...

  19. Taxonomy Icon Data: Pacific electric ray [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Pacific electric ray Torpedo californica Chordata/Vertebrata/Pisciformes Torpedo_californica_L.png Torpedo..._californica_NL.png Torpedo_californica_S.png Torpedo_californica_NS.png http://biosc...iencedbc.jp/taxonomy_icon/icon.cgi?i=Torpedo+californica&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Torpedo...+californica&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Torpedo...+californica&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Torpedo+californica&t=NS ...

  20. Taxonomy Icon Data: Japanese tree frog [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Japanese tree frog Hyla japonica Chordata/Vertebrata/Amphibia Hyla_japonica_L.png Hyla_jap...onica_NL.png Hyla_japonica_S.png Hyla_japonica_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Hyla+jap...onica&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Hyla+japonica&t=NL http://biosciencedbc....jp/taxonomy_icon/icon.cgi?i=Hyla+japonica&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Hyla+jap

  1. Taxonomy Icon Data: Japanese giant salamander [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Japanese giant salamander Andrias japonicus Chordata/Vertebrata/Amphibia Andrias_japonicus_L.png Andrias_jap...onicus_NL.png Andrias_japonicus_S.png Andrias_japonicus_NS.png http://biosciencedbc....jp/taxonomy_icon/icon.cgi?i=Andrias+japonicus&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Andrias+jap...onicus&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Andrias+japonicus...&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Andrias+japonicus&t=NS ...

  2. A review of the taxonomy of chondrichthyan fishes: a modern perspective.

    Science.gov (United States)

    White, W T; Last, P R

    2012-04-01

    Taxonomic clarity is a fundamental requirement as it forms the foundation of all other life sciences. In the last decade, chondrichthyan taxonomy has undergone a scientific renaissance with >180 new species formally described. This effort encompasses c. 15% of the global chondrichthyan fauna, which consists of 1185 currently recognized species. The important role of chondrichthyan taxonomy for conservation management has been highlighted in recent years with new species descriptions or taxonomic resolution of a number of threatened species. These include Australian gulper (genus Centrophorus) and speartooth sharks (genus Glyphis) in coastal waters of Australia and Borneo. Closer examination of other wide-ranging species, for which the taxonomy was thought to be stable, has shown that they consist of species complexes, e.g. manta rays (Manta spp.) and spotted eagle rays (the Aetobatus narinari complex), and highlights the need for critical re-examination of other wide-ranging species. Molecular methods have provided another useful tool to taxonomists and they have proven to assist greatly with identifying cryptic species and species complexes. The limitations of particular molecular methods being used need, however, to be carefully considered and there are some concerns about how these are being integrated with classical taxonomy. The fundamental importance of taxonomic nomenclature to life sciences is often poorly understood but striving for nomenclatural stability is a critical component of taxonomy. Similarly, biological collections are an extremely vital asset to both taxonomists and the broader scientific community. These collections are becoming increasingly important due in part to molecular species identification initiatives such as the Barcode of Life which has resulted in a large number of voucher specimens linked to tissue samples being deposited. Biological collections are also proving to be imperative in biodiversity studies as they contain a 'gold mine

  3. Molecular typing of Sarcocystis neurona: current status and future trends.

    Science.gov (United States)

    Elsheikha, Hany M; Mansfield, Linda S

    2007-10-21

    Sarcocystis neurona is an important protozoal pathogen because it causes the serious neurological disease equine protozoal myeloencephalitis (EPM). The capacity of this organism to cause a wide spectrum of neurological signs in horses and the broad geographic distribution of observed cases in the Americas drive the need for sensitive, reliable and rapid typing methods to characterize strains. Various molecular methods have been developed and used to diagnose EPM due to S. neurona, to identify S. neurona isolates and to determine the heterogeneity and evolutionary relatedness within this species and related Sarcocystis spp. These methods included sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), immuno-fluorescent assay (IFA), slide agglutination test (SAT), SnSAG-specific ELISA, random amplified polymorphic DNA (RAPD), PCR-based restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) fingerprinting, and sequence analysis of surface protein genes, ribosomal genes, microsatellite alleles and other molecular markers. Here, the utility of these molecular methods is reviewed and evaluated with respect to the need for molecular approaches that utilize well-characterized polymorphic, simple, independent, and stable genetic markers. These tools have the potential to add to knowledge of the genetic population structure of S. neurona and to provide new insights into the pathogenesis of EPM and S. neurona epidemiology. In particular, these methods provide new tools to address the hypothesis that particular genetic variants are associated with adverse clinical outcomes (severe pathotypes). The ultimate goal is to utilize them in future studies to improve treatment and prevention strategies.

  4. Josephson current through a molecular transistor in a dissipative environment

    DEFF Research Database (Denmark)

    Novotny, T; Rossini, Gianpaolo; Flensberg, Karsten

    2005-01-01

    We study the Josephson coupling between two superconductors through a single correlated molecular level, including Coulomb interaction on the level and coupling to a bosonic environment. All calculations are done to the lowest, i.e., the fourth, order in the tunneling coupling and we find...

  5. Using current molecular techniques for rapid differentiation of ...

    African Journals Online (AJOL)

    Typhoid fever is responsible for the deaths of many people annually. However, conventional and timeconsuming detection methods for Salmonella Typhi still dominate. By using a molecular based approach, it was possible to identify Salmonella Typhi by amplifying two specific genes (viaB and tyv) and by using RFLP ...

  6. Reference materials for molecular diagnostics: Current achievements and future strategies.

    Science.gov (United States)

    Jing, Rongrong; Wang, Huimin; Ju, Shaoqing; Cui, Ming

    2018-06-01

    Molecular diagnoses have become more widespread in many areas of laboratory medicine where qualitative or quantitative approaches are used to detect nucleic acids. The increasing number of assay methods and the targets for molecular diagnostics contribute to variability in the test results among clinical laboratories. Thus, reference materials (RMs) are required to enhance the comparability of results. This review focuses on the definition of RMs as well as the production and characteristics of higher order RMs from different organizations and their future strategies. We describe the recent progress in RMs, including the definition of RMs by the Joint Committee for Guides in Metrology, as well as the production and characteristics of higher order RMs by international official bodies. There is an urgent need for RMs in nucleic acid testing, especially higher order RMs. To advance the harmonization and standardization of clinical nucleic acid detection, cooperation between the above organizations is proposed and different approaches to higher order RMs development are also needed. Copyright © 2018 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  7. Gliomatosis cerebri: Prognosis based on current molecular markers.

    Science.gov (United States)

    Maharaj, Monish M; Phan, Kevin; Xu, Joshua; Fairhall, Jacob; Reddy, Rajesh; Rao, Prashanth J V

    2017-09-01

    This study aims to review the literature and identify key molecular markers affecting the prognosis of Gliomatosis cerebri (2) to evaluate the level of evidence and identify outstanding markers requiring further study. A literature search was conducted across 5 major databases using the key terms: "Molecular markers" AND "Gliomatosis cerebri" OR "diffuse astrocytoma." Critical appraisal and data presentation was performed inline with the PRISMA guidelines. Following search strategy implementation, 11 studies were included in the final review process. Our data demonstrates significant prognostic value associated with IDH1 132H mutation and variable evidence surrounding the role of INA expression, MGMT promoter methylation and other factors. However, there are significant limitations in the level of evidence obtained. As the genetic basis for the pathogenesis of Gliomatosis cerebri continues to widen, there is little data on markers aside from IDH1 mutation available. IDH1 132H mutation has been demonstrated to have significant effect on survival, particularly in patients with Gliomatosis cerebri type 2. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Molecular techniques for MRSA typing: current issues and perspectives

    Directory of Open Access Journals (Sweden)

    P. A. Trindade

    Full Text Available Staphylococcus aureus has long been recognised as an important pathogen in human disease. Serious staphylococcal infections can frequently occur in inpatients and may lead to dire consequences, especially as to therapy with antimicrobial agents. The increase in the frequency of Methicillin-Resistant Staphylococcus aureus (MRSA as the causal agent of nosocomial infection and the possibility of emergence of resistance to vancomycin demands a quick and trustworthy characterization of isolates and identification of clonal spread within hospitals. Enough information must be generated to permit the implementation of appropriate measures for control of infection, so that outbreaks can be contained. Molecular typing techniques reviewed in this manuscript include: plasmid profile analysis, analysis of chromosomal DNA after enzymatic restriction, Southern blotting, pulsed field gel electrophoresis (PFGE, techniques involving polymerase chain reaction and multilocus sequence typing (MLST. Repetitive DNA Sequence PCR (rep-PCR may be used for screening due to its practicality, low cost and reproducibility. Because of its high discriminatory power Pulsed-Field Gel Electrophoresis (PFGE still remains the gold standard for MRSA typing. New techniques with higher reproducibility and discriminatory power, such as Multi-Locus Sequence Typing (MLST, are appearing. These are mostly useful for global epidemiology studies. Molecular typing techniques are invaluable tools for the assessment of putative MRSA outbreaks and so should be extensively used for this purpose.

  9. Molecular techniques for MRSA typing: current issues and perspectives

    Directory of Open Access Journals (Sweden)

    Trindade P. A.

    2003-01-01

    Full Text Available Staphylococcus aureus has long been recognised as an important pathogen in human disease. Serious staphylococcal infections can frequently occur in inpatients and may lead to dire consequences, especially as to therapy with antimicrobial agents. The increase in the frequency of Methicillin-Resistant Staphylococcus aureus (MRSA as the causal agent of nosocomial infection and the possibility of emergence of resistance to vancomycin demands a quick and trustworthy characterization of isolates and identification of clonal spread within hospitals. Enough information must be generated to permit the implementation of appropriate measures for control of infection, so that outbreaks can be contained. Molecular typing techniques reviewed in this manuscript include: plasmid profile analysis, analysis of chromosomal DNA after enzymatic restriction, Southern blotting, pulsed field gel electrophoresis (PFGE, techniques involving polymerase chain reaction and multilocus sequence typing (MLST. Repetitive DNA Sequence PCR (rep-PCR may be used for screening due to its practicality, low cost and reproducibility. Because of its high discriminatory power Pulsed-Field Gel Electrophoresis (PFGE still remains the gold standard for MRSA typing. New techniques with higher reproducibility and discriminatory power, such as Multi-Locus Sequence Typing (MLST, are appearing. These are mostly useful for global epidemiology studies. Molecular typing techniques are invaluable tools for the assessment of putative MRSA outbreaks and so should be extensively used for this purpose.

  10. Diagnosis - the limiting focus of taxonomy.

    Science.gov (United States)

    Sturmberg, Joachim P; Martin, Carmel M

    2016-02-01

    The focus on the diagnosis is a pivotal aspect of medical practice since antiquity. Diagnostic taxonomy helped to categorize ailments to improve medical care, and in its social sense resulted in validation of the sick role for some, but marginalization or stigmatization for others. In the medical industrial complex, diagnostic taxonomy structured health care financing, management and practitioner remuneration. However, with increasing demands from multiple agencies, there are increasing unintended and unwarranted consequences of our current taxonomies and diagnostic processes resulting from the conglomeration of underpinning concepts, theories, information and motivations. We argue that the increasing focus on the diagnosis resulted in excessive compartmentalization - 'partialism' - of medical practice, diminishing medical care and being naively simplistic in light of the emerging understanding of the interconnected nature of the diseasome. The human is a complex organic system of interconnecting dynamics and feedback loops responding to internal and external forces including genetic, epigenetic and environmental attractors, rather than the sum of multiple discrete organs which can develop isolated diseases or multiple morbidities. Solutions to these unintended consequences of many contemporary health system processes involve revisiting the nature of diagnostic taxonomies and the processes of their construction. A dynamic taxonomic framework would shift to more relevant attractors at personal, clinical and health system levels recognizing the non-linear nature of health and disease. Human health at an individual, group and population level is the ability to adapt to internal and external stressors with resilience throughout the life course, yet diagnostic taxonomies are increasingly constructed around fixed anchors. Understanding diagnosis as dissecting, pigeonholing or bean counting (learning by dividing) is no longer useful, the challenge for the future is to

  11. Current trends in molecular diagnostics of chronic myeloid leukemia.

    Science.gov (United States)

    Vinhas, Raquel; Cordeiro, Milton; Pedrosa, Pedro; Fernandes, Alexandra R; Baptista, Pedro V

    2017-08-01

    Nearly 1.5 million people worldwide suffer from chronic myeloid leukemia (CML), characterized by the genetic translocation t(9;22)(q34;q11.2), involving the fusion of the Abelson oncogene (ABL1) with the breakpoint cluster region (BCR) gene. Early onset diagnosis coupled to current therapeutics allow for a treatment success rate of 90, which has focused research on the development of novel diagnostics approaches. In this review, we present a critical perspective on current strategies for CML diagnostics, comparing to gold standard methodologies and with an eye on the future trends on nanotheranostics.

  12. Molecular Pathogenesis and Current Therapy in Intrahepatic Cholangiocarcinoma

    DEFF Research Database (Denmark)

    Høgdall, Dan Taksony Solyom; O'Rourke, Colm J; Taranta, Andrzej

    2016-01-01

    , the context of tumor plasticity and the causative features driving the disease. Molecular profiling and pathological techniques have begun to underline persistent alterations that may trigger inherited drug resistance (a hallmark of hepatobiliary and pancreatic cancers), metastasis and disease recurrence......Intrahepatic cholangiocarcinoma (iCCA) comprises one of the most rapidly evolving cancer types. An underlying chronic inflammatory liver disease that precedes liver cancer development for several decades and creates a pro-oncogenic microenvironment frequently impairs progress in therapeutic...... clinical strategies and patient outcome. This was achieved for other cancers, such as breast carcinoma, facilitated by the delineation of patient subsets and of precision therapies. In iCCA, many questions persevere as to the evolutionary process and cellular origin of the initial transforming event...

  13. Molecular complexity of primary open angle glaucoma: current ...

    Indian Academy of Sciences (India)

    2009-12-31

    Dec 31, 2009 ... ment nor does it develop any glaucomatous phenotype (Kim ... vestigial genomic region; only to cause harm in case of any .... level, current knowledge of genetic studies suggests that the ...... rizes the unfolding network of events in primary open angle glaucoma (POAG) and has been created based on the ...

  14. Molecular structure-adsorption study on current textile dyes.

    Science.gov (United States)

    Örücü, E; Tugcu, G; Saçan, M T

    2014-01-01

    This study was performed to investigate the adsorption of a diverse set of textile dyes onto granulated activated carbon (GAC). The adsorption experiments were carried out in a batch system. The Langmuir and Freundlich isotherm models were applied to experimental data and the isotherm constants were calculated for 33 anthraquinone and azo dyes. The adsorption equilibrium data fitted more adequately to the Langmuir isotherm model than the Freundlich isotherm model. Added to a qualitative analysis of experimental results, multiple linear regression (MLR), support vector regression (SVR) and back propagation neural network (BPNN) methods were used to develop quantitative structure-property relationship (QSPR) models with the novel adsorption data. The data were divided randomly into training and test sets. The predictive ability of all models was evaluated using the test set. Descriptors were selected with a genetic algorithm (GA) using QSARINS software. Results related to QSPR models on the adsorption capacity of GAC showed that molecular structure of dyes was represented by ionization potential based on two-dimensional topological distances, chromophoric features and a property filter index. Comparison of the performance of the models demonstrated the superiority of the BPNN over GA-MLR and SVR models.

  15. Current Trends in the Molecular Classification of Renal Neoplasms

    Directory of Open Access Journals (Sweden)

    Andrew N. Young

    2006-01-01

    Full Text Available Renal cell carcinoma (RCC is the most common form of kidney cancer in adults. RCC is a significant challenge for pathologic diagnosis and clinical management. The primary approach to diagnosis is by light microscopy, using the World Health Organization (WHO classification system, which defines histopathologic tumor subtypes with distinct clinical behavior and underlying genetic mutations. However, light microscopic diagnosis of RCC subtypes is often difficult due to variable histology. In addition, the clinical behavior of RCC is highly variable and therapeutic response rates are poor. Few clinical assays are available to predict outcome in RCC or correlate behavior with histology. Therefore, novel RCC classification systems based on gene expression should be useful for diagnosis, prognosis, and treatment. Recent microarray studies have shown that renal tumors are characterized by distinct gene expression profiles, which can be used to discover novel diagnostic and prognostic biomarkers. Here, we review clinical features of kidney cancer, the WHO classification system, and the growing role of molecular classification for diagnosis, prognosis, and therapy of this disease.

  16. Reconstitution of Biological Molecular generators of electric current. Bacteriorhodopsin.

    Science.gov (United States)

    Drachev, L A; Frolov, V N; Kaulen, A D; Liberman, E A; Ostroumov, S A; Plakunova, V G; Semenov, A Y; Skulachev, V P

    1976-11-25

    1. Photoinduced generation of electric current by bacteriorhodopsin, incorporated into the planar phospholipid membrane, has been directly measured with conventional electrometer techniques. 2. Two methods for bacteriorhodopsin incorporation have been developed: (a) formation of planar membrane from a mixture of decane solution of phospholipids and of the fraction of violet fragments of the Halobacterium halobium membrane (bacteriorhodopsin sheets), and (b) adhesion of bacteriorhodopsin-containing reconstituted spherical membranes (proteoliposomes) to the planar membrane in the presence of Ca2+ or some other cations. In both cases, illumination was found to induce electric current generation directed across the planar membrane, an effect which was measured by macroelectrodes immersed into electrolyte solutions on both sides of the membrane. 3. The maximal values of the transmembrane electric potential were of about 150 mV at a current of about 10(-11) A. The electromotive force measured by means of counterbalancing the photoeffect by an external battery, was found to reach the value of 300 mV. 4. The action spectrum of the photoeffect coincides with the bacteriorhodopsin absorption spectrum (maximum about 570 nm). 5. Both components of the electrochemical potential of H+ ions (electric potential and delta pH) across the planar membrane affect the bacteriorhodopsin photoelectric response in a fashion which could be expected if bacteriorhodopsin were a light-dependent electrogenic proton pump. 6. La3+ ions were shown to inhibit operation of those bacteriorhodopsin which pump out H+ ions from the La3+-containing compartment. 7. The photoeffect, mediated by proteoliposomes associated with thick planar membrane, is decreased by gramicidin A at concentrations which do not influence the planar membrane resistance in the light. On the contrary, a protonophorous uncoupler, trichlorocarbonylcyanidephenylhydrazone, decreases the photoeffect only if it is added at a

  17. Voltage Sensing in Membranes: From Macroscopic Currents to Molecular Motions.

    Science.gov (United States)

    Freites, J Alfredo; Tobias, Douglas J

    2015-06-01

    Voltage-sensing domains (VSDs) are integral membrane protein units that sense changes in membrane electric potential, and through the resulting conformational changes, regulate a specific function. VSDs confer voltage-sensitivity to a large superfamily of membrane proteins that includes voltage-gated Na[Formula: see text], K[Formula: see text], Ca[Formula: see text] ,and H[Formula: see text] selective channels, hyperpolarization-activated cyclic nucleotide-gated channels, and voltage-sensing phosphatases. VSDs consist of four transmembrane segments (termed S1 through S4). Their most salient structural feature is the highly conserved positions for charged residues in their sequences. S4 exhibits at least three conserved triplet repeats composed of one basic residue (mostly arginine) followed by two hydrophobic residues. These S4 basic side chains participate in a state-dependent internal salt-bridge network with at least four acidic residues in S1-S3. The signature of voltage-dependent activation in electrophysiology experiments is a transient current (termed gating or sensing current) upon a change in applied membrane potential as the basic side chains in S4 move across the membrane electric field. Thus, the unique structural features of the VSD architecture allow for competing requirements: maintaining a series of stable transmembrane conformations, while allowing charge motion, as briefly reviewed here.

  18. Taxonomy Icon Data: African savanna elephant [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available African savanna elephant Loxodonta africana Chordata/Vertebrata/Mammalia/Theria/Eutheria/etc. Loxodonta_afri...cana_L.png Loxodonta_africana_NL.png Loxodonta_africana_S.png Loxodonta_africana_NS....png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Loxodonta+africana&t=L http://biosciencedbc.jp/taxonom...y_icon/icon.cgi?i=Loxodonta+africana&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Loxodonta+afric...ana&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Loxodonta+africana&t=NS ...

  19. Taxonomy Icon Data: North Pacific right whale [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available North Pacific right whale Eubalaena japonica Chordata/Vertebrata/Mammalia/Theria/Eu...theria/Cetacea Eubalaena_japonica_L.png Eubalaena_japonica_NL.png Eubalaena_japonica_S.png Eubalaena_japonic...a_NS.png http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Eubalaena+japonica&t=L http://biosciencedbc.jp/tax...onomy_icon/icon.cgi?i=Eubalaena+japonica&t=NL http://biosciencedbc.jp/taxonomy_ic...on/icon.cgi?i=Eubalaena+japonica&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Eubalaena+japonica&t=NS ...

  20. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  1. Taxonomy Icon Data: Synechocystis sp.PCC 6803 [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Synechocystis sp.PCC 6803 Synechocystis sp.PCC 6803 Synechocystis_sp_PCC_6803_L.png Synecho...cystis_sp_PCC_6803_NL.png Synechocystis_sp_PCC_6803_S.png Synechocystis_sp_PCC_6803_NS.png http://bi...osciencedbc.jp/taxonomy_icon/icon.cgi?i=Synechocystis+sp%2ePCC+6803&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Synecho...cystis+sp%2ePCC+6803&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Synecho...cystis+sp%2ePCC+6803&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Synechocystis

  2. Deep Learning in Nuclear Medicine and Molecular Imaging: Current Perspectives and Future Directions.

    Science.gov (United States)

    Choi, Hongyoon

    2018-04-01

    Recent advances in deep learning have impacted various scientific and industrial fields. Due to the rapid application of deep learning in biomedical data, molecular imaging has also started to adopt this technique. In this regard, it is expected that deep learning will potentially affect the roles of molecular imaging experts as well as clinical decision making. This review firstly offers a basic overview of deep learning particularly for image data analysis to give knowledge to nuclear medicine physicians and researchers. Because of the unique characteristics and distinctive aims of various types of molecular imaging, deep learning applications can be different from other fields. In this context, the review deals with current perspectives of deep learning in molecular imaging particularly in terms of development of biomarkers. Finally, future challenges of deep learning application for molecular imaging and future roles of experts in molecular imaging will be discussed.

  3. Constructing a Business Model Taxonomy

    DEFF Research Database (Denmark)

    Groth, Pernille; Nielsen, Christian

    2015-01-01

    the quality of business model taxonomy studies in the future are identified. Originality/Value: The paper highlights the benefits and potential implications of designing business model taxonomy studies and makes the case for ensuring the quality of future studies relating to e.g. performance. Reviewing......Abstract Purpose: The paper proposes a research design recipe capable of leading to future business model taxonomies and discusses the potential benefits and implications of achieving this goal. Design/Methodology/Approach: The paper provides a review of relevant scholarly literature about business...... models to clarify the subject as well as highlighting the importance of past studies of business model classifications. In addition it reviews the scholarly literature on relevant methodological approaches, such as cluster analysis and latent class analysis, for constructing a business model taxonomy...

  4. A taxonomy of inductive problems.

    Science.gov (United States)

    Kemp, Charles; Jern, Alan

    2014-02-01

    Inductive inferences about objects, features, categories, and relations have been studied for many years, but there are few attempts to chart the range of inductive problems that humans are able to solve. We present a taxonomy of inductive problems that helps to clarify the relationships between familiar inductive problems such as generalization, categorization, and identification, and that introduces new inductive problems for psychological investigation. Our taxonomy is founded on the idea that semantic knowledge is organized into systems of objects, features, categories, and relations, and we attempt to characterize all of the inductive problems that can arise when these systems are partially observed. Recent studies have begun to address some of the new problems in our taxonomy, and future work should aim to develop unified theories of inductive reasoning that explain how people solve all of the problems in the taxonomy.

  5. A taxonomy for human reliability analysis

    International Nuclear Information System (INIS)

    Beattie, J.D.; Iwasa-Madge, K.M.

    1984-01-01

    A human interaction taxonomy (classification scheme) was developed to facilitate human reliability analysis in a probabilistic safety evaluation of a nuclear power plant, being performed at Ontario Hydro. A human interaction occurs, by definition, when operators or maintainers manipulate, or respond to indication from, a plant component or system. The taxonomy aids the fault tree analyst by acting as a heuristic device. It helps define the range and type of human errors to be identified in the construction of fault trees, while keeping the identification by different analysts consistent. It decreases the workload associated with preliminary quantification of the large number of identified interactions by including a category called 'simple interactions'. Fault tree analysts quantify these according to a procedure developed by a team of human reliability specialists. The interactions which do not fit into this category are called 'complex' and are quantified by the human reliability team. The taxonomy is currently being used in fault tree construction in a probabilistic safety evaluation. As far as can be determined at this early stage, the potential benefits of consistency and completeness in identifying human interactions and streamlining the initial quantification are being realized

  6. A Taxonomy of Manufacturing Strategies

    OpenAIRE

    Jeffrey G. Miller; Aleda V. Roth

    1994-01-01

    This paper describes the development and analysis of a numerical taxonomy of manufacturing strategies. The taxonomy was developed with standard methods of cluster analysis, and is based on the relative importance attached to eleven competitive capabilities defining the manufacturing task of 164 large American manufacturing business units. Three distinct clusters of manufacturing strategy groups were observed. Though there is an industry effect, all three manufacturing strategy types are obser...

  7. The Distributed Wind Cost Taxonomy

    Energy Technology Data Exchange (ETDEWEB)

    Forsyth, Trudy; Jimenez, Tony; Preus, Robert; Tegen, Suzanne; Baring-Gould, Ian

    2017-03-28

    To date, there has been no standard method or tool to analyze the installed and operational costs for distributed wind turbine systems. This report describes the development of a classification system, or taxonomy, for distributed wind turbine project costs. The taxonomy establishes a framework to help collect, sort, and compare distributed wind cost data that mirrors how the industry categorizes information. The taxonomy organizes costs so they can be aggregated from installers, developers, vendors, and other sources without losing cost details. Developing a peer-reviewed taxonomy is valuable to industry stakeholders because a common understanding the details of distributed wind turbine costs and balance of station costs is a first step to identifying potential high-value cost reduction opportunities. Addressing cost reduction potential can help increase distributed wind's competitiveness and propel the U.S. distributed wind industry forward. The taxonomy can also be used to perform cost comparisons between technologies and track trends for distributed wind industry costs in the future. As an initial application and piloting of the taxonomy, preliminary cost data were collected for projects of different sizes and from different regions across the contiguous United States. Following the methods described in this report, these data are placed into the established cost categories.

  8. Current-induced forces: a new mechanism to induce negative differential resistance and current-switching effect in molecular junctions

    Science.gov (United States)

    Gu, Lei; Fu, Hua-Hua

    2015-12-01

    Current-induced forces can excite molecules, polymers and other low-dimensional materials, which in turn leads to an effective gate voltage through Holstein interaction. Here, by taking a short asymmetric DNA junction as an example, and using the Langevin approach, we find that when suppression of charge transport by the effective gate voltage surpasses the current increase from an elevated voltage bias, the current-voltage (I-V) curves display strong negative differential resistance (NDR) and perfect current-switching characteristics. The asymmetric DNA chain differs in mechanical stability under inverse voltages and the I-V curve is asymmetric about inverse biases, which can be used to understand recent transport experiments on DNA chains, and meanwhile provides a new strategy to realize NDR in molecular junctions and other low-dimensional quantum systems.

  9. Current-induced forces: a new mechanism to induce negative differential resistance and current-switching effect in molecular junctions

    International Nuclear Information System (INIS)

    Gu, Lei; Fu, Hua-Hua

    2015-01-01

    Current-induced forces can excite molecules, polymers and other low-dimensional materials, which in turn leads to an effective gate voltage through Holstein interaction. Here, by taking a short asymmetric DNA junction as an example, and using the Langevin approach, we find that when suppression of charge transport by the effective gate voltage surpasses the current increase from an elevated voltage bias, the current-voltage (I–V) curves display strong negative differential resistance (NDR) and perfect current-switching characteristics. The asymmetric DNA chain differs in mechanical stability under inverse voltages and the I–V curve is asymmetric about inverse biases, which can be used to understand recent transport experiments on DNA chains, and meanwhile provides a new strategy to realize NDR in molecular junctions and other low-dimensional quantum systems. (paper)

  10. Jaguar taxonomy and genetic diversity for southern Arizona, United States, and Sonora, Mexico

    Science.gov (United States)

    Culver, Melanie; Hein, Alexander Ochoa

    2016-06-28

    Executive SummaryThe jaguar is the largest Neotropical felid and the only extant representative of the genus Panthera in the Americas. In recorded history, the jaguars range has extended from the Southern United States, throughout Mexico, to Central and South America, and they occupy a wide variety of habitats. A previous jaguar genetic study found high historical levels of gene flow among jaguar populations over broad areas but did not include any samples of jaguar from the States of Arizona, United States, or Sonora, Mexico. Arizona and Sonora have been part of the historical distribution of jaguars; however, poaching and habitat fragmentation have limited their distribution until they were declared extinct in the United States and endangered in Sonora. Therefore, a need was apparent to have this northernmost (Arizona/Sonora) jaguar population included in an overall jaguar molecular taxonomy and genetic diversity analyses. In this study, we used molecular genetic markers to examine diversity and taxonomy for jaguars in the Northwestern Jaguar Recovery Unit (NJRU; Sonora, Sinaloa, and Jalisco, Mexico; and southern Arizona and New Mexico, United States) relative to jaguars in other parts of the jaguar range (Central and South America). The objectives of this study were to:Collect opportunistic jaguar samples (hide, blood, hair, saliva, and scat), from historical and current individuals, that originated in NJRU areas of Arizona, New Mexico, and Sonora;Use these samples to assess molecular taxonomy of NJRU jaguars compared to data from a previous study of jaguars rangewide; andDevelop suggestions for conservation of NJRU jaguars based on the results.

  11. Pumping $ac$ Josephson current in the Single Molecular Magnets by spin nutation

    OpenAIRE

    Abdollahipour, B.; Abouie, J.; Rostami, A. A.

    2012-01-01

    We demonstrate that an {\\it ac} Josephson current is pumped through the Single Molecular Magnets (SMM) by the spin nutation. The spin nutation is generated by applying a time dependent magnetic field to the SMM. We obtain the flowing charge current through the junction by working in the tunneling limit and employing Green's function technique. At the resonance conditions some discontinuities and divergencies are appeared in the normal and Josephson currents, respectively. Such discontinuities...

  12. Current and future molecular diagnostics in non-small-cell lung cancer.

    Science.gov (United States)

    Li, Chun Man; Chu, Wing Ying; Wong, Di Lun; Tsang, Hin Fung; Tsui, Nancy Bo Yin; Chan, Charles Ming Lok; Xue, Vivian Wei Wen; Siu, Parco Ming Fai; Yung, Benjamin Yat Ming; Chan, Lawrence Wing Chi; Wong, Sze Chuen Cesar

    2015-01-01

    The molecular investigation of lung cancer has opened up an advanced area for the diagnosis and therapeutic management of lung cancer patients. Gene alterations in cancer initiation and progression provide not only information on molecular changes in lung cancer but also opportunities in advanced therapeutic regime by personalized targeted therapy. EGFR mutations and ALK rearrangement are important predictive biomarkers for the efficiency of tyrosine kinase inhibitor treatment in lung cancer patients. Moreover, epigenetic aberration and microRNA dysregulation are recent advances in the early detection and monitoring of lung cancer. Although a wide range of molecular tests are available, standardization and validation of assay protocols are essential for the quality of the test outcome. In this review, current and new advancements of molecular biomarkers for non-small-cell lung cancer will be discussed. Recommendations on future development of molecular diagnostic services will also be explored.

  13. Dose response models and a quantitative microbial risk assessment framework for the Mycobacterium avium complex that account for recent developments in molecular biology, taxonomy, and epidemiology.

    Science.gov (United States)

    Hamilton, Kerry A; Weir, Mark H; Haas, Charles N

    2017-02-01

    Mycobacterium avium complex (MAC) is a group of environmentally-transmitted pathogens of great public health importance. This group is known to be harbored, amplified, and selected for more human-virulent characteristics by amoeba species in aquatic biofilms. However, a quantitative microbial risk assessment (QMRA) has not been performed due to the lack of dose response models resulting from significant heterogeneity within even a single species or subspecies of MAC, as well as the range of human susceptibilities to mycobacterial disease. The primary human-relevant species and subspecies responsible for the majority of the human disease burden and present in drinking water, biofilms, and soil are M. avium subsp. hominissuis, M. intracellulare, and M. chimaera. A critical review of the published literature identified important health endpoints, exposure routes, and susceptible populations for MAC risk assessment. In addition, data sets for quantitative dose-response functions were extracted from published in vivo animal dosing experiments. As a result, seven new exponential dose response models for human-relevant species of MAC with endpoints of lung lesions, death, disseminated infection, liver infection, and lymph node lesions are proposed. Although current physical and biochemical tests used in clinical settings do not differentiate between M. avium and M. intracellulare, differentiating between environmental species and subspecies of the MAC can aid in the assessment of health risks and control of MAC sources. A framework is proposed for incorporating the proposed dose response models into susceptible population- and exposure route-specific QMRA models. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Nematode taxonomy: from morphology to metabarcoding

    Science.gov (United States)

    Ahmed, M.; Sapp, M.; Prior, T.; Karssen, G.; Back, M.

    2015-11-01

    Nematodes represent a species rich and morphologically diverse group of metazoans inhabiting both aquatic and terrestrial environments. Their role as biological indicators and as key players in nutrient cycling has been well documented. Some groups of nematodes are also known to cause significant losses to crop production. In spite of this, knowledge of their diversity is still limited due to the difficulty in achieving species identification using morphological characters. Molecular methodology has provided very useful means of circumventing the numerous limitations associated with classical morphology based identification. We discuss herein the history and the progress made within the field of nematode systematics, the limitations of classical taxonomy and how the advent of high throughput sequencing is facilitating advanced ecological and molecular studies.

  15. a Comparison of Morphological Taxonomy and Next Generation DNA Sequencing for the Assessment of Zooplankton Diversity

    Science.gov (United States)

    Harvey, J.; Fisher, J. L.; Johnson, S.; Morgan, S.; Peterson, W. T.; Satterthwaite, E. V.; Vrijenhoek, R. C.

    2016-02-01

    Our ability to accurately characterize the diversity of planktonic organisms is affected by both the methods we use to collect water samples and our approaches to assessing sample contents. Plankton nets collect organisms from high volumes of water, but integrate sample contents along the net's path. In contrast, plankton pumps collect water from discrete depths. Autonomous underwater vehicles (AUVs) can collect water samples with pinpoint accuracy from physical features such as upwelling fronts or biological features such as phytoplankton blooms, but sample volumes are necessarily much smaller than those possible with nets. Characterization of plankton diversity and abundances in water samples may also vary with the assessment method we apply. Morphological taxonomy provides visual identification and enumeration of organisms via microscopy, but is labor intensive. Next generation DNA sequencing (NGS) shows great promise for assessing plankton diversity in water samples but accurate assessment of relative abundances may not be possible in all cases. Comparison of morphological taxonomy to molecular approaches is necessary to identify areas of overlap and also areas of disagreement between these methods. We have compared morphological taxonomic assessments to mitochondrial COI and nuclear 28S ribosomal RNA NGS results for plankton net samples collected in Monterey bay, California. We have made a similar comparison for plankton pump samples, and have also applied our NGS methods to targeted, small volume water samples collected by an AUV. Our goal is to communicate current results and lessons learned regarding application of traditional taxonomy and novel molecular approaches to the study of plankton diversity in spatially and temporally variable, coastal marine environments.

  16. Magnetic Switching of a Single Molecular Magnet due to Spin-Polarized Current

    OpenAIRE

    Misiorny, Maciej; Barnas, Józef

    2006-01-01

    Magnetic switching of a single molecular magnet (SMM) due to spin-polarized current flowing between ferromagnetic metallic electrodes is investigated theoretically. Magnetic moments of the electrodes are assumed to be collinear and parallel to the magnetic easy axis of the molecule. Electrons tunneling through a barrier between magnetic leads are coupled to the SMM via exchange interaction. The current flowing through the system as well as the spin relaxation times of the SMM are calculated f...

  17. Discovery of energetic molecular ions (NO+ and O2+) in the storm time ring current

    International Nuclear Information System (INIS)

    Klecker, B.; Moebius, E.; Hovestadt, D.; Scholer, M.; Gloeckler, G.; Ipavich, F.M.

    1986-01-01

    A few hours after the onset of a large geomagnetic storm on September 4, 1984, energetic molecular ions in the mass range 28--32, predminantly NO + and O 2 + , have been discovered in the outer ring current at L--7. The data have been obtained with the time-of-flight spectrometer SULEICA on the AMPTE/IRM spacecraft. We find at 160 keV/e a mean abundance ratio of the molecular ions relative to O + ions of 0.031 +- 0.004. During quiet times no molecular ions are observed, the 1 sigma upper limit of the ratio derived by averaging over several quiet periods is 0.003. The observations demonstrate the injection of ionospheric plasma into the storm time ring current and the subsequent acceleration to energies of several hundred keV on a time scale of a few hours after the onset of the magnetic storm

  18. Instruments and Taxonomy of Workplace Bullying in Health Care Organizations

    Directory of Open Access Journals (Sweden)

    Eun-Jun Park, PhD, RN

    2017-12-01

    Full Text Available Summary: Purpose: This study was aimed to evaluate the methodological issues and comprehensiveness of workplace bullying instruments and to suggest a taxonomy of psychological abuse. Methods: Nineteen instruments applied in health care organizations and 469 questionnaire items mainly regarding psychological abuse were collected through a literature review. Three researchers classified the questionnaire items according to a “taxonomy of psychological abuse in the workplace.” Results: Many instruments of workplace bullying were developed in the 2000s using a reflective measurement model, but their psychometric property was not sufficient and the measurement model is questioned. Based on the questionnaire items, the “taxonomy of psychological abuse in the workplace” was modified by adding two new subcategories (unachievable work and unfair treatment and clarifying some operational definitions. According to the modified taxonomy of 11 (subcategories, the reviewed instruments assessed 6.5 (subcategories on average. No instrument measured all (subcategories. Category 4.2 (disrespect, humiliation, and rejection of the person was measured in all instruments, followed by Categories 5 (professional discredit and denigration and 1.2 (social isolation behaviors. Conclusion: The current instruments are not comprehensive enough. It is suggested that the modified taxonomy is verified and guide more reliable and inclusive instruments in the future. Furthermore, a formative measurement model, which defines a bullying as an inventory of different types of behaviors, should be used. Keywords: aggression, bullying, hostility, mobbing, surveys and questionnaires

  19. ICTV Virus Taxonomy Profile: Rhabdoviridae.

    Science.gov (United States)

    Walker, Peter J; Blasdell, Kim R; Calisher, Charles H; Dietzgen, Ralf G; Kondo, Hideki; Kurath, Gael; Longdon, Ben; Stone, David M; Tesh, Robert B; Tordo, Noël; Vasilakis, Nikos; Whitfield, Anna E; Nbsp Ictv Report Consortium

    2018-04-01

    The family Rhabdoviridae comprises viruses with negative-sense (-) single-stranded RNA genomes of 10.8-16.1 kb. Virions are typically enveloped with bullet-shaped or bacilliform morphology but can also be non-enveloped filaments. Rhabdoviruses infect plants and animals including mammals, birds, reptiles and fish, as well as arthropods which serve as single hosts or act as biological vectors for transmission to animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish and agricultural crops. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of Rhabdoviridae, which is available at www.ictv.global/report/rhabdoviridae.

  20. Fast transient current response to switching events in short chains of molecular islands

    Czech Academy of Sciences Publication Activity Database

    Kalvová, Anděla; Špička, Václav; Velický, B.

    2013-01-01

    Roč. 26, č. 4 (2013), s. 773-777 ISSN 1557-1939 R&D Projects: GA ČR GAP204/12/0897 Institutional support: RVO:68378271 Keywords : nonequilibrium * molecular islands * initial correlations * transient currents Subject RIV: BE - Theoretical Physics Impact factor: 0.930, year: 2013

  1. DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation.

    Science.gov (United States)

    Sheth, Bhavisha P; Thaker, Vrinda S

    2017-07-01

    Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification (traditional taxonomy and DNA barcoding), the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ∼41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.

  2. The morphological and molecular changes of brain cells exposed to direct current electric field stimulation.

    Science.gov (United States)

    Pelletier, Simon J; Lagacé, Marie; St-Amour, Isabelle; Arsenault, Dany; Cisbani, Giulia; Chabrat, Audrey; Fecteau, Shirley; Lévesque, Martin; Cicchetti, Francesca

    2014-12-07

    The application of low-intensity direct current electric fields has been experimentally used in the clinic to treat a number of brain disorders, predominantly using transcranial direct current stimulation approaches. However, the cellular and molecular changes induced by such treatment remain largely unknown. Here, we tested various intensities of direct current electric fields (0, 25, 50, and 100V/m) in a well-controlled in vitro environment in order to investigate the responses of neurons, microglia, and astrocytes to this type of stimulation. This included morphological assessments of the cells, viability, as well as shape and fiber outgrowth relative to the orientation of the direct current electric field. We also undertook enzyme-linked immunosorbent assays and western immunoblotting to identify which molecular pathways were affected by direct current electric fields. In response to direct current electric field, neurons developed an elongated cell body shape with neurite outgrowth that was associated with a significant increase in growth associated protein-43. Fetal midbrain dopaminergic explants grown in a collagen gel matrix also showed a reorientation of their neurites towards the cathode. BV2 microglial cells adopted distinct morphological changes with an increase in cyclooxygenase-2 expression, but these were dependent on whether they had already been activated with lipopolysaccharide. Finally, astrocytes displayed elongated cell bodies with cellular filopodia that were oriented perpendicularly to the direct current electric field. We show that cells of the central nervous system can respond to direct current electric fields both in terms of their morphological shape and molecular expression of certain proteins, and this in turn can help us to begin understand the mechanisms underlying the clinical benefits of direct current electric field. © The Author 2015. Published by Oxford University Press on behalf of CINP.

  3. Current and future molecular diagnostics in colorectal cancer and colorectal adenoma.

    Science.gov (United States)

    Tsang, Andy Hin-Fung; Cheng, Ka-Ho; Wong, Apple Siu-Ping; Ng, Simon Siu-Man; Ma, Brigette Buig-Yue; Chan, Charles Ming-Lok; Tsui, Nancy Bo-Yin; Chan, Lawrence Wing-Chi; Yung, Benjamin Yat-Ming; Wong, Sze-Chuen Cesar

    2014-04-14

    Colorectal cancer (CRC) is one of the most prevalent cancers in developed countries. On the other hand, CRC is also one of the most curable cancers if it is detected in early stages through regular colonoscopy or sigmoidoscopy. Since CRC develops slowly from precancerous lesions, early detection can reduce both the incidence and mortality of the disease. Fecal occult blood test is a widely used non-invasive screening tool for CRC. Although fecal occult blood test is simple and cost-effective in screening CRC, there is room for improvement in terms of the accuracy of the test. Genetic dysregulations have been found to play an important role in CRC development. With better understanding of the molecular basis of CRC, there is a growing expectation on the development of diagnostic tests based on more sensitive and specific molecular markers and those tests may provide a breakthrough to the limitations of current screening tests for CRC. In this review, the molecular basis of CRC development, the characteristics and applications of different non-invasive molecular biomarkers, as well as the technologies available for the detection were discussed. This review intended to provide a summary on the current and future molecular diagnostics in CRC and its pre-malignant state, colorectal adenoma.

  4. ICTV Virus Taxonomy Profile: Pleolipoviridae

    Czech Academy of Sciences Publication Activity Database

    Bamford, D.H.; Pietila, M.K.; Roine, E.; Atanasova, N.S.; Dienstbier, Ana; Oksanen, H.M.

    2017-01-01

    Roč. 98, č. 12 (2017), s. 2916-2917 ISSN 0022-1317 Institutional support: RVO:61388971 Keywords : Pleolipoviridae * taxonomy * Halorubrum pleomorphic virus 1 Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 2.838, year: 2016

  5. Chemical and molecular factors in irritable bowel syndrome: current knowledge, challenges, and unanswered questions.

    Science.gov (United States)

    Camilleri, Michael; Oduyebo, Ibironke; Halawi, Houssam

    2016-11-01

    Several chemical and molecular factors in the intestine are reported to be altered and to have a potentially significant role in irritable bowel syndrome (IBS), particularly in IBS with diarrhea. These include bile acids; short-chain fatty acids; mucosal barrier proteins; mast cell products such as histamine, proteases, and tryptase; enteroendocrine cell products; and mucosal mRNAs, proteins, and microRNAs. This article reviews the current knowledge and unanswered questions in the pathobiology of the chemical and molecular factors in IBS. Evidence continues to point to significant roles in pathogenesis of these chemical and molecular mechanisms, which may therefore constitute potential targets for future research and therapy. However, it is still necessary to address the interaction between these factors in the gut and to appraise how they may influence hypervigilance in the central nervous system in patients with IBS. Copyright © 2016 the American Physiological Society.

  6. Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

    Science.gov (United States)

    Reinhold, William C

    2015-12-10

    There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

  7. The Molecular Biology of Soft-Tissue Sarcomas and Current Trends in Therapy

    Directory of Open Access Journals (Sweden)

    Jorge Quesada

    2012-01-01

    Full Text Available Basic research in sarcoma models has been fundamental in the discovery of scientific milestones leading to a better understanding of the molecular biology of cancer. Yet, clinical research in sarcoma has lagged behind other cancers because of the multiple clinical and pathological entities that characterize sarcomas and their rarity. Sarcomas encompass a very heterogeneous group of tumors with diverse pathological and clinical overlapping characteristics. Molecular testing has been fundamental in the identification and better definition of more specific entities among this vast array of malignancies. A group of sarcomas are distinguished by specific molecular aberrations such as somatic mutations, intergene deletions, gene amplifications, reciprocal translocations, and complex karyotypes. These and other discoveries have led to a better understanding of the growth signals and the molecular pathways involved in the development of these tumors. These findings are leading to treatment strategies currently under intense investigation. Disruption of the growth signals is being targeted with antagonistic antibodies, tyrosine kinase inhibitors, and inhibitors of several downstream molecules in diverse molecular pathways. Preliminary clinical trials, supported by solid basic research and strong preclinical evidence, promises a new era in the clinical management of these broad spectrum of malignant tumors.

  8. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

    NARCIS (Netherlands)

    Belkum, van A.; Struelens, M.; Visser, de J.A.G.M.; Verburgh, H.; Tibayrenc., M.

    2001-01-01

    Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing

  9. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

    NARCIS (Netherlands)

    A.F. van Belkum (Alex); M. Struelens; A. de Visser (Arjan); H.A. Verbrugh (Henri); M. Tibayrench

    2001-01-01

    textabstractCurrently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and

  10. Comment: 235 [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available u University (currently National Research Institute of Brewing)) licensed under CC Attribution2.1 Japan 撮影: ...水谷治(東北大学(現 酒類総研)) Photo: Osamu Mizutani (Tohoku University (currently National Research Institute of Brewing)) bando 2010/08/04 09:28:07 2010/08/04 11:18:35 ...

  11. Understanding the molecular mechanism of pulse current charging for stable lithium-metal batteries

    Science.gov (United States)

    Li, Qi; Tan, Shen; Li, Linlin; Lu, Yingying; He, Yi

    2017-01-01

    High energy and safe electrochemical storage are critical components in multiple emerging fields of technologies. Rechargeable lithium-metal batteries are considered to be promising alternatives for current lithium-ion batteries, leading to as much as a 10-fold improvement in anode storage capacity (from 372 to 3860 mAh g−1). One of the major challenges for commercializing lithium-metal batteries is the reliability and safety issue, which is often associated with uneven lithium electrodeposition (lithium dendrites) during the charging stage of the battery cycling process. We report that stable lithium-metal batteries can be achieved by simply charging cells with square-wave pulse current. We investigated the effects of charging period and frequency as well as the mechanisms that govern this process at the molecular level. Molecular simulations were performed to study the diffusion and the solvation structure of lithium cations (Li+) in bulk electrolyte. The model predicts that loose association between cations and anions can enhance the transport of Li+ and eventually stabilize the lithium electrodeposition. We also performed galvanostatic measurements to evaluate the cycling behavior and cell lifetime under pulsed electric field and found that the cell lifetime can be more than doubled using certain pulse current waveforms. Both experimental and simulation results demonstrate that the effectiveness of pulse current charging on dendrite suppression can be optimized by choosing proper time- and frequency-dependent pulses. This work provides a molecular basis for understanding the mechanisms of pulse current charging to mitigating lithium dendrites and designing pulse current waveforms for stable lithium-metal batteries. PMID:28776039

  12. Team errors: definition and taxonomy

    International Nuclear Information System (INIS)

    Sasou, Kunihide; Reason, James

    1999-01-01

    In error analysis or error management, the focus is usually upon individuals who have made errors. In large complex systems, however, most people work in teams or groups. Considering this working environment, insufficient emphasis has been given to 'team errors'. This paper discusses the definition of team errors and its taxonomy. These notions are also applied to events that have occurred in the nuclear power industry, aviation industry and shipping industry. The paper also discusses the relations between team errors and Performance Shaping Factors (PSFs). As a result, the proposed definition and taxonomy are found to be useful in categorizing team errors. The analysis also reveals that deficiencies in communication, resource/task management, excessive authority gradient, excessive professional courtesy will cause team errors. Handling human errors as team errors provides an opportunity to reduce human errors

  13. ICTV Virus Taxonomy Profile: Pneumoviridae.

    Science.gov (United States)

    Rima, Bert; Collins, Peter; Easton, Andrew; Fouchier, Ron; Kurath, Gael; Lamb, Robert A; Lee, Benhur; Maisner, Andrea; Rota, Paul; Wang, Linfa; Ictv Report Consortium

    2017-12-01

    The family Pneumoviridae comprises large enveloped negative-sense RNA viruses. This taxon was formerly a subfamily within the Paramyxoviridae, but was reclassified in 2016 as a family with two genera, Orthopneumovirus and Metapneumovirus. Pneumoviruses infect a range of mammalian species, while some members of the Metapneumovirus genus may also infect birds. Some viruses are specific and pathogenic for humans, such as human respiratory syncytial virus and human metapneumovirus. There are no known vectors for pneumoviruses and transmission is thought to be primarily by aerosol droplets and contact. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Pneumoviridae, which is available at www.ictv.global/report/pneumoviridae.

  14. ICTV Virus Taxonomy Profile: Hepeviridae.

    Science.gov (United States)

    Purdy, Michael A; Harrison, Tim J; Jameel, S; Meng, X-J; Okamoto, H; Van der Poel, W H M; Smith, Donald B; Ictv Report Consortium

    2017-11-01

    The family Hepeviridae includes enterically transmitted small non-enveloped positive-sense RNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Extrahepatic manifestations of Guillain-Barré syndrome, neuralgic amyotrophy, glomerulonephritis and pancreatitis have been described in humans. Avian hepatitis E virus causes hepatitis-splenomegaly syndrome in chickens. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Hepeviridae, which is available at www.ictv.global/report/hepeviridae.

  15. ICTV Virus Taxonomy Profile: Picornaviridae.

    Science.gov (United States)

    Zell, R; Delwart, E; Gorbalenya, A E; Hovi, T; King, A M Q; Knowles, N J; Lindberg, A M; Pallansch, M A; Palmenberg, A C; Reuter, G; Simmonds, P; Skern, T; Stanway, G; Yamashita, T; Ictv Report Consortium

    2017-10-01

    The family Picornaviridae comprises small non-enveloped viruses with RNA genomes of 6.7 to 10.1 kb, and contains >30 genera and >75 species. Most of the known picornaviruses infect mammals and birds, but some have also been detected in reptiles, amphibians and fish. Many picornaviruses are important human and veterinary pathogens and may cause diseases of the central nervous system, heart, liver, skin, gastrointestinal tract or upper respiratory tract. Most picornaviruses are transmitted by the faecal-oral or respiratory routes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Picornaviridae, which is available at www.ictv.global/report/picornaviridae.

  16. Taxonomy of the extrasolar planet.

    Science.gov (United States)

    Plávalová, Eva

    2012-04-01

    When a star is described as a spectral class G2V, we know that the star is similar to our Sun. We know its approximate mass, temperature, age, and size. When working with an extrasolar planet database, it is very useful to have a taxonomy scale (classification) such as, for example, the Harvard classification for stars. The taxonomy has to be easily interpreted and present the most relevant information about extrasolar planets. I propose an extrasolar planet taxonomy scale with four parameters. The first parameter concerns the mass of an extrasolar planet in the form of units of the mass of other known planets, where M represents the mass of Mercury, E that of Earth, N Neptune, and J Jupiter. The second parameter is the planet's distance from its parent star (semimajor axis) described in a logarithm with base 10. The third parameter is the mean Dyson temperature of the extrasolar planet, for which I established four main temperature classes: F represents the Freezing class, W the Water class, G the Gaseous class, and R the Roasters class. I devised one additional class, however: P, the Pulsar class, which concerns extrasolar planets orbiting pulsar stars. The fourth parameter is eccentricity. If the attributes of the surface of the extrasolar planet are known, we are able to establish this additional parameter where t represents a terrestrial planet, g a gaseous planet, and i an ice planet. According to this taxonomy scale, for example, Earth is 1E0W0t, Neptune is 1N1.5F0i, and extrasolar planet 55 Cnc e is 9E-1.8R1.

  17. Evaluating a medical error taxonomy.

    OpenAIRE

    Brixey, Juliana; Johnson, Todd R.; Zhang, Jiajie

    2002-01-01

    Healthcare has been slow in using human factors principles to reduce medical errors. The Center for Devices and Radiological Health (CDRH) recognizes that a lack of attention to human factors during product development may lead to errors that have the potential for patient injury, or even death. In response to the need for reducing medication errors, the National Coordinating Council for Medication Errors Reporting and Prevention (NCC MERP) released the NCC MERP taxonomy that provides a stand...

  18. Spumaretroviruses: Updated taxonomy and nomenclature.

    Science.gov (United States)

    Khan, Arifa S; Bodem, Jochen; Buseyne, Florence; Gessain, Antoine; Johnson, Welkin; Kuhn, Jens H; Kuzmak, Jacek; Lindemann, Dirk; Linial, Maxine L; Löchelt, Martin; Materniak-Kornas, Magdalena; Soares, Marcelo A; Switzer, William M

    2018-03-01

    Spumaretroviruses, commonly referred to as foamy viruses, are complex retroviruses belonging to the subfamily Spumaretrovirinae, family Retroviridae, which naturally infect a variety of animals including nonhuman primates (NHPs). Additionally, cross-species transmissions of simian foamy viruses (SFVs) to humans have occurred following exposure to tissues of infected NHPs. Recent research has led to the identification of previously unknown exogenous foamy viruses, and to the discovery of endogenous spumaretrovirus sequences in a variety of host genomes. Here, we describe an updated spumaretrovirus taxonomy that has been recently accepted by the International Committee on Taxonomy of Viruses (ICTV) Executive Committee, and describe a virus nomenclature that is generally consistent with that used for other retroviruses, such as lentiviruses and deltaretroviruses. This taxonomy can be applied to distinguish different, but closely related, primate (e.g., human, ape, simian) foamy viruses as well as those from other hosts. This proposal accounts for host-virus co-speciation and cross-species transmission. Published by Elsevier Inc.

  19. Current status of molecular biological techniques for plant breeding in the Republic of Korea

    Energy Technology Data Exchange (ETDEWEB)

    Sohn, Seong-Han; Lee, Si-Myung; Park, Bum-Seok; Yun, In-Sun; Goo, Doe-Hoe; Kim, Seok-Dong [Rural Development Administration, National Institute of Agricultural Science and Technology, Suwon (Korea)

    2002-02-01

    Classical plant breeding has played an important role in developing new varieties in current agriculture. For decades, the technique of cross-pollination has been popular for breeding in cereal and horticultural crops to introduce special traits. However, recently the molecular techniques get widely accepted as an alternative tool in both introducing a useful trait for developing the new cultivars and investigating the characteristics of a trait in plant, like the identification of a gene. Using the advanced molecular technique, several genetically modified (GM) crops (e.g., Roundup Ready Soybean, YieldGard, LibertyLink etc.) became commercially cultivated and appeared in the global market since 1996. The GM crops, commercially available at the moment, could be regarded as successful achievements in history of crop breeding conferring the specific gene into economically valuable crops to make them better. Along with such achievements, on the other hand these new crops have also caused the controversial debate on the safety of GM crops as human consumption and environmental release as well. Nevertheless, molecular techniques are widespread and popular in both investigating the basic science of plant biology and breeding new varieties compared to their conventional counterparts. Thus, the Department of Bioresources at the National Institute of Agricultural Science and Technology (NIAST) has been using the molecular biological techniques as a complimentary tool for the improvement of crop varieties for almost two decades. (author)

  20. Balance Sheet Taxonomy

    Directory of Open Access Journals (Sweden)

    Ecaterina Necsulescu

    2011-05-01

    Full Text Available The general objective of the financial statements is to provide information about the financial position, financial performance and cash flows of an entity, information that is useful for a wide range of users. For the current paper is very interesting to take into account is the presentation of the important role given to assets even in defining the subject of accounting, both in economic and financial concept.

  1. Molecular Targets for PET Imaging of Activated Microglia: The Current Situation and Future Expectations.

    Science.gov (United States)

    Tronel, Claire; Largeau, Bérenger; Santiago Ribeiro, Maria Joao; Guilloteau, Denis; Dupont, Anne-Claire; Arlicot, Nicolas

    2017-04-11

    Microglia, as cellular mediators of neuroinflammation, are implicated in the pathogenesis of a wide range of neurodegenerative diseases. Positron emission tomography (PET) imaging of microglia has matured over the last 20 years, through the development of radiopharmaceuticals targeting several molecular biomarkers of microglial activation and, among these, mainly the translocator protein-18 kDa (TSPO). Nevertheless, current limitations of TSPO as a PET microglial biomarker exist, such as low brain density, even in a neurodegenerative setting, expression by other cells than the microglia (astrocytes, peripheral macrophages in the case of blood brain barrier breakdown), genetic polymorphism, inducing a variation for most of TSPO PET radiopharmaceuticals' binding affinity, or similar expression in activated microglia regardless of its polarization (pro- or anti-inflammatory state), and these limitations narrow its potential interest. We overview alternative molecular targets, for which dedicated radiopharmaceuticals have been proposed, including receptors (purinergic receptors P2X7, cannabinoid receptors, α7 and α4β2 nicotinic acetylcholine receptors, adenosine 2A receptor, folate receptor β) and enzymes (cyclooxygenase, nitric oxide synthase, matrix metalloproteinase, β-glucuronidase, and enzymes of the kynurenine pathway), with a particular focus on their respective contribution for the understanding of microglial involvement in neurodegenerative diseases. We discuss opportunities for these potential molecular targets for PET imaging regarding their selectivity for microglia expression and polarization, in relation to the mechanisms by which microglia actively participate in both toxic and neuroprotective actions in brain diseases, and then take into account current clinicians' expectations.

  2. Ab initio theory for current-induced molecular switching: Melamine on Cu(001)

    KAUST Repository

    Ohto, Tatsuhiko

    2013-05-28

    Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green\\'s function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current. © 2013 American Physical Society.

  3. Magnetic switching of a single molecular magnet due to spin-polarized current

    Science.gov (United States)

    Misiorny, Maciej; Barnaś, Józef

    2007-04-01

    Magnetic switching of a single molecular magnet (SMM) due to spin-polarized current flowing between ferromagnetic metallic leads (electrodes) is investigated theoretically. Magnetic moments of the leads are assumed to be collinear and parallel to the magnetic easy axis of the molecule. Electrons tunneling through the barrier between magnetic leads are coupled to the SMM via exchange interaction. The current flowing through the system, as well as the spin relaxation times of the SMM, are calculated from the Fermi golden rule. It is shown that spin of the SMM can be reversed by applying a certain voltage between the two magnetic electrodes. Moreover, the switching may be visible in the corresponding current-voltage characteristics.

  4. Ab initio theory for current-induced molecular switching: Melamine on Cu(001)

    KAUST Repository

    Ohto, Tatsuhiko; Rungger, Ivan; Yamashita, Koichi; Nakamura, Hisao; Sanvito, Stefano

    2013-01-01

    Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green's function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current. © 2013 American Physical Society.

  5. COPD: time to improve its taxonomy?

    Directory of Open Access Journals (Sweden)

    Bartolomé R. Celli

    2018-02-01

    Full Text Available Due to well-conducted epidemiological studies and advances in genetics, molecular biology, translational research, the advent of computed tomography of the lungs and bioinformatics, the diagnosis of chronic obstructive pulmonary disease (COPD as a single entity caused by susceptibility to cigarette smoke is no longer tenable. Furthermore, the once-accepted concept that COPD results from a rapid and progressive loss of lung function over time is not true for a sizeable proportion of adults with the disease. Now we know that some genetic predisposition and/or different environmental interactions (nutritional, infectious, pollution and immunological may negatively modulate post-natal lung development and lead to poorly reversible airflow limitation later in life, consistent with COPD. We believe it is time to rethink the taxonomy of this disease based on the evidence at hand. To do so, we have followed the principles outlined in the 1980s by J.D. Scadding who proposed that diseases can be defined by four key characteristics: 1 clinical description (syndrome, 2 disorder of structure (morbid anatomy, 3 disorder of function (pathophysiology and 4 causation (aetiology. Here, we propose a pragmatic approach to the taxonomy of COPD based on different processes that result in a similar syndromic presentation. It can accommodate changes over time, as the pathobiology that may lead to COPD expands. We hope that stakeholders in the field may find it useful to better define the patients now boxed into one single entity, so that specific studies can be designed and conducted for each type of COPDs.

  6. Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease.

    Science.gov (United States)

    Ellingford, Jamie M; Barton, Stephanie; Bhaskar, Sanjeev; Williams, Simon G; Sergouniotis, Panagiotis I; O'Sullivan, James; Lamb, Janine A; Perveen, Rahat; Hall, Georgina; Newman, William G; Bishop, Paul N; Roberts, Stephen A; Leach, Rick; Tearle, Rick; Bayliss, Stuart; Ramsden, Simon C; Nemeth, Andrea H; Black, Graeme C M

    2016-05-01

    To compare the efficacy of whole genome sequencing (WGS) with targeted next-generation sequencing (NGS) in the diagnosis of inherited retinal disease (IRD). Case series. A total of 562 patients diagnosed with IRD. We performed a direct comparative analysis of current molecular diagnostics with WGS. We retrospectively reviewed the findings from a diagnostic NGS DNA test for 562 patients with IRD. A subset of 46 of 562 patients (encompassing potential clinical outcomes of diagnostic analysis) also underwent WGS, and we compared mutation detection rates and molecular diagnostic yields. In addition, we compared the sensitivity and specificity of the 2 techniques to identify known single nucleotide variants (SNVs) using 6 control samples with publically available genotype data. Diagnostic yield of genomic testing. Across known disease-causing genes, targeted NGS and WGS achieved similar levels of sensitivity and specificity for SNV detection. However, WGS also identified 14 clinically relevant genetic variants through WGS that had not been identified by NGS diagnostic testing for the 46 individuals with IRD. These variants included large deletions and variants in noncoding regions of the genome. Identification of these variants confirmed a molecular diagnosis of IRD for 11 of the 33 individuals referred for WGS who had not obtained a molecular diagnosis through targeted NGS testing. Weighted estimates, accounting for population structure, suggest that WGS methods could result in an overall 29% (95% confidence interval, 15-45) uplift in diagnostic yield. We show that WGS methods can detect disease-causing genetic variants missed by current NGS diagnostic methodologies for IRD and thereby demonstrate the clinical utility and additional value of WGS. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

  7. Sistemática, taxonomía y domesticación de alpacas y llamas: nueva evidencia cromosómica y molecular Systematics, taxonomy and domestication of alpaca and llama: new chromosomal and molecular evidence

    Directory of Open Access Journals (Sweden)

    JUAN C MARÍN

    2007-06-01

    Full Text Available Existen cuatro especies de camélidos sudamericanos, dos de ellos silvestres, guanaco (Lama guanicoe y vicuña (Vicugna vicugna, y dos formas domésticas, alpaca (Lama pacos y llama (Lama glama, cuyo origen ha sido objeto de debate. En el presente estudio la variación en el patrón de bandas G de los cromosomas de llamas y alpacas y la secuencia de dos genes mitocondriales han sido usados para estudiar el origen y la clasificación de llamas y alpacas. Patrones de bandas cromosómicas similares fueron observados en las cuatro especies de Lamini, incluso similares a los descritos para camello, Camelus bactrianus. Sin embargo, se encontraron finas y consistentes diferencias en los brazos cortos del cromosoma 1, permitiendo separar a camellos, guanacos y llamas, de las de vicuñas y alpacas. Este patrón fue consistente incluso en un híbrido guanaco x alpaca. Relaciones equivalentes fueron encontradas en las secuencias completas del gen para citocromo b, así como en el árbol de expansión mínima de las secuencias parciales de la región control, agrupando a guanacos con llamas y a vicuñas con alpacas. Los análisis filogenéticos mostraron a V. vicugna y a L. guanicoe como grupos recíprocamente monofHéticos. El análisis de las secuencias de ambos genes mostró dos ciados entre las vicuñas, concordantes con las subespecies reconocidas para esta especie, pero los resultados obtenidos para guanacos no reflejaron la existencia de las cuatro subespecies previamente propuestas. El análisis combinado de variaciones cromosómicas y moleculares demostraron una alta similitud genética entre alpacas y vicuñas, así como entre llamas y guanacos. Aunque se revela hibridización direccional, nuestros resultados apoyan fuertemente la hipótesis de que la llama se deriva de L. guanicoe, y la alpaca de V. vicugna, apoyando la reclasificación de la alpaca como V. pacosFour camelid species exist in South America: two wild, the guanaco (Lama guanicoe and

  8. A taxonomy of integral reaction path analysis

    Energy Technology Data Exchange (ETDEWEB)

    Grcar, Joseph F.; Day, Marcus S.; Bell, John B.

    2004-12-23

    W. C. Gardiner observed that achieving understanding through combustion modeling is limited by the ability to recognize the implications of what has been computed and to draw conclusions about the elementary steps underlying the reaction mechanism. This difficulty can be overcome in part by making better use of reaction path analysis in the context of multidimensional flame simulations. Following a survey of current practice, an integral reaction flux is formulated in terms of conserved scalars that can be calculated in a fully automated way. Conditional analyses are then introduced, and a taxonomy for bidirectional path analysis is explored. Many examples illustrate the resulting path analysis and uncover some new results about nonpremixed methane-air laminar jets.

  9. Open-boundary Ehrenfest molecular dynamics: towards a model of current induced heating in nanowires

    International Nuclear Information System (INIS)

    Horsfield, Andrew P; Bowler, D R; Fisher, A J

    2004-01-01

    We present a time-dependent method based on the single-particle electron density matrix that allows the electronic and ionic degrees of freedom to be modelled within the Ehrenfest approximation in the presence of open boundaries. We describe a practical implementation using tight binding, and use it to investigate steady-state conduction through a single-atom device and to perform molecular dynamics. We find that in the Ehrenfest approximation an electric current allows both ionic heating and cooling to take place, depending on the bias. (letter to the editor)

  10. Expanding the taxonomy of the diagnostic criteria for temporomandibular disorders.

    Science.gov (United States)

    Peck, C C; Goulet, J-P; Lobbezoo, F; Schiffman, E L; Alstergren, P; Anderson, G C; de Leeuw, R; Jensen, R; Michelotti, A; Ohrbach, R; Petersson, A; List, T

    2014-01-01

    There is a need to expand the current temporomandibular disorders' (TMDs) classification to include less common but clinically important disorders. The immediate aim was to develop a consensus-based classification system and associated diagnostic criteria that have clinical and research utility for less common TMDs. The long-term aim was to establish a foundation, vis-à-vis this classification system, that will stimulate data collection, validity testing and further criteria refinement. A working group [members of the International RDC/TMD Consortium Network of the International Association for Dental Research (IADR), members of the Orofacial Pain Special Interest Group (SIG) of the International Association for the Study of Pain (IASP), and members from other professional societies] reviewed disorders for inclusion based on clinical significance, the availability of plausible diagnostic criteria and the ability to operationalise and study the criteria. The disorders were derived from the literature when possible and based on expert opinion as necessary. The expanded TMDs taxonomy was presented for feedback at international meetings. Of 56 disorders considered, 37 were included in the expanded taxonomy and were placed into the following four categories: temporomandibular joint disorders, masticatory muscle disorders, headache disorders and disorders affecting associated structures. Those excluded were extremely uncommon, lacking operationalised diagnostic criteria, not clearly related to TMDs, or not sufficiently distinct from disorders already included within the taxonomy. The expanded TMDs taxonomy offers an integrated approach to clinical diagnosis and provides a framework for further research to operationalise and test the proposed taxonomy and diagnostic criteria. © 2014 John Wiley & Sons Ltd.

  11. A refined taxonomy of behaviour change techniques to help people change their physical activity and healthy eating behaviours: the CALO-RE taxonomy.

    Science.gov (United States)

    Michie, Susan; Ashford, Stefanie; Sniehotta, Falko F; Dombrowski, Stephan U; Bishop, Alex; French, David P

    2011-11-01

    Current reporting of intervention content in published research articles and protocols is generally poor, with great diversity of terminology, resulting in low replicability. This study aimed to extend the scope and improve the reliability of a 26-item taxonomy of behaviour change techniques developed by Abraham and Michie [Abraham, C. and Michie, S. (2008). A taxonomy of behaviour change techniques used in interventions. Health Psychology, 27(3), 379-387.] in order to optimise the reporting and scientific study of behaviour change interventions. Three UK study centres collaborated in applying this existing taxonomy to two systematic reviews of interventions to increase physical activity and healthy eating. The taxonomy was refined in iterative steps of (1) coding intervention descriptions, and assessing inter-rater reliability, (2) identifying gaps and problems across study centres and (3) refining the labels and definitions based on consensus discussions. Labels and definitions were improved for all techniques, conceptual overlap between categories was resolved, some categories were split and 14 techniques were added, resulting in a 40-item taxonomy. Inter-rater reliability, assessed on 50 published intervention descriptions, was good (kappa = 0.79). This taxonomy can be used to improve the specification of interventions in published reports, thus improving replication, implementation and evidence syntheses. This will strengthen the scientific study of behaviour change and intervention development.

  12. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

    Science.gov (United States)

    McDonald, Daniel; Price, Morgan N; Goodrich, Julia; Nawrocki, Eric P; DeSantis, Todd Z; Probst, Alexander; Andersen, Gary L; Knight, Rob; Hugenholtz, Philip

    2012-03-01

    Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

  13. Een revisie van de taxonomie van gifkikkers

    NARCIS (Netherlands)

    Poelman, E.H.

    2007-01-01

    Recent kwam het lang verwachte ruim tweehonderdvijftig pagina`s tellende manuscript uit met daarin een revisie van de taxonomie van gifkikkers. De auteurs onder leiding van Taran Grant stellen een nieuwe taxonomie voor, die de familie Dendrobatidae met haar tien algemener geaccepteerde genera

  14. A taxonomy of distributed denial of service attacks

    DEFF Research Database (Denmark)

    De Donno, Michele; Giaretta, Alberto; Dragoni, Nicola

    2017-01-01

    Distributed Denial of Service (DDoS) attacks which are now even more powerful and easier to achieve than the past. Understanding how these attacks work, in all their different forms, represents a first crucial step to tackle this urgent issue. To this end, in this paper we propose a new up-to-date taxonomy...... and a comprehensive classification of current DDoS attacks....

  15. Generalized metamaterials: Definitions and taxonomy.

    Science.gov (United States)

    Kim, Noori; Yoon, Yong-Jin; Allen, Jont B

    2016-06-01

    This article reviews the development of metamaterials (MM), starting from Newton's discovery of the wave equation, and ends with a discussion of the need for a technical taxonomy (classification) of these materials, along with a better defined definition of metamaterials. It is intended to be a technical definition of metamaterials, based on a historical perspective. The evolution of MMs began with the discovery of the wave equation, traceable back to Newton's calculation of the speed of sound. The theory of sound evolved to include quasi-statics (Helmholtz) and the circuit equations of Kirchhoff's circuit laws, leading to the ultimate development of Maxwell's equations and the equation for the speed of light. Be it light, or sound, the speed of the wave-front travel defines the wavelength, and thus the quasi-static (QS) approximation. But there is much more at stake than QSs. Taxonomy requires a proper statement of the laws of physics, which includes at least the six basic network postulates: (P1) causality (non-causal/acausal), (P2) linearity (non-linear), (P3) real (complex) time response, (P4) passive (active), (P5) time-invariant (time varying), and (P6) reciprocal (non-reciprocal). These six postulates are extended to include MMs.

  16. GEM Building Taxonomy (Version 2.0)

    Science.gov (United States)

    Brzev, S.; Scawthorn, C.; Charleson, A.W.; Allen, L.; Greene, M.; Jaiswal, Kishor; Silva, V.

    2013-01-01

    This report documents the development and applications of the Building Taxonomy for the Global Earthquake Model (GEM). The purpose of the GEM Building Taxonomy is to describe and classify buildings in a uniform manner as a key step towards assessing their seismic risk, Criteria for development of the GEM Building Taxonomy were that the Taxonomy be relevant to seismic performance of different construction types; be comprehensive yet simple; be collapsible; adhere to principles that are familiar to the range of users; and ultimately be extensible to non-buildings and other hazards. The taxonomy was developed in conjunction with other GEM researchers and builds on the knowledge base from other taxonomies, including the EERI and IAEE World Housing Encyclopedia, PAGER-STR, and HAZUS. The taxonomy is organized as a series of expandable tables, which contain information pertaining to various building attributes. Each attribute describes a specific characteristic of an individual building or a class of buildings that could potentially affect their seismic performance. The following 13 attributes have been included in the GEM Building Taxonomy Version 2.0 (v2.0): 1.) direction, 2.)material of the lateral load-resisting system, 3.) lateral load-resisting system, 4.) height, 5.) date of construction of retrofit, 6.) occupancy, 7.) building position within a block, 8.) shape of the building plan, 9.) structural irregularity, 10.) exterior walls, 11.) roof, 12.) floor, 13.) foundation system. The report illustrates the pratical use of the GEM Building Taxonomy by discussing example case studies, in which the building-specific characteristics are mapped directly using GEM taxonomic attributes and the corresponding taxonomic string is constructed for that building, with "/" slash marks separating attributes. For example, for the building shown to the right, the GEM Taxonomy string is: DX1/MUR+CLBRS+MOCL2/LWAL3/

  17. Taxonomy of the ant genus Nesomyrmex Wheeler (Formicidae, Myrmicinae in the Afrotropical region, with a review of current species groups and description of a new species of the N. angulatus group from Mozambique

    Directory of Open Access Journals (Sweden)

    Francisco Hita Garcia

    2017-01-01

    Full Text Available This study reviews the taxonomy of the ant genus Nesomyrmex Wheeler, 1910 in the Afrotropical region. Previous revisionary studies are discussed and four species groups are proposed on the basis of external morphology. The N. angulatus group contains seven species that are widely distributed throughout the whole Afrotropical region, with one species also occurring in the Palaearctic and Malagasy regions. The N. cataulacoides group is monotypic, with one morphologically bizarre species found in Equatorial rain forests. The N. humerosus group is also monotypic and occurs in East Africa. The last and by far most species-rich group is the N. simoni group that contains 17 species, all of which are endemic to South Africa. The four groups are defined for the first time for the region, and an illustrated identification key is provided. Furthermore, the N. angulatus group is more thoroughly reviewed. One new species from Mozambique is described, N. inhaca sp. nov., and species accounts for the other six are provided. Also, an illustrated identification key to the species of the N. angulatus group is presented.

  18. Taxonomy

    DEFF Research Database (Denmark)

    Stauffer, Jr., Jay Richard; Madsen, Henry; Konings, Adrianus

    2007-01-01

    We have observed a dramatic decrease in the abundance of snail-eating fishes and an increase in the prevalence of schistosomiasis among village residents and expatriate tourists at Lake Malawi, Africa, over the past two decades. We hypothesized that these observations were linked by a cause-and-e...... identified. Before we can identify the interactions among these components of the system and effectively manage snail-eating fishes, we must be able to accurately delimit the taxonomic units (e.g., species, populations, and demes) within each of the above groups....

  19. Quality control for terms and definitions in ontologies and taxonomies

    Directory of Open Access Journals (Sweden)

    Rüegg Alexander

    2006-04-01

    Full Text Available Abstract Background Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO, the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.

  20. Current Understanding of Molecular Pathology and Treatment of Cardiomyopathy in Duchenne Muscular Dystrophy

    Directory of Open Access Journals (Sweden)

    Tirsa L. E. van Westering

    2015-05-01

    Full Text Available Duchenne muscular dystrophy (DMD is a genetic muscle disorder caused by mutations in the Dmd gene resulting in the loss of the protein dystrophin. Patients do not only experience skeletal muscle degeneration, but also develop severe cardiomyopathy by their second decade, one of the main causes of death. The absence of dystrophin in the heart renders cardiomyocytes more sensitive to stretch-induced damage. Moreover, it pathologically alters intracellular calcium (Ca2+ concentration, neuronal nitric oxide synthase (nNOS localization and mitochondrial function and leads to inflammation and necrosis, all contributing to the development of cardiomyopathy. Current therapies only treat symptoms and therefore the need for targeting the genetic defect is immense. Several preclinical therapies are undergoing development, including utrophin up-regulation, stop codon read-through therapy, viral gene therapy, cell-based therapy and exon skipping. Some of these therapies are undergoing clinical trials, but these have predominantly focused on skeletal muscle correction. However, improving skeletal muscle function without addressing cardiac aspects of the disease may aggravate cardiomyopathy and therefore it is essential that preclinical and clinical focus include improving heart function. This review consolidates what is known regarding molecular pathology of the DMD heart, specifically focusing on intracellular Ca2+, nNOS and mitochondrial dysregulation. It briefly discusses the current treatment options and then elaborates on the preclinical therapeutic approaches currently under development to restore dystrophin thereby improving pathology, with a focus on the heart.

  1. Molecular Diagnostics for Precision Medicine in Colorectal Cancer: Current Status and Future Perspective

    Directory of Open Access Journals (Sweden)

    Guoli Chen

    2016-01-01

    Full Text Available Precision medicine, a concept that has recently emerged and has been widely discussed, emphasizes tailoring medical care to individuals largely based on information acquired from molecular diagnostic testing. As a vital aspect of precision cancer medicine, targeted therapy has been proven to be efficacious and less toxic for cancer treatment. Colorectal cancer (CRC is one of the most common cancers and among the leading causes for cancer related deaths in the United States and worldwide. By far, CRC has been one of the most successful examples in the field of precision cancer medicine, applying molecular tests to guide targeted therapy. In this review, we summarize the current guidelines for anti-EGFR therapy, revisit the roles of pathologists in an era of precision cancer medicine, demonstrate the transition from traditional “one test-one drug” assays to multiplex assays, especially by using next-generation sequencing platforms in the clinical diagnostic laboratories, and discuss the future perspectives of tumor heterogeneity associated with anti-EGFR resistance and immune checkpoint blockage therapy in CRC.

  2. Ab initio molecular dynamics: basic concepts, current trends and novel applications

    International Nuclear Information System (INIS)

    Tuckerman, Mark E

    2002-01-01

    The field of ab initio molecular dynamics (AIMD), in which finite temperature molecular dynamics (MD) trajectories are generated with forces obtained from accurate 'on the fly' electronic structure calculations, is a rapidly evolving and growing technology that allows chemical processes in condensed phases to be studied in an accurate and unbiased way. This article is intended to present the basics of the AIMD method as well as to provide a broad survey of the state of the art of the field and showcase some of its capabilities. Beginning with a derivation of the method from the Born-Oppenheimer approximation, issues including the density functional representation of electronic structure, basis sets, calculation of observables and the Car-Parrinello extended Lagrangian algorithm are discussed. A number of example applications, including liquid structure and dynamics and aqueous proton transport, are presented in order to highlight some of the current capabilities of the approach. Finally, advanced topics such as inclusion of nuclear quantum effects, excited states and scaling issues are addressed. (topical review)

  3. Current Methods in the Molecular Typing of Mycobacterium tuberculosis and Other Mycobacteria

    Science.gov (United States)

    van Ingen, Jakko; Dziadek, Jarosław; Mazur, Paweł K.; Bielecki, Jacek

    2014-01-01

    In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individual Mycobacterium strains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on the Mycobacterium species under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing of M. tuberculosis and some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed. PMID:24527454

  4. Molecular Diagnostics for Precision Medicine in Colorectal Cancer: Current Status and Future Perspective.

    Science.gov (United States)

    Chen, Guoli; Yang, Zhaohai; Eshleman, James R; Netto, George J; Lin, Ming-Tseh

    2016-01-01

    Precision medicine, a concept that has recently emerged and has been widely discussed, emphasizes tailoring medical care to individuals largely based on information acquired from molecular diagnostic testing. As a vital aspect of precision cancer medicine, targeted therapy has been proven to be efficacious and less toxic for cancer treatment. Colorectal cancer (CRC) is one of the most common cancers and among the leading causes for cancer related deaths in the United States and worldwide. By far, CRC has been one of the most successful examples in the field of precision cancer medicine, applying molecular tests to guide targeted therapy. In this review, we summarize the current guidelines for anti-EGFR therapy, revisit the roles of pathologists in an era of precision cancer medicine, demonstrate the transition from traditional "one test-one drug" assays to multiplex assays, especially by using next-generation sequencing platforms in the clinical diagnostic laboratories, and discuss the future perspectives of tumor heterogeneity associated with anti-EGFR resistance and immune checkpoint blockage therapy in CRC.

  5. Multilevel Molecular Modeling Approach for a Rational Design of Ionic Current Sensors for Nanofluidics.

    Science.gov (United States)

    Kirch, Alexsandro; de Almeida, James M; Miranda, Caetano R

    2018-05-10

    The complexity displayed by nanofluidic-based systems involves electronic and dynamic aspects occurring across different size and time scales. To properly model such kind of system, we introduced a top-down multilevel approach, combining molecular dynamics simulations (MD) with first-principles electronic transport calculations. The potential of this technique was demonstrated by investigating how the water and ionic flow through a (6,6) carbon nanotube (CNT) influences its electronic transport properties. We showed that the confinement on the CNT favors the partially hydrated Na, Cl, and Li ions to exchange charge with the nanotube. This leads to a change in the electronic transmittance, allowing for the distinguishing of cations from anions. Such an ionic trace may handle an indirect measurement of the ionic current that is recorded as a sensing output. With this case study, we are able to show the potential of this top-down multilevel approach, to be applied on the design of novel nanofluidic devices.

  6. Cancer of the Pancreas: Molecular Pathways and Current Advancement in Treatment.

    Science.gov (United States)

    Polireddy, Kishore; Chen, Qi

    2016-01-01

    Pancreatic cancer is one of the most lethal cancers among all malignances, with a median overall survival of cancers harbor a variety of genetic alternations that render it difficult to treat even with targeted therapy. Recent studies revealed that pancreatic cancers are highly enriched with a cancer stem cell (CSC) population, which is resistant to chemotherapeutic drugs, and therefore escapes chemotherapy and promotes tumor recurrence. Cancer cell epithelial to mesenchymal transition (EMT) is highly associated with metastasis, generation of CSCs, and treatment resistance in pancreatic cancer. Reviewed here are the molecular biology of pancreatic cancer, the major signaling pathways regulating pancreatic cancer EMT and CSCs, and the advancement in current clinical and experimental treatments for pancreatic cancer.

  7. Fragment-orbital tunneling currents and electronic couplings for analysis of molecular charge-transfer systems.

    Science.gov (United States)

    Hwang, Sang-Yeon; Kim, Jaewook; Kim, Woo Youn

    2018-04-04

    In theoretical charge-transfer research, calculation of the electronic coupling element is crucial for examining the degree of the electronic donor-acceptor interaction. The tunneling current (TC), representing the magnitudes and directions of electron flow, provides a way of evaluating electronic couplings, along with the ability of visualizing how electrons flow in systems. Here, we applied the TC theory to π-conjugated organic dimer systems, in the form of our fragment-orbital tunneling current (FOTC) method, which uses the frontier molecular-orbitals of system fragments as diabatic states. For a comprehensive test of FOTC, we assessed how reasonable the computed electronic couplings and the corresponding TC densities are for the hole- and electron-transfer databases HAB11 and HAB7. FOTC gave 12.5% mean relative unsigned error with regard to the high-level ab initio reference. The shown performance is comparable with that of fragment-orbital density functional theory, which gave the same error by 20.6% or 13.9% depending on the formulation. In the test of a set of nucleobase π stacks, we showed that the original TC expression is also applicable to nondegenerate cases under the condition that the overlap between the charge distributions of diabatic states is small enough to offset the energy difference. Lastly, we carried out visual analysis on the FOTC densities of thiophene dimers with different intermolecular alignments. The result depicts an intimate topological connection between the system geometry and electron flow. Our work provides quantitative and qualitative grounds for FOTC, showing it to be a versatile tool in characterization of molecular charge-transfer systems.

  8. Phylogeny and taxonomy of the scab and spot anthracnose fungus Elsinoë (Myriangiales, Dothideomycetes).

    Science.gov (United States)

    Fan, X L; Barreto, R W; Groenewald, J Z; Bezerra, J D P; Pereira, O L; Cheewangkoon, R; Mostert, L; Tian, C M; Crous, P W

    2017-06-01

    Species of Elsinoë are phytopathogens causing scab and spot anthracnose on many plants, including some economically important crops such as avocado, citrus, grapevines, and ornamentals such as poinsettias, field crops and woody hosts. Disease symptoms are often easily recognisable, and referred to as signature-bearing diseases, for the cork-like appearance of older infected tissues with scab-like appearance. In some Elsinoë -host associations the resulting symptoms are better described as spot anthracnose. Additionally the infected plants may also show mild to severe distortions of infected organs. Isolation of Elsinoë in pure culture can be very challenging and examination of specimens collected in the field is often frustrating because of the lack of fertile structures. Current criteria for species recognition and host specificity in Elsinoë are unclear due to overlapping morphological characteristics, and the lack of molecular and pathogenicity data. In the present study we revised the taxonomy of Elsinoë based on DNA sequence and morphological data derived from 119 isolates, representing 67 host genera from 17 countries, including 64 ex-type cultures. Combined analyses of ITS, LSU, rpb2 and TEF1-α DNA sequence data were used to reconstruct the backbone phylogeny of the genus Elsinoë . Based on the single nomenclature for fungi, 26 new combinations are proposed in Elsinoë for species that were originally described in Sphaceloma . A total of 13 species are epitypified with notes on their taxonomy and phylogeny. A further eight new species are introduced, leading to a total of 75 Elsinoë species supported by molecular data in the present study. For the most part species of Elsinoë appear to be host specific, although the majority of the species treated are known only from a few isolates, and further collections and pathogenicity studies will be required to reconfirm this conclusion.

  9. Phylogeny and taxonomy of the scab and spot anthracnose fungus Elsinoë (Myriangiales, Dothideomycetes

    Directory of Open Access Journals (Sweden)

    X.L. Fan

    2017-06-01

    Full Text Available Species of Elsinoë are phytopathogens causing scab and spot anthracnose on many plants, including some economically important crops such as avocado, citrus, grapevines, and ornamentals such as poinsettias, field crops and woody hosts. Disease symptoms are often easily recognisable, and referred to as signature-bearing diseases, for the cork-like appearance of older infected tissues with scab-like appearance. In some Elsinoë-host associations the resulting symptoms are better described as spot anthracnose. Additionally the infected plants may also show mild to severe distortions of infected organs. Isolation of Elsinoë in pure culture can be very challenging and examination of specimens collected in the field is often frustrating because of the lack of fertile structures. Current criteria for species recognition and host specificity in Elsinoë are unclear due to overlapping morphological characteristics, and the lack of molecular and pathogenicity data. In the present study we revised the taxonomy of Elsinoë based on DNA sequence and morphological data derived from 119 isolates, representing 67 host genera from 17 countries, including 64 ex-type cultures. Combined analyses of ITS, LSU, rpb2 and TEF1-α DNA sequence data were used to reconstruct the backbone phylogeny of the genus Elsinoë. Based on the single nomenclature for fungi, 26 new combinations are proposed in Elsinoë for species that were originally described in Sphaceloma. A total of 13 species are epitypified with notes on their taxonomy and phylogeny. A further eight new species are introduced, leading to a total of 75 Elsinoë species supported by molecular data in the present study. For the most part species of Elsinoë appear to be host specific, although the majority of the species treated are known only from a few isolates, and further collections and pathogenicity studies will be required to reconfirm this conclusion.

  10. CURRENT APPROACHES TO THE LABORATORY DIAGNOSIS OF RHEUMATIC DISEASES: ROLE OF MOLECULAR AND CELLULAR BIOMARKERS

    Directory of Open Access Journals (Sweden)

    E. N. Aleksandrova

    2016-01-01

    .The alternative therapies of RD include the use of low-molecular-weight chemically synthesized agents that suppress the activity of tyrosine kinases. The important area of this therapy is to restore immunological tolerance and to correct autoimmune disorders by means of autologous hematopoietic stem cells, mesenchymal stromal cells, autologous tolerogenic dendritic cells, regulatory T and B cells, gene therapy, and peptide antigens. The prospects for the laboratory diagnosis of RD are associated with the necessity of harmonizing and standardizing the current methods to determine autoantibodies and with the search for and clinical validation of novel proteomic, transcriptomic, and genomic biomarkers.

  11. Taxonomy of oxalotrophic Methylobacterium strains

    Science.gov (United States)

    Sahin, Nurettin; Kato, Yuko; Yilmaz, Ferah

    2008-10-01

    Most of the oxalotrophic bacteria are facultative methylotrophs and play important ecological roles in soil fertility and cycling of elements. This study gives a detailed picture of the taxonomy and diversity of these bacteria and provides new information about the taxonomical variability within the genus Methylobacterium. Twelve mesophilic, pink-pigmented, and facultatively methylotrophic oxalate-oxidizing strains were included in this work that had been previously isolated from the soil and some plant tissues by the potassium oxalate enrichment method. The isolates were characterized using biochemical tests, cellular lipid profiles, spectral characteristics of carotenoid pigments, G+C content of the DNA, and 16S rDNA sequencing. The taxonomic similarities among the strains were analyzed using the simple matching ( S SM) and Jaccard ( S J) coefficients, and the UPGMA clustering algorithm. The phylogenetic position of the strains was inferred by the neighbor-joining method on the basis of the 16S rDNA sequences. All isolates were Gram-negative, facultatively methylotrophic, oxidase and catalase positive, and required no growth factors. Based on the results of numerical taxonomy, the strains formed four closely related clusters sharing ≥85% similarity. Analysis of the 16S rDNA sequences demonstrated that oxalotrophic, pink-pigmented, and facultatively methylotrophic strains could be identified as members of the genus Methylobacterium. Except for M. variabile and M. aquaticum, all of the Methylobacterium type strains tested had the ability of oxalate utilization. Our results indicate that the capability of oxalate utilization seems to be an uncommon trait and could be used as a valuable taxonomic criterion for differentiation of Methylobacterium species.

  12. The evolution of trypanosomatid taxonomy.

    Science.gov (United States)

    Kaufer, Alexa; Ellis, John; Stark, Damien; Barratt, Joel

    2017-06-08

    Trypanosomatids are protozoan parasites of the class Kinetoplastida predominately restricted to invertebrate hosts (i.e. possess a monoxenous life-cycle). However, several genera are pathogenic to humans, animals and plants, and have an invertebrate vector that facilitates their transmission (i.e. possess a dixenous life-cycle). Phytomonas is one dixenous genus that includes several plant pathogens transmitted by phytophagous insects. Trypanosoma and Leishmania are dixenous genera that infect vertebrates, including humans, and are transmitted by hematophagous invertebrates. Traditionally, monoxenous trypanosomatids such as Leptomonas were distinguished from morphologically similar dixenous species based on their restriction to an invertebrate host. Nonetheless, this criterion is somewhat flawed as exemplified by Leptomonas seymouri which reportedly infects vertebrates opportunistically. Similarly, Novymonas and Zelonia are presumably monoxenous genera yet sit comfortably in the dixenous clade occupied by Leishmania. The isolation of Leishmania macropodum from a biting midge (Forcipomyia spp.) rather than a phlebotomine sand fly calls into question the exclusivity of the Leishmania-sand fly relationship, and its suitability for defining the Leishmania genus. It is now accepted that classic genus-defining characteristics based on parasite morphology and host range are insufficient to form the sole basis of trypanosomatid taxonomy as this has led to several instances of paraphyly. While improvements have been made, resolution of evolutionary relationships within the Trypanosomatidae is confounded by our incomplete knowledge of its true diversity. The known trypanosomatids probably represent a fraction of those that exist and isolation of new species will help resolve relationships in this group with greater accuracy. This review incites a dialogue on how our understanding of the relationships between certain trypanosomatids has shifted, and discusses new knowledge

  13. Building a taxonomy of GI knowledge

    DEFF Research Database (Denmark)

    Arleth, Mette

    2004-01-01

    This paper reports on and ongoing study concerning non-professional users` understanding of GI. Online access to GI are offered by many public authorities, in order to make the public able to serve them selves online and gain insight in the physical planning and area administration. The aim...... of this project is to investigate how and how well non-professional users actually understand GI. For that purpose a taxonomy of GI knowledge is built, drawing on Bloom`s taxonomy. The elements of this taxonomy are described after a presentation of the main research question of the study, the applications chosen...

  14. Organising knowledge taxonomies, knowledge and organisational effectiveness

    CERN Document Server

    Lambe, Patrick

    2007-01-01

    Taxonomies are often thought to play a niche role within content-oriented knowledge management projects. They are thought to be 'nice to have' but not essential. In this ground-breaking book, Patrick Lambe shows how they play an integral role in helping organizations coordinate and communicate effectively. Through a series of case studies, he demonstrates the range of ways in which taxonomies can help organizations to leverage and articulate their knowledge. A step-by-step guide in the book to running a taxonomy project is full of practical advice for knowledge managers and business owners ali

  15. The Importance of Biopsy in the Era of Molecular Medicine.

    Science.gov (United States)

    Ziv, Etay; Durack, Jeremy C; Solomon, Stephen B

    Recent advances in the molecular characterization of cancers have triggered interest in developing a new taxonomy of disease in oncology with the goal of using the molecular profile of a patient's tumor to predict response to treatment. Image-guided needle biopsy is central to this "precision medicine" effort. In this review, we first discuss the current role of biopsy in relation to clinical examples of molecular medicine. We then outline important bottlenecks to the advancement of precision medicine and highlight the potential role of image-guided biopsy to address these challenges.

  16. Current clinical practice: differential management of uveal melanoma in the era of molecular tumor analyses

    Directory of Open Access Journals (Sweden)

    Aaberg Jr TM

    2014-12-01

    Full Text Available Thomas M Aaberg Jr,1 Robert W Cook,2 Kristen Oelschlager,2 Derek Maetzold,2 P Kumar Rao,3 John O Mason III41Michigan State University Medical School and Retina Specialists of Michigan, Grand Rapids, MI, 2Castle Biosciences, Friendswood, TX, 3Washington University School of Medicine in St Louis, St Louis, MO, 4Retina Consultants of Alabama and University of Alabama Birmingham, Birmingham, AL, USA Objective: Assess current clinical practices for uveal melanoma (UM and the impact of molecular prognostic testing on treatment decisions.Design: Cross-sectional survey and sequential medical records review.Participants: Ophthalmologists who treat UM.Methods: (A Medical records review of all Medicare beneficiaries tested by UM gene expression profile in 2012, conducted under an institutional review board-approved protocol. (B 109 ophthalmologists specializing in the treatment of UM were invited to participate in 24-question survey in 2012; 72 were invited to participate in a 23-question survey in 2014.Main outcome measures: Responses analyzed by descriptive statistics, frequency analyses (percentages, Tukey, histograms, and Fisher’s exact test. Descriptive presentation of essay answers.Results: The review of Medicare medical records included 191 evaluable patients, 88 (46% with documented medical treatment actions or institutional policies related to surveillance plans. Of these 88, all gene expression profiling (GEP Class 1 UM patients were treated with low-intensity surveillance. All GEP Class 2 UM patients were treated with high-intensity surveillance (P<0.0001 versus Class 1. There were 36 (19% with information concerning referrals after initial diagnosis. Of these 36, all 23 Class 2 patients were referred to medical oncology; however, none of the 13 Class 1 patients were referred (P<0.0001 versus Class 1. Only Class 2 patients were recommended for adjunctive treatment regimens. 2012 survey: 50 respondents with an annual median of 35 new UM

  17. Unravelling the tangled taxonomies of health informatics

    Directory of Open Access Journals (Sweden)

    David Barrett

    2014-08-01

    Full Text Available Even though informatics is a term used commonly in healthcare, it can be a confusing and disengaging one. Many definitions exist in the literature, and attempts have been made to develop a clear taxonomy. Despite this, informatics is still a term that lacks clarity in both its scope and the classification of sub-terms that it encompasses.This paper reviews the importance of an agreed taxonomy and explores the challenges of establishing exactly what is meant by health informatics (HI. It reviews what a taxonomy should do, summarises previous attempts at categorising and organising HI and suggests the elements to consider when seeking to develop a system of classification.The paper does not provide all the answers, but it does clarify the questions. By plotting a path towards a taxonomy of HI, it will be possible to enhance understanding and optimise the benefits of embracing technology in clinical practice.

  18. EPA's Information Architecture and Web Taxonomy

    Science.gov (United States)

    EPA's Information Architecture creates a topical organization of our website, instead of an ownership-based organization. The EPA Web Taxonomy allows audiences easy access to relevant information from EPA programs, by using a common vocabulary.

  19. Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects

    Directory of Open Access Journals (Sweden)

    Waqas Malik

    2014-01-01

    Full Text Available Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L. is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i comparative analysis of low- and high-throughput marker technologies available in cotton, (ii genetic diversity in the available wild and improved gene pools of cotton, (iii identification of the genomic regions within cotton genome underlying economic traits, and (iv marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands.

  20. Molecular subtyping of cancer: current status and moving toward clinical applications.

    Science.gov (United States)

    Zhao, Lan; Lee, Victor H F; Ng, Michael K; Yan, Hong; Bijlsma, Maarten F

    2018-04-12

    Cancer is a collection of genetic diseases, with large phenotypic differences and genetic heterogeneity between different types of cancers and even within the same cancer type. Recent advances in genome-wide profiling provide an opportunity to investigate global molecular changes during the development and progression of cancer. Meanwhile, numerous statistical and machine learning algorithms have been designed for the processing and interpretation of high-throughput molecular data. Molecular subtyping studies have allowed the allocation of cancer into homogeneous groups that are considered to harbor similar molecular and clinical characteristics. Furthermore, this has helped researchers to identify both actionable targets for drug design as well as biomarkers for response prediction. In this review, we introduce five frequently applied techniques for generating molecular data, which are microarray, RNA sequencing, quantitative polymerase chain reaction, NanoString and tissue microarray. Commonly used molecular data for cancer subtyping and clinical applications are discussed. Next, we summarize a workflow for molecular subtyping of cancer, including data preprocessing, cluster analysis, supervised classification and subtype characterizations. Finally, we identify and describe four major challenges in the molecular subtyping of cancer that may preclude clinical implementation. We suggest that standardized methods should be established to help identify intrinsic subgroup signatures and build robust classifiers that pave the way toward stratified treatment of cancer patients.

  1. The taxobook principles and practices of building taxonomies

    CERN Document Server

    Hlava, Marjorie

    2014-01-01

    This book outlines the basic principles of creation and maintenance of taxonomies and thesauri. It also provides step by step instructions for building a taxonomy or thesaurus and discusses the various ways to get started on a taxonomy construction project.Often, the first step is to get management and budgetary approval, so I start this book with a discussion of reasons to embark on the taxonomy journey. From there I move on to a discussion of metadata and how taxonomies and metadata are related, and then consider how, where, and why taxonomies are used.Information architecture has its corner

  2. A taxonomy of anatomical and pathological entities to support commenting on radiographs (preliminary clinical evaluation)

    International Nuclear Information System (INIS)

    Cosson, Philip; Dash, Robert

    2015-01-01

    It has been shown that radiographers have a lot to offer the patient by providing their expert opinion in a timely intervention; including the possibility of Radiographer Led Discharge. Some excellent paper based ‘commenting’ systems have been developed locally and the Society and College of Radiographers has issued national guidance with a pro-forma to support implementation. However, delivery and audit of the PCE service can be burdensome. There is also an ongoing training need linked in to annual reviews. This paper provides a brief introduction to the field of controlled vocabularies and ontologies in radiology and serves to identify their potential for PCE systems. The current work has constructed a prototype taxonomy and accompanying ontology (list of relationships) that enable the generation of radiographer comments using an electronic, fast, and structured web based interface. For example, in the current implementation any one of thousands of possible unique comments could be constructed by making just six selections from filtered lists of terms. The prototype taxonomy has been tested to refine and validate the concept. The resulting taxonomy and its evolution is described here. Finally, the taxonomy was trialled by 23 participants who generated structured PCE's after reviewing 27 cases on DICOM workstations. An analysis of agreement between participants and the ‘gold standard’ is presented. In conclusion, a taxonomy has been created that would provide for: a standardised framework for training staff and students, efficient and robust delivery of the service, and audit of individual practice

  3. Molecular current switch: principles and photoelectronic characterization of the model system

    Czech Academy of Sciences Publication Activity Database

    Vala, M.; Weiter, M.; Nešpůrek, Stanislav

    2005-01-01

    Roč. 15, č. 3 (2005), s. 28 ISSN 1210-7409 Institutional research plan: CEZ:AV0Z40500505 Keywords : molecular electronics * photochromism * charge transport Subject RIV: CD - Macromolecular Chemistry

  4. Molecular Phytopathology: Current Approaches and Main Directions in Diagnostics of Woody Plant Diseases

    Directory of Open Access Journals (Sweden)

    O. Yu. Baranov

    2014-08-01

    Full Text Available In the article the authors describe the prospects for diagnosis of woody plants diseases based on the use of modern methods of molecular plant pathology. The metagenomic approach based on the analysis of complex pathogens, including non-pathogenic microflora is described. The use the multicopy universal loci characterized by a number of advantages in determining taxonomic affiliation of infectious agents during phytopathological molecular analysis is proposed.

  5. Review of current classification, molecular alterations, and tyrosine kinase inhibitor therapies in myeloproliferative disorders with hypereosinophilia

    Directory of Open Access Journals (Sweden)

    Havelange V

    2013-08-01

    Full Text Available Violaine Havelange,1,2 Jean-Baptiste Demoulin1 1de Duve Institute, Université catholique de Louvain, Brussels, Belgium; 2Department of Hematology, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium Abstract: Recent advances in our understanding of the molecular mechanisms underlying hypereosinophilia have led to the development of a 'molecular' classification of myeloproliferative disorders with eosinophilia. The revised 2008 World Health Organization classification of myeloid neoplasms included a new category called “myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB or FGFR1.” Despite the molecular heterogeneity of PDGFR (platelet-derived growth factor receptor rearrangements, tyrosine kinase inhibitors at low dose induce rapid and complete hematological remission in the majority of these patients. Other kinase inhibitors are promising. Further discoveries of new molecular alterations will direct the development of new specific inhibitors. In this review, an update of the classifications of myeloproliferative disorders associated with hypereosinophilia is discussed together with open and controversial questions. Molecular mechanisms and promising results of tyrosine kinase inhibitor treatments are reviewed. Keywords: hypereosinophilia, classification, myeloproliferative disorders, molecular alterations, tyrosine kinase inhibitor

  6. Towards an Artificial Space Object Taxonomy

    Science.gov (United States)

    Wilkins, M.; Schumacher, P.; Jah, M.; Pfeffer, A.

    2013-09-01

    Object recognition is the first step in positively identifying a resident space object (RSO), i.e. assigning an RSO to a category such as GPS satellite or space debris. Object identification is the process of deciding that two RSOs are in fact one and the same. Provided we have appropriately defined a satellite taxonomy that allows us to place a given RSO into a particular class of object without any ambiguity, one can assess the probability of assignment to a particular class by determining how well the object satisfies the unique criteria of belonging to that class. Ultimately, tree-based taxonomies delineate unique signatures by defining the minimum amount of information required to positively identify a RSO. Therefore, taxonomic trees can be used to depict hypotheses in a Bayesian object recognition and identification process. This work describes a new RSO taxonomy along with specific reasoning behind the choice of groupings. An alternative taxonomy was recently presented at the Sixth Conference on Space Debris in Darmstadt, Germany. [1] The best example of a taxonomy that enjoys almost universal scientific acceptance is the classical Linnaean biological taxonomy. A strength of Linnaean taxonomy is that it can be used to organize the different kinds of living organisms, simply and practically. Every species can be given a unique name. This uniqueness and stability are a result of the acceptance by biologists specializing in taxonomy, not merely of the binomial names themselves. Fundamentally, the taxonomy is governed by rules for the use of these names, and these are laid down in formal Nomenclature Codes. We seek to provide a similar formal nomenclature system for RSOs through a defined tree-based taxonomy structure. Each categorization, beginning with the most general or inclusive, at any level is called a taxon. Taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a diagnosis, a statement intended to supply characters that

  7. Forensic Taxonomy of Android Social Apps.

    Science.gov (United States)

    Azfar, Abdullah; Choo, Kim-Kwang Raymond; Liu, Lin

    2017-03-01

    An Android social app taxonomy incorporating artifacts that are of forensic interest will enable users and forensic investigators to identify the personally identifiable information (PII) stored by the apps. In this study, 30 popular Android social apps were examined. Artifacts of forensic interest (e.g., contacts lists, chronology of messages, and timestamp of an added contact) were recovered. In addition, images were located, and Facebook token strings used to tie account identities and gain access to information entered into Facebook by a user were identified. Based on the findings, a two-dimensional taxonomy of the forensic artifacts of the social apps is proposed. A comparative summary of existing forensic taxonomies of different categories of Android apps, designed to facilitate timely collection and analysis of evidentiary materials from Android devices, is presented. © 2016 American Academy of Forensic Sciences.

  8. Tephritid taxonomy into the 21st century - Research opportunities and applications

    International Nuclear Information System (INIS)

    Drew, R.A.I.; Romig, M.C.

    2000-01-01

    We write with the firm conviction that taxonomic research forms the essential foundation for all other areas of investigation within the field of biology. This has been well demonstrated in the Tephritidae and is a position at which we have arrived through many years' experience in fruit fly systematic research covering taxonomy, behaviour, biology, ecology and pest control. The importance of sound taxonomic research is highlighted at this time by the known presence of many sibling species complexes across the family. Within the Dacinae, for example, major pest species often occur within groups of closely related species, most of which are not pests. The dorsalis complex of Southeast Asia and the musae complex of Papua New Guinea are examples. Tephritid taxonomy has a long history (over two centuries) and rich heritage with some 4,500 species having been described since the mid-1700s. This research has been carried out in major research centres around the world and particularly in Australia, Europe, Hawaii, mainland USA and South Africa. In Mexico in February 1998, a significant meeting was held on the biology/behaviour and taxonomy of Tephritidae. Specialist researchers in this area presented valuable and interesting data on 'Phylogeny and Evolution of Behaviour' in fruit flies. In summarising current knowledge on the taxonomy and biology of the Tephritidae, the meeting highlighted the outstanding achievements of taxonomy in its contributions to both basic research and pest management programmes over many decades of tephritid studies world-wide. This presentation provides a link between the meetings in Mexico and Penang and enables us to present a summary of our current knowledge and genuine valuable applications of tephritid taxonomy to the overall fruit fly research and pest management effort. In doing this, this presentation also fits into the theme of this conference in Penang, 'Fruit Flies- current global scenario'

  9. A taxonomy of behaviour change methods: an Intervention Mapping approach

    OpenAIRE

    Kok, Gerjo; Gottlieb, Nell H.; Peters, Gjalt-Jorn Y.; Mullen, Patricia Dolan; Parcel, Guy S.; Ruiter, Robert A.C.; Fern?ndez, Mar?a E.; Markham, Christine; Bartholomew, L. Kay

    2015-01-01

    ABSTRACT In this paper, we introduce the Intervention Mapping (IM) taxonomy of behaviour change methods and its potential to be developed into a coding taxonomy. That is, although IM and its taxonomy of behaviour change methods are not in fact new, because IM was originally developed as a tool for intervention development, this potential was not immediately apparent. Second, in explaining the IM taxonomy and defining the relevant constructs, we call attention to the existence of parameters fo...

  10. Current applications of molecular imaging and luminescence-based techniques in traditional Chinese medicine.

    Science.gov (United States)

    Li, Jinhui; Wan, Haitong; Zhang, Hong; Tian, Mei

    2011-09-01

    Traditional Chinese medicine (TCM), which is fundamentally different from Western medicine, has been widely investigated using various approaches. Cellular- or molecular-based imaging has been used to investigate and illuminate the various challenges identified and progress made using therapeutic methods in TCM. Insight into the processes of TCM at the cellular and molecular changes and the ability to image these processes will enhance our understanding of various diseases of TCM and will provide new tools to diagnose and treat patients. Various TCM therapies including herbs and formulations, acupuncture and moxibustion, massage, Gua Sha, and diet therapy have been analyzed using positron emission tomography, single photon emission computed tomography, functional magnetic resonance imaging and ultrasound and optical imaging. These imaging tools have kept pace with developments in molecular biology, nuclear medicine, and computer technology. We provide an overview of recent developments in demystifying ancient knowledge - like the power of energy flow and blood flow meridians, and serial naturopathies - which are essential to visually and vividly recognize the body using modern technology. In TCM, treatment can be individualized in a holistic or systematic view that is consistent with molecular imaging technologies. Future studies might include using molecular imaging in conjunction with TCM to easily diagnose or monitor patients naturally and noninvasively. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  11. Constructing a working taxonomy of functional Ada software components for real-time embedded system applications

    Science.gov (United States)

    Wallace, Robert

    1986-01-01

    A major impediment to a systematic attack on Ada software reusability is the lack of an effective taxonomy for software component functions. The scope of all possible applications of Ada software is considered too great to allow the practical development of a working taxonomy. Instead, for the purposes herein, the scope of Ada software application is limited to device and subsystem control in real-time embedded systems. A functional approach is taken in constructing the taxonomy tree for identified Ada domain. The use of modular software functions as a starting point fits well with the object oriented programming philosophy of Ada. Examples of the types of functions represented within the working taxonomy are real time kernels, interrupt service routines, synchronization and message passing, data conversion, digital filtering and signal conditioning, and device control. The constructed taxonomy is proposed as a framework from which a need analysis can be performed to reveal voids in current Ada real-time embedded programming efforts for Space Station.

  12. Cybercrimes: A Proposed Taxonomy and Challenges

    Directory of Open Access Journals (Sweden)

    Harmandeep Singh Brar

    2018-01-01

    Full Text Available Cybersecurity is one of the most important concepts of cyberworld which provides protection to the cyberspace from various types of cybercrimes. This paper provides an updated survey of cybersecurity. We conduct the survey of security of recent prominent researches and categorize the recent incidents in context to various fundamental principles of cybersecurity. We have proposed a new taxonomy of cybercrime which can cover all types of cyberattacks. We have analyzed various cyberattacks as per the updated cybercrime taxonomy to identify the challenges in the field of cybersecurity and highlight various research directions as future work in this field.

  13. A Taxonomy of Human Translation Styles

    DEFF Research Database (Denmark)

    Carl, Michael; Dragsted, Barbara; Lykke Jakobsen, Arnt

    2011-01-01

    on the translators' activity data, we develop a taxonomy of translation styles. The taxonomy could serve to inform the development of advanced translation assistance tools and provide a basis for a felicitous and grounded integration of human machine interaction in translation.......While the translation profession becomes increasingly technological, we are still far from understanding how humans actually translate and how they could be best supported by machines. In this paper we outline a method which helps to uncover characteristics of human translation processes. Based...

  14. The past, the present and the future of eutardigrade taxonomy

    Directory of Open Access Journals (Sweden)

    Giovanni Pilato

    2013-03-01

    Full Text Available The Author first recalls the past of eutardigrade taxonomy and indicates the main factors that for a long time restrained its progress. One consequence of a superficial analysis is that very wide individual variability has been erroneously attributed to many species, and this has become the main problem for tardigrade taxonomists. The situation began to change after 1969 because of the first attempts to eliminate the above mentioned problems. Novelties gave impetus to the revision of tardigrade taxonomy, and genuine systematics, finally based on phylogenetics, became popular. Today the morphological characters are considered more in depth and studies utilising DNA sequences are more in fashion; they are surely useful and allow the distinction of morphologically very similar species. However, in the author’s opinion, this progress will be possible only if the molecular studies are always associated with careful morphological studies, which, in the meantime, will be more and more detailed also thanks to the use of the Scanning Electron Microscopy (SEM.

  15. Taxonomies of Educational Technology Uses: Dewey, Chip and Me

    Science.gov (United States)

    Levin, James A.

    2014-01-01

    In the early 1990s, Chip Bruce created a taxonomy of education technology uses, which the author of the article helped to expand and evaluate. This taxonomy is based on John Dewey's "four impulses of the child": inquiry, construction, communication, and expression. This taxonomy has helped people interested in the uses of…

  16. The genus Gloriosa (Colchicaceae) : ethnobotany, phylogeny and taxonomy

    NARCIS (Netherlands)

    Maroyi, A.

    2012-01-01

    This thesis focuses on the ethnobotany, phylogeny and taxonomy of the genus Gloriosa L. over its distributional range. Some Gloriosa species are known to have economic and commercial value, but the genus is also well known for its complex alpha taxonomy. An appropriate taxonomy for this group is of

  17. A new taxonomy of sublinear keyword pattern matching algorithms

    NARCIS (Netherlands)

    Cleophas, L.G.W.A.; Watson, B.W.; Zwaan, G.

    2004-01-01

    Abstract This paper presents a new taxonomy of sublinear (multiple) keyword pattern matching algorithms. Based on an earlier taxonomy by Watson and Zwaan [WZ96, WZ95], this new taxonomy includes not only suffix-based algorithms related to the Boyer-Moore, Commentz-Walter and Fan-Su algorithms, but

  18. Study on different influence of pyrimidine and phenyl on current-voltage characteristics of molecular devices

    International Nuclear Information System (INIS)

    Fu Xiaoxiao; Li Zongliang

    2011-01-01

    By using ab initio method and elastic scattering Green's function theory, electronic transport properties of symmetric tetraphenyl and non-symmetric diblock dipyrimidinyldiphenyl molecules are investigated. The numerical results show that, the tetraphenyl molecule has better electronic conductivity than the diblock molecule. The diblock molecule exhibits pronounced rectification behavior. Some molecular orbitals of the tetraphenyl molecule are delocalized into the two gold electrodes simultaneously which results in the better electronic conductivity. However, the non-symmetric structure of diblock molecule leads to the localization of the molecular orbitals, which is a disadvantage to the electronic transport. (authors)

  19. Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

    Directory of Open Access Journals (Sweden)

    Matsen Frederick A

    2012-05-01

    Full Text Available Abstract Background Although taxonomy is often used informally to evaluate the results of phylogenetic inference and the root of phylogenetic trees, algorithmic methods to do so are lacking. Results In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem to express the difference between a taxonomy and a phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. Conclusions The algorithms in this paper, and the associated freely-available software, will help biologists better use and understand taxonomically labeled phylogenetic trees.

  20. Molecular Phylogenetics of the Serranid Subfamily Epinephelinae: Speciation and Biogeography in a Nearshore Marine Fish Clade

    OpenAIRE

    Craig, Matthew T,

    2005-01-01

    The processes that shape present day distributions of marine organisms have remained a central topic in evolutionary biology, conservation biology, and ecology. In this thesis, genetic data from mitochondrial and nuclear genes were used to create a phylogenetic hypothesis for the groupers of the subfamily Epinephelinae as a means of evaluating the current taxonomy of the group and the geography of speciation in marine organisms. The molecular phylogenetic hypothesis presented in Chap...

  1. Unconventional Current Scaling and Edge Effects for Charge Transport through Molecular Clusters

    DEFF Research Database (Denmark)

    Obersteiner, Veronika; Huhs, Georg; Papior, Nick Rübner

    2017-01-01

    Metal-molecule-metal junctions are the key components of molecular electronics circuits. Gaining a microscopic understanding of their conducting properties is central to advancing the field. In the present contribution we highlight the fundamental differences between single-molecule and ensemble ...

  2. Molecular current modulator consisting of conjugated polymer chain with chemically attached photoactive side groups

    Czech Academy of Sciences Publication Activity Database

    Nešpůrek, Stanislav; Sworakowski, J.

    2001-01-01

    Roč. 393, 1-2 (2001), s. 168-176 ISSN 0040-6090 R&D Projects: GA AV ČR IAA1050901; GA AV ČR KSK4050111 Institutional research plan: CEZ:AV0Z4050913 Keywords : molecular electronics * photoconductivity * polymers Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.266, year: 2001

  3. Current and future molecular approaches to investigate the white pine blister rust pathosystem

    Science.gov (United States)

    B. A. Richardson; A. K. M. Ekramoddoulah; J.-J. Liu; M.-S. Kim; N. B. Klopfenstein

    2010-01-01

    Molecular genetics is proving to be especially useful for addressing a wide variety of research and management questions on the white pine blister rust pathosystem. White pine blister rust, caused by Cronartium ribicola, is an ideal model for studying biogeography, genetics, and evolution because: (1) it involves an introduced pathogen; (2) it includes multiple primary...

  4. Current Status of Conventional and Molecular Interventions for Blast Resistance in Rice

    Directory of Open Access Journals (Sweden)

    Deepti Srivastava

    2017-11-01

    Full Text Available Pyricularia oryzae anamorph of Magnaporthe oryzae is one of the most notorious fungal pathogens causing severe economic loss in rice production worldwide. Various methods, viz. cultural, biological and molecular approaches, are utilized to counteract this pathogen. Moreover, some tolerant or resistant rice varieties have been developed with the help of breeding programmes. Isolation and molecular characterization of different blast resistance genes now open the gate for new possibilities to elucidate the actual allelic variants of these genes via various molecular breeding and transgenic approaches. However, the behavioral pattern of this fungus breakups the resistance barriers in the resistant or tolerant rice varieties. This host-pathogen barrier will be possibly countered in future research by comparative genomics data from available genome sequence data of rice and M. oryzae for durable resistance. Present review emphasized fascinating recent updates, new molecular breeding approaches, transgenic and genomics approaches (i.e. miRNA and genome editing for the management of blast disease in rice. The updated information will be helpful for the durable, resistance breeding programme in rice against blast pathogen.

  5. Magnetic resonance imaging of vulnerable atherosclerotic plaques: current imaging strategies and molecular imaging probes

    NARCIS (Netherlands)

    Briley-Saebo, Karen C.; Mulder, Willem J. M.; Mani, Venkatesh; Hyafil, Fabien; Amirbekian, Vardan; Aguinaldo, Juan Gilberto S.; Fisher, Edward A.; Fayad, Zahi A.

    2007-01-01

    The vulnerability or destabilization of atherosclerotic plaques has been directly linked to plaque composition. Imaging modalities, such as magnetic resonance (MR) imaging, that allow for evaluation of plaque composition at a cellular and molecular level, could further improve the detection of

  6. Understanding the molecular target therapy and it's approved synchronous use with radiation therapy in current Indian oncology practice

    International Nuclear Information System (INIS)

    Gupta, Puneet; Dohhen, Umesh Kumar; Romana; Srivastava, Priyanka

    2012-01-01

    The molecular targeted drugs (MTD) are of two types; large and small. The large molecular targeted drugs (LMTD) cannot cross the cancer cell membrane whereas those that cross the cancer cell membrane are nicknamed small molecular target drugs (SMTD). India has availability of almost all MTD originals approved by USA Food and Drug administration. However a few LMTD like inj vectibix, inj Zevalin, Inj Bexar etc.; and SMTD like cap Tipifarnib approved for AML, are not available in India currently although approved and available in USA. The MTD may he used alone as singlet; along with chemotherapy as doublet or triplet; or along with radiation and chemotherapy combo (nicknamed chemo-radiation-bio therapy). The molecular target therapy approved by USA and/or European FDA and currently available in India and used along with radiation therapy with or without chemotherapy, indication wise are; Brain Tumor Inj Nimotuzumab (LMTD) and Inj bevacizumab (LMTD) in Glioblasoma Multiforme; for Carcinoma Head and neck Inj Cetuximab and Inj Nimotuzumab (LMTT), Tab Geftinib (SMTD). (author)

  7. Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

    OpenAIRE

    van Belkum, Alex; Struelens, Marc; de Visser, Arjan; Verbrugh, Henri; Tibayrenc, Michel

    2001-01-01

    Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. ...

  8. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.

    OpenAIRE

    Belkum, Alex; Struelens, M.; Visser, Arjan; Verbrugh, Henri; Tibayrench, M.

    2001-01-01

    textabstractCurrently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiologi...

  9. An Empirical Taxonomy of Social-Psychological Risk Indicators in Youth Suicide

    Science.gov (United States)

    Hyde, Toni; Kirkland, John; Bimler, David; Pechtel, Pia

    2005-01-01

    The current study integrates descriptive (though primarily social-psychological) statements about youth suicide into a coherent, empirically supported taxonomy. Drawing from relevant literature, a set of 107 items characterizing these contributions about youth suicide was created. Seventy-two participants sorted these statements according to their…

  10. Constructive Alignment and the SOLO Taxonomy

    DEFF Research Database (Denmark)

    Brabrand, Claus; Dahl, Bettina

    2008-01-01

    the science faculties at University of Aarhus, Denmark (AU) and the University of Southern Denmark (SDU) that had been rewritten to explicitly incorporate course objectives, interpreted as intended learning outcomes (ILOs), using the principles of Constructive Alignment and the SOLO Taxonomy. In this paper we...

  11. A Diagnostic Taxonomy of Adult Career Problems.

    Science.gov (United States)

    Campbell, Robert E.; Cellini, James V.

    1981-01-01

    Developed a taxonomy for the differential diagnosis of adult career development problems. Problem categories identified were: (1) problems in career decision making; (2) problems in implementing career plans; (3) problems in organizational/institutional performance; and (4) problems in organizational/institutional adaption. (Author)

  12. A Taxonomy for Mannerisms of Blind Children.

    Science.gov (United States)

    Eichel, Valerie J.

    1979-01-01

    The investigation involving 24 blind children (2-11 years old) set out to develop and validate a coding procedure which employed a set of 34 descriptors with their corresponding definitions. The use of the taxonomy enabled a detailed, systematic study of manneristic behavior in blind children. (Author/SBH)

  13. Towards a taxonomy for project management competences

    NARCIS (Netherlands)

    Dr Ruben Vrijhoef; Steven Nijhuis; J. Kessels

    2016-01-01

    Presented at Conference: IPMA World Conference 2014, At Rotterdam, The Netherlands, Volume: 28 A taxonomy is used for classifying things in general. For the purpose of this paper it is a systematic classification of competences into hierarchical groups where each sublevel constitutes a breakdown of

  14. An Android Communication App Forensic Taxonomy.

    Science.gov (United States)

    Azfar, Abdullah; Choo, Kim-Kwang Raymond; Liu, Lin

    2016-09-01

    Due to the popularity of Android devices and applications (apps), Android forensics is one of the most studied topics within mobile forensics. Communication apps, such as instant messaging and Voice over IP (VoIP), are one popular app category used by mobile device users, including criminals. Therefore, a taxonomy outlining artifacts of forensic interest involving the use of Android communication apps will facilitate the timely collection and analysis of evidentiary materials from such apps. In this paper, 30 popular Android communication apps were examined, where a logical extraction of the Android phone images was collected using XRY, a widely used mobile forensic tool. Various information of forensic interest, such as contact lists and chronology of messages, was recovered. Based on the findings, a two-dimensional taxonomy of the forensic artifacts of the communication apps is proposed, with the app categories in one dimension and the classes of artifacts in the other dimension. Finally, the artifacts identified in the study of the 30 communication apps are summarized using the taxonomy. It is expected that the proposed taxonomy and the forensic findings in this paper will assist forensic investigations involving Android communication apps. © 2016 American Academy of Forensic Sciences.

  15. Numerical Investigation of the Microscopic Heat Current Inside a Nanofluid System Based on Molecular Dynamics Simulation and Wavelet Analysis.

    Science.gov (United States)

    Jia, Tao; Gao, Di

    2018-04-03

    Molecular dynamics simulation is employed to investigate the microscopic heat current inside an argon-copper nanofluid. Wavelet analysis of the microscopic heat current inside the nanofluid system is conducted. The signal of the microscopic heat current is decomposed into two parts: one is the approximation part; the other is the detail part. The approximation part is associated with the low-frequency part of the signal, and the detail part is associated with the high-frequency part of the signal. Both the probability distributions of the high-frequency and the low-frequency parts of the signals demonstrate Gaussian-like characteristics. The curves fit to data of the probability distribution of the microscopic heat current are established, and the parameters including the mean value and the standard deviation in the mathematical formulas of the curves show dramatic changes for the cases before and after adding copper nanoparticles into the argon base fluid.

  16. [The current status and outlook for molecular genetic methods in solving the tasks of medical microbiology].

    Science.gov (United States)

    Gintsburg, A L; Zigangirova, N A; Romanova, Iu M

    1999-01-01

    The article deals with modern methods, viz. PCR, molecular display and genotherapy, which permit the new approach to the solution of problems connected with the identification of infective agents, the study of the mechanisms of the pathogenesis of infectious diseases and their treatment. In this article concrete examples, clearly demonstrating how each of the above-mentioned technologies makes it possible to broaden the circle of problems solved in infectious pathology of man, are presented.

  17. The current contribution of molecular factors to risk estimation in neuroblastoma patients.

    Science.gov (United States)

    Berthold, F; Sahin, K; Hero, B; Christiansen, H; Gehring, M; Harms, D; Horz, S; Lampert, F; Schwab, M; Terpe, J

    1997-10-01

    The association of molecular characteristics with prognosis has been reported, but not their relationship with each other and their impact in the context of known clinical risk factors. In this study, data of 1249 consecutive intent-to-treat-neuroblastoma patients with more than 1 year follow-up were examined by multivariate analysis using loglinear and Cox proportional hazard regression models on a stage-related basis (stages 1-3: 600, 4S: 116, 4: 533). In a first step, risk factors were identified from 18 selected clinical variables, and risk groups defined. The second step investigated whether molecular characteristics (MYCN, LOH 1p, del 1p, CD44, N-ras, NGF-R, bcl-2, APO-1 (CD95)) contributed additional prognostic information to the model. The loglinear model demonstrated several interactions between clinical factors. By the Cox regression model, seven independent clinical risk factors were found for stages 1-3, seven for stage 4 and two for stage 4S. By subsequent introduction of all molecular variables, MYCN amplification only added significant prognostic information to the clinical factors in localised and stage 4 neuroblastoma. The models allowed the definition of risk groups for stages 1-3 patients by age (e beta = 5.09) and MYCN (e beta = 4.26), for stage 4 by MYCN (e beta = 2.78) and number of symptoms (e beta = 2.44) and for stage 4S by platelet count (e beta = 3.91) and general condition (e beta = 2.99). Molecular factors and in particular MYCN contribute significantly to risk estimation. In conjunction with clinical factors, they are powerful tools to define risk groups in neuroblastoma.

  18. Taxonomy for Common-Cause Failure Vulnerability and Mitigation

    Energy Technology Data Exchange (ETDEWEB)

    Wood, Richard Thomas [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Korsah, Kofi [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Mullens, James Allen [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Pullum, Laura L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-09-01

    Applying current guidance and practices for common-cause failure (CCF) mitigation to digital instrumentation and control (I&C) systems has proven problematic, and the regulatory environment has been unpredictable. The potential for CCF vulnerability inhibits I&C modernization, thereby challenging the long-term sustainability of existing plants. For new plants and advanced reactor concepts, concern about CCF vulnerability in highly integrated digital I&C systems imposes a design burden that results in higher costs and increased complexity. The regulatory uncertainty in determining which mitigation strategies will be acceptable (e.g., what diversity is needed and how much is sufficient) drives designers to adopt complicated, costly solutions devised for existing plants. To address the conditions that constrain the transition to digital I&C technology by the US nuclear industry, crosscutting research is needed to resolve uncertainty, demonstrate necessary characteristics, and establish an objective basis for qualification of digital technology for nuclear power plant (NPP) I&C applications. To fulfill this research need, Oak Ridge National Laboratory is investigating mitigation of CCF vulnerability for nuclear-qualified applications. The outcome of this research is expected to contribute to a fundamentally sound, comprehensive basis to qualify digital technology for nuclear power applications. This report documents the development of a CCF taxonomy. The basis for the CCF taxonomy was generated by determining consistent terminology and establishing a classification approach. The terminology is based on definitions from standards, guides, and relevant nuclear power industry technical reports. The classification approach is derived from identified classification schemes focused on I&C systems and key characteristics, including failure modes. The CCF taxonomy provides the basis for a systematic organization of key systems aspects relevant to analyzing the potential for

  19. The molecular biology of prostate cancer: current understanding and clinical implications.

    Science.gov (United States)

    Gandhi, Jason; Afridi, Adil; Vatsia, Sohrab; Joshi, Gargi; Joshi, Gunjan; Kaplan, Steven A; Smith, Noel L; Khan, Sardar Ali

    2018-04-01

    With continuous progress over the past few decades in understanding diagnosis, treatment, and genetics, much has been learned about the prostate cancer-diagnosed genome. A comprehensive MEDLINE® and Google scholar literature search was conducted using keyword variations relating to the genetics of prostate cancer such as chromosomal alterations, androgen receptor, castration-resistant, inheritance, polymorphisms, oncogenes, metastasis, biomarkers, and immunotherapy. Traditionally, androgen receptors (AR) have been the focus of research. Recently, identification of recurrent chromosomal alterations that lead to either multiplication of regions (gain-of-function) or deletion of regions (loss-of-function) has opened the door to greater genetic accessibility. These chromosomal aberrations lead to variation in copy number and gene expression. Some of these chromosomal alterations are inherited, while others undergo somatic mutations during disease progression. Inherited gene mutations that make one susceptible to prostate cancer have been identified with familial-linked studies. Somatic genes that progress tumorigenesis have also been identified. Research on the molecular biology of prostate cancer has characterized these genes into tumor suppressor genes or oncogenes. Additionally, genome-wide assay studies have identified many high-risk single-nucleotide polymorphisms recurrent throughout the prostate cancer-diagnosed genome. Castration-resistant prostate cancer is the most aggressive form of prostate cancer, and its research has elucidated many types of mutations associated with AR itself, including enhanced expression and amplification, point mutations, and alternative splicing. Understanding the molecular biology of prostate cancer has permitted more accurate identification using advanced biomarkers and therapy for aggressive forms using immunotherapy. An age-related disease, prostate cancer commands profound attention. With increasing life expectancy and the

  20. Current perspectives in the use of molecular imaging to target surgical treatments for genitourinary cancers.

    Science.gov (United States)

    Greco, Francesco; Cadeddu, Jeffrey A; Gill, Inderbir S; Kaouk, Jihad H; Remzi, Mesut; Thompson, R Houston; van Leeuwen, Fijs W B; van der Poel, Henk G; Fornara, Paolo; Rassweiler, Jens

    2014-05-01

    Molecular imaging (MI) entails the visualisation, characterisation, and measurement of biologic processes at the molecular and cellular levels in humans and other living systems. Translating this technology to interventions in real-time enables interventional MI/image-guided surgery, for example, by providing better detection of tumours and their dimensions. To summarise and critically analyse the available evidence on image-guided surgery for genitourinary (GU) oncologic diseases. A comprehensive literature review was performed using PubMed and the Thomson Reuters Web of Science. In the free-text protocol, the following terms were applied: molecular imaging, genitourinary oncologic surgery, surgical navigation, image-guided surgery, and augmented reality. Review articles, editorials, commentaries, and letters to the editor were included if deemed to contain relevant information. We selected 79 articles according to the search strategy based on the Preferred Reporting Items for Systematic Reviews and Meta-analysis criteria and the IDEAL method. MI techniques included optical imaging and fluorescent techniques, the augmented reality (AR) navigation system, magnetic resonance imaging spectroscopy, positron emission tomography, and single-photon emission computed tomography. Experimental studies on the AR navigation system were restricted to the detection and therapy of adrenal and renal malignancies and in the relatively infrequent cases of prostate cancer, whereas fluorescence techniques and optical imaging presented a wide application of intraoperative GU oncologic surgery. In most cases, image-guided surgery was shown to improve the surgical resectability of tumours. Based on the evidence to date, image-guided surgery has promise in the near future for multiple GU malignancies. Further optimisation of targeted imaging agents, along with the integration of imaging modalities, is necessary to further enhance intraoperative GU oncologic surgery. Copyright © 2013

  1. CpG Methylation Analysis—Current Status of Clinical Assays and Potential Applications in Molecular Diagnostics

    Science.gov (United States)

    Sepulveda, Antonia R.; Jones, Dan; Ogino, Shuji; Samowitz, Wade; Gulley, Margaret L.; Edwards, Robin; Levenson, Victor; Pratt, Victoria M.; Yang, Bin; Nafa, Khedoudja; Yan, Liying; Vitazka, Patrick

    2009-01-01

    Methylation of CpG islands in gene promoter regions is a major molecular mechanism of gene silencing and underlies both cancer development and progression. In molecular oncology, testing for the CpG methylation of tissue DNA has emerged as a clinically useful tool for tumor detection, outcome prediction, and treatment selection, as well as for assessing the efficacy of treatment with the use of demethylating agents and monitoring for tumor recurrence. In addition, because CpG methylation occurs early in pre-neoplastic tissues, methylation tests may be useful as markers of cancer risk in patients with either infectious or inflammatory conditions. The Methylation Working Group of the Clinical Practice Committee of the Association of Molecular Pathology has reviewed the current state of clinical testing in this area. We report here our summary of both the advantages and disadvantages of various methods, as well as the needs for standardization and reporting. We then conclude by summarizing the most promising areas for future clinical testing in cancer molecular diagnostics. PMID:19541921

  2. Molecular and cellular biology of cerebral arteriovenous malformations: a review of current concepts and future trends in treatment.

    Science.gov (United States)

    Rangel-Castilla, Leonardo; Russin, Jonathan J; Martinez-Del-Campo, Eduardo; Soriano-Baron, Hector; Spetzler, Robert F; Nakaji, Peter

    2014-09-01

    Arteriovenous malformations (AVMs) are classically described as congenital static lesions. However, in addition to rupturing, AVMs can undergo growth, remodeling, and regression. These phenomena are directly related to cellular, molecular, and physiological processes. Understanding these relationships is essential to direct future diagnostic and therapeutic strategies. The authors performed a search of the contemporary literature to review current information regarding the molecular and cellular biology of AVMs and how this biology will impact their potential future management. A PubMed search was performed using the key words "genetic," "molecular," "brain," "cerebral," "arteriovenous," "malformation," "rupture," "management," "embolization," and "radiosurgery." Only English-language papers were considered. The reference lists of all papers selected for full-text assessment were reviewed. Current concepts in genetic polymorphisms, growth factors, angiopoietins, apoptosis, endothelial cells, pathophysiology, clinical syndromes, medical treatment (including tetracycline and microRNA-18a), radiation therapy, endovascular embolization, and surgical treatment as they apply to AVMs are discussed. Understanding the complex cellular biology, physiology, hemodynamics, and flow-related phenomena of AVMs is critical for defining and predicting their behavior, developing novel drug treatments, and improving endovascular and surgical therapies.

  3. Cellular and Molecular Mechanisms in Perioperative Hepatic Protection: A Review of Current Interventions

    Directory of Open Access Journals (Sweden)

    Zahra Talebi

    2017-05-01

    Full Text Available Liver is one of the most important organs needing great concern during the perioperative period. There are a number of different mechanisms that interact with liver cells and might affect their integrity and cell live. Though these mechanisms are not all the same, there is a great common point: all affect the metabolic pathways of the liver. Ischemia, anesthetic drug effects and other perioperative insults may affect the liver. Disturbance in an organ’s blood flow is an inherent part of diverse surgical procedures, which leads to lack of oxygen and nutrient supply. These ischemic periods can be particularly long in case of liver surgeries, such as resection of large hepatic tumors, management of hepatic trauma and liver transplant. Once the blood flow and oxygen supply are restored, the interruption of blood flow affects the oxygen dependent cells in liver, which require mitochondrial oxidative phosphorylation for their metabolism. Molecular mechanisms such as Redox status, ionic interchange disturbances as well as different mediators and cells like KC, SEC, dendritic cells, leukocytes, and lymphocytes, are involved in the process ultimately leading to cell death by apoptosis and necrosis. This review provides an overview on the cellular and molecular mechanisms involved in liver injuries, categorizing these mechanisms in 3 different classes: preoperative mechanisms, intraoperative mechanisms and postoperative mechanisms. Each of them are discussed in a different part of the manuscript

  4. Molecular phylogeny of Pasiphaeidae (Crustacea, Decapoda, Caridea) reveals systematic incongruence of the current classification.

    Science.gov (United States)

    Liao, Yunshi; De Grave, Sammy; Ho, Tsz Wai; Ip, Brian H Y; Tsang, Ling Ming; Chan, Tin-Yam; Chu, Ka Hou

    2017-10-01

    Caridean shrimps constitute one of the most diverse groups of decapod crustaceans, notwithstanding their poorly resolved infraordinal relationships. One of the systematically controversial families in Caridea is the predominantly pelagic Pasiphaeidae, comprises 101 species in seven genera. Pasiphaeidae species exhibit high morphological disparity, as well as ecological niche width, inhabiting shallow to very deep waters (>4000m). The present work presents the first molecular phylogeny of the family, based on a combined dataset of six mitochondrial and nuclear gene markers (12S rDNA, 16S rDNA, histone 3, sodium-potassium ATPase α-subunit, enolase and ATP synthase β-subunit) from 33 species belonged to six genera of Pasiphaeidae with 19 species from 12 other caridean families as outgroup taxa. Maximum likelihood and Bayesian inference analyses conducted on the concatenated dataset of 2265bp suggest the family Pasiphaeidae is not monophyletic, with Psathyrocaris more closely related to other carideans than to the other five pasiphaeid genera included in this analysis. Leptochela occupies a sister position to the remaining genera and is genetically quite distant from them. At the generic level, the analysis supports the monophyly of Pasiphaea, Leptochela and Psathyrocaris, while Eupasiphae is shown to be paraphyletic, closely related to Parapasiphae and Glyphus. The present molecular result strongly implies that certain morphological characters used in the present systematic delineation within Pasiphaeidae may not be synapomorphies and the classification within the family needs to be urgently revised. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances.

    Science.gov (United States)

    Wagner, James M; Alper, Hal S

    2016-04-01

    Coupling the tools of synthetic biology with traditional molecular genetic techniques can enable the rapid prototyping and optimization of yeast strains. While the era of yeast synthetic biology began in the well-characterized model organism Saccharomyces cerevisiae, it is swiftly expanding to include non-conventional yeast production systems such as Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. These yeasts already have roles in the manufacture of vaccines, therapeutic proteins, food additives, and biorenewable chemicals, but recent synthetic biology advances have the potential to greatly expand and diversify their impact on biotechnology. In this review, we summarize the development of synthetic biological tools (including promoters and terminators) and enabling molecular genetics approaches that have been applied in these four promising alternative biomanufacturing platforms. An emphasis is placed on synthetic parts and genome editing tools. Finally, we discuss examples of synthetic tools developed in other organisms that can be adapted or optimized for these hosts in the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Molecular Epidemiologic Typing Systems of Bacterial Pathogens: Current Issues and Perpectives

    Directory of Open Access Journals (Sweden)

    Struelens Marc J

    1998-01-01

    Full Text Available The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s ? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection. Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.

  7. Constructing Taxonomies to Identify Distinctive Forms of Primary Healthcare Organizations

    Science.gov (United States)

    Borgès Da Silva, Roxane; Pineault, Raynald; Hamel, Marjolaine; Levesque, Jean-Frédéric; Roberge, Danièle; Lamarche, Paul

    2013-01-01

    Background. Primary healthcare (PHC) renewal gives rise to important challenges for policy makers, managers, and researchers in most countries. Evaluating new emerging forms of organizations is therefore of prime importance in assessing the impact of these policies. This paper presents a set of methods related to the configurational approach and an organizational taxonomy derived from our analysis. Methods. In 2005, we carried out a study on PHC in two health and social services regions of Quebec that included urban, suburban, and rural areas. An organizational survey was conducted in 473 PHC practices. We used multidimensional nonparametric statistical methods, namely, multiple correspondence and principal component analyses, and an ascending hierarchical classification method to construct a taxonomy of organizations. Results. PHC organizations were classified into five distinct models: four professional and one community. Study findings indicate that the professional integrated coordination and the community model have great potential for organizational development since they are closest to the ideal type promoted by current reforms. Conclusion. Results showed that the configurational approach is useful to assess complex phenomena such as the organization of PHC. The analysis highlights the most promising organizational models. Our study enhances our understanding of organizational change in health services organizations. PMID:24959575

  8. Building a Framework for a Dual Task Taxonomy

    Directory of Open Access Journals (Sweden)

    Tara L. McIsaac

    2015-01-01

    Full Text Available The study of dual task interference has gained increasing attention in the literature for the past 35 years, with six MEDLINE citations in 1979 growing to 351 citations indexed in 2014 and a peak of 454 cited papers in 2013. Increasingly, researchers are examining dual task cost in individuals with pathology, including those with neurodegenerative diseases. While the influence of these papers has extended from the laboratory to the clinic, the field has evolved without clear definitions of commonly used terms and with extreme variations in experimental procedures. As a result, it is difficult to examine the interference literature as a single body of work. In this paper we present a new taxonomy for classifying cognitive-motor and motor-motor interference within the study of dual task behaviors that connects traditional concepts of learning and principles of motor control with current issues of multitasking analysis. As a first step in the process we provide an operational definition of dual task, distinguishing it from a complex single task. We present this new taxonomy, inclusive of both cognitive and motor modalities, as a working model; one that we hope will generate discussion and create a framework from which one can view previous studies and develop questions of interest.

  9. Current status and future perspectives on molecular and serological methods in diagnostic mycology.

    Science.gov (United States)

    Lau, Anna; Chen, Sharon; Sleiman, Sue; Sorrell, Tania

    2009-11-01

    Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex xMAP) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum beta-D-glucan test have value for diagnosing infection and monitoring therapeutic response.

  10. Molecular diagnostics to identify fungal plant pathogens – A review of current methods

    OpenAIRE

    Bernreiter, Andreas

    2017-01-01

    La siguiente revisión ofrece una visión amplia de los métodos actuales utilizados para la identificación de hongos fitopatógenos. Además, se presentan estudios previos centrados en patógenos relevantes para el Ecuador y una breve discusión sobre el futuro del diagnóstico en fitopatología. En la actualidad, las herramientas de diagnóstico que aplican biología molecular se basan en la tecnología de reacción en cadena de la polimerasa (PCR). Se presenta una selección de tecnologías basadas en PC...

  11. Molecular basis of hepatic fibrosis and current status of its diagnosis and treatment

    Directory of Open Access Journals (Sweden)

    LI Yan

    2018-01-01

    Full Text Available During the process of acute or chronic liver injury, hepatic stellate cells interact with various types of cells such as hepatic parenchymal cells, Kupffer cells, and liver sinusoidal endothelial cells to mediate extracellular matrix deposition and sinusoid capillarization and thus initiate the process of hepatic fibrosis. The nature of hepatic fibrosis is repair response after liver injury. Liver biopsy is regarded as the gold standard for the diagnosis of hepatic fibrosis; however, it is generally associated with the risk of bleeding and even death. Noninvasive diagnostic methods for liver fibrosis mainly include serum biomarkers, imaging techniques, and predictive statistical model, but such methods cannot completely replace liver biopsy. At present, the treatment of hepatic fibrosis focuses on the research and development of new drugs targeting primary disease, hepatic stellate cells, or balance of extracellular matrix synthesis/degradation. The research on the molecular mechanism of hepatic fibrosis provides a solid theoretical basis for exploring the treatment of hepatic fibrosis.

  12. Molecular taxonomy of Plagioscion Heckel (Perciformes, Sciaenidae and evidence from mtDNA RFLP markers for an invasive species in the Paraná river, Southern Brazil Taxonomia molecular de Plagioscion Heckel (Perciformes, Sciaenidae e evidências de marcadores moleculares RFLPs de mtDNA para uma espécie invasora no rio Paraná, Sul do Brasil

    Directory of Open Access Journals (Sweden)

    Rodrigo A. Torres

    2006-12-01

    Full Text Available Mitochondrial RFLP markers were developed to examine whether Plagioscion squamosissimus (Heckel, 1840 is invasive in natural environments of the congener P. ternetzi in the Paraná river, in southern Brazil. Specimens of P. squamosissimus and of the putative P. ternetzi (Boulenger, 1895 were obtained from the Negro river (Manaus, Amazonas, Brazil and from Paraná river, respectively. Fragments of the cytochrome b gene (900bp were amplified by PCR and four restriction enzymes (Eco RI, Mbo I, Bam HI and Alu I yielded the mitochondrial markers. An additional RFLP analysis with a cytochrome b gene sequence of Plagioncion sp. from GeneBank was carried out to validate the prior analysis. No genetic differentiation was found among either sample. While molecular variation in the cytochrome b analysis was no substantial among individuals, the combined analysis was important for demonstrating that there is no evidence for differentiation of the putative sample P. ternetzi from that of P. squamosissimus. The ecological implications of the introduced occurrence of P. squamosissimus, as well as the role of molecular taxonomic approaches for biodiversity studies are discussed.Marcadores RFLPs mitocondriais foram desenvolvidos para verificar se Plagioscion squamosissimus (Heckel, 1840 é invasora nos ambientes naturais da espécie congênere P. ternetzi no rio Paraná, no sul do Brasil. Exemplares de Plagioscion squamosissimus e supostamente de P. ternetzi (Boulenger, 1895 foram obtidos, respectivamente, do rio Negro (Manaus, AM, Brasil e rio Paraná (Foz do Iguaçu, PR, Brasil. Foram amplificados, via PCR, fragmentos de cerca de 900pb do Citocromo b e foram utilizadas quatro enzimas de restrição (Eco RI, Mbo I, Bam HI e Alu I para os fins de geração dos marcadores moleculares. Foi desenvolvida, a partir de uma seqüência de Citocromo b de Plagioscion sp. (genebank, uma análise de RFLP adicional, objetivando validar a primeira análise acima mencionada

  13. The ACTTION–APS–AAPM Pain Taxonomy (AAAPT) Multidimensional Approach to Classifying Acute Pain Conditions

    Science.gov (United States)

    Kent, Michael L.; Tighe, Patrick J.; Belfer, Inna; Brennan, Timothy J.; Bruehl, Stephen; Brummett, Chad M.; Buckenmaier, Chester C.; Buvanendran, Asokumar; Cohen, Robert I.; Desjardins, Paul; Edwards, David; Fillingim, Roger; Gewandter, Jennifer; Gordon, Debra B.; Hurley, Robert W.; Kehlet, Henrik; Loeser, John D.; Mackey, Sean; McLean, Samuel A.; Polomano, Rosemary; Rahman, Siamak; Raja, Srinivasa; Rowbotham, Michael; Suresh, Santhanam; Schachtel, Bernard; Schreiber, Kristin; Schumacher, Mark; Stacey, Brett; Stanos, Steven; Todd, Knox; Turk, Dennis C.; Weisman, Steven J.; Wu, Christopher; Carr, Daniel B.; Dworkin, Robert H.; Terman, Gregory

    2017-01-01

    , despite the advent of modern multimodal analgesic strategies. Mismanaged acute pain has a broad societal impact as significant numbers of patients may progress to suffer from chronic pain. An acute pain taxonomy provides a much-needed standardization of clinical diagnostic criteria, which benefits clinical care, research, education, and public policy. For the purposes of the present taxonomy, acute pain is considered to last up to seven days, with prolongation to 30 days being common. The current understanding of acute pain mechanisms poorly differentiates between acute and chronic pain and is often insufficient to distinguish among many types of acute pain conditions. Given the usefulness of the AAPT multidimensional framework, the AAAPT undertook a similar approach to organizing various acute pain conditions. PMID:28482098

  14. "Communicate to vaccinate": the development of a taxonomy of communication interventions to improve routine childhood vaccination.

    Science.gov (United States)

    Willis, Natalie; Hill, Sophie; Kaufman, Jessica; Lewin, Simon; Kis-Rigo, John; De Castro Freire, Sara Bensaude; Bosch-Capblanch, Xavier; Glenton, Claire; Lin, Vivian; Robinson, Priscilla; Wiysonge, Charles S

    2013-05-11

    members or volunteers; and health care providers. Our taxonomy illuminates and organises this field and identifies the range of available communication interventions to increase routine childhood vaccination uptake. We have utilised a variety of data sources, capturing information from rigorous evaluations such as randomised trials as well as experiences and knowledge of practitioners and vaccination stakeholders. The taxonomy reflects current public health practice and can guide the future development of vaccination programmes.

  15. The ACTTION-APS-AAPM Pain Taxonomy (AAAPT) Multidimensional Approach to Classifying Acute Pain Conditions.

    Science.gov (United States)

    Kent, Michael L; Tighe, Patrick J; Belfer, Inna; Brennan, Timothy J; Bruehl, Stephen; Brummett, Chad M; Buckenmaier, Chester C; Buvanendran, Asokumar; Cohen, Robert I; Desjardins, Paul; Edwards, David; Fillingim, Roger; Gewandter, Jennifer; Gordon, Debra B; Hurley, Robert W; Kehlet, Henrik; Loeser, John D; Mackey, Sean; McLean, Samuel A; Polomano, Rosemary; Rahman, Siamak; Raja, Srinivasa; Rowbotham, Michael; Suresh, Santhanam; Schachtel, Bernard; Schreiber, Kristin; Schumacher, Mark; Stacey, Brett; Stanos, Steven; Todd, Knox; Turk, Dennis C; Weisman, Steven J; Wu, Christopher; Carr, Daniel B; Dworkin, Robert H; Terman, Gregory

    2017-05-01

    . Mismanaged acute pain has a broad societal impact as significant numbers of patients may progress to suffer from chronic pain. An acute pain taxonomy provides a much-needed standardization of clinical diagnostic criteria, which benefits clinical care, research, education, and public policy. For the purposes of the present taxonomy, acute pain is considered to last up to seven days, with prolongation to 30 days being common. The current understanding of acute pain mechanisms poorly differentiates between acute and chronic pain and is often insufficient to distinguish among many types of acute pain conditions. Given the usefulness of the AAPT multidimensional framework, the AAAPT undertook a similar approach to organizing various acute pain conditions. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Species identification of Aspergillus section Flavi isolates from Portuguese almonds using phenotypic, including MALDI-TOF ICMS, and molecular approaches

    OpenAIRE

    Rodrigues, Paula; Venâncio, Armando; Lima, Nelson

    2011-01-01

    Section Flavi is one of the most significant Sections in the genus Aspergillus. Taxonomy of this section currently depends on multivariate approaches, entailing phenotypic and molecular traits. This work aimed to identify isolates from section Flavi by combining various classic phenotypic and genotypic methods as well as the novel approach based on spectral analysis by MALDI-TOF ICMS, and to evaluate the discriminatory power of the various approaches in species identification. Methods and ...

  17. Toward a comprehensive taxonomy of human motives

    Science.gov (United States)

    Talevich, Jennifer R.; Walsh, David A.; Iyer, Ravi; Chopra, Gurveen

    2017-01-01

    A major success in personality has been the development of a consensual structure of traits. However, much less progress has been made on the structure of an equally important aspect of human psychology: motives. We present an empirically and theoretically structured hierarchical taxonomy of 161 motives gleaned from a literature review from McDougall to the present and based on the cluster analysis of similarity judgments among these 161 motives, a broader sampling of motives than previous work. At the broadest level were: Meaning, Communion, and Agency. These divided into nine clusters: Morality & Virtue, Religion & Spirituality, Self-Actualization, Avoidance, Social Relating, Family, Health, Mastery & Competence, and Financial & Occupational Success. Each divided into more concrete clusters to form 5 levels. We discuss contributions to research on motives, especially recent work on goal systems, and the aiding of communication and systematization of research. Finally, we compare the taxonomy to other motive organizations. PMID:28231252

  18. How apomictic taxa are treated in current taxonomy: A review

    Czech Academy of Sciences Publication Activity Database

    Majeský, L.; Krahulec, František; Vašut, R.J.

    2017-01-01

    Roč. 66, č. 5 (2017), s. 1017-1040 ISSN 0040-0262 Institutional support: RVO:67985939 Keywords : apomixis * hybridization * species concept Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 2.447, year: 2016

  19. Towards a taxonomy of digital work

    OpenAIRE

    Mrass, Volkmar; Li, Mahei Manhai; Peters, Christoph

    2017-01-01

    Despite the increasing importance of digitization for economy and society, there is few structuring of the very heterogenous kinds of digital work. Representatives from business, politics and science need a basis for the development of strategies to encounter the challenges that result from this digitization. We aim at delivering a contribution to that basis by systematically investigating what different types of digital work exist and by developing a taxonomy. As a first important step towar...

  20. An Empirical Taxonomy of Crowdfunding Intermediaries

    OpenAIRE

    Haas, Philipp; Blohm, Ivo; Leimeister, Jan Marco

    2014-01-01

    Due to the recent popularity of crowdfunding, a broad magnitude of crowdfunding intermediaries has emerged, while research on crowdfunding intermediaries has been largely neglected. As a consequence, existing classifications of crowdfunding intermediaries are conceptual, lack theoretical grounding, and are not empirically validated. Thus, we develop an empirical taxonomy of crowdfunding intermediaries, which is grounded in the theories of two-sided markets and financial intermediation. Integr...

  1. An inclusive taxonomy of behavioral biases

    OpenAIRE

    David Peón; Manel Antelo; Anxo Calvo-Silvosa

    2017-01-01

    This paper overviews the theoretical and empirical research on behavioral biases and their influence in the literature. To provide a systematic exposition, we present a unified framework that takes the reader through an original taxonomy, based on the reviews of relevant authors in the field. In particular, we establish three broad categories that may be distinguished: heuristics and biases; choices, values and frames; and social factors. We then describe the main biases within each category,...

  2. Ab initio and empirical studies on the asymmetry of molecular current-voltage characteristics

    International Nuclear Information System (INIS)

    Hoft, R C; Armstrong, N; Ford, M J; Cortie, M B

    2007-01-01

    We perform theoretical calculations of the tunnelling current through various small organic molecules sandwiched between gold electrodes by using both a tunnel barrier model and an ab initio transport code. The height of the tunnelling barrier is taken to be the work function of gold as modified by the adsorbed molecule and calculated from an ab initio electronic structure code. The current-voltage characteristics of these molecules are compared. Asymmetry is introduced into the system in two ways: an asymmetric molecule and a gap between the molecule and the right electrode. The latter is a realistic situation in scanning probe experiments. The asymmetry is also realized in the tunnel barrier model by two distinct work functions on the left and right electrodes. Significant asymmetry is observed in the ab initio i(V) curves. The tunnel barrier i(V) curves show much less pronounced asymmetry. The relative sizes of the currents through the molecules are compared. In addition, the performance of the WKB approximation is compared to the results obtained from the exact Schroedinger solution to the tunnelling barrier problem

  3. DNA Variations in Oculocutaneous Albinism: An Updated Mutation List and Current Outstanding Issues in Molecular Diagnostics

    Science.gov (United States)

    Simeonov, Dimitre R.; Wang, Xinjing; Wang, Chen; Sergeev, Yuri; Dolinska, Monika; Bower, Matthew; Fischer, Roxanne; Winer, David; Dubrovsky, Genia; Balog, Joan Z.; Huizing, Marjan; Hart, Rachel; Zein, Wadih M.; Gahl, William A.; Brooks, Brian P.; Adams, David R.

    2014-01-01

    Oculocutaneous albinism (OCA) is a rare genetic disorder of melanin synthesis that results in hypopigmented hair, skin, and eyes. There are four types of OCA, caused by mutations in TYR (OCA-1), OCA2 (OCA-2), TYRP1 (OCA-3), or SLC45A2 (OCA-4). Here we report 22 novel mutations; 14 from a cohort of 61 patients seen as part of the NIH OCA Natural History Study and 8 from a prior study at the University of Minnesota. We also include a comprehensive list of almost 600 previously reported OCA mutations, along with ethnicity information, carrier frequencies, and in silico pathogenicity predictions. In addition to discussing the clinical and molecular features of OCA, we address the cases of apparent missing heritability. In our cohort, 25% of patients did not have two mutations in a single OCA gene. We demonstrate the utility of multiple detection methods to reveal mutations missed by Sanger sequencing. Finally, we review the TYR p.R402Q temperature sensitive variant and confirm its association with cases of albinism with only one identifiable TYR mutation. PMID:23504663

  4. Molecular Biosensors for Electrochemical Detection of Infectious Pathogens in Liquid Biopsies: Current Trends and Challenges.

    Science.gov (United States)

    Campuzano, Susana; Yáñez-Sedeño, Paloma; Pingarrón, José Manuel

    2017-11-03

    Rapid and reliable diagnosis of infectious diseases caused by pathogens, and timely initiation of appropriate treatment are critical determinants to promote optimal clinical outcomes and general public health. Conventional in vitro diagnostics for infectious diseases are time-consuming and require centralized laboratories, experienced personnel and bulky equipment. Recent advances in electrochemical affinity biosensors have demonstrated to surpass conventional standards in regards to time, simplicity, accuracy and cost in this field. The tremendous potential offered by electrochemical affinity biosensors to detect on-site infectious pathogens at clinically relevant levels in scarcely treated body fluids is clearly stated in this review. The development and application of selected examples using different specific receptors, assay formats and electrochemical approaches focusing on the determination of specific circulating biomarkers of different molecular (genetic, regulatory and functional) levels associated with bacterial and viral pathogens are critically discussed. Existing challenges still to be addressed and future directions in this rapidly advancing and highly interesting field are also briefly pointed out.

  5. Current molecular profile of juvenile nasopharyngeal angiofibroma: First comprehensive study from India.

    Science.gov (United States)

    Pandey, Praveen; Mishra, Anupam; Tripathi, Ashoak Mani; Verma, Veerendra; Trivedi, Ritu; Singh, Hitendra Prakash; Kumar, Sunil; Patel, Brijesh; Singh, Vinay; Pandey, Shivani; Pandey, Amita; Mishra, Subhash Chandra

    2017-03-01

    An attempt is made to analyze the molecular behavior of juvenile nasopharyngeal angiofibroma (JNA). Case Series METHODS: Quantification of mRNAs expression was undertaken through real-time polymerase chain reaction in JNA (9-24) samples for VEGF-A, basic fibroblast growth factor (b-FGF), platelet-derived growth factor PDGF-A, KIT proto-oncogene receptor tyrosine kinase (c-Kit), Avian myelomatosis viral oncogene homolog (c-Myc), Harvey rat sarcoma viral oncogene homolog (H-Ras), tumor suppressor gene TP53, and androgen receptor and interleukin 6 (IL-6). The β-catenin expression was evaluated by western blot in 16 samples. Nasal polyp was taken as control. A significantly increased (P < 0.01) expression of c-myc, VEGFA, bFGF, PDGFA, c-kit, and TP53 was seen, along with enhanced expression of β-catenin. A massive enhancement of H-Ras expression was seen for the first time. Androgen receptor expression was no different, whereas IL-6 despite showing upregulation trend was not significant. The enhanced expressions of various markers suggest their potential role in JNA. Although the biological significance of c-kit, c-myc, and one of the novel markers H-Ras has yet to be defined, their significant expression may have a therapeutic importance. NA. Laryngoscope, 127:E100-E106, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

  6. Current immunological and molecular biological perspectives on seafood allergy: a comprehensive review.

    Science.gov (United States)

    Leung, Nicki Y H; Wai, Christine Y Y; Shu, ShangAn; Wang, Jinjun; Kenny, Thomas P; Chu, Ka Hou; Leung, Patrick S C

    2014-06-01

    Seafood is an important component in human diet and nutrition worldwide. However, seafood also constitutes one of the most important groups of foods in the induction of immediate (type I) food hypersensitivity, which significantly impacts the quality of life and healthcare cost. Extensive efforts within the past two decades have revealed the molecular identities and immunological properties of the major fish and shellfish allergens. The major allergen involved in allergy and cross-reactivity among different fish species was identified as parvalbumin while that responsible for shellfish (crustaceans and mollusks) allergy was identified as tropomyosin. The cloning and expression of the recombinant forms of these seafood allergens facilitate the investigation on the detailed mechanisms leading to seafood allergies, mapping of IgE-binding epitopes, and assessment of their allergenicity and stability. Future research focusing on the immunological cross-reactivity and discovery of novel allergens will greatly facilitate the management of seafood allergies and the design of effective and life-long allergen-specific immunotherapies.

  7. DEVELOPMENTAL TAXONOMY OF CONDUCT DISORDER

    Directory of Open Access Journals (Sweden)

    Jelena Kostić

    2015-12-01

    Full Text Available Conduct disorder is a heterogeneous disorder in terms of etiology, course and prognosis, and currently, there is no singular model that would describe the development of the disorder. The results of empirical research on males confirm this heterogeneity, as they point out to two possible developmental pathways: childhood-onset and adolescentonset type. This paper presents the basic elements of developmental taxonomic theory which argues that there are two different developmental pathways to conduct disorder which have different causes and serve as the basis for the current typology of conduct disorders in the classification systems. Such a typology of conduct disorders in the diagnostic classification allows better understanding, prognosis and choice of treatment.

  8. DEVELOPMENTAL TAXONOMY OF CONDUCT DISORDER

    OpenAIRE

    Jelena Kostić; Milkica Nešić; Jasminka Marković; Miodrag Stanković

    2015-01-01

    Conduct disorder is a heterogeneous disorder in terms of etiology, course and prognosis, and currently, there is no singular model that would describe the development of the disorder. The results of empirical research on males confirm this heterogeneity, as they point out to two possible developmental pathways: childhood-onset and adolescentonset type. This paper presents the basic elements of developmental taxonomic theory which argues that there are two different developmental pathways to c...

  9. Integrated biochemical, molecular genetic, and bioacoustical analysis of mesoscale variability of the euphausiid Nematoscelis difficilis in the California Current

    Science.gov (United States)

    Bucklin, Ann; Wiebe, Peter H.; Smolenack, Sara B.; Copley, Nancy J.; Clarke, M. Elizabeth

    2002-03-01

    Integrated assessment of the euphausiid Nematoscelis difficilis (Crustacea; Euphausiacea) and the zooplankton assemblage of the California Current was designed to investigate individual, population, and community responses to mesoscale variability in biological and physical characters of the ocean. Zooplankton samples and observational data were collected along a cross-shelf transect of the California Current in association with the California Cooperative Fisheries Investigations (CalCOFI) Survey during October 1996. The transect crossed three domains defined by temperature and salinity: nearshore, mid-Current, and offshore. Individual N. difficilis differed in physiological condition along the transect, with higher size-corrected concentrations of four central metabolic enzymes (citrate synthetase, hexokinase, lactate dehydrogenase (LDH), and phosphoglucose isomerase (PGI)) for euphausiids collected in nearshore waters than in mid-Current and offshore waters. There was little variation in the DNA sequences of the genes encoding PGI and LDH (all DNA changes were either silent or heterozygous base substitutions), suggesting that differences in enzyme concentration did not result from underlying molecular genetic variation. The population genetic makeup of N. difficilis varied from sample to sample based on haplotype frequencies of mitochondrial cytochrome oxidase I (mtCOI; P=0.029). There were significant differences between pooled nearshore and offshore samples, based on allele frequencies at two sites of common substitutions in the mtCOI sequence ( P=0.020 and 0.026). Silhouette and bioacoustical backscattering measurements of the zooplankton assemblage of the top 100 m showed marked diel vertical migration of the scattering layer, of which euphausiids were a small but significant fraction. The biochemical and molecular assays are used as indices of complex physiological (i.e., growth and condition) and genetic (i.e., mortality) processes; the bioacoustical

  10. Current and Emerging Technologies for Probing Molecular Signatures of Traumatic Brain Injury

    Directory of Open Access Journals (Sweden)

    Ari Ercole

    2017-08-01

    Full Text Available Traumatic brain injury (TBI is understood as an interplay between the initial injury, subsequent secondary injuries, and a complex host response all of which are highly heterogeneous. An understanding of the underlying biology suggests a number of windows where mechanistically inspired interventions could be targeted. Unfortunately, biologically plausible therapies have to-date failed to translate into clinical practice. While a number of stereotypical pathways are now understood to be involved, current clinical characterization is too crude for it to be possible to characterize the biological phenotype in a truly mechanistically meaningful way. In this review, we examine current and emerging technologies for fuller biochemical characterization by the simultaneous measurement of multiple, diverse biomarkers. We describe how clinically available techniques such as cerebral microdialysis can be leveraged to give mechanistic insights into TBI pathobiology and how multiplex proteomic and metabolomic techniques can give a more complete description of the underlying biology. We also describe spatially resolved label-free multiplex techniques capable of probing structural differences in chemical signatures. Finally, we touch on the bioinformatics challenges that result from the acquisition of such large amounts of chemical data in the search for a more mechanistically complete description of the TBI phenotype.

  11. Targeted Therapy Database (TTD): a model to match patient's molecular profile with current knowledge on cancer biology.

    Science.gov (United States)

    Mocellin, Simone; Shrager, Jeff; Scolyer, Richard; Pasquali, Sandro; Verdi, Daunia; Marincola, Francesco M; Briarava, Marta; Gobbel, Randy; Rossi, Carlo; Nitti, Donato

    2010-08-10

    The efficacy of current anticancer treatments is far from satisfactory and many patients still die of their disease. A general agreement exists on the urgency of developing molecularly targeted therapies, although their implementation in the clinical setting is in its infancy. In fact, despite the wealth of preclinical studies addressing these issues, the difficulty of testing each targeted therapy hypothesis in the clinical arena represents an intrinsic obstacle. As a consequence, we are witnessing a paradoxical situation where most hypotheses about the molecular and cellular biology of cancer remain clinically untested and therefore do not translate into a therapeutic benefit for patients. To present a computational method aimed to comprehensively exploit the scientific knowledge in order to foster the development of personalized cancer treatment by matching the patient's molecular profile with the available evidence on targeted therapy. To this aim we focused on melanoma, an increasingly diagnosed malignancy for which the need for novel therapeutic approaches is paradigmatic since no effective treatment is available in the advanced setting. Relevant data were manually extracted from peer-reviewed full-text original articles describing any type of anti-melanoma targeted therapy tested in any type of experimental or clinical model. To this purpose, Medline, Embase, Cancerlit and the Cochrane databases were searched. We created a manually annotated database (Targeted Therapy Database, TTD) where the relevant data are gathered in a formal representation that can be computationally analyzed. Dedicated algorithms were set up for the identification of the prevalent therapeutic hypotheses based on the available evidence and for ranking treatments based on the molecular profile of individual patients. In this essay we describe the principles and computational algorithms of an original method developed to fully exploit the available knowledge on cancer biology with the

  12. Identification of a current hot spot of HIV type 1 transmission in Mongolia by molecular epidemiological analysis.

    Science.gov (United States)

    Davaalkham, Jagdagsuren; Unenchimeg, Puntsag; Baigalmaa, Chultem; Erdenetuya, Gombo; Nyamkhuu, Dulmaa; Shiino, Teiichiro; Tsuchiya, Kiyoto; Hayashida, Tsunefusa; Gatanaga, Hiroyuki; Oka, Shinichi

    2011-10-01

    We investigated the current molecular epidemiological status of HIV-1 in Mongolia, a country with very low incidence of HIV-1 though with rapid expansion in recent years. HIV-1 pol (1065 nt) and env (447 nt) genes were sequenced to construct phylogenetic trees. The evolutionary rates, molecular clock phylogenies, and other evolutionary parameters were estimated from heterochronous genomic sequences of HIV-1 subtype B by the Bayesian Markov chain Monte Carlo method. We obtained 41 sera from 56 reported HIV-1-positive cases as of May 2009. The main route of infection was men who have sex with men (MSM). Dominant subtypes were subtype B in 32 cases (78%) followed by subtype CRF02_AG (9.8%). The phylogenetic analysis of the pol gene identified two clusters in subtype B sequences. Cluster 1 consisted of 21 cases including MSM and other routes of infection, and cluster 2 consisted of eight MSM cases. The tree analyses demonstrated very short branch lengths in cluster 1, suggesting a surprisingly active expansion of HIV-1 transmission during a short period with the same ancestor virus. Evolutionary analysis indicated that the outbreak started around the early 2000s. This study identified a current hot spot of HIV-1 transmission and potential seed of the epidemic in Mongolia. Comprehensive preventive measures targeting this group are urgently needed.

  13. An integrative view of cisplatin-induced renal and cardiac toxicities: molecular mechanisms, current treatment challenges and potential protective measures

    Science.gov (United States)

    Dugbartey, George J.; Peppone, Luke J.; de Graaf, Inge A.M.

    2017-01-01

    Cisplatin is currently one of the most widely-used chemotherapeutic agents against various malignancies. Its clinical application is limited, however, by inherent renal and cardiac toxicities and other side effects, of which the underlying mechanisms are only partly understood. Experimental studies show cisplatin generates reactive oxygen species, which impair the cell’s antioxidant defense system, causing oxidative stress and potentiating injury, thereby culminating in kidney and heart failure. Understanding the molecular mechanisms of cisplatin-induced renal and cardiac toxicities may allow clinicians to prevent or treat this problem better and may also provide a model for investigating drug-induced organ toxicity in general. This review discusses some of the major molecular mechanisms of cisplatin-induced renal and cardiac toxicities including disruption of ionic homeostasis and energy status of the cell leading to cell injury and cell death. We highlight clinical manifestations of both toxicities as well as (novel)biomarkers such as kidney injury molecule-1 (KIM-1), tissue inhibitor of metalloproteinase-1 (TIMP-1) and N-terminal pro-B-type natriuretic peptide (NT-proBNP). We also present some current treatment challenges and propose potential protective strategies with novel pharmacological compounds that might mitigate or prevent these toxicities, which include the use of hydrogen sulfide. PMID:27717837

  14. Molecular and elemental effects underlying the biochemical action of transcranial direct current stimulation (tDCS) in appetite control

    Science.gov (United States)

    Surowka, Artur D.; Ziomber, Agata; Czyzycki, Mateusz; Migliori, Alessandro; Kasper, Kaja; Szczerbowska-Boruchowska, Magdalena

    2018-04-01

    Recent studies highlight that obesity may alter the electric activity in brain areas triggering appetite and craving. Transcranial direct current brain stimulation (tDCS) has recently emerged as a safe alternative for treating food addiction via modulating cortical excitability without any high-risk surgical procedure to be utilized. As for anodal-type tDCS (atDCS), we observe increased excitability and spontaneous firing of the cortical neurons, whilst for the cathodal-type tDCS (ctDCS) a significant decrease is induced. Unfortunately, for the method to be fully used in a clinical setting, its biochemical action mechanism must be precisely defined, although it is proposed that molecular remodelling processes play in concert with brain activity changes involving the ions of: Na, Cl, K and Ca. Herein, we proposed for the first time Fourier transform infrared (FTIR) and synchrotron X-ray fluorescence (SRXRF) microprobes for a combined molecular and elemental analysis in the brain areas implicated appetite control, upon experimental treatment by either atDCS or ctDCS. The study, although preliminary, shows that by stimulating the prefrontal cortex in the rats fed high-caloric nutrients, the feeding behavior can be significantly changed, resulting in significantly inhibited appetite. Both, atDCS and ctDCS produced significant molecular changes involving qualitative and structural properties of lipids, whereas atDCS was found with a somewhat more significant effect on protein secondary structure in all the brain areas investigated. Also, tDCS was reported to reduce surface masses of Na, Cl, K, and Ca in almost all brain areas investigated, although the atDCS deemed to have a stronger neuro-modulating effect. Taken together, one can report that tDCS is an effective treatment technique, and its action mechanism in the appetite control seems to involve a variety of lipid-, protein- and metal/non-metal-ion-driven biochemical changes, regardless the current polarization.

  15. A Reasoning Technique for Taxonomy Expert System of Living Organisms

    OpenAIRE

    desiani, anita; Firdaus, Firdaus; Maiyanti, Sri Indra

    2016-01-01

    Taxonomy of living organisms can help scientists to sort organisms in order and help them to identify new organisms by finding out which their groups. It also is easier to study organisms when they are sorted in groups. Taxonomy of living organisms system is a important basic part of ecology system. Researcher should know about any organisms that they noted in an ecology. Integration between classification taxonomy of Living Organisms and technology information will have many advantages for ...

  16. Mathematics, curriculum and assessment: The role of taxonomies in the quest for coherence

    Directory of Open Access Journals (Sweden)

    Caroline Long

    2014-12-01

    Full Text Available A challenge encountered when monitoring mathematics teaching and learning at high school is that taxonomies such as Bloom’s, and variations of this work, are not entirely adequate for providing meaningful feedback to teachers beyond very general cognitive categories that are difficult to interpret. Challenges of this nature are also encountered in the setting of examinations, where the requirement is to cover a range of skills and cognitive domains. The contestation as to the cognitive level is inevitable as it is necessary to analyse the relationship between the problem and the learners’ background experience. The challenge in the project described in this article was to find descriptive terms that would be meaningful to teachers. The first attempt at providing explicit feedback was to apply the assessment frameworks that include a content component and a cognitive component, namely knowledge, routine procedures, complex procedures and problem solving, currently used in the South African curriculum documents. The second attempt investigated various taxonomies, including those used in international assessments and in mathematics education research, for constructs that teachers of mathematics might find meaningful. The final outcome of this investigation was to apply the dimensions required to understand a mathematical concept proposed by Usiskin (2012: the skills-algorithm, property-proof, use-application and representation-metaphor dimension. A feature of these dimensions is that they are not hierarchical; rather, within each of the dimensions, the mathematical task may demand recall but may also demand the highest level of creativity. For our purpose, we developed a two-way matrix using Usiskin’s dimensions on one axis and a variation of Bloom’s revised taxonomy on the second axis. Our findings are that this two-way matrix provides an alternative to current taxonomies, is more directly applicable to mathematics and provides the

  17. Comparative studies of high-frequency and direct current molecular gas discharges

    International Nuclear Information System (INIS)

    Goichman, V.H.; Goldfarb, V.M.; Tendler, M.B.

    1975-01-01

    Electron gas parameters, gas temperatures, ionization and thermal instability are found to be markedly different in direct current glow discharges from capactive electrodless high frequency discharge even when equal net power input is provided. It is reasonable to expect that the combined discharge containing both types of discharges mentioned above may be expected to improve significantly both the steady-state and transient characteristics of the plasma. The characteristics of different discharges in air, nitrogen air-CO 2 -He mixture have been compared. Because of the lack of the direct electrical methods for measurements of the hf plasma, exphasis in this investigation has been laid on both theoretical) based on the analytical expression for electron energy distribution function received previously and experimental spectroscopic evaluations of the plasma parameters. (Auth.)

  18. A Rain Taxonomy for Degraded Visual Environment Mitigation

    Science.gov (United States)

    Gatlin, P. N.; Petersen, W. A.

    2018-01-01

    This Technical Memorandum (TM) provides a description of a rainfall taxonomy that defines the detailed characteristics of naturally occurring rainfall. The taxonomy is based on raindrop size measurements collected around the globe and encompasses several different climate types. Included in this TM is a description of these rainfall observations, an explanation of methods used to process those data, and resultant metrics comprising the rain taxonomy database. Each of the categories in the rain taxonomy are characterized by a unique set of raindrop sizes that can be used in simulations of electromagnetic wave propagation through a rain medium.

  19. Taxonomy and biogeography of Stephanoxis Simon, 1897 (Aves: Trochilidae

    Directory of Open Access Journals (Sweden)

    Vagner Cavarzere

    2014-01-01

    Full Text Available After the description in the 19th century of two hummingbird species currently allocated to the genus Stephanoxis, Peters (1945 merged both taxa into a single species without providing any rationale. Here we re-evaluate the taxonomy and species limits of the representatives of this genus based on an extensive number of specimens. We demonstrate these taxa are better treated as full species under both the Biological and Phylogenetic Species Concepts due to their well-defined range and plumage patterns and reciprocally diagnosability. They have distinct, allopatric distributions segregated by a 160 km gap between the Serra do Mar, to the east, and Serra de Paranapiacaba, to the west, in the state of São Paulo. Stephanoxis species have ranges which are congruent with other montane bird species’ suggesting shared vicariance events during preterit interglacial periods.

  20. Transporter taxonomy - a comparison of different transport protein classification schemes.

    Science.gov (United States)

    Viereck, Michael; Gaulton, Anna; Digles, Daniela; Ecker, Gerhard F

    2014-06-01

    Currently, there are more than 800 well characterized human membrane transport proteins (including channels and transporters) and there are estimates that about 10% (approx. 2000) of all human genes are related to transport. Membrane transport proteins are of interest as potential drug targets, for drug delivery, and as a cause of side effects and drug–drug interactions. In light of the development of Open PHACTS, which provides an open pharmacological space, we analyzed selected membrane transport protein classification schemes (Transporter Classification Database, ChEMBL, IUPHAR/BPS Guide to Pharmacology, and Gene Ontology) for their ability to serve as a basis for pharmacology driven protein classification. A comparison of these membrane transport protein classification schemes by using a set of clinically relevant transporters as use-case reveals the strengths and weaknesses of the different taxonomy approaches.

  1. Current-voltage curves for molecular junctions computed using all-electron basis sets

    International Nuclear Information System (INIS)

    Bauschlicher, Charles W.; Lawson, John W.

    2006-01-01

    We present current-voltage (I-V) curves computed using all-electron basis sets on the conducting molecule. The all-electron results are very similar to previous results obtained using effective core potentials (ECP). A hybrid integration scheme is used that keeps the all-electron calculations cost competitive with respect to the ECP calculations. By neglecting the coupling of states to the contacts below a fixed energy cutoff, the density matrix for the core electrons can be evaluated analytically. The full density matrix is formed by adding this core contribution to the valence part that is evaluated numerically. Expanding the definition of the core in the all-electron calculations significantly reduces the computational effort and, up to biases of about 2 V, the results are very similar to those obtained using more rigorous approaches. The convergence of the I-V curves and transmission coefficients with respect to basis set is discussed. The addition of diffuse functions is critical in approaching basis set completeness

  2. Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments.

    Science.gov (United States)

    Chen, Jing; Dick, Richard; Lin, Jih-Gaw; Gu, Ji-Dong

    2016-12-01

    Nitrite-dependent anaerobic methane oxidation (n-damo) process uniquely links microbial nitrogen and carbon cycles. Research on n-damo bacteria progresses quickly with experimental evidences through enrichment cultures. Polymerase chain reaction (PCR)-based methods for detecting them in various natural ecosystems and engineered systems play a very important role in the discovery of their distribution, abundance, and biodiversity in the ecosystems. Important characteristics of n-damo enrichments were obtained and their key significance in microbial nitrogen and carbon cycles was investigated. The molecular methods currently used in detecting n-damo bacteria were comprehensively reviewed and discussed for their strengths and limitations in applications with a wide range of samples. The pmoA gene-based PCR primers for n-damo bacterial detection were evaluated and, in particular, several incorrectly stated PCR primer nucleotide sequences in the published papers were also pointed out to allow correct applications of the PCR primers in current and future investigations. Furthermore, this review also offers the future perspectives of n-damo bacteria based on current information and methods available for a better acquisition of new knowledge about this group of bacteria.

  3. Moving towards a molecular taxonomy of autoimmune rheumatic diseases

    NARCIS (Netherlands)

    Barturen, Guillermo; Beretta, Lorenzo; Cervera, Ricard; van Vollenhoven, Ronald; Alarcón-Riquelme, Marta E.

    2018-01-01

    Autoimmune rheumatic diseases pose many problems that have, in general, already been solved in the field of cancer. The heterogeneity of each disease, the clinical similarities and differences between different autoimmune rheumatic diseases and the large number of patients that remain without a

  4. Identification of bacterial strains in viili by molecular taxonomy and ...

    African Journals Online (AJOL)

    Viili, also known as viilia, is a traditional fermented dairy product, which is popular in ... In this study, culture-dependent and independent methods had been used to ... Also, their synergistic effects on milk curd and exopolysaccharides (EPSs) ...

  5. Molecular phylogeny and taxonomy of the genus Veloporphyrellus

    Science.gov (United States)

    Yan-Chun Li; Beatriz Ortiz-Santana; Nian-Kai Zeng; Bang Feng; Zhu L. Yang

    2014-01-01

    Veloporphyrellus is a genus known from North and Central America, southeastern Asia, and Africa. Because species of this genus are phenotypically similar to some taxa in several genera, such as Boletellus, Leccinum, Strobilomyces, Suillus and Tylopilus s.l. belonging to Boletales, its phylogenetic disposition has...

  6. Expanding the Taxonomy of the Diagnostic Criteria for Temporomandibular Disorders (DC/TMD)

    Science.gov (United States)

    Peck, Christopher C.; Goulet, Jean-Paul; Lobbezoo, Frank; Schiffman, Eric L.; Alstergren, Per; Anderson, Gary C.; de Leeuw, Reny; Jensen, Rigmor; Michelotti, Ambra; Ohrbach, Richard; Petersson, Arne; List, Thomas

    2014-01-01

    Background There is a need to expand the current temporomandibular disorder (TMD) classification to include less common, but clinically important disorders. The immediate aim was to develop a consensus-based classification system and associated diagnostic criteria that have clinical and research utility for less common TMDs. The long-term aim was to establish a foundation, vis-à-vis this classification system, that will stimulate data collection, validity testing, and further criteria refinement. Methods A working group [members of the International RDC/TMD Consortium Network of the International Association for Dental Research (IADR), members of the Orofacial Pain Special Interest Group (SIG) of the International Association for the Study of Pain (IASP), and members from other professional societies] reviewed disorders for inclusion based on clinical significance, the availability of plausible diagnostic criteria, and the ability to operationalize and study the criteria. The disorders were derived from the literature when possible and based on expert opinion as necessary. The expanded TMD taxonomy was presented for feedback at international meetings. Results Of 56 disorders considered, 37 were included in the expanded taxonomy and were placed into the following four categories: temporomandibular joint disorders, masticatory muscle disorders, headache disorders, and disorders affecting associated structures. Those excluded were extremely uncommon, lacking operationalized diagnostic criteria, not clearly related to TMDs, or not sufficiently distinct from disorders already included within the taxonomy. Conclusions The expanded TMD taxonomy offers an integrated approach to clinical diagnosis and provides a framework for further research to operationalize and test the proposed taxonomy and diagnostic criteria. PMID:24443898

  7. The ALI-ARMS Code for Modeling Atmospheric non-LTE Molecular Band Emissions: Current Status and Applications

    Science.gov (United States)

    Kutepov, A. A.; Feofilov, A. G.; Manuilova, R. O.; Yankovsky, V. A.; Rezac, L.; Pesnell, W. D.; Goldberg, R. A.

    2008-01-01

    The Accelerated Lambda Iteration (ALI) technique was developed in stellar astrophysics at the beginning of 1990s for solving the non-LTE radiative transfer problem in atomic lines and multiplets in stellar atmospheres. It was later successfully applied to modeling the non-LTE emissions and radiative cooling/heating in the vibrational-rotational bands of molecules in planetary atmospheres. Similar to the standard lambda iterations ALI operates with the matrices of minimal dimension. However, it provides higher convergence rate and stability due to removing from the iterating process the photons trapped in the optically thick line cores. In the current ALI-ARMS (ALI for Atmospheric Radiation and Molecular Spectra) code version additional acceleration of calculations is provided by utilizing the opacity distribution function (ODF) approach and "decoupling". The former allows replacing the band branches by single lines of special shape, whereas the latter treats non-linearity caused by strong near-resonant vibration-vibrational level coupling without additional linearizing the statistical equilibrium equations. Latest code application for the non-LTE diagnostics of the molecular band emissions of Earth's and Martian atmospheres as well as for the non-LTE IR cooling/heating calculations are discussed.

  8. Taxonomy of the nuclear plant operator's role

    International Nuclear Information System (INIS)

    Kisner, R.A.; Fullerton, A.M.; Frey, P.R.; Dougherty, E.M.

    1981-01-01

    A program is presently under way at the Oak Ridge National Laboratory (ORNL) to define the functional design requirements of operational aids for nuclear power plant operators. A first and important step in defining these requirements is to develop an understanding of the operator's role or function. This paper describes a taxonomy of operator functions that applies during all operational modes and conditions of the plant. Other topics such as the influence of automation, role acceptance, and the operator's role during emergencies are also discussed. This systematic approach has revealed several areas which have potential for improving the operator's ability to perform his role

  9. Constructive Alignment and the SOLO Taxonomy:

    DEFF Research Database (Denmark)

    Brabrand, Claus; Dahl, Bettina

    2008-01-01

    explain and discuss these principles, give examples of how the new syllabi were constructed, and describe the process by which they were formed. We also explain and discuss the results of a comparative study comparing the competences of Computer Science with those of Mathematics (and classical Natural...... the science faculties at University of Aarhus, Denmark (AU) and the University of Southern Denmark (SDU) that had been rewritten to explicitly incorporate course objectives, interpreted as intended learning outcomes (ILOs), using the principles of Constructive Alignment and the SOLO Taxonomy. In this paper we...

  10. An inclusive taxonomy of behavioral biases

    Directory of Open Access Journals (Sweden)

    David Peón

    2017-07-01

    Full Text Available This paper overviews the theoretical and empirical research on behavioral biases and their influence in the literature. To provide a systematic exposition, we present a unified framework that takes the reader through an original taxonomy, based on the reviews of relevant authors in the field. In particular, we establish three broad categories that may be distinguished: heuristics and biases; choices, values and frames; and social factors. We then describe the main biases within each category, and revise the main theoretical and empirical developments, linking each bias with other biases and anomalies that are related to them, according to the literature.

  11. Molecular dynamics simulations of metallic friction and of its dependence on electric currents - development and first results

    Science.gov (United States)

    Meintanis, Evangelos Anastasios

    We have extended the HOLA molecular dynamics (MD) code to run slider-on-block friction experiments for Al and Cu. Both objects are allowed to evolve freely and show marked deformation despite the hardness difference. We recover realistic coefficients of friction and verify the importance of cold-welding and plastic deformations in dry sliding friction. Our first data also show a mechanism for decoupling between load and friction at high velocities. Such a mechanism can explain an increase in the coefficient of friction of metals with velocity. The study of the effects of currents on our system required the development of a suitable electrodynamic (ED) solver, as the disparity of MD and ED time scales threatened the efficiency of our code. Our first simulations combining ED and MD are presented.

  12. Theoretical investigation on current-voltage characteristics in all-carbon molecular device with different contact geometries

    International Nuclear Information System (INIS)

    Ye Fuqiu; Fan Zhiqiang; He Jun; Peng Jun; Tang Liming

    2012-01-01

    Applying nonequilibrium Green's functions in combination with the first-principles density-functional theory, we investigate electronic transport properties of an all-carbon molecular device consisting of one phenalenyl molecule and two zigzag graphene nanoribbons. The results show that the electronic transport properties are strongly dependent on the contact geometry and device's currents can drop obviously when the connect sites change from second-nearest sites from the central atom of the molecule (S site) to third-nearest sites from the central atom of the molecule (T site). More importantly, the negative differential resistance behavior is only observed on the negative bias region when the molecule connects the graphene nanoribbons through two T sites.

  13. Targeted Therapy Database (TTD: a model to match patient's molecular profile with current knowledge on cancer biology.

    Directory of Open Access Journals (Sweden)

    Simone Mocellin

    Full Text Available BACKGROUND: The efficacy of current anticancer treatments is far from satisfactory and many patients still die of their disease. A general agreement exists on the urgency of developing molecularly targeted therapies, although their implementation in the clinical setting is in its infancy. In fact, despite the wealth of preclinical studies addressing these issues, the difficulty of testing each targeted therapy hypothesis in the clinical arena represents an intrinsic obstacle. As a consequence, we are witnessing a paradoxical situation where most hypotheses about the molecular and cellular biology of cancer remain clinically untested and therefore do not translate into a therapeutic benefit for patients. OBJECTIVE: To present a computational method aimed to comprehensively exploit the scientific knowledge in order to foster the development of personalized cancer treatment by matching the patient's molecular profile with the available evidence on targeted therapy. METHODS: To this aim we focused on melanoma, an increasingly diagnosed malignancy for which the need for novel therapeutic approaches is paradigmatic since no effective treatment is available in the advanced setting. Relevant data were manually extracted from peer-reviewed full-text original articles describing any type of anti-melanoma targeted therapy tested in any type of experimental or clinical model. To this purpose, Medline, Embase, Cancerlit and the Cochrane databases were searched. RESULTS AND CONCLUSIONS: We created a manually annotated database (Targeted Therapy Database, TTD where the relevant data are gathered in a formal representation that can be computationally analyzed. Dedicated algorithms were set up for the identification of the prevalent therapeutic hypotheses based on the available evidence and for ranking treatments based on the molecular profile of individual patients. In this essay we describe the principles and computational algorithms of an original method

  14. Taxonomy of Streptomyces strains isolated from rhizospheres of ...

    African Journals Online (AJOL)

    Taxonomy of Streptomyces strains isolated from rhizospheres of various plant species grown in Taif region, KSA, having antagonistic activities against some microbial tissue ... African Journal of Biotechnology ... Keywords: Taxonomy, Streptomyces, microbial tissue culture contaminants, antagonistic activities, 16S rRNA

  15. Understanding the Advising Learning Process Using Learning Taxonomies

    Science.gov (United States)

    Muehleck, Jeanette K.; Smith, Cathleen L.; Allen, Janine M.

    2014-01-01

    To better understand the learning that transpires in advising, we used Anderson et al.'s (2001) revision of Bloom's (1956) taxonomy and Krathwohl, Bloom, and Masia's (1964) affective taxonomy to analyze eight student-reported advising outcomes from Smith and Allen (2014). Using the cognitive processes and knowledge domains of Anderson et al.'s…

  16. Rethinking Bloom's Taxonomy: Implications for Testing and Assessment.

    Science.gov (United States)

    Anderson, Lorin W.

    This paper describes a work in progress on a second edition of "Taxonomy of Educational Objectives, The Classification of Educational Goals, Handbook I: Cognitive Domain," also known as "Bloom's Taxonomy" (B. Bloom and others, Eds., 1956). The new edition will be grounded in the collective wisdom of the original…

  17. Nuclear Medicine Technologists' Perception and Current Assessment of Quality: A Society of Nuclear Medicine and Molecular Imaging Technologist Section Survey.

    Science.gov (United States)

    Mann, April; Farrell, Mary Beth; Williams, Jessica; Basso, Danny

    2017-06-01

    In 2015, the Society of Nuclear Medicine and Molecular Imaging Technologist Section (SNMMI-TS) launched a multiyear quality initiative to help prepare the technologist workforce for an evidence-based health-care delivery system that focuses on quality. To best implement the quality strategy, the SNMMI-TS first surveyed technologists to ascertain their perception of quality and current measurement of quality indicators. Methods: An internet survey was sent to 27,989 e-mail contacts. Questions related to demographic data, perceptions of quality, quality measurement, and opinions on the minimum level of education are discussed in this article. Results: A total of 4,007 (14.3%) responses were received. When asked to list 3 words or phrases that represent quality, there were a plethora of different responses. The top 3 responses were image quality, quality control, and technologist education or competency. Surveying patient satisfaction was the most common quality measure (80.9%), followed by evaluation of image quality (78.2%). Evaluation of image quality (90.3%) and equipment functionality (89.4%) were considered the most effective measures. Technologists' differentiation between quality, quality improvement, quality control, quality assurance, and quality assessment seemed ambiguous. Respondents were confident in their ability to assess and improve quality at their workplace (91.9%) and agreed their colleagues were committed to delivering quality work. Of note, 70.7% of respondents believed that quality is directly related to the technologist's level of education. Correspondingly, respondents felt there should be a minimum level of education (99.5%) and that certification or registry should be required (74.4%). Most respondents (59.6%) felt that a Bachelor's degree should be the minimum level of education, followed by an Associate's degree (40.4%). Conclusion: To best help nuclear medicine technologists provide quality care, the SNMMI-TS queried technologists to

  18. A preliminary taxonomy of medical errors in family practice.

    Science.gov (United States)

    Dovey, S M; Meyers, D S; Phillips, R L; Green, L A; Fryer, G E; Galliher, J M; Kappus, J; Grob, P

    2002-09-01

    To develop a preliminary taxonomy of primary care medical errors. Qualitative analysis to identify categories of error reported during a randomized controlled trial of computer and paper reporting methods. The National Network for Family Practice and Primary Care Research. Family physicians. Medical error category, context, and consequence. Forty two physicians made 344 reports: 284 (82.6%) arose from healthcare systems dysfunction; 46 (13.4%) were errors due to gaps in knowledge or skills; and 14 (4.1%) were reports of adverse events, not errors. The main subcategories were: administrative failure (102; 30.9% of errors), investigation failures (82; 24.8%), treatment delivery lapses (76; 23.0%), miscommunication (19; 5.8%), payment systems problems (4; 1.2%), error in the execution of a clinical task (19; 5.8%), wrong treatment decision (14; 4.2%), and wrong diagnosis (13; 3.9%). Most reports were of errors that were recognized and occurred in reporters' practices. Affected patients ranged in age from 8 months to 100 years, were of both sexes, and represented all major US ethnic groups. Almost half the reports were of events which had adverse consequences. Ten errors resulted in patients being admitted to hospital and one patient died. This medical error taxonomy, developed from self-reports of errors observed by family physicians during their routine clinical practice, emphasizes problems in healthcare processes and acknowledges medical errors arising from shortfalls in clinical knowledge and skills. Patient safety strategies with most effect in primary care settings need to be broader than the current focus on medication errors.

  19. Digital Libraries: The Challenge of Integrating Instagram with a Taxonomy for Content Management

    OpenAIRE

    Simona Ibba; Filippo Eros Pani

    2016-01-01

    Interoperability and social implication are two current challenges in the digital library (DL) context. To resolve the problem of interoperability, our work aims to find a relationship between the main metadata schemas. In particular, we want to formalize knowledge through the creation of a metadata taxonomy built with the analysis and the integration of existing schemas associated with DLs. We developed a method to integrate and combine Instagram metadata and hashtags. The final result is a ...

  20. Planetary Taxonomy: Label Round Bodies "Worlds"

    Science.gov (United States)

    Margot, Jean-Luc; Levison, H. F.

    2009-05-01

    The classification of planetary bodies is as important to Astronomy as taxonomy is to other sciences. The etymological, historical, and IAU definitions of planet rely on a dynamical criterion, but some authors prefer a geophysical criterion based on "roundness". Although the former criterion is superior when it comes to classifying newly discovered objects, the conflict need not exist if we agree to identify the subset of "round" planetary objects as "worlds". This addition to the taxonomy would conveniently recognize that "round" objects such as Earth, Europa, Titan, Triton, and Pluto share some common planetary-type processes regardless of their distance from the host star. Some of these worlds are planets, others are not. Defining how round is round and handling the inevitable transition objects are non-trivial tasks. Because images at sufficient resolution are not available for the overwhelming majority of newly discovered objects, the degree of roundness is not a directly observable property and is inherently problematic as a basis for classification. We can tolerate some uncertainty in establishing the "world" status of a newly discovered object, and still establish its planet or satellite status with existing dynamical criteria. Because orbital parameters are directly observable, and because mass can often be measured either from orbital perturbations or from the presence of companions, the dynamics provide a robust and practical planet classification scheme. It may also be possible to determine which bodies are dynamically dominant from observations of the population magnitude/size distribution.

  1. Molecular Dynamics Study of the Separation Behavior at the Interface between PVDF Binder and Copper Current Collector

    Directory of Open Access Journals (Sweden)

    Seungjun Lee

    2016-01-01

    Full Text Available In Li-ion batteries, the mechanical strengths at the interfaces of binder/particle and binder/current collector play an important role in maintaining the mechanical integrity of the composite electrode. In this work, the separation behaviors between polyvinylidene fluoride (PVDF binders and copper current collectors are studied in the opening and sliding modes using molecular dynamics (MD simulations. The simulation shows that the separation occurs inside the PVDF rather than at the interface due to the strong adhesion between PVDF and copper. This fracture behavior is different from the behavior of the PVDF/graphite basal plane that shows a clear separation at the interface. The results suggest that the adhesion strength of the PVDF/copper is stronger than that of the PVDF/graphite basal plane. The methodology used in MD simulation can directly evaluate the adhesion strength at the interfaces of various materials between binders, substrates, and particles at the atomic scales. The proposed method can therefore provide a guideline for the design of the electrode in order to enhance the mechanical integrity for better battery performance.

  2. A literature review on the levels of automation during the years. What are the different taxonomies that have been proposed?

    Science.gov (United States)

    Vagia, Marialena; Transeth, Aksel A; Fjerdingen, Sigurd A

    2016-03-01

    In this paper we present a literature review of the evolution of the levels of autonomy from the end of the 1950s up until now. The motivation of this study was primarily to gather and to compare the literature that exists, on taxonomies on levels of automation. Technical developments within both computer hardware and software have made it possible to introduce autonomy into virtually all aspects of human-machine systems. The current study, is focusing on how different authors treat the problem of different levels of automation. The outcome of this study is to present the differences between the proposed levels of automation and the various taxonomies, giving the potential users a number of choices in order to decide which taxonomy satisfies their needs better. In addition, this paper surveys deals with the term adaptive automation, which seems to be a new trend in the literature on autonomy. Copyright © 2015 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  3. Does the name really matter? The importance of botanical nomenclature and plant taxonomy in biomedical research.

    Science.gov (United States)

    Bennett, Bradley C; Balick, Michael J

    2014-03-28

    Medical research on plant-derived compounds requires a breadth of expertise from field to laboratory and clinical skills. Too often basic botanical skills are evidently lacking, especially with respect to plant taxonomy and botanical nomenclature. Binomial and familial names, synonyms and author citations are often misconstrued. The correct botanical name, linked to a vouchered specimen, is the sine qua non of phytomedical research. Without the unique identifier of a proper binomial, research cannot accurately be linked to the existing literature. Perhaps more significant, is the ambiguity of species determinations that ensues of from poor taxonomic practices. This uncertainty, not surprisingly, obstructs reproducibility of results-the cornerstone of science. Based on our combined six decades of experience with medicinal plants, we discuss the problems of inaccurate taxonomy and botanical nomenclature in biomedical research. This problems appear all too frequently in manuscripts and grant applications that we review and they extend to the published literature. We also review the literature on the importance of taxonomy in other disciplines that relate to medicinal plant research. In most cases, questions regarding orthography, synonymy, author citations, and current family designations of most plant binomials can be resolved using widely-available online databases and other electronic resources. Some complex problems require consultation with a professional plant taxonomist, which also is important for accurate identification of voucher specimens. Researchers should provide the currently accepted binomial and complete author citation, provide relevant synonyms, and employ the Angiosperm Phylogeny Group III family name. Taxonomy is a vital adjunct not only to plant-medicine research but to virtually every field of science. Medicinal plant researchers can increase the precision and utility of their investigations by following sound practices with respect to botanical

  4. Digital Libraries: The Challenge of Integrating Instagram with a Taxonomy for Content Management

    Directory of Open Access Journals (Sweden)

    Simona Ibba

    2016-05-01

    Full Text Available Interoperability and social implication are two current challenges in the digital library (DL context. To resolve the problem of interoperability, our work aims to find a relationship between the main metadata schemas. In particular, we want to formalize knowledge through the creation of a metadata taxonomy built with the analysis and the integration of existing schemas associated with DLs. We developed a method to integrate and combine Instagram metadata and hashtags. The final result is a taxonomy, which provides innovative metadata with respect to the classification of resources, as images of Instagram and the user-generated content, that play a primary role in the context of modern DLs. The possibility of Instagram to localize the photos inserted by users allows us to interpret the most relevant and interesting informative content for a specific user type and in a specific location and to improve access, visibility and searching of library content.

  5. Shedding subspecies: The influence of genetics on reptile subspecies taxonomy.

    Science.gov (United States)

    Torstrom, Shannon M; Pangle, Kevin L; Swanson, Bradley J

    2014-07-01

    The subspecies concept influences multiple aspects of biology and management. The 'molecular revolution' altered traditional methods (morphological traits) of subspecies classification by applying genetic analyses resulting in alternative or contradictory classifications. We evaluated recent reptile literature for bias in the recommendations regarding subspecies status when genetic data were included. Reviewing characteristics of the study, genetic variables, genetic distance values and noting the species concepts, we found that subspecies were more likely elevated to species when using genetic analysis. However, there was no predictive relationship between variables used and taxonomic recommendation. There was a significant difference between the median genetic distance values when researchers elevated or collapsed a subspecies. Our review found nine different concepts of species used when recommending taxonomic change, and studies incorporating multiple species concepts were more likely to recommend a taxonomic change. Since using genetic techniques significantly alter reptile taxonomy there is a need to establish a standard method to determine the species-subspecies boundary in order to effectively use the subspecies classification for research and conservation purposes. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Leaf arrangements are invalid in the taxonomy of orchid species

    Directory of Open Access Journals (Sweden)

    Anna Jakubska-Busse

    2017-07-01

    Full Text Available The selection and validation of proper distinguishing characters are of crucial importance in taxonomic revisions. The modern classifications of orchids utilize the molecular tools, but still the selection and identification of the material used in these studies is for the most part related to general species morphology. One of the vegetative characters quoted in orchid manuals is leaf arrangement. However, phyllotactic diversity and ontogenetic changeability have not been analysed in detail in reference to particular taxonomic groups. Therefore, we evaluated the usefulness of leaf arrangements in the taxonomy of the genus Epipactis Zinn, 1757. Typical leaf arrangements in shoots of this genus are described as distichous or spiral. However, in the course of field research and screening of herbarium materials, we indisputably disproved the presence of distichous phyllotaxis in the species Epipactis purpurata Sm. and confirmed the spiral Fibonacci pattern as the dominant leaf arrangement. In addition, detailed analyses revealed the presence of atypical decussate phyllotaxis in this species, as well as demonstrated the ontogenetic formation of pseudowhorls. These findings confirm ontogenetic variability and plasticity in E. purpurata. Our results are discussed in the context of their significance in delimitations of complex taxa within the genus Epipactis.

  7. Norms for environmentally responsible behaviour: An extended taxonomy and a preliminary assessment

    DEFF Research Database (Denmark)

    Thøgersen, John

    The currently used concept of personal or moral norms is ambiguous with regard to its motivational content. Therefore, a revision of the norm taxonomy is suggested, implying a distinction between three types of personal norms, called introjected, identified, and integrated norms. A preliminary as...... is also supported, with the reservation that the different behavioural references are more than just different methods of measuring the same latent construct(s). People evidently hold different norms for different environmentally responsible behaviours.......The currently used concept of personal or moral norms is ambiguous with regard to its motivational content. Therefore, a revision of the norm taxonomy is suggested, implying a distinction between three types of personal norms, called introjected, identified, and integrated norms. A preliminary...... assessment of the taxonomy is carried out based of a survey of a random sample of Danish residents 18 years or older. A range of norm constructs were measured with regard to four environmentally relevant behaviours: buying organic milk, buying energy saving light bulbs, source-separating compostable kitchen...

  8. Surface potential, charging and local current transport of individual Ge quantum dots grown by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Singha, R.K. [Department of Physics, Visva-Bharati, Santiniketan 731235 (India); Manna, S.; Bar, R.; Das, S. [Department of Physics, Indian Institute of Technology-Kharagpur, Kharagpur 721302 (India); Ray, S.K., E-mail: physkr@phy.iitkgp.ernet.in [Department of Physics, Indian Institute of Technology-Kharagpur, Kharagpur 721302 (India)

    2017-06-15

    Highlights: We have elaborately explained the individual Ge QD charging phenomena and current transport, which is very important to understand the Ge/Si nano devices. This paper will give a flavor to properly understand these phenomena linked together along with the photocurrent mechanism which is related to the Ge/Si valence band offset. • Both the CAFM and KPFM techniques point out the functionality of doping nature of the underneath Si substrate on the aforementioned characteristics of Ge QDs. • Analysis of the surface potential mapping using KPFM technique yields an approximate valence band offset measurement which is required to understand the intra-valence transition of holes for the realization of long wavelength infrared photodetector. • KPFM and CAFM can be utilized to explore the charging/discharging phenomena of dots and their composition variations. • Current-voltage (I–V) characteristics of the individual Ge QD strongly depends on the individual QD size. • Energy band diagrams for diamond tip and Ge QD shows the higher barrier for electrons and lower barrier for holes allowing the easy tunneling for holes to dominate the transport. - Abstract: It is fundamentally important to understand the nanoscale electronic properties of a single quantum dot (QD) contrary to an ensemble of QDs. Kelvin probe force microscopy (KPFM) and conductive atomic force microscopy (CAFM) are two important tools, which could be employed to probe surface potential, charging phenomena, and current transport mechanism of individual QD. We demonstrate the aforementioned characteristics of self-assembled Ge QDs, which was grown on Si substrates by solid source molecular beam epitaxy driven by the Stranski-Krastanov method. Study reveals that each Ge QD acts as charge storage node even at zero applied bias. The shape, size and density of QDs could be well probed by CAFM and KPFM, whereas QD facets could be better resolved by the conductive tip. The CAFM investigation

  9. Taxonomi för databashanterare

    OpenAIRE

    Österberg, Alexander

    2017-01-01

    Syftet med denna undersökning är att ta fram en taxonomi för databashanteringssystem (DBMS) som kan förenkla valet av DBMS, då det kan vara en lång och komplicerad process. Taxonomin klassificerar kriterier hos DBMS som anses viktiga i en litteraturstudie av flertalet artiklar. Arbetet visar även på en strukturerad process för att gå från krav till val av databashanterare i form av ett poängsystem som använder sig av taxonomin och DBMS rangordning på olika kriterier. Valprocessen tar ställnin...

  10. Taxonomy for competency-based dental curricula.

    Science.gov (United States)

    Beltrán-Neira, Roberto J; Beltrán-Aguilar, Eugenio D

    2004-09-01

    The objective of this article is to propose a classification of dental competencies. Interest in dental competencies has grown consistently during the last three decades. However, the dental education literature suggests that the term "competency" is understood and used differently by dental schools around the world. The taxonomic classification of dental competencies we propose follows a systematic approach starting at the highest level of complexity, i.e., the professional profile the teaching institution envisions for its graduates, and following in a decreasing degree of complexity to competency function, task, step, movement, and moment. This taxonomy has proved to be useful for more than thirty years in the Dental School of the Peruvian University Cayetano Heredia. Graduates of this school are successful practitioners, teachers, and researchers in Peru and other countries. The classification proposed here should clarify terms, facilitate curriculum design and learning assessment, stimulate further discussion on the matter, and facilitate communication among the dental education establishment.

  11. Ontologies, taxonomies and thesauri in systems science and systematics

    CERN Document Server

    Currás, Emilia

    2010-01-01

    The originality of this book, which deals with such a new subject matter, lies in the application of methods and concepts never used before - such as ontologies and taxonomies, as well as thesauri - to the ordering of knowledge based on primary information. Chapters in the book also examine the study of ontologies, taxonomies and thesauri from the perspective of systematics and general systems theory. Ontologies, Taxonomies and Thesauri in Systems Science and Systematics will be extremely useful to those operating within the network of related fields, which includes documentation and informati

  12. Fish Ontology framework for taxonomy-based fish recognition

    Science.gov (United States)

    Ali, Najib M.; Khan, Haris A.; Then, Amy Y-Hui; Ving Ching, Chong; Gaur, Manas

    2017-01-01

    Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO), an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users. PMID:28929028

  13. Fish Ontology framework for taxonomy-based fish recognition

    Directory of Open Access Journals (Sweden)

    Najib M. Ali

    2017-09-01

    Full Text Available Life science ontologies play an important role in Semantic Web. Given the diversity in fish species and the associated wealth of information, it is imperative to develop an ontology capable of linking and integrating this information in an automated fashion. As such, we introduce the Fish Ontology (FO, an automated classification architecture of existing fish taxa which provides taxonomic information on unknown fish based on metadata restrictions. It is designed to support knowledge discovery, provide semantic annotation of fish and fisheries resources, data integration, and information retrieval. Automated classification for unknown specimens is a unique feature that currently does not appear to exist in other known ontologies. Examples of automated classification for major groups of fish are demonstrated, showing the inferred information by introducing several restrictions at the species or specimen level. The current version of FO has 1,830 classes, includes widely used fisheries terminology, and models major aspects of fish taxonomy, grouping, and character. With more than 30,000 known fish species globally, the FO will be an indispensable tool for fish scientists and other interested users.

  14. Towards a new taxonomy of idiopathic orofacial pain.

    Science.gov (United States)

    Woda, Alain; Tubert-Jeannin, Stéphanie; Bouhassira, Didier; Attal, Nadine; Fleiter, Bernard; Goulet, Jean-Paul; Gremeau-Richard, Christelle; Navez, Marie Louise; Picard, Pascale; Pionchon, Paul; Albuisson, Eliane

    2005-08-01

    There is no current consensus on the taxonomy of the different forms of idiopathic orofacial pain (stomatodynia, atypical odontalgia, atypical facial pain, facial arthromyalgia), which are sometimes considered as separate entities and sometimes grouped together. In the present prospective multicentric study, we used a systematic approach to help to place these different painful syndromes in the general classification of chronic facial pain. This multicenter study was carried out on 245 consecutive patients presenting with chronic facial pain (>4 months duration). Each patient was seen by two experts who proposed a diagnosis, administered a 111-item questionnaire and filled out a standardized 68-item examination form. Statistical processing included univariate analysis and several forms of multidimensional analysis. Migraines (n=37), tension-type headache (n=26), post-traumatic neuralgia (n=20) and trigeminal neuralgia (n=13) tended to cluster independently. When signs and symptoms describing topographic features were not included in the list of variables, the idiopathic orofacial pain patients tended to cluster in a single group. Inside this large cluster, only stomatodynia (n=42) emerged as a distinct homogenous subgroup. In contrast, facial arthromyalgia (n=46) and an entity formed with atypical facial pain (n=25) and atypical odontalgia (n=13) could only be individualised by variables reflecting topographical characteristics. These data provide grounds for an evidence-based classification of idiopathic facial pain entities and indicate that the current sub-classification of these syndromes relies primarily on the topography of the symptoms.

  15. A Taxonomy of Information Technology-Enhanced Pricing Strategies

    NARCIS (Netherlands)

    Dixit, A.; Whipple, T.W.; Zinkhan, G.M.; Gailey, E.

    2008-01-01

    As a result of evolving technology, opportunities for innovative pricing strategies continuously emerge. The authors provide an updated taxonomy to show how such emerging strategies relate to recent technological advances. Specifically, they cite increased availability of information, enhanced

  16. The HCBS Taxonomy- A New Language for Classifying Home...

    Data.gov (United States)

    U.S. Department of Health & Human Services — The home- and community-based services (HCBS) taxonomy provides a common language for describing and categorizing HCBS across Medicaid programs. Prior to the...

  17. Biogeography and taxonomy of racket-tail hummingbirds (Aves: Trochilidae: Ocreatus): evidence for species delimitation from morphology and display behavior.

    Science.gov (United States)

    Schuchmann, Karl-L; Weller, André-A; Jürgens, Dietmar

    2016-11-27

    We analyzed geographic variation, biogeography, and intrageneric relationships of racket-tail hummingbirds Ocreatus (Aves, Trochilidae). Presently, the genus is usually considered monospecific, with O. underwoodii including eight subspecies (polystictus, discifer, underwoodii, incommodus, melanantherus, peruanus, annae, addae), although up to three species have been recognized by some authors. In order to evaluate the current taxonomy we studied geographic variation in coloration, mensural characters, and behavioral data of all Ocreatus taxa. We briefly review the taxonomic history of the genus. Applying the Biological Species Concept, species delimitation was based on a qualitative-quantitative criteria analysis including an evaluation of character states. Our results indicate that the genus should be considered a superspecies with four species, the monotypic Ocreatus addae, O. annae, and O. peruanus, and the polytypic O. underwoodii (including the subspecies underwoodii, discifer, incommodus, melanantherus, polystictus). In this taxonomic treatment, O. annae becomes an endemic species to Peru and O. addae is endemic to Bolivia. We recommend additional sampling of distributional, ethological, and molecular data for an improved resolution of the evolutionary history of Ocreatus.

  18. A taxonomy of behaviour change methods: an Intervention Mapping approach.

    Science.gov (United States)

    Kok, Gerjo; Gottlieb, Nell H; Peters, Gjalt-Jorn Y; Mullen, Patricia Dolan; Parcel, Guy S; Ruiter, Robert A C; Fernández, María E; Markham, Christine; Bartholomew, L Kay

    2016-09-01

    In this paper, we introduce the Intervention Mapping (IM) taxonomy of behaviour change methods and its potential to be developed into a coding taxonomy. That is, although IM and its taxonomy of behaviour change methods are not in fact new, because IM was originally developed as a tool for intervention development, this potential was not immediately apparent. Second, in explaining the IM taxonomy and defining the relevant constructs, we call attention to the existence of parameters for effectiveness of methods, and explicate the related distinction between theory-based methods and practical applications and the probability that poor translation of methods may lead to erroneous conclusions as to method-effectiveness. Third, we recommend a minimal set of intervention characteristics that may be reported when intervention descriptions and evaluations are published. Specifying these characteristics can greatly enhance the quality of our meta-analyses and other literature syntheses. In conclusion, the dynamics of behaviour change are such that any taxonomy of methods of behaviour change needs to acknowledge the importance of, and provide instruments for dealing with, three conditions for effectiveness for behaviour change methods. For a behaviour change method to be effective: (1) it must target a determinant that predicts behaviour; (2) it must be able to change that determinant; (3) it must be translated into a practical application in a way that preserves the parameters for effectiveness and fits with the target population, culture, and context. Thus, taxonomies of methods of behaviour change must distinguish the specific determinants that are targeted, practical, specific applications, and the theory-based methods they embody. In addition, taxonomies should acknowledge that the lists of behaviour change methods will be used by, and should be used by, intervention developers. Ideally, the taxonomy should be readily usable for this goal; but alternatively, it should be

  19. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences

    Directory of Open Access Journals (Sweden)

    Robert C. Edgar

    2018-04-01

    Full Text Available Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA is a fundamental task in microbiology. Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%, all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. Accuracy was found to fall rapidly with identity; for example, better methods were found to have V4 genus prediction accuracy of ∼100% at 100% identity but ∼50% at 97% identity. The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal.

  20. Adoption of geodemographic and ethno-cultural taxonomies for analysing Big Data

    Directory of Open Access Journals (Sweden)

    Richard James Webber

    2015-05-01

    Full Text Available This paper is intended to contribute to the discussion of the differential level of adoption of Big Data among research communities. Recognising the impracticality of conducting an audit across all forms and uses of Big Data, we have restricted our enquiry to one very specific form of Big Data, namely general purpose taxonomies, of which Mosaic, Acorn and Origins are examples, that rely on data from a variety of Big Data feeds. The intention of these taxonomies is to enable the records of consumers and citizens held on Big Data datasets to be coded according to type of residential neighbourhood or ethno-cultural heritage without any use of questionnaires. Based on our respective experience in the academic social sciences, in government and in the design and marketing of these taxonomies, we identify the features of these classifications which appear to render them attractive or problematic to different categories of potential user or researcher depending on how the relationship is conceived. We conclude by identifying seven classifications of user or potential user who, on account of their background, current position and future career expectations, tend to respond in different ways to the opportunity to adopt these generic systems as aids for understanding social processes.

  1. Current and calcium responses to local activation of axonal NMDA receptors in developing cerebellar molecular layer interneurons.

    Directory of Open Access Journals (Sweden)

    Bénédicte Rossi

    Full Text Available In developing cerebellar molecular layer interneurons (MLIs, NMDA increases spontaneous GABA release. This effect had been attributed to either direct activation of presynaptic NMDA receptors (preNMDARs or an indirect pathway involving activation of somato-dendritic NMDARs followed by passive spread of somatic depolarization along the axon and activation of axonal voltage dependent Ca(2+ channels (VDCCs. Using Ca(2+ imaging and electrophysiology, we searched for preNMDARs by uncaging NMDAR agonists either broadly throughout the whole field or locally at specific axonal locations. Releasing either NMDA or glutamate in the presence of NBQX using short laser pulses elicited current transients that were highly sensitive to the location of the spot and restricted to a small number of varicosities. The signal was abolished in the presence of high Mg(2+ or by the addition of APV. Similar paradigms yielded restricted Ca(2+ transients in interneurons loaded with a Ca(2+ indicator. We found that the synaptic effects of NMDA were not inhibited by blocking VDCCs but were impaired in the presence of the ryanodine receptor antagonist dantrolene. Furthermore, in voltage clamped cells, bath applied NMDA triggers Ca(2+ elevations and induces neurotransmitter release in the axonal compartment. Our results suggest the existence of preNMDARs in developing MLIs and propose their involvement in the NMDA-evoked increase in GABA release by triggering a Ca(2+-induced Ca(2+ release process mediated by presynaptic Ca(2+ stores. Such a mechanism is likely to exert a crucial role in various forms of Ca(2+-mediated synaptic plasticity.

  2. “Communicate to vaccinate”: the development of a taxonomy of communication interventions to improve routine childhood vaccination

    Science.gov (United States)

    2013-01-01

    -to-be-parents; communities, community members or volunteers; and health care providers. Conclusions Our taxonomy illuminates and organises this field and identifies the range of available communication interventions to increase routine childhood vaccination uptake. We have utilised a variety of data sources, capturing information from rigorous evaluations such as randomised trials as well as experiences and knowledge of practitioners and vaccination stakeholders. The taxonomy reflects current public health practice and can guide the future development of vaccination programmes. PMID:23663327

  3. New Augmented Reality Taxonomy: Technologies and Features of Augmented Environment.

    OpenAIRE

    Hugues , Olivier; Fuchs , Philippe; Nannipieri , Olivier

    2011-01-01

    978-1-4614-0063-9; This article has a dual aim: firstly to define augmented reality (AR) en- vironments and secondly, based on our definition, a new taxonomy enabling these environments to be classified. After briefly reviewing existing classifica- tions, we define AR by its purpose, ie. to enable someone to create sensory- motor and cognitive activities in a new space combining the real environment and a virtual environment. Below we present our functional taxonomy of AR environments. We div...

  4. Norms for environmentally responsible behaviour: An extended taxonomy

    DEFF Research Database (Denmark)

    Thøgersen, John

    2006-01-01

    and shopping. Also the frequency of the four behaviours was measured. The revised taxonomy has content, discriminant, predictive, and nomological validity and satisfactory test-retest reliability. The most internalized of the new norm constructs, integrated norms, is most strongly correlated with conventional...... measures of personal and moral norms. However, other constructs in the proposed taxonomy still contribute significantly to predicting conventional norm measures after controlling for integrated norms. This documents the motivational ambiguity of the conventional personal norm construct. The patterns...

  5. A taxonomy of epithelial human cancer and their metastases

    Directory of Open Access Journals (Sweden)

    De Moor Bart

    2009-12-01

    . Moreover, a signature was developed based on our unsupervised clustering of breast tumors and this was predictive for disease-specific survival in three independent studies. Next, the metastases from ovarian, breast, lung and vulva cluster with their tissue of origin while metastases from colon showed a bimodal distribution. A significant part clusters with tissue of origin while the remaining tumors cluster with the tissue of destination. Conclusion Our molecular taxonomy of epithelial human cancer indicates surprising correlations over tissues. This may have a significant impact on the classification of many cancer sites and may guide pathologists, both in research and daily practice. Moreover, these results based on unsupervised analysis yielded a signature predictive of clinical outcome in breast cancer. Additionally, we hypothesize that metastases from gastrointestinal origin either remember their tissue of origin or adapt to the tissue of destination. More specifically, colon metastases in the liver show strong evidence for such a bimodal tissue specific profile.

  6. A Taxonomy of Medical Uncertainties in Clinical Genome Sequencing

    Science.gov (United States)

    Han, Paul K. J.; Umstead, Kendall L.; Bernhardt, Barbara A.; Green, Robert C.; Joffe, Steven; Koenig, Barbara; Krantz, Ian; Waterston, Leo B.; Biesecker, Leslie G.; Biesecker, Barbara B.

    2017-01-01

    Purpose Clinical next generation sequencing (CNGS) is introducing new opportunities and challenges into the practice of medicine. Simultaneously, these technologies are generating uncertainties of unprecedented scale that laboratories, clinicians, and patients are required to address and manage. We describe in this report the conceptual design of a new taxonomy of uncertainties around the use of CNGS in health care. Methods Interviews to delineate the dimensions of uncertainty in CNGS were conducted with genomics experts, and themes were extracted in order to expand upon a previously published three-dimensional taxonomy of medical uncertainty. In parallel we developed an interactive website to disseminate the CNGS taxonomy to researchers and engage them in its continued refinement. Results The proposed taxonomy divides uncertainty along three axes: source, issue, and locus, and further discriminates the uncertainties into five layers with multiple domains. Using a hypothetical clinical example, we illustrate how the taxonomy can be applied to findings from CNGS and used to guide stakeholders through interpretation and implementation of variant results. Conclusion The utility of the proposed taxonomy lies in promoting consistency in describing dimensions of uncertainty in publications and presentations, to facilitate research design and management of the uncertainties inherent in the implementation of CNGS. PMID:28102863

  7. A value-based taxonomy of improvement approaches in healthcare.

    Science.gov (United States)

    Colldén, Christian; Gremyr, Ida; Hellström, Andreas; Sporraeus, Daniella

    2017-06-19

    Purpose The concept of value is becoming increasingly fashionable in healthcare and various improvement approaches (IAs) have been introduced with the aim of increasing value. The purpose of this paper is to construct a taxonomy that supports the management of parallel IAs in healthcare. Design/methodology/approach Based on previous research, this paper proposes a taxonomy that includes the dimensions of view on value and organizational focus; three contemporary IAs - lean, value-based healthcare, and patient-centered care - are related to the taxonomy. An illustrative qualitative case study in the context of psychiatric (psychosis) care is then presented that contains data from 23 interviews and focuses on the value concept, IAs, and the proposed taxonomy. Findings Respondents recognized the dimensions of the proposed taxonomy and indicated its usefulness as support for choosing and combining different IAs into a coherent management model, and for facilitating dialog about IAs. The findings also suggested that the view of value as "health outcomes" is widespread, but healthcare professionals are less likely than managers to also view value as a process. Originality/value The conceptual contribution of this paper is to delineate some important characteristics of IAs in relation to the emerging "value era". It also highlights the coexistence of different IAs in healthcare management practice. A taxonomy is proposed that can help managers choose, adapt, and combine IAs in local management models.

  8. Transient magnetic currents through a molecular bridge: limits to reduction of non-equilibrium Green's functions to a generalized master equation

    Czech Academy of Sciences Publication Activity Database

    Kalvová, Anděla; Velický, B.; Špička, Václav

    2017-01-01

    Roč. 30, č. 3 (2017), s. 807-811 ISSN 1557-1939 Institutional support: RVO:68378271 Keywords : non-equilibrium * initial conditions * transient currents * molecular islands Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 1.180, year: 2016

  9. DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies

    OpenAIRE

    Pires, Amanda Ciprandi; Marinoni, Luciane

    2010-01-01

    The taxonomic crisis, emphasized in recent years, is marked by the lack of popularity (lack of interest in taxonomy) and financial incentives to study biodiversity. This situation, coupled with the issues involved with the necessity of knowing many yet undiscovered species, has meant that new technologies, including the use of DNA, have emerged to revitalize taxonomy. Part of the scientific community, however, has rejected the use of these innovative ideas. DNA barcoding has especially been t...

  10. An End-to-End DNA Taxonomy Methodology for Benthic Biodiversity Survey in the Clarion-Clipperton Zone, Central Pacific Abyss

    Directory of Open Access Journals (Sweden)

    Adrian G. Glover

    2015-12-01

    Full Text Available Recent years have seen increased survey and sampling expeditions to the Clarion-Clipperton Zone (CCZ, central Pacific Ocean abyss, driven by commercial interests from contractors in the potential extraction of polymetallic nodules in the region. Part of the International Seabed Authority (ISA regulatory requirements are that these contractors undertake environmental research expeditions to their CCZ exploration claims following guidelines approved by the ISA Legal and Technical Commission (ISA, 2010. Section 9 (e of these guidelines instructs contractors to “…collect data on the sea floor communities specifically relating to megafauna, macrofauna, meiofauna, microfauna, nodule fauna and demersal scavengers”. There are a number of methodological challenges to this, including the water depth (4000–5000 m, extremely warm surface waters (~28 °C compared to bottom water (~1.5 °C and great distances to ports requiring a large and long seagoing expedition with only a limited number of scientists. Both scientists and regulators have recently realized that a major gap in our knowledge of the region is the fundamental taxonomy of the animals that live there; this is essential to inform our knowledge of the biogeography, natural history and ultimately our stewardship of the region. Recognising this, the ISA is currently sponsoring a series of taxonomic workshops on the CCZ fauna and to assist in this process we present here a series of methodological pipelines for DNA taxonomy (incorporating both molecular and morphological data of the macrofauna and megafauna from the CCZ benthic habitat in the recent ABYSSLINE cruise program to the UK-1 exploration claim. A major problem on recent CCZ cruises has been the collection of high-quality samples suitable for both morphology and DNA taxonomy, coupled with a workflow that ensures these data are made available. The DNA sequencing techniques themselves are relatively standard, once good samples have been

  11. Genome-Based Microbial Taxonomy Coming of Age.

    Science.gov (United States)

    Hugenholtz, Philip; Skarshewski, Adam; Parks, Donovan H

    2016-06-01

    Reconstructing the complete evolutionary history of extant life on our planet will be one of the most fundamental accomplishments of scientific endeavor, akin to the completion of the periodic table, which revolutionized chemistry. The road to this goal is via comparative genomics because genomes are our most comprehensive and objective evolutionary documents. The genomes of plant and animal species have been systematically targeted over the past decade to provide coverage of the tree of life. However, multicellular organisms only emerged in the last 550 million years of more than three billion years of biological evolution and thus comprise a small fraction of total biological diversity. The bulk of biodiversity, both past and present, is microbial. We have only scratched the surface in our understanding of the microbial world, as most microorganisms cannot be readily grown in the laboratory and remain unknown to science. Ground-breaking, culture-independent molecular techniques developed over the past 30 years have opened the door to this so-called microbial dark matter with an accelerating momentum driven by exponential increases in sequencing capacity. We are on the verge of obtaining representative genomes across all life for the first time. However, historical use of morphology, biochemical properties, behavioral traits, and single-marker genes to infer organismal relationships mean that the existing highly incomplete tree is riddled with taxonomic errors. Concerted efforts are now needed to synthesize and integrate the burgeoning genomic data resources into a coherent universal tree of life and genome-based taxonomy. Copyright © 2016 Cold Spring Harbor Laboratory Press; all rights reserved.

  12. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology.

    Science.gov (United States)

    Sibley, Christopher D; Peirano, Gisele; Church, Deirdre L

    2012-04-01

    Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Current research in nuclear medicine and molecular imaging in Italy: highlights of the 10th National Congress of the Italian Association of Nuclear Medicine and Molecular Imaging.

    Science.gov (United States)

    Cuocolo, A

    2011-06-01

    The 10th National Congress of the Italian Association of Nuclear Medicine and Molecular Imaging (AIMN) took place in Rimini on March 18-21, 2011 under the chairmanship of Professor Stefano Fanti. The program was of excellent quality and put a further step for the settlement of the standardized AIMN congress structure. A large industrial exhibition demonstrated the latest technological innovations and developments within the field. The congress was a great success with more than 1100 total participants and more than 360 abstracts received. Of these, 40 abstracts were accepted for oral and 285 for poster presentations. The original investigations presented were related to different areas of nuclear medicine and molecular imaging, with particular focus on advances in instrumentation and data processing, progress in radiochemistry and pharmacy, novel diagnostics and therapeutics, and new insights in well established areas of clinical application, such as oncology, cardiology, neurology, psychiatry, endocrinology, paediatrics, and infection and inflammation. Noteworthy, several presentations at this congress, focusing on quantitative interpretation of the imaging data and on pragmatic endpoints, such as adverse outcomes, identified when nuclear medicine procedures achieved clinical effectiveness for patient care and patient management and further demonstrated that nuclear medicine plays a crucial role in the contemporary medical scenario. This highlights lecture is only a brief summary of the large amount of data presented and discussed, which can be found in much greater detail in the congress abstract book, published as volume 55, supplement 1 of the Q J Nucl Med Mol Imaging in April 2011.

  14. Computational modeling of the behavior of nuclear materials (2). Molecular simulations for nuclear materials. Current situation and future perspective

    International Nuclear Information System (INIS)

    Okita, Taira; Itakura, Mitsuhiro

    2017-01-01

    Molecular simulations for nuclear materials aim to reproduce atomistic-scale phenomena induced by irradiation and infer the change in material properties. In the present work, recent progress in this field is presented. In particular, the following three topics are explained: (1) Quantification of lattice defects formation process induced by fast neutron collision. (2) Identification of dislocation-channeling mechanism induced by interactions between defect clusters and dislocations. (3) Modeling of the three dimensional movement of defect clusters using molecular dynamics and kinetic Monte Carlo simulations. (author)

  15. A taxonomy of control in intensified processes

    International Nuclear Information System (INIS)

    Barzin, R.; Abd Shukor, S.R.; Ahmad, A.L.

    2006-01-01

    Process Intensification (PI) is a revolutionary approach to design, development and implementation of process and plant. PI technology offers improved environment in a chemical process in terms of better products, and processes which are safer, cleaner, smaller - and cheaper. PI is a strategy of making dramatic reductions in the size of unit operations within chemical plants, in order to achieve given production objectives. However, PI technology would be handicapped if such system is not properly controlled. There are some foreseeable problems in order to control such processes for instance, dynamic interaction between components that make up a control loop, response time of the instrumentations, availability of proper sensor and etc. In some cases, in order to control these systems, advanced control solutions have been applied i.e. model predictive controllers (MPC) and its different algorithms such as quadratic generalized predictive control (QGPC) and self tuning quadratic generalized predictive control (STQGPC). Nevertheless in some cases simpler solutions could be applied to control such system for example proportional integral controller in the control of reactive distillation systems. As mentioned, conventional control systems like proportional-integral, proportional-integral-derivative (PID) controllers and their different structures can be used in PI systems but due to inherent nonlinearity and fast responsiveness of PI systems, digital controllers-regarding to their robustness-are mostly applied in order to control PI systems. Regarding to the fact that choosing the appropriate control strategy is the most essential part of making PI systems possible to be handle easily, taxonomy of the usage of various control structure in controlling PI systems is proposed. This paper offers an overview and discussion on identifying potential problems of instrumentation in PI technology and available control strategies

  16. Climbing Bloom's taxonomy pyramid: Lessons from a graduate histology course.

    Science.gov (United States)

    Zaidi, Nikki B; Hwang, Charles; Scott, Sara; Stallard, Stefanie; Purkiss, Joel; Hortsch, Michael

    2017-09-01

    Bloom's taxonomy was adopted to create a subject-specific scoring tool for histology multiple-choice questions (MCQs). This Bloom's Taxonomy Histology Tool (BTHT) was used to analyze teacher- and student-generated quiz and examination questions from a graduate level histology course. Multiple-choice questions using histological images were generally assigned a higher BTHT level than simple text questions. The type of microscopy technique (light or electron microscopy) used for these image-based questions did not result in any significant differences in their Bloom's taxonomy scores. The BTHT levels for teacher-generated MCQs correlated positively with higher discrimination indices and inversely with the percent of students answering these questions correctly (difficulty index), suggesting that higher-level Bloom's taxonomy questions differentiate well between higher- and lower-performing students. When examining BTHT scores for MCQs that were written by students in a Multiple-Choice Item Development Assignment (MCIDA) there was no significant correlation between these scores and the students' ability to answer teacher-generated MCQs. This suggests that the ability to answer histology MCQs relies on a different skill set than the aptitude to construct higher-level Bloom's taxonomy questions. However, students significantly improved their average BTHT scores from the midterm to the final MCIDA task, which indicates that practice, experience and feedback increased their MCQ writing proficiency. Anat Sci Educ 10: 456-464. © 2017 American Association of Anatomists. © 2017 American Association of Anatomists.

  17. An Analytical Overview of Spirituality in NANDA-I Taxonomies.

    Science.gov (United States)

    Mesquita, Ana Cláudia; Caldeira, Sílvia; Chaves, Erika; Carvalho, Emilia Campos de

    2017-03-01

    To discuss the approach of spirituality in NANDA-I taxonomies, based on the elements that characterize this phenomenon. This study was based on concepts that are usually adopted in the literature for defining spirituality and on the analysis of the NANDA-I taxonomies from I to III. Spirituality is included in all taxonomies but all three are missing some attributes to guarantee the completeness of this dimension for nursing diagnosis. Taxonomy III makes different approaches to spirituality and some inconsistencies. Contribute to the development and review of the new proposal for taxonomy. Discutir a abordagem à espiritualidade nas taxonomias da NANDA-I, baseada nos elementos que caracterizam este fenômeno. MÉTODOS: Este estudo foi baseado em conceitos usualmente adotados na literatura de enfermagem para definir espiritualidade e na análise das taxonomias da NANDA-I, desde a I à III. A espiritualidade está incluída nas taxonomias, porém estas carecem de atributos do seu conceito. CONCLUSÕES: A taxonomia III faz diferentes abordagens à espiritualidade, porém com algumas inconsistências identificadas. IMPLICAÇÕES PARA A ENFERMAGEM: Esta análise pode contribuir para o desenvolvimento e revisão da taxonomia III. © 2017 NANDA International, Inc.

  18. The ACTTION-American Pain Society Pain Taxonomy (AAPT): an evidence-based and multidimensional approach to classifying chronic pain conditions.

    Science.gov (United States)

    Fillingim, Roger B; Bruehl, Stephen; Dworkin, Robert H; Dworkin, Samuel F; Loeser, John D; Turk, Dennis C; Widerstrom-Noga, Eva; Arnold, Lesley; Bennett, Robert; Edwards, Robert R; Freeman, Roy; Gewandter, Jennifer; Hertz, Sharon; Hochberg, Marc; Krane, Elliot; Mantyh, Patrick W; Markman, John; Neogi, Tuhina; Ohrbach, Richard; Paice, Judith A; Porreca, Frank; Rappaport, Bob A; Smith, Shannon M; Smith, Thomas J; Sullivan, Mark D; Verne, G Nicholas; Wasan, Ajay D; Wesselmann, Ursula

    2014-03-01

    Current approaches to classification of chronic pain conditions suffer from the absence of a systematically implemented and evidence-based taxonomy. Moreover, existing diagnostic approaches typically fail to incorporate available knowledge regarding the biopsychosocial mechanisms contributing to pain conditions. To address these gaps, the Analgesic, Anesthetic, and Addiction Clinical Trial Translations Innovations Opportunities and Networks (ACTTION) public-private partnership with the U.S. Food and Drug Administration and the American Pain Society (APS) have joined together to develop an evidence-based chronic pain classification system called the ACTTION-APS Pain Taxonomy. This paper describes the outcome of an ACTTION-APS consensus meeting, at which experts agreed on a structure for this new taxonomy of chronic pain conditions. Several major issues around which discussion revolved are presented and summarized, and the structure of the taxonomy is presented. ACTTION-APS Pain Taxonomy will include the following dimensions: 1) core diagnostic criteria; 2) common features; 3) common medical comorbidities; 4) neurobiological, psychosocial, and functional consequences; and 5) putative neurobiological and psychosocial mechanisms, risk factors, and protective factors. In coming months, expert working groups will apply this taxonomy to clusters of chronic pain conditions, thereby developing a set of diagnostic criteria that have been consistently and systematically implemented across nearly all common chronic pain conditions. It is anticipated that the availability of this evidence-based and mechanistic approach to pain classification will be of substantial benefit to chronic pain research and treatment. The ACTTION-APS Pain Taxonomy is an evidence-based chronic pain classification system designed to classify chronic pain along the following dimensions: 1) core diagnostic criteria; 2) common features; 3) common medical comorbidities; 4) neurobiological, psychosocial

  19. NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics.

    Science.gov (United States)

    Tsang, Hin-Fung; Xue, Vivian Weiwen; Koh, Su-Pin; Chiu, Ya-Ming; Ng, Lawrence Po-Wah; Wong, Sze-Chuen Cesar

    2017-01-01

    Formalin-fixed, paraffin-embedded (FFPE) tissue sample is a gold mine of resources for molecular diagnosis and retrospective clinical studies. Although molecular technologies have expanded the range of mutations identified in FFPE samples, the applications of existing technologies are limited by the low nucleic acids yield and poor extraction quality. As a result, the routine clinical applications of molecular diagnosis using FFPE samples has been associated with many practical challenges. NanoString technologies utilize a novel digital color-coded barcode technology based on direct multiplexed measurement of gene expression and offer high levels of precision and sensitivity. Each color-coded barcode is attached to a single target-specific probe corresponding to a single gene which can be individually counted without amplification. Therefore, NanoString is especially useful for measuring gene expression in degraded clinical specimens. Areas covered: This article describes the applications of NanoString technologies in molecular diagnostics and challenges associated with its applications and the future development. Expert commentary: Although NanoString technology is still in the early stages of clinical use, it is expected that NanoString-based cancer expression panels would play more important roles in the future in classifying cancer patients and in predicting the response to therapy for better personal therapeutic care.

  20. A systematic review of molecular imaging (PET and SPECT) in autism spectrum disorder: current state and future research opportunities.

    Science.gov (United States)

    Zürcher, Nicole R; Bhanot, Anisha; McDougle, Christopher J; Hooker, Jacob M

    2015-05-01

    Non-invasive positron emission tomography (PET) and single-photon emission computed tomography (SPECT) are techniques used to quantify molecular interactions, biological processes and protein concentration and distribution. In the central nervous system, these molecular imaging techniques can provide critical insights into neurotransmitter receptors and their occupancy by neurotransmitters or drugs. In recent years, there has been an increase in the number of studies that have investigated neurotransmitters in autism spectrum disorder (ASD), while earlier studies mostly focused on cerebral blood flow and glucose metabolism. The underlying and contributing mechanisms of ASD are largely undetermined and ASD diagnosis relies on the behavioral phenotype. Discovery of biochemical endophenotypes would represent a milestone in autism research that could potentially lead to ASD subtype stratification and the development of novel therapeutic drugs. This review characterizes the prior use of molecular imaging by PET and SPECT in ASD, addresses methodological challenges and highlights areas of future opportunity for contributions from molecular imaging to understand ASD pathophysiology. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Reads2Type: a web application for rapid microbial taxonomy identification

    DEFF Research Database (Denmark)

    Saputra, Dhany; Rasmussen, Simon; Larsen, Mette Voldby

    2015-01-01

    genome of microbial isolates. Therefore we have developed Reads2Type, a web-based tool for taxonomy identification based on whole bacterial genome sequence data. Raw sequencing data provided by the user are mapped against a set of marker probes that are derived from currently available bacteria complete......, as the entire computational analysis is done on the computer of whom utilizes the web application. This also prevents data privacy issues to arise. The Reads2Type tool is available at http://www.cbs.dtu.dk/~dhany/reads2type.html ....

  2. DNA Taxonomy - the Riddle of Oxychloë (Juncaceae)

    DEFF Research Database (Denmark)

    Kristiansen, Kim Anker; Cilieborg, Malene Skovsted; Drábková, Lenka

    2005-01-01

    is fatal, but if no voucher exists, bad sequences and bad taxonomy may be forever linked. Previous phylogenetic analyses of rbcL sequences have indicated that the small, south hemisphere, genus Oxychloë (Juncaceae) surprisingly either is embedded within or is a sister group to the Cyperaceae....... This is not in accordance with traditional or current morphological data. By studying five new accessions, representing four species of Oxychloë, and re-examining the two vouchers of O. andina that were used in previous phylogenies, it has been possible to show that these two sequences are erroneous. One is a chimeric...

  3. The Hierarchical Taxonomy of Psychopathology (HiTOP) : A Dimensional Alternative to Traditional Nosologies

    NARCIS (Netherlands)

    Kotov, Roman; Krueger, Robert F.; Watson, David; Achenbach, Thomas M.; Althoff, Robert R.; Bagby, R. Michael; Brown, Timothy A.; Carpenter, William T.; Caspi, Avshalom; Clark, Lee Anna; Eaton, Nicholas R.; Forbes, Miriam K.; Forbush, Kelsie T.; Goldberg, David; Hasin, Deborah; Hyman, Steven E.; Ivanova, Masha Y.; Lynam, Donald R.; Markon, Kristian; Miller, Joshua D.; Moffitt, Terrie E.; Morey, Leslie C.; Mullins-Sweatt, Stephanie N.; Ormel, Johan; Patrick, Christopher J.; Regier, Darrel A.; Rescorla, Leslie; Ruggero, Camilo J.; Samuel, Douglas B.; Sellbom, Martin; Simms, Leonard J.; Skodol, Andrew E.; Slade, Tim; South, Susan C.; Tackett, Jennifer L.; Waldman, Irwin D.; Waszczuk, Monika A.; Widiger, Thomas A.; Wright, Aidan G. C.; Zimmerman, Mark

    The reliability and validity of traditional taxonomies are limited by arbitrary boundaries between psychopathology and normality, often unclear boundaries between disorders, frequent disorder co-occurrence, heterogeneity within disorders, and diagnostic instability. These taxonomies went beyond

  4. Let’s rise up to unite taxonomy and technology

    Science.gov (United States)

    2017-01-01

    What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional “model” organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance. PMID:28820884

  5. Let's rise up to unite taxonomy and technology.

    Directory of Open Access Journals (Sweden)

    Holly M Bik

    2017-08-01

    Full Text Available What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional "model" organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance.

  6. Let's rise up to unite taxonomy and technology.

    Science.gov (United States)

    Bik, Holly M

    2017-08-01

    What do you think of when you think of taxonomy? An 18th century gentlemen in breeches? Or perhaps botany drawings hung on the walls of a boutique hotel? Such old-fashioned conceptions to the contrary, taxonomy is alive today although constantly struggling for survival and recognition. The scientific community is losing valuable resources as taxonomy experts age and retire, and funding for morphological studies and species descriptions remains stagnant. At the same time, organismal knowledge (morphology, ecology, physiology) has never been more important: genomic studies are becoming more taxon focused, the scientific community is recognizing the limitations of traditional "model" organisms, and taxonomic expertise is desperately needed to fight against global biodiversity declines resulting from human impacts. There has never been a better time for a taxonomic renaissance.

  7. Current update on established and novel biomarkers in salivary gland carcinoma pathology and the molecular pathways involved.

    Science.gov (United States)

    Stenner, Markus; Klussmann, J Peter

    2009-03-01

    This review aims to take stock of the new information that has accumulated over the past decade on the molecular pathology of salivary gland cancer. Emphasis will be placed on established and novel immunohistochemical markers, the pathways involved, and on findings of prognostic importance as well as new therapeutic concepts. Whenever reasonable, analogies to tumors of better explored, histologically related glandular organs such as pancreas and breast are established.

  8. VecScreen_plus_taxonomy: imposing a tax(onomy) increase on vector contamination screening.

    Science.gov (United States)

    Schäffer, Alejandro A; Nawrocki, Eric P; Choi, Yoon; Kitts, Paul A; Karsch-Mizrachi, Ilene; McVeigh, Richard

    2018-03-01

    Nucleic acid sequences in public databases should not contain vector contamination, but many sequences in GenBank do (or did) contain vectors. The National Center for Biotechnology Information uses the program VecScreen to screen submitted sequences for contamination. Additional tools are needed to distinguish true-positive (contamination) from false-positive (not contamination) VecScreen matches. A principal reason for false-positive VecScreen matches is that the sequence and the matching vector subsequence originate from closely related or identical organisms (for example, both originate in Escherichia coli). We collected information on the taxonomy of sources of vector segments in the UniVec database used by VecScreen. We used that information in two overlapping software pipelines for retrospective analysis of contamination in GenBank and for prospective analysis of contamination in new sequence submissions. Using the retrospective pipeline, we identified and corrected over 8000 contaminated sequences in the nonredundant nucleotide database. The prospective analysis pipeline has been in production use since April 2017 to evaluate some new GenBank submissions. Data on the sources of UniVec entries were included in release 10.0 (ftp://ftp.ncbi.nih.gov/pub/UniVec/). The main software is freely available at https://github.com/aaschaffer/vecscreen_plus_taxonomy. aschaffe@helix.nih.gov. Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2017. This work is written by US Government employees and are in the public domain in the US.

  9. Current Molecular Targeted Therapy in Advanced Gastric Cancer: A Comprehensive Review of Therapeutic Mechanism, Clinical Trials, and Practical Application

    Directory of Open Access Journals (Sweden)

    Kaichun Li

    2016-01-01

    Full Text Available Despite the great progress in the treatment of gastric cancer, it is still the third leading cause of cancer death worldwide. Patients often miss the opportunity for a surgical cure, because the cancer has already developed into advanced cancer when identified. Compared to best supportive care, chemotherapy can improve quality of life and prolong survival time, but the overall survival is often short. Due to the molecular study of gastric cancer, new molecular targeted drugs have entered the clinical use. Trastuzumab, an antibody targeting human epidermal growth factor receptor 2 (HER2, can significantly improve survival in advanced gastric cancer patients with HER2 overexpression. Second-line treatment of advanced gastric cancer with ramucirumab, an antibody targeting VEGFR-2, alone or in combination with paclitaxel, has been proved to provide a beneficial effect. The VEGFR-2 tyrosine kinase inhibitor, apatinib, can improve the survival of advanced gastric cancer patients after second-line chemotherapy failure. Unfortunately, none of the EGFR targeting antibodies (cetuximab or panitumumab, VEGF targeting monoclonal antibodies (bevacizumab, mTOR inhibitor (everolimus, or HGF/MET pathway targeting drugs has a significant survival benefit. Many other clinical trials based on molecular markers are underway. This review will summarize targeted therapies for advanced gastric cancer.

  10. Taxonomy of the genus Brachyteles Spix, 1823 and its phylogenetic position within the subfamily Atelinae Gray, 1825

    OpenAIRE

    José Eduardo Serrano Villavicencio

    2016-01-01

    Muriquis, genus Brachyteles Spix, 1823, are the largest of the extant New World primates, and they are one of the three extant genera of the subfamily Atelinae along with Ateles (spider monkeys) and Lagothrix (wooly monkeys). The taxonomy of Brachyteles has constantly changed since its first description in the 19th century. First treated as a monotypic genus, and after several modifications in the number of species, Brachyteles currently contains two species, B. arachnoides (Southern muriqui)...

  11. A Practitioner's Perspective on Taxonomy, Ontology and Findability

    Science.gov (United States)

    Berndt, Sarah

    2011-01-01

    This slide presentation reviews the presenters perspective on developing a taxonomy for JSC to capitalize on the accomplishments of yesterday, while maintaining the flexibility needed for the evolving information of today. A clear vision and scope for the semantic system is integral to its success. The vision for the JSC Taxonomy is to connect information stovepipes to present a unified view for information and knowledge across the Center, across organizations, and across decades. Semantic search at JSC means seamless integration of disparate information sets into a single interface. Ever increasing use, interest, and organizational participation mark successful integration and provide the framework for future application.

  12. Taxonomy, Ontology and Semantics at Johnson Space Center

    Science.gov (United States)

    Berndt, Sarah Ann

    2011-01-01

    At NASA Johnson Space Center (JSC), the Chief Knowledge Officer has been developing the JSC Taxonomy to capitalize on the accomplishments of yesterday while maintaining the flexibility needed for the evolving information environment of today. A clear vision and scope for the semantic system is integral to its success. The vision for the JSC Taxonomy is to connect information stovepipes to present a unified view for information and knowledge across the Center, across organizations, and across decades. Semantic search at JSC means seemless integration of disparate information sets into a single interface. Ever increasing use, interest, and organizational participation mark successful integration and provide the framework for future application.

  13. Web analytics as tool for improvement of website taxonomies

    DEFF Research Database (Denmark)

    Jonasen, Tanja Svarre; Ådland, Marit Kristine; Lykke, Marianne

    The poster examines how web analytics can be used to provide information about users and inform design and redesign of taxonomies. It uses a case study of the website Cancer.dk by the Danish Cancer Society. The society is a private organization with an overall goal to prevent the development...... provides information about e.g. subjects of interest, searching behaviour, browsing patterns in website structure as well as tag clouds, page views. The poster discusses benefits and challenges of the two web metrics, with a model of how to use search and tag data for the design of taxonomies, e.g. choice...

  14. Modern Grid Initiative Distribution Taxonomy Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Schneider, Kevin P.; Chen, Yousu; Chassin, David P.; Pratt, Robert G.; Engel, David W.; Thompson, Sandra E.

    2008-11-01

    This is the final report for the development of a toxonomy of prototypical electrical distribution feeders. Two of the primary goals of the Department of Energy's (DOE) Modern Grid Initiative (MGI) are 'to accelerate the modernization of our nation's electricity grid' and to 'support demonstrations of systems of key technologies that can serve as the foundation for an integrated, modern power grid'. A key component to the realization of these goals is the effective implementation of new, as well as existing, 'smart grid technologies'. Possibly the largest barrier that has been identified in the deployment of smart grid technologies is the inability to evaluate how their deployment will affect the electricity infrastructure, both locally and on a regional scale. The inability to evaluate the impacts of these technologies is primarily due to the lack of detailed electrical distribution feeder information. While detailed distribution feeder information does reside with the various distribution utilities, there is no central repository of information that can be openly accessed. The role of Pacific Northwest National Laboratory (PNNL) in the MGI for FY08 was to collect distribution feeder models, in the SynerGEE{reg_sign} format, from electric utilities around the nation so that they could be analyzed to identify regional differences in feeder design and operation. Based on this analysis PNNL developed a taxonomy of 24 prototypical feeder models in the GridLAB-D simulations environment that contain the fundamental characteristics of non-urban core, radial distribution feeders from the various regions of the U.S. Weighting factors for these feeders are also presented so that they can be used to generate a representative sample for various regions within the United States. The final product presented in this report is a toolset that enables the evaluation of new smart grid technologies, with the ability to aggregate their effects

  15. Taxonomy and phylogeny of the genus citrus based on the nuclear ribosomal dna its region sequence

    International Nuclear Information System (INIS)

    Sun, Y.L.

    2015-01-01

    The genus Citrus (Aurantioideae, Rutaceae) is the sole source of the citrus fruits of commerce showing high economic values. In this study, the taxonomy and phylogeny of Citrus species is evaluated using sequence analysis of the ITS region of nrDNA. This study is based on 26 plants materials belonging to 22 Citrus species having wild, domesticated, and cultivated species. Through DNA alignment of the ITS sequence, ITS1 and ITS2 regions showed relatively high variations of sequence length and nucleotide among these Citrus species. According to previous six-tribe discrimination theory by Swingle and Reece, the grouping in our ITS phylogenetic tree reconstructed by ITS sequences was not related to tribe discrimination but species discrimination. However, the molecular analysis could provide more information on citrus taxonomy. Combined with ITS sequences of other subgenera in then true citrus fruit tree group, the ITS phylogenetic tree indicated subgenera Citrus was monophyletic and nearer to Fortunella, Poncirus, and Clymenia compared to Microcitrus and Eremocitrus. Abundant sequence variations of the ITS region shown in this study would help species identification and tribe differentiation of the genus Citrus. (author)

  16. A PROPOSED TAXONOMY OF THE PERCEPTUAL DOMAIN AND SOME SUGGESTED APPLICATIONS.

    Science.gov (United States)

    MOORE, MAXINE R.

    THIS PROPOSAL FOR A PRELIMINARY TAXONOMY OF THE PERCEPTUAL DOMAIN, ORGANIZED ON THE PRINCIPLE OF INTEGRATION, DREW ON GUILFORD'S THEORETICAL AND FACTOR-ANALYTICAL WORK, ON WITKIN'S FIGURE-GROUND STUDIES, AND ON THE "TAXONOMY OF EDUCATIONAL OBJECTIVES" MODELS. THE TAXONOMY CATEGORIES ARE SENSATION, FIGURE PERCEPTION, SYMBOL PERCEPTION, PERCEPTION…

  17. Bloom's Taxonomy: Improving Assessment and Teaching-Learning Process

    Science.gov (United States)

    Chandio, Muhammad Tufail; Pandhiani, Saima Murtaza; Iqbal, Rabia

    2016-01-01

    This research study critically analyzes the scope and contribution of Bloom's Taxonomy in both assessment and teaching-learning process. Bloom's Taxonomy consists of six stages, namely; remembering, understanding, applying, analyzing, evaluating and creating and moves from lower degree to the higher degree. The study applies Bloom's Taxonomy to…

  18. Integrative taxonomy supports new candidate fish species in a poorly studied neotropical region: the Jequitinhonha River Basin.

    Science.gov (United States)

    Pugedo, Marina Lages; de Andrade Neto, Francisco Ricardo; Pessali, Tiago Casarim; Birindelli, José Luís Olivan; Carvalho, Daniel Cardoso

    2016-06-01

    Molecular identification through DNA barcoding has been proposed as a way to standardize a global biodiversity identification system using a partial sequence of the mitochondrial COI gene. We applied an integrative approach using DNA barcoding and traditional morphology-based bioassessment to identify fish from a neotropical region possessing low taxonomic knowledge: the Jequitinhonha River Basin (Southeastern Brazil). The Jequitinhonha River Basin (JRB) has a high rate of endemism and is considered an area of high priority for fish conservation, with estimates indicating the presence of around 110 native and non-indigenous species. DNA barcodes were obtained from 260 individuals belonging to 52 species distributed among 35 genera, 21 families and 6 orders, including threatened and rare species such as Rhamdia jequitinhonha and Steindachneridion amblyurum. The mean Kimura two-parameter genetic distances within species, genera and families were: 0.44, 12.16 and 20.58 %, respectively. Mean intraspecific genetic variation ranged from 0 to 11.43 %, and high values (>2 %) were recovered for five species. Species with a deep intraspecific distance, possibly flagging overlooked taxa, were detected within the genus Pimelodella. Fifteen species, only identified to the genus level, had unique BINs, with a nearest neighbor distance over 2 % and therefore, potential new candidate species supported by DNA barcoding. The integrative taxonomy approach using DNA barcoding and traditional taxonomy may be a remedy to taxonomy impediment, accelerating species identification by flagging potential new candidate species and to adequately conserve the megadiverse neotropical ichthyofauna.

  19. What are the currently available and in development molecular markers for bladder cancer? Will they prove to be useful in the future?

    Science.gov (United States)

    Abdulmajed, Mohamed Ismat; Sancak, Eyüp Burak; Reşorlu, Berkan; Al-Chalaby, Gydhia Zuhair

    2014-12-01

    Urothelial carcinoma is the 9(th) most common cancer worldwide. Most urothelial tumors are non-muscle invasive on presentation. However, two-thirds of non-invasive bladder cancers will eventually recur with a 25% risk of progression to muscle-invasive bladder cancer. Tumor stage, histological grade and pathological invasion of blood vessels and lymphatic tissue are the main indicators for urothelial cancer prognosis. The gold standard for diagnosing bladder cancer is conventional white-light cystoscopy and biopsy. Urine cytology is a highly specific, sensitive test for high-grade tumors or carcinoma in situ (CIS). Urinary NMP22 has an overall sensitivity and specificity for detecting bladder cancer of 49% and 87%, respectively. However, there are false-positive results in the presence of urinary tract infection or hematuria. The detection of specific gene mutations related to urothelial cancers has been studied and employed to reproduce markers helpful for diagnosis. According to current studies, molecular markers can be used to predict tumor recurrence. From a prognostic point of view, new molecular markers have yet to be established as reliable indicators of tumor aggressiveness. We aimed to review the molecular markers with possible prognostic significance that have been discussed in the literature. This review examined the literature for various molecular markers under development for bladder cancer in an attempt to optimize patient care and reduce the costs of treating these patients.

  20. Change of the dominant luminescent mechanism with increasing current density in molecularly doped organic light-emitting devices

    International Nuclear Information System (INIS)

    Zhou Liang; Zhang Hongjie; Meng Qingguo; Liu Fengyi; Yu Jiangbo; Deng Ruiping; Peng Zeping; Li Zhefeng; Guo Zhiyong

    2007-01-01

    We have fabricated and measured a series of electroluminescent devices with the structure of ITO/TPD/Eu(TTA) 3 phen (x):CBP/BCP/ALQ/LiF/Al, where x is the weight percentage of Eu(TTA) 3 phen (from 0% to 6%). At very low current density, carrier trapping is the dominant luminescent mechanism and the 4% doped device shows the highest electroluminescence (EL) efficiency among all these devices. With increasing current density, Foerster energy transfer participates in EL process. At the current density of 10.0 and 80.0 mA/cm 2 , 2% and 3% doped devices show the highest EL efficiency, respectively. From analysis of the EL spectra and the EL efficiency-current density characteristics, we found that the EL efficiency is manipulated by Foerster energy transfer efficiency at high current density. So we suggest that the dominant luminescent mechanism changes gradually from carrier trapping to Foerster energy transfer with increasing current density. Moreover, the conversion of dominant EL mechanism was suspected to be partly responsible for the EL efficiency roll-off because of the lower EL quantum efficiency of Foerster energy transfer compared with carrier trapping

  1. The Current Status of the Disease Caused by Enterovirus 71 Infections: Epidemiology, Pathogenesis, Molecular Epidemiology, and Vaccine Development

    Science.gov (United States)

    Chang, Ping-Chin; Chen, Shou-Chien; Chen, Kow-Tong

    2016-01-01

    Enterovirus 71 (EV71) infections have a major public health impact in the Asia-Pacific region. We reviewed the epidemiology, pathogenesis, and molecular epidemiology of EV71 infection as well as EV71 vaccine development. Previous studies were found using the search terms “enterovirus 71” and “epidemiology” or “pathogenesis” or “molecular epidemiology” or “vaccine” in Medline and PubMed. Articles that were not published in the English language, manuscripts without an abstract, and opinion articles were excluded from the review. The reported epidemiology of cases caused by EV71 infection varied from country to country; seasonal variations in incidence were observed. Most cases of EV71 infection that resulted in hospitalization for complications occurred in children less than five years old. The brainstem was the most likely major target of EV71 infection. The emergence of the EV71 epidemic in the Asia-Pacific region has been associated with the circulation of different genetic lineages (genotypes B3, B4, C1, C2, and C4) that appear to be undergoing rapid evolutionary changes. The relationship between the gene structure of the EV71 virus and the factors that ensure its survival, circulation, and evasion of immunity is still unknown. EV71 infection has emerged as an important global public health problem. Vaccine development, including the development of inactivated whole-virus live attenuated, subviral particles, and DNA vaccines, has been progressing. PMID:27618078

  2. Unique molecular signatures as a hallmark of patients with metastatic breast cancer: implications for current treatment paradigms.

    Science.gov (United States)

    Wheler, Jennifer J; Parker, Barbara A; Lee, Jack J; Atkins, Johnique T; Janku, Filip; Tsimberidou, Apostolia M; Zinner, Ralph; Subbiah, Vivek; Fu, Siqing; Schwab, Richard; Moulder, Stacy; Valero, Vicente; Schwaederle, Maria; Yelensky, Roman; Miller, Vincent A; Stephens, M Philip J; Meric-Bernstam, Funda; Kurzrock, Razelle

    2014-05-15

    Our analysis of the tumors of 57 women with metastatic breast cancer with next generation sequencing (NGS) demonstrates that each patient's tumor is unique in its molecular fingerprint. We observed 216 somatic aberrations in 70 different genes, including 131 distinct aberrations. The most common gene alterations (in order of decreasing frequency) included: TP53, PIK3CA, CCND1, MYC, HER2 (ERBB2), MCL1, PTEN, FGFR1, GATA3, NF1, PIK3R1, BRCA2, EGFR, IRS2, CDH1, CDKN2A, FGF19, FGF3 and FGF4. Aberrations included mutations (46%), amplifications (45%), deletions (5%), splices (2%), truncations (1%), fusions (0.5%) and rearrangements (0.5%), with multiple distinct variants within the same gene. Many of these aberrations represent druggable targets, either through direct pathway inhibition or through an associated pathway (via 'crosstalk'). The 'molecular individuality' of these tumors suggests that a customized strategy, using an "N-of-One" model of precision medicine, may represent an optimal approach for the treatment of patients with advanced tumors.

  3. The Current Status of the Disease Caused by Enterovirus 71 Infections: Epidemiology, Pathogenesis, Molecular Epidemiology, and Vaccine Development.

    Science.gov (United States)

    Chang, Ping-Chin; Chen, Shou-Chien; Chen, Kow-Tong

    2016-09-09

    Enterovirus 71 (EV71) infections have a major public health impact in the Asia-Pacific region. We reviewed the epidemiology, pathogenesis, and molecular epidemiology of EV71 infection as well as EV71 vaccine development. Previous studies were found using the search terms "enterovirus 71" and "epidemiology" or "pathogenesis" or "molecular epidemiology" or "vaccine" in Medline and PubMed. Articles that were not published in the English language, manuscripts without an abstract, and opinion articles were excluded from the review. The reported epidemiology of cases caused by EV71 infection varied from country to country; seasonal variations in incidence were observed. Most cases of EV71 infection that resulted in hospitalization for complications occurred in children less than five years old. The brainstem was the most likely major target of EV71 infection. The emergence of the EV71 epidemic in the Asia-Pacific region has been associated with the circulation of different genetic lineages (genotypes B3, B4, C1, C2, and C4) that appear to be undergoing rapid evolutionary changes. The relationship between the gene structure of the EV71 virus and the factors that ensure its survival, circulation, and evasion of immunity is still unknown. EV71 infection has emerged as an important global public health problem. Vaccine development, including the development of inactivated whole-virus live attenuated, subviral particles, and DNA vaccines, has been progressing.

  4. Social Media Use in Chronic Disease: A Systematic Review and Novel Taxonomy.

    Science.gov (United States)

    Patel, Rajesh; Chang, Tammy; Greysen, S Ryan; Chopra, Vineet

    2015-12-01

    The purpose of this study is to evaluate clinical outcomes from applications of contemporary social media in chronic disease; to develop a conceptual taxonomy to categorize, summarize, and then analyze the current evidence base; and to suggest a framework for future studies on this topic. We performed a systematic review of MEDLINE via PubMed (January 2000 to January 2015) of studies reporting clinical outcomes on leading contemporary social media (ie, Facebook, Twitter, Wikipedia, YouTube) use in 10 chronic diseases. Two reviewers independently performed data extraction and quality assessment; characterization of study outcomes as positive, negative, neutral, or undefined impact; and inductive, thematic analysis to develop our taxonomy. Of 378 citations identified, 42 studies examining the use of Facebook (n = 16), blogs (n = 13), Twitter (n = 8), wikis (n = 5), and YouTube (n = 4) on outcomes in cancer (n = 14), depression (n = 13), obesity (n = 9), diabetes (n = 4), heart disease (n = 3), stroke (n = 2), and chronic lower respiratory tract infection (n = 1) were included. Studies were classified as support (n = 16), patient education (n = 10), disease modification (n = 6), disease management (n = 5), and diagnosis (n = 5) within our taxonomy. The overall impact of social media on chronic disease was variable, with 48% of studies indicating benefit, 45% neutral or undefined, and 7% suggesting harm. Among studies that showed benefit, 85% used either Facebook or blogs, and 40% were based within the domain of support. Using social media to provide social, emotional, or experiential support in chronic disease, especially with Facebook and blogs, appears most likely to improve patient care. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Towards Web 3.0: taxonomies and ontologies for medical education -- a systematic review.

    Science.gov (United States)

    Blaum, Wolf E; Jarczweski, Anne; Balzer, Felix; Stötzner, Philip; Ahlers, Olaf

    2013-01-01

    Both for curricular development and mapping, as well as for orientation within the mounting supply of learning resources in medical education, the Semantic Web ("Web 3.0") poses a low-threshold, effective tool that enables identification of content related items across system boundaries. Replacement of the currently required manual with an automatically generated link, which is based on content and semantics, requires the use of a suitably structured vocabulary for a machine-readable description of object content. Aim of this study is to compile the existing taxonomies and ontologies used for the annotation of medical content and learning resources, to compare those using selected criteria, and to verify their suitability in the context described above. Based on a systematic literature search, existing taxonomies and ontologies for the description of medical learning resources were identified. Through web searches and/or direct contact with the respective editors, each of the structured vocabularies thus identified were examined in regards to topic, structure, language, scope, maintenance, and technology of the taxonomy/ontology. In addition, suitability for use in the Semantic Web was verified. Among 20 identified publications, 14 structured vocabularies were identified, which differed rather strongly in regards to language, scope, currency, and maintenance. None of the identified vocabularies fulfilled the necessary criteria for content description of medical curricula and learning resources in the German-speaking world. While moving towards Web 3.0, a significant problem lies in the selection and use of an appropriate German vocabulary for the machine-readable description of object content. Possible solutions include development, translation and/or combination of existing vocabularies, possibly including partial translations of English vocabularies.

  6. Taxonomy, distribution and ecology of Bolboschoenus in Europe

    Czech Academy of Sciences Publication Activity Database

    Hroudová, Zdenka; Zákravský, Petr; Ducháček, M.; Marhold, K.

    2007-01-01

    Roč. 44, č. 2 (2007), s. 81-102 ISSN 0003-3847 R&D Projects: GA AV ČR IAA6005905; GA ČR GA521/04/0997 Institutional research plan: CEZ:AV0Z60050516 Keywords : taxonomy * distribution * ecology Subject RIV: EF - Botanics Impact factor: 0.408, year: 2007

  7. Computer-assisted tree taxonomy by automated image recognition

    NARCIS (Netherlands)

    Pauwels, E.J.; Zeeuw, P.M.de; Ranguelova, E.B.

    2009-01-01

    We present an algorithm that performs image-based queries within the domain of tree taxonomy. As such, it serves as an example relevant to many other potential applications within the field of biodiversity and photo-identification. Unsupervised matching results are produced through a chain of

  8. Use of Bloom's Taxonomy in Developing Reading Comprehension Specifications

    Science.gov (United States)

    Luebke, Stephen; Lorie, James

    2013-01-01

    This article is a brief account of the use of Bloom's Taxonomy of Educational Objectives (Bloom, Engelhart, Furst, Hill, & Krathwohl, 1956) by staff of the Law School Admission Council in the 1990 development of redesigned specifications for the Reading Comprehension section of the Law School Admission Test. Summary item statistics for the…

  9. Developing Learning Objectives for Accounting Ethics Using Bloom's Taxonomy

    Science.gov (United States)

    Kidwell, Linda A.; Fisher, Dann G.; Braun, Robert L.; Swanson, Diane L.

    2013-01-01

    The purpose of our article is to offer a set of core knowledge learning objectives for accounting ethics education. Using Bloom's taxonomy of educational objectives, we develop learning objectives in six content areas: codes of ethical conduct, corporate governance, the accounting profession, moral development, classical ethics theories, and…

  10. Development of a Taxonomy of Keywords for Engineering Education Research

    Science.gov (United States)

    Finelli, Cynthia J.; Borrego, Maura; Rasoulifar, Golnoosh

    2016-01-01

    The diversity of engineering education research provides an opportunity for cross-fertilisation of ideas and creativity, but it also can result in fragmentation of the field and duplication of effort. One solution is to establish a standardised taxonomy of engineering education terms to map the field and communicate and connect research…

  11. The construction of a joint taxonomy of traits and situations

    NARCIS (Netherlands)

    van den Berge, Maarten; De Raad, B.

    2001-01-01

    This study implements the first steps to be taken in the Construction of a taxonomy of situations front a trait psychological perspective. Taking the AB(5)C model of personality characteristics (De Raad et al., 1992) as a point of departure, a collection of situations that is linked to the

  12. Taxonomy for complexity theory in the context of maternity care

    NARCIS (Netherlands)

    Nieuwenhuize, M.; Downe, S.; Gottfreðsdóttir, H.; Rijnders, M.; Preez, A. du; Vaz Rebelo, P.

    2015-01-01

    Background The linear focus of ‘normal science’ is unable toadequately take account of the complex interactions that direct health care systems. There is a turn towards complexity theory as a more appropriate framework for understanding system behaviour. However, a comprehensive taxonomy for

  13. Soil Taxonomy and land evaluation for forest establishment

    Science.gov (United States)

    Haruyoshi Ikawa

    1992-01-01

    Soil Taxonomy, the United States system of soil classification, can be used for land evaluation for selected purposes. One use is forest establishment in the tropics, and the soil family category is especially functional for this purpose. The soil family is a bionomial name with descriptions usually of soil texture, mineralogy, and soil temperature classes. If the...

  14. Taxonomies of Educational Objectives and Theories of Classification.

    Science.gov (United States)

    Travers, Robert M. W.

    1980-01-01

    Classification is the taxonomic science in which a system of categories is established and in which the categories have some logical structure. Scientific classifications have included those by Aristotle, Linnaeus, and Lavoisier. Educational taxonomies include those developed by Bloom, Herbart, Dewey, and Piaget. The problems of taxonomy…

  15. Applying a Knowledge Management Taxonomy to Secondary Schools

    Science.gov (United States)

    Thambi, Melinda; O'Toole, Paddy

    2012-01-01

    The purpose of this article is to examine the relevance of a corporate-based taxonomy of knowledge management to secondary schooling. Do the principles of knowledge management from the corporate world translate to the world of education; specifically, secondary schooling? This article examines categories of knowledge management articulated in…

  16. On Dramatic Instruction: Towards a Taxonomy of Methods.

    Science.gov (United States)

    Courtney, Richard

    1987-01-01

    Examines the many possible methods used by instructors who work with dramatic action: in educational drama, drama therapy, social drama, and theater. Discusses an emergent taxonomy whereby instructors choose either spontaneous/formal, overt/covert/, or intrinsic/extrinsic methods. (JC)

  17. The International Association for Plant Taxonomy (IAPT) Announces ...

    African Journals Online (AJOL)

    The International Association for Plant Taxonomy (IAPT) Announces: Registration of Plant Names, Test and Trial Phase (1998-1999). KL Wilson. Abstract. Journal of East African Natural History Vol. 85 (1&2) 1996: 91-93. AJOL African Journals Online. HOW TO USE AJOL... for Researchers · for Librarians · for Authors ...

  18. Taxonomies, Folksonomies, and Semantics: Establishing Functional Meaning in Navigational Structures

    Science.gov (United States)

    Bacha, Jeffrey A.

    2012-01-01

    This article argues for the establishment of a usability process that incorporates the study of "words" and "word phrases." It demonstrates how semantically mapping a navigational taxonomy can help the developers of digital environments establish a more focused sense of functional meaning for the users of their digital designs.

  19. Taxonomy of Lecture Note-Taking Skills and Subskills

    Science.gov (United States)

    Al-Musalli, Alaa M.

    2015-01-01

    Note taking (NT) in lectures is as active a skill as listening, which stimulates it, and as challenging as writing, which is the end product. Literature on lecture NT misses an integration of the processes involved in listening with those in NT. In this article, a taxonomy is proposed of lecture NT skills and subskills based on a similar list…

  20. An error taxonomy system for analysis of haemodialysis incidents.

    Science.gov (United States)

    Gu, Xiuzhu; Itoh, Kenji; Suzuki, Satoshi

    2014-12-01

    This paper describes the development of a haemodialysis error taxonomy system for analysing incidents and predicting the safety status of a dialysis organisation. The error taxonomy system was developed by adapting an error taxonomy system which assumed no specific specialty to haemodialysis situations. Its application was conducted with 1,909 incident reports collected from two dialysis facilities in Japan. Over 70% of haemodialysis incidents were reported as problems or complications related to dialyser, circuit, medication and setting of dialysis condition. Approximately 70% of errors took place immediately before and after the four hours of haemodialysis therapy. Error types most frequently made in the dialysis unit were omission and qualitative errors. Failures or complications classified to staff human factors, communication, task and organisational factors were found in most dialysis incidents. Device/equipment/materials, medicine and clinical documents were most likely to be involved in errors. Haemodialysis nurses were involved in more incidents related to medicine and documents, whereas dialysis technologists made more errors with device/equipment/materials. This error taxonomy system is able to investigate incidents and adverse events occurring in the dialysis setting but is also able to estimate safety-related status of an organisation, such as reporting culture. © 2014 European Dialysis and Transplant Nurses Association/European Renal Care Association.

  1. Redesign of a Life Span Development Course Using Fink's Taxonomy

    Science.gov (United States)

    Fallahi, Carolyn R.

    2008-01-01

    This study compared a traditional lecture-based life span development course to the same course redesigned using Fink's (2003) taxonomy of significant learning. The goals, activities, and feedback within the course corresponded to Fink's 6 taxa (knowledge, application, integration, human dimension, caring, learning how to learn). Undergraduates in…

  2. Regional floras, a significant modern trend in plant taxonomy

    NARCIS (Netherlands)

    Steenis, van C.G.G.J.

    1959-01-01

    Besides through monographic work plant taxonomy has a second way of framing synthetic attempts and that is by compiling Florulas and Floras, containing a complete account of the flora of parts of the globe, of cities, islets, islands, states, countries, or continents. Irrespective of their style,

  3. A Taxonomy of Human-Agent Team Collaborations

    NARCIS (Netherlands)

    Neef, R.M.

    2006-01-01

    Future command teams will be heavily supported by artificial actors. This paper introduces a taxonomy of collaboration types in human – agent teams. Using two classifying dimensions, coordination type and collaboration type, eight different classes of human – agent collaborations transpire. These

  4. A Taxonomy of Privacy Constructs for Privacy-Sensitive Robotics

    OpenAIRE

    Rueben, Matthew; Grimm, Cindy M.; Bernieri, Frank J.; Smart, William D.

    2017-01-01

    The introduction of robots into our society will also introduce new concerns about personal privacy. In order to study these concerns, we must do human-subject experiments that involve measuring privacy-relevant constructs. This paper presents a taxonomy of privacy constructs based on a review of the privacy literature. Future work in operationalizing privacy constructs for HRI studies is also discussed.

  5. Taxonomies of Higher Educational Institutions Predicted from Organizational Climate.

    Science.gov (United States)

    Lysons, Art

    1990-01-01

    Application of the Perceived Climate Questionnaire involving senior-level staff from Australian institutions used climate factors as the basis for testing hypothesized taxonomies of the institutions. Results reinforce the relevance of contemporary management theories and demonstrate the importance of leadership styles in organizational…

  6. Conception of Learning Outcomes in the Bloom's Taxonomy Affective Domain

    Science.gov (United States)

    Savickiene, Izabela

    2010-01-01

    The article raises a problematic issue regarding an insufficient base of the conception of learning outcomes in the Bloom's taxonomy affective domain. The search for solutions introduces the conception of teaching and learning in the affective domain as well as presents validity criteria of learning outcomes in the affective domain. The…

  7. The Unfortunate Consequences of Bloom's Taxonomy

    Science.gov (United States)

    Case, Roland

    2013-01-01

    The sequenced levels of thinking articulated in Bloom's original taxonomy (or in the multitude of subsequent variations) is the most widely known list in education. In addition to enduring popularity, it is arguably one of the most destructive theories in education. In this article, the author explains what makes it so damaging and how…

  8. Taxonomy of the family Arenaviridae and the order Bunyavirales

    NARCIS (Netherlands)

    Maes, Piet; Alkhovsky, Sergey V.; Bào, Yīmíng; Beer, Martin; Birkhead, Monica; Briese, Thomas; Buchmeier, Michael J.; Calisher, Charles H.; Charrel, Rémi N.; Choi, Il Ryong; Clegg, Christopher S.; Torre, de la Juan Carlos; Delwart, Eric; DeRisi, Joseph L.; Bello, Di Patrick L.; Serio, Di Francesco; Digiaro, Michele; Dolja, Valerian V.; Drosten, Christian; Druciarek, Tobiasz Z.; Du, Jiang; Ebihara, Hideki; Elbeaino, Toufic; Gergerich, Rose C.; Gillis, Amethyst N.; Gonzalez, Jean Paul J.; Haenni, Anne Lise; Hepojoki, Jussi; Hetzel, Udo; Hồ, Thiện; Hóng, Ní; Jain, Rakesh K.; Jansen van Vuren, Petrus; Jin, Qi; Jonson, Miranda Gilda; Junglen, Sandra; Keller, Karen E.; Kemp, Alan; Kipar, Anja; Kondov, Nikola O.; Koonin, Eugene V.; Kormelink, Richard; Korzyukov, Yegor; Krupovic, Mart; Lambert, Amy J.; Laney, Alma G.; LeBreton, Matthew; Lukashevich, Igor S.; Marklewitz, Marco; Markotter, Wanda; Martelli, Giovanni P.; Martin, Robert R.; Mielke-Ehret, Nicole; Mühlbach, Hans Peter; Navarro, Beatriz; Ng, Terry Fei Fan; Nunes, Márcio Roberto Teixeira; Palacios, Gustavo; Pawęska, Janusz T.; Peters, Clarence J.; Plyusnin, Alexander; Radoshitzky, Sheli R.; Romanowski, Víctor; Salmenperä, Pertteli; Salvato, Maria S.; Sanfaçon, Hélène; Sasaya, Takahide; Schmaljohn, Connie; Schneider, Bradley S.; Shirako, Yukio; Siddell, Stuart; Sironen, Tarja A.; Stenglein, Mark D.; Storm, Nadia; Sudini, Harikishan; Tesh, Robert B.; Tzanetakis, Ioannis E.; Uppala, Mangala; Vapalahti, Olli; Vasilakis, Nikos; Walker, Peter J.; Wáng, Guópíng; Wáng, Lìpíng; Wáng, Yànxiăng; Wèi, Tàiyún; Wiley, Michael R.; Wolf, Yuri I.; Wolfe, Nathan D.; Wú, Zhìqiáng; Xú, Wénxìng; Yang, Li; Yāng, Zuòkūn; Yeh, Shyi Dong; Zhāng, Yǒng Zhèn; Zhèng, Yàzhōu; Zhou, Xueping; Zhū, Chénxī; Zirkel, Florian; Kuhn, Jens H.

    2018-01-01

    In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by

  9. Taxonomy, phylogeny, and coevolution of pines and their stem rusts

    Science.gov (United States)

    C. I. Millar; B. B. Kinloch

    1991-01-01

    We review and reinterpret major events in the evolution of pines and their stem rusts using information from their taxonomy, genetics, biogeography, and fossil history. Understanding of pine evolution has been significantly revised in the last 20 years. Pines appear to have evolved early in the Mesozoic and to have diversified and migrated throughout middle latitudes...

  10. Fail Better: Toward a Taxonomy of E-Learning Error

    Science.gov (United States)

    Priem, Jason

    2010-01-01

    The study of student error, important across many fields of educational research, has begun to attract interest in the field of e-learning, particularly in relation to usability. However, it remains unclear when errors should be avoided (as usability failures) or embraced (as learning opportunities). Many domains have benefited from taxonomies of…

  11. Merlin C. Wittrock and the Revision of Bloom's Taxonomy

    Science.gov (United States)

    Krathwohl, David R.; Anderson, Lorin W.

    2010-01-01

    Merl Wittrock, a cognitive psychologist who had proposed a generative model of learning, was an essential member of the group that over a period of 5 years revised the "Taxonomy of Educational Objectives," originally published in 1956. This article describes the development of that 2001 revision (Anderson and Krathwohl, Editors) and Merl's…

  12. Living Behaviors and Molecular Characterization of Benthic Foraminifera in the Arabian Gulf

    Science.gov (United States)

    Arslan, Muhammad; Kaminski, Michael; Khalil, Amjad; Holzmann, Maria

    2016-04-01

    The benthic foraminifera are among the major carbonate producers in modern Arabian Gulf waters and are found living in all marine habitats. They have been recognized as proxies to assess paleoenvironmental changes, however, their biological behaviors in modern environments needs to be further studied. The current study attempts to explain the biology of benthic foraminifera in terms of their living behaviors and molecular characterization, from different regions of the western side of the Arabian Gulf. Accordingly, two major groups of benthic foraminifera, namely rotaliids and miliolids, are examined under laboratory conditions. Results illustrate that the rotaliids are more resistant to environmental changes than miliolids, as their granular reticulopodial network is stronger than among the miliolids, with high cytoplasmic streaming. The pseudopodia extend out from both primary and secondary apertures, and aid the organism in locomotion by attaching to the wall of hard substrate. As a result they drag their whole bodies toward the direction of motion. In rotaliids, the movement rate is high and is attributed to the extension of pseudopodia through all apertures, compared with miliolids in which pseudopodia extend out from the primary aperture only. The innate behavior of both groups was observed as a function of external stimulus, i.e., light, nutrients, and availability of substrate. The observation on average life span reflected that the rotaliids was able to survive longer than miliolids. Molecular analysis reveals the presence of four groups, i.e., Ammonia, Murrayinella, Glabratellina, and Elphidium which support the morphological taxonomy at the genus level. However, BLAST analysis contradicts the species level taxonomy, which challenges the classification based upon hard-shell morphology. Nevertheless, monophyletic clustering is observed among all major groups. The study concludes that the morphological taxonomy needs to be augmented by molecular analysis

  13. Application of Modern Experimental Technique to Solve Morphological Complexity in Plants Taxonomy

    Directory of Open Access Journals (Sweden)

    SURANTO

    2000-07-01

    Full Text Available Modern taxonomy has two approaches, i.e. classical and experimental taxonomy. Classical taxonomy uses morphological characters, while experimental taxonomy uses broader methods including chemistry, physics and mathematics, in the form of laboratory data that are revealed together with the progress of optical technique (microscope, chemistry methods (chromatography, electrophoresis, etc. Modern taxonomy tends to use series of interrelated data. More data used would result in more validity and give better clarification of taxonomic status. A lot of modern taxonomic data such as palynology, cytotaxonomy (cytology, chemical constituent (chemotaxonomy, isozyme and DNA sequencing were used recently.

  14. A philosophical taxonomy of ethically significant moral distress.

    Science.gov (United States)

    Thomas, Tessy A; McCullough, Laurence B

    2015-02-01

    Moral distress is one of the core topics of clinical ethics. Although there is a large and growing empirical literature on the psychological aspects of moral distress, scholars, and empirical investigators of moral distress have recently called for greater conceptual clarity. To meet this recognized need, we provide a philosophical taxonomy of the categories of what we call ethically significant moral distress: the judgment that one is not able, to differing degrees, to act on one's moral knowledge about what one ought to do. We begin by unpacking the philosophical components of Andrew Jameton's original formulation from his landmark 1984 work and identify two key respects in which that formulation remains unclear: the origins of moral knowledge and impediments to acting on that moral knowledge. We then selectively review subsequent literature that shows that there is more than one concept of moral distress and that explores the origin of the values implicated in moral distress and impediments to acting on those values. This review sets the stage for identifying the elements of a philosophical taxonomy of ethically significant moral distress. The taxonomy uses these elements to create six categories of ethically significant moral distress: challenges to, threats to, and violations of professional integrity; and challenges to, threats to, and violations of individual integrity. We close with suggestions about how the proposed philosophical taxonomy of ethically significant moral distress sheds light on the concepts of moral residue and crescendo effect of moral distress and how the proposed taxonomy might usefully guide prevention of and future qualitative and quantitative empirical research on ethically significant moral distress. © The Author 2014. Published by Oxford University Press, on behalf of the Journal of Medicine and Philosophy Inc. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Diversity of marine planktonic ostracods in South China Sea: a DNA taxonomy approach.

    Science.gov (United States)

    Xu, Lei; Wang, Lianggen; Ning, Jiajia; Li, Hong; Ji, Yingying; Du, Feiyan

    2018-04-19

    Ostracods (Crustacea, Ostracoda) are small bivalved crustaceans, contributing over 200 described species to the marine zooplankton community. They are widely distributed and are relatively abundant components of the mesozooplankton, playing an important role in the transport of organic matter to deep layers. However, identification of ostracods based on micro-morphological characters is extremely difficult and time-consuming. Previous fragmentary taxonomic studies of ostracods in the South China Sea (SCA), were based solely on morphology. Here, by analysing the mitochondrial COI gene, we explore the taxa across the SCA using molecular tools for the first time. Our results show that sequence divergence among species varies within a large range, from 12.93% to 35.82%. Sixteen of the taxonomic units recovered by DNA taxonomy agree well with morphology, but Paraconchoecia oblonga, Conchoecia magna and Halocypris brevirostris split into two clades each, each of which contains cryptic species.

  16. Powdery mildew of Chrysanthemum × morifolium: phylogeny and taxonomy in the context of Golovinomyces species on Asteraceae hosts.

    Science.gov (United States)

    Bradshaw, Michael; Braun, Uwe; Götz, Monika; Meeboon, Jamjan; Takamatsu, Susumu

    2017-01-01

    The taxonomic history of the common powdery mildew of Chrysanthemum × morifolium (chrysanthemum, florist's daisy), originally described in Germany as Oidium chrysanthemi, is discussed. The position of O. chrysanthemi was investigated on the basis of morphological traits and molecular phylogenetic analyses. Based on the results of this study, this species, which is closely related to Golovinomyces artemisae, was reassessed and reallocated to Golovinomyces. The phylogenetic analysis and taxonomic reassessment of the chrysanthemum powdery mildew is supplemented by a morphological description, a summary of its worldwide distribution data, and a brief discussion of the introduction of this fungus to North America. G. chrysanthemi differs from true G. artemisiae in that it has much longer conidiophores, is not constricted at the base, and has much larger and most importantly longer conidia. The close affinity of Golovinomyces to Artemisia and Chrysanthemum species signifies a coevolutionary event between the powdery mildews concerned and their host species in the subtribe Artemisiinae (Asteraceae tribe Anthemideae). This conclusion is fully supported by the current phylogeny and taxonomy of the host plant genera and the coevolution that occurred with the host and pathogen. The following powdery mildew species, which are associated with hosts belonging to the tribe Anthemideae of the Asteraceae, are epitypified: Alphitomorpha depressa β artemisiae (≡ Alphitomorpha artemisiae), Erysiphe artemisiae, and Oidium chrysanthemi. Erysiphe macrocarpa is neotypified. Their sequences were retrieved from the epitype collections and have been added to the phylogenetic tree. Golovinomyces orontii, an additional powdery mildew species on Chrysanthemum ×morifolium, is reported. This species is rarely found as a spontaneous infection and was obtained from inoculation experiments.

  17. Operationalizing value-based pricing of medicines : a taxonomy of approaches.

    Science.gov (United States)

    Sussex, Jon; Towse, Adrian; Devlin, Nancy

    2013-01-01

    The UK Government is proposing a novel form of price regulation for branded medicines, which it has dubbed 'value-based pricing' (VBP). The specifics of how VBP will work are unclear. We provide an account of the possible means by which VBP of medicines might be operationalized, and a taxonomy to describe and categorize the various approaches. We begin with a brief discussion of the UK Government's proposal for VBP and proceed to define a taxonomy of approaches to VBP. The taxonomy has five main dimensions: (1) what is identified as being of value, (2) how each element is measured, (3) how it is valued, (4) how the different elements of value are aggregated, and (5) how the result is then used to determine the price of a medicine. We take as our starting point that VBP will include a measure of health gain and that, as proposed by the UK Government, this will be built on the QALY. Our principal interest is in the way criteria other than QALYs are taken into account, including severity of illness, the extent of unmet need, and wider societal considerations such as impacts on carers. We set out to: (1) identify and describe the full range of alternative means by which 'value' might be measured and valued, (2) identify and describe the options available for aggregating the different components of value to establish a maximum price, and (3) note the challenges and relative advantages associated with these approaches. We review the means by which aspects of VBP are currently operationalized in a selection of countries and place these, and proposals for the UK, in the context of our taxonomy. Finally, we give an initial assessment of the challenges, pros and cons of each approach. We conclude that identifying where VBP should lie on each of the five dimensions entails value judgements: there are no simple 'right or wrong' solutions. If a wider definition of value than incremental QALYs gained is adopted, as is desirable, then a pragmatic way to aggregate the different

  18. DArT whole genome profiling provides insights on the evolution and taxonomy of edible Banana (Musa spp.)

    Czech Academy of Sciences Publication Activity Database

    Sardos, J.; Perrier, X.; Doležel, Jaroslav; Hřibová, Eva; Christelová, Pavla; Van den Houwe, I.; Kilian, A.; Roux, N.

    2016-01-01

    Roč. 118, č. 7 (2016), s. 1269-1278 ISSN 0305-7364 R&D Projects: GA MŠk(CZ) LO1204; GA MŠk LG15017 Institutional support: RVO:61389030 Keywords : multilocus genotype data * arrays technology dart * genetic diversity * population-structure * balbisiana colla * acuminata colla * markers * identification * aflp * domestication * Musa acuminata * Musa balbisiana * Musa spp. * banana * DArT * domestication * taxonomy * classification * domestication Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 4.041, year: 2016

  19. Diffuse low-grade glioma: a review on the new molecular classification, natural history and current management strategies.

    Science.gov (United States)

    Delgado-López, P D; Corrales-García, E M; Martino, J; Lastra-Aras, E; Dueñas-Polo, M T

    2017-08-01

    The management of diffuse supratentorial WHO grade II glioma remains a challenge because of the infiltrative nature of the tumor, which precludes curative therapy after total or even supratotal resection. When possible, functional-guided resection is the preferred initial treatment. Total and subtotal resections correlate with increased overall survival. High-risk patients (age >40, partial resection), especially IDH-mutated and 1p19q-codeleted oligodendroglial lesions, benefit from surgery plus adjuvant chemoradiation. Under the new 2016 WHO brain tumor classification, which now incorporates molecular parameters, all diffusely infiltrating gliomas are grouped together since they share specific genetic mutations and prognostic factors. Although low-grade gliomas cannot be regarded as benign tumors, large observational studies have shown that median survival can actually be doubled if an early, aggressive, multi-stage and personalized therapy is applied, as compared to prior wait-and-see policy series. Patients need an honest long-term therapeutic strategy that should ideally anticipate neurological, cognitive and histopathologic worsening.

  20. Current Opinion in Endocrinology, Diabetes, and Obesity “Pituitary gigantism: Update on Molecular Biology and Management”

    Science.gov (United States)

    Lodish, Maya B.; Trivellin, Giampaolo; Stratakis, Constantine A.

    2016-01-01

    Purpose of review To provide an update on the mechanisms leading to pituitary gigantism, as well as to familiarize the practitioner with the implication of these genetic findings on treatment decisions. Recent findings Prior studies have identified gigantism as a feature of a number of monogenic disorders, including mutations in the aryl hydrocarbon receptor interacting protein (AIP) gene, multiple endocrine neoplasia types 1 and 4, McCune Albright Syndrome, Carney Complex, and the paraganglioma, pheochromocytoma and pituitary adenoma association (3PA) due to succinate dehydrogenase defects. We recently described a previously uncharacterized form of early-onset pediatric gigantism caused by microduplications on chromosome Xq26.3 and we termed it X-LAG (X-linked acrogigantism). The age of onset of increased growth in X-LAG is significantly younger than other pituitary gigantism cases, and control of growth hormone excess is particularly challenging. Summary Knowledge of the molecular defects that underlie pituitary tumorigenesis is crucial for patient care as they guide early intervention, screening for associated conditions, genetic counseling, surgical approach (partial or total hypophysectomy), and choice of medical management. Recently described microduplications of Xq26.3 account for more than 80% of the cases of early-onset pediatric gigantism. Early recognition of X-LAG may improve outcomes, as successful control of growth hormone excess requires extensive anterior pituitary resection and are difficult to manage with medical therapy alone. PMID:26574647

  1. A Taxonomy for Enhancing Usability, Flexibility, and Security of User Authentication

    Directory of Open Access Journals (Sweden)

    Susan Gottschlich

    2017-12-01

    Full Text Available Two technology trends – a move toward software defined capabilities and toward networked devices – support both unprecedented innovations and requirements for security. A fundamental aspect of security is user authentication, which allows devices and software applications to establish their user’s identity and identity is in turn used to establish which of its capabilities the user is authorized to access. While multiple authentication steps, known as multifactor authentication, are being used more widely throughout the military, government, businesses, and consumer sectors, the selection and implementation of which authentication factors to require is typically defined by security policy. Security policy is in turn typically established by a security organization that may have no formal metrics or means to guide its selection of authentication factors. This paper will present a taxonomy for describing authentication factors including important attributes that characterize authentication robustness to aid in the selection of factors that are consistent with the user’s mission. One particular authentication factor that I have developed will be discussed in the context of this taxonomy to motivate the need to broaden current definitions and security policies. The ultimate goal of this paper is to inspire the development of standards for authentication technologies to both support mission aware authentication innovation and to inform decision making about security policies concerning user authentication and authorization. Further, this paper aims to demonstrate that such an approach will fundamentally enhance both security and usability of increasingly networked, software-defined devices, equipment and software applications.

  2. Synthesis of phylogeny and taxonomy into a comprehensive tree of life

    Science.gov (United States)

    Hinchliff, Cody E.; Smith, Stephen A.; Allman, James F.; Burleigh, J. Gordon; Chaudhary, Ruchi; Coghill, Lyndon M.; Crandall, Keith A.; Deng, Jiabin; Drew, Bryan T.; Gazis, Romina; Gude, Karl; Hibbett, David S.; Katz, Laura A.; Laughinghouse, H. Dail; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltis, Douglas E.; Williams, Tiffani; Cranston, Karen A.

    2015-01-01

    Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips—the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point for community contribution. This comprehensive tree will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change, agriculture, and genomics. PMID:26385966

  3. Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

    Science.gov (United States)

    van Belkum, Alex; Struelens, Marc; de Visser, Arjan; Verbrugh, Henri; Tibayrenc, Michel

    2001-01-01

    Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made. PMID:11432813

  4. Making US Soil Taxonomy more scientifically applicable to environmental and food security issues.

    Science.gov (United States)

    Monger, Curtis; Lindbo, David L.; Wysocki, Doug; Schoeneberger, Phil; Libohova, Zamir

    2017-04-01

    US Department of Agriculture began mapping soils in the 1890s on a county-by-county basis until most of the conterminous United States was mapped by the late 1930s. This first-generation mapping was followed by a second-generation that re-mapped the US beginning in the 1940s. Soil classification during these periods evolved into the current system of Soil Taxonomy which is based on (1) soil features as natural phenomena and on (2) soil properties important for agriculture and other land uses. While this system has enabled communication among soil surveyors, the scientific applicability of Soil Taxonomy to address environmental and food security issues has been under-utilized. In particular, little effort has been exerted to understand how soil taxa interact and function together as larger units—as soil systems. Thus, much soil-geomorphic understanding that could be applied to process-based modeling remains unexploited. The challenge for soil taxonomists in the United States and elsewhere is to expand their expertise and work with modelers to explore how soil taxa are linked to each other, how they influence water, nutrient, and pollutant flow through the landscape, how they interact with ecology, and how they change with human land use.

  5. Toward a clarification of the taxonomy of "bias" in epidemiology textbooks.

    Science.gov (United States)

    Schwartz, Sharon; Campbell, Ulka B; Gatto, Nicolle M; Gordon, Kirsha

    2015-03-01

    Epidemiology textbooks typically divide biases into 3 general categories-confounding, selection bias, and information bias. Despite the ubiquity of this categorization, authors often use these terms to mean different things. This hinders communication among epidemiologists and confuses students who are just learning about the field. To understand the sources of this problem, we reviewed current general epidemiology textbooks to examine how the authors defined and categorized biases. We found that much of the confusion arises from different definitions of "validity" and from a mixing of 3 overlapping organizational features in defining and differentiating among confounding, selection bias, and information bias: consequence, the result of the problem; cause, the processes that give rise to the problem; and cure, how these biases can be addressed once they occur. By contrast, a consistent taxonomy would provide (1) a clear and consistent definition of what unites confounding, selection bias, and information bias and (2) a clear articulation and consistent application of the feature that distinguishes these categories. Based on a distillation of these textbook discussions, we provide an example of a taxonomy that we think meets these criteria.

  6. Defining the value of injection current and effective electrical contact area for EGaIn-based molecular tunneling junctions.

    Science.gov (United States)

    Simeone, Felice C; Yoon, Hyo Jae; Thuo, Martin M; Barber, Jabulani R; Smith, Barbara; Whitesides, George M

    2013-12-04

    Analysis of rates of tunneling across self-assembled monolayers (SAMs) of n-alkanethiolates SCn (with n = number of carbon atoms) incorporated in junctions having structure Ag(TS)-SAM//Ga2O3/EGaIn leads to a value for the injection tunnel current density J0 (i.e., the current flowing through an ideal junction with n = 0) of 10(3.6±0.3) A·cm(-2) (V = +0.5 V). This estimation of J0 does not involve an extrapolation in length, because it was possible to measure current densities across SAMs over the range of lengths n = 1-18. This value of J0 is estimated under the assumption that values of the geometrical contact area equal the values of the effective electrical contact area. Detailed experimental analysis, however, indicates that the roughness of the Ga2O3 layer, and that of the Ag(TS)-SAM, determine values of the effective electrical contact area that are ~10(-4) the corresponding values of the geometrical contact area. Conversion of the values of geometrical contact area into the corresponding values of effective electrical contact area results in J0(+0.5 V) = 10(7.6±0.8) A·cm(-2), which is compatible with values reported for junctions using top-electrodes of evaporated Au, and graphene, and also comparable with values of J0 estimated from tunneling through single molecules. For these EGaIn-based junctions, the value of the tunneling decay factor β (β = 0.75 ± 0.02 Å(-1); β = 0.92 ± 0.02 nC(-1)) falls within the consensus range across different types of junctions (β = 0.73-0.89 Å(-1); β = 0.9-1.1 nC(-1)). A comparison of the characteristics of conical Ga2O3/EGaIn tips with the characteristics of other top-electrodes suggests that the EGaIn-based electrodes provide a particularly attractive technology for physical-organic studies of charge transport across SAMs.

  7. Taxonomy of Means and Ends in Aquaculture Production—Part 2: The Technical Solutions of Controlling Solids, Dissolved Gasses and pH

    Directory of Open Access Journals (Sweden)

    Bjorgvin Vilbergsson

    2016-09-01

    Full Text Available In engineering design, knowing the relationship between the means (technique and the end (desired function or outcome is essential. The means in Aquaculture are technical solutions like airlifts that are used to achive desired functionality (an end like controlling dissolved gasses. In previous work, the authors identified possible functions by viewing aquaculture production systems as transformation processes in which inputs are transformed by treatment techniques (means and produce outputs (ends. The current work creates an overview of technical solutions of treatment functions for both design and research purposes. A comprehensive literature review of all areas of technical solutions is identified and categorized into a visual taxonomy of the treatment functions for controlling solids, controlling dissolved gasses and controlling pH alkalinity and hardness. This article is the second in a sequence of four and partly presents the treatments functions in the taxonomy. The other articles in this series present complementary aspects of this research: Part 1, A transformational view on aquaculture and functions divided into input, treatment and output functions; Part 2, The current taxonomy paper; Part 3, The second part of the taxonomy; and Part 4, Mapping of the means (techniques for multiple treatment functions.

  8. The molecular biology of ilarviruses.

    Science.gov (United States)

    Pallas, Vicente; Aparicio, Frederic; Herranz, Mari C; Sanchez-Navarro, Jesus A; Scott, Simon W

    2013-01-01

    Ilarviruses were among the first 16 groups of plant viruses approved by ICTV. Like Alfalfa mosaic virus (AMV), bromoviruses, and cucumoviruses they are isometric viruses and possess a single-stranded, tripartite RNA genome. However, unlike these other three groups, ilarviruses were recognized as being recalcitrant subjects for research (their ready lability is reflected in the sigla used to create the group name) and were renowned as unpromising subjects for the production of antisera. However, it was recognized that they shared properties with AMV when the phenomenon of genome activation, in which the coat protein (CP) of the virus is required to be present to initiate infection, was demonstrated to cross group boundaries. The CP of AMV could activate the genome of an ilarvirus and vice versa. Development of the molecular information for ilarviruses lagged behind the knowledge available for the more extensively studied AMV, bromoviruses, and cucumoviruses. In the past 20 years, genomic data for most known ilarviruses have been developed facilitating their detection and allowing the factors involved in the molecular biology of the genus to be investigated. Much information has been obtained using Prunus necrotic ringspot virus and the more extensively studied AMV. A relationship between some ilarviruses and the cucumoviruses has been defined with the recognition that members of both genera encode a 2b protein involved in RNA silencing and long distance viral movement. Here, we present a review of the current knowledge of both the taxonomy and the molecular biology of this genus of agronomically and horticulturally important viruses. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Developing "Personality" Taxonomies: Metatheoretical and Methodological Rationales Underlying Selection Approaches, Methods of Data Generation and Reduction Principles.

    Science.gov (United States)

    Uher, Jana

    2015-12-01

    Taxonomic "personality" models are widely used in research and applied fields. This article applies the Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals (TPS-Paradigm) to scrutinise the three methodological steps that are required for developing comprehensive "personality" taxonomies: 1) the approaches used to select the phenomena and events to be studied, 2) the methods used to generate data about the selected phenomena and events and 3) the reduction principles used to extract the "most important" individual-specific variations for constructing "personality" taxonomies. Analyses of some currently popular taxonomies reveal frequent mismatches between the researchers' explicit and implicit metatheories about "personality" and the abilities of previous methodologies to capture the particular kinds of phenomena toward which they are targeted. Serious deficiencies that preclude scientific quantifications are identified in standardised questionnaires, psychology's established standard method of investigation. These mismatches and deficiencies derive from the lack of an explicit formulation and critical reflection on the philosophical and metatheoretical assumptions being made by scientists and from the established practice of radically matching the methodological tools to researchers' preconceived ideas and to pre-existing statistical theories rather than to the particular phenomena and individuals under study. These findings raise serious doubts about the ability of previous taxonomies to appropriately and comprehensively reflect the phenomena towards which they are targeted and the structures of individual-specificity occurring in them. The article elaborates and illustrates with empirical examples methodological principles that allow researchers to appropriately meet the metatheoretical requirements and that are suitable for comprehensively exploring individuals' "personality".

  10. Developing Integrated Taxonomies for a Tiered Information Architecture

    Science.gov (United States)

    Dutra, Jayne E.

    2006-01-01

    This viewgraph presentation reviews the concept of developing taxonomies for an information architecture. In order to assist people in accessing information required to access information and retrieval, including cross repository searching, a system of nested taxonomies is being developed. Another facet of this developmental project is collecting and documenting attributes about people, to allow for several uses: access management, i.e., who are you and what can you see?; targeted content delivery i.e., what content helps you get your work done?; w ork force planning i.e., what skill sets do you have that we can appl y to work?; and IT Services i.e., How can we provision you with the proper IT services?

  11. NASA Taxonomies for Searching Problem Reports and FMEAs

    Science.gov (United States)

    Malin, Jane T.; Throop, David R.

    2006-01-01

    Many types of hazard and risk analyses are used during the life cycle of complex systems, including Failure Modes and Effects Analysis (FMEA), Hazard Analysis, Fault Tree and Event Tree Analysis, Probabilistic Risk Assessment, Reliability Analysis and analysis of Problem Reporting and Corrective Action (PRACA) databases. The success of these methods depends on the availability of input data and the analysts knowledge. Standard nomenclature can increase the reusability of hazard, risk and problem data. When nomenclature in the source texts is not standard, taxonomies with mapping words (sets of rough synonyms) can be combined with semantic search to identify items and tag them with metadata based on a rich standard nomenclature. Semantic search uses word meanings in the context of parsed phrases to find matches. The NASA taxonomies provide the word meanings. Spacecraft taxonomies and ontologies (generalization hierarchies with attributes and relationships, based on terms meanings) are being developed for types of subsystems, functions, entities, hazards and failures. The ontologies are broad and general, covering hardware, software and human systems. Semantic search of Space Station texts was used to validate and extend the taxonomies. The taxonomies have also been used to extract system connectivity (interaction) models and functions from requirements text. Now the Reconciler semantic search tool and the taxonomies are being applied to improve search in the Space Shuttle PRACA database, to discover recurring patterns of failure. Usual methods of string search and keyword search fall short because the entries are terse and have numerous shortcuts (irregular abbreviations, nonstandard acronyms, cryptic codes) and modifier words cannot be used in sentence context to refine the search. The limited and fixed FMEA categories associated with the entries do not make the fine distinctions needed in the search. The approach assigns PRACA report titles to problem classes in

  12. Benchmarking of methods for genomic taxonomy

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Lukjancenko, Oksana

    2014-01-01

    . Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene...

  13. Research into the development of a knowledge acquisition taxonomy

    Science.gov (United States)

    Fink, Pamela K.; Herren, L. Tandy

    1991-01-01

    The focus of the research was on the development of a problem solving taxonomy that can support and direct the knowledge engineering process during the development of an intelligent tutoring system. The results of the research are necessarily general. Being only a small initial attempt at a fundamental problem in artificial intelligence and cognitive psychology, the process has had to be bootstrapped and the results can only provide pointers to further, more formal research designs.

  14. Evaluating ILI Advanced Series through Bloom's Revised Taxonomy

    OpenAIRE

    MAHDIPOUR, Nasim; SADEGHI, Bahador

    2015-01-01

    Abstract. This study investigated Iran Language Institute Advanced Series in terms of learning objectives based on Bloom's Revised Taxonomy. It examined the cognitive, affective and psychomotor domains to see how the critical thinking skills are used and to what extent these books are different from each other. For these purposes, the frequencies, percentages and Standard Residual were analyzed. Results revealed that the lower-order cognitive skills (i.e. remembering, understanding and applyi...

  15. Building the Layers of a New Manufacturing Taxonomy

    DEFF Research Database (Denmark)

    Kapetaniou, Chrystalla; Rieple, Alison; Pilkington, Alan

    2017-01-01

    Recent innovations in 3D printing technologies and processes have influenced how products are designed, built and delivered. However, there is a significant gap in our knowledge of how 3D printing is impacting on manufacturing eco-systems within different industries and contexts. Drawing...... inspiration from earlier manufacturing taxonomies as well as the competitive dynamics literature which provides insights into industries' moves from straightforwardly rivalrous frameworks, through competitive-cooperative exemplars, into the more recent relational-based competition. Basing our analysis...

  16. Using HET taxonomy to help stop human error

    OpenAIRE

    Li, Wen-Chin; Harris, Don; Stanton, Neville A.; Hsu, Yueh-Ling; Chang, Danny; Wang, Thomas; Young, Hong-Tsu

    2010-01-01

    Flight crews make positive contributions to the safety of aviation operations. Pilots have to assess continuously changing situations, evaluate potential risks, and make quick decisions. However, even well-trained and experienced pilots make errors. Accident investigations have identified that pilots’ performance is influenced significantly by the design of the flightdeck interface. This research applies hierarchical task analysis (HTA) and utilizes the Human Error Template (HET) taxonomy to ...

  17. A Hierarchical Causal Taxonomy of Psychopathology across the Life Span

    Science.gov (United States)

    Lahey, Benjamin B.; Krueger, Robert F.; Rathouz, Paul J.; Waldman, Irwin D.; Zald, David H.

    2016-01-01

    We propose a taxonomy of psychopathology based on patterns of shared causal influences identified in a review of multivariate behavior genetic studies that distinguish genetic and environmental influences that are either common to multiple dimensions of psychopathology or unique to each dimension. At the phenotypic level, first-order dimensions are defined by correlations among symptoms; correlations among first-order dimensions similarly define higher-order domains (e.g., internalizing or externalizing psychopathology). We hypothesize that the robust phenotypic correlations among first-order dimensions reflect a hierarchy of increasingly specific etiologic influences. Some nonspecific etiologic factors increase risk for all first-order dimensions of psychopathology to varying degrees through a general factor of psychopathology. Other nonspecific etiologic factors increase risk only for all first-order dimensions within a more specific higher-order domain. Furthermore, each first-order dimension has its own unique causal influences. Genetic and environmental influences common to family members tend to be nonspecific, whereas environmental influences unique to each individual are more dimension-specific. We posit that these causal influences on psychopathology are moderated by sex and developmental processes. This causal taxonomy also provides a novel framework for understanding the heterogeneity of each first-order dimension: Different persons exhibiting similar symptoms may be influenced by different combinations of etiologic influences from each of the three levels of the etiologic hierarchy. Furthermore, we relate the proposed causal taxonomy to transdimensional psychobiological processes, which also impact the heterogeneity of each psychopathology dimension. This causal taxonomy implies the need for changes in strategies for studying the etiology, psychobiology, prevention, and treatment of psychopathology. PMID:28004947

  18. Taxonomy of the genus Arachis (Leguminosae

    Directory of Open Access Journals (Sweden)

    Antonio Krapovickas

    2007-01-01

    the ideas presented. It is evident that the genetic distances separating the sections are far from being of the same magnitude. The presumably older sections (Triseminatae, Trierectoides, Erectoides, Extranervosae and Heteranthae, except for section Erectoides, are much more isolated from the remaining sections and from each other than those taken to be of more recent origin (Procumbentes, Caulorrhizae, Rhizomatosae and Arachis. Section Arachis is by far the largest, containing about 40% of the species described. Species of this section appear to be spreading into new territory and to be invading areas occupied by species of other sections. They grow intermixed with populations of Extranervosae in the upper Paraguay basin and occupy common ground with section Procumbentes in the Gran Pantanal. They have reached the shores of La Plata and the southeastern coast of Brazil and grow from Yala in NW Argentina to the Tocantins in NE Brazil. They include the worldwide cultivar, A. hypogaea. Essentially every published work on the botanical history and taxonomy of Arachis is presented here in the individual specimen references and in the general bibliography. The history of A. hypogaeafrom the early 16th Century to more recent times, along with the common names in several native American languages, provide a perspective on the antiquity of this cultivar and the level of civilization required for its creation. Six appendices provide supporting data and matters of record. Diagnostic keys to the sections and to the species within each section select the more sharply distinguishing characteristics of the sections and species. Nineteen line drawings capture the sectional and species structures of whole plants, root systems, fruit orientations, agametic reproductions from fruiting structures, carpel shapes and surface features of leaves and stems.

  19. Histopathological, Molecular, and Genetic Profile of Hereditary Diffuse Gastric Cancer: Current Knowledge and Challenges for the Future.

    Science.gov (United States)

    van der Post, Rachel S; Gullo, Irene; Oliveira, Carla; Tang, Laura H; Grabsch, Heike I; O'Donovan, Maria; Fitzgerald, Rebecca C; van Krieken, Han; Carneiro, Fátima

    Familial clustering is seen in 10 % of gastric cancer cases and approximately 1-3 % of gastric cancer arises in the setting of hereditary diffuse gastric cancer (HDGC). In families with HDGC, gastric cancer presents at young age. HDGC is predominantly caused by germline mutations in CDH1 and in a minority by mutations in other genes, including CTNNA1. Early stage HDGC is characterized by a few, up to dozens of intramucosal foci of signet ring cell carcinoma and its precursor lesions. These include in situ signet ring cell carcinoma and pagetoid spread of signet ring cells. Advanced HDGC presents as poorly cohesive/diffuse type carcinoma, normally with very few typical signet ring cells, and has a poor prognosis. Currently, it is unknown which factors drive the progression towards aggressive disease, but it is clear that most intramucosal lesions will not have such progression.Immunohistochemical profile of early and advanced HDGC is often characterized by abnormal E-cadherin immunoexpression, including absent or reduced membranous expression, as well as "dotted" or cytoplasmic expression. However, membranous expression of E-cadherin does not exclude HDGC. Intramucosal HDGC (pT1a) presents with an "indolent" phenotype, characterized by typical signet ring cells without immunoexpression of Ki-67 and p53, while advanced carcinomas (pT > 1) display an "aggressive" phenotype with pleomorphic cells, that are immunoreactive for Ki-67 and p53. These features show that the IHC profile is different between intramucosal and more advanced HDGC, providing evidence of phenotypic heterogeneity, and may help to define predictive biomarkers of progression from indolent to aggressive, widely invasive carcinomas.

  20. Scientific Teaching: Defining a Taxonomy of Observable Practices

    Science.gov (United States)

    Couch, Brian A.; Brown, Tanya L.; Schelpat, Tyler J.; Graham, Mark J.; Knight, Jennifer K.

    2015-01-01

    Over the past several decades, numerous reports have been published advocating for changes to undergraduate science education. These national calls inspired the formation of the National Academies Summer Institutes on Undergraduate Education in Biology (SI), a group of regional workshops to help faculty members learn and implement interactive teaching methods. The SI curriculum promotes a pedagogical framework called Scientific Teaching (ST), which aims to bring the vitality of modern research into the classroom by engaging students in the scientific discovery process and using student data to inform the ongoing development of teaching methods. With the spread of ST, the need emerges to systematically define its components in order to establish a common description for education researchers and practitioners. We describe the development of a taxonomy detailing ST’s core elements and provide data from classroom observations and faculty surveys in support of its applicability within undergraduate science courses. The final taxonomy consists of 15 pedagogical goals and 37 supporting practices, specifying observable behaviors, artifacts, and features associated with ST. This taxonomy will support future educational efforts by providing a framework for researchers studying the processes and outcomes of ST-based course transformations as well as a concise guide for faculty members developing classes. PMID:25713097

  1. A taxonomy of dignity: a grounded theory study

    Directory of Open Access Journals (Sweden)

    Jacobson Nora

    2009-02-01

    Full Text Available Abstract Background This paper has its origins in Jonathan Mann's insight that the experience of dignity may explain the reciprocal relationships between health and human rights. It follows his call for a taxonomy of dignity: "a coherent vocabulary and framework to characterize dignity." Methods Grounded theory procedures were use to analyze literature pertaining to dignity and to conduct and analyze 64 semi-structured interviews with persons marginalized by their health or social status, individuals who provide health or social services to these populations, and people working in the field of health and human rights. Results The taxonomy presented identifies two main forms of dignity–human dignity and social dignity–and describes several elements of these forms, including the social processes that violate or promote them, the conditions under which such violations and promotions occur, the objects of violation and promotion, and the consequences of dignity violation. Together, these forms and elements point to a theory of dignity as a quality of individuals and collectives that is constituted through interaction and interpretation and structured by conditions pertaining to actors, relationships, settings, and the broader social order. Conclusion The taxonomy has several implications for work in health and human rights. It suggests a map to possible points of intervention and provides a language in which to talk about dignity.

  2. Thermophilic fungi in the new age of fungal taxonomy.

    Science.gov (United States)

    de Oliveira, Tássio Brito; Gomes, Eleni; Rodrigues, Andre

    2015-01-01

    Thermophilic fungi are of wide interest due to their potential to produce heat-tolerant enzymes for biotechnological processes. However, the taxonomy of such organisms remains obscure, especially given new developments in the nomenclature of fungi. Here, we examine the taxonomy of the thermophilic fungi most commonly used in industry in light of the recent taxonomic changes following the adoption of the International Code of Nomenclature for Algae, Fungi and Plants and also based on the movement One Fungus = One Name. Despite the widespread use of these fungi in applied research, several thermotolerant fungi still remain classified as thermophiles. Furthermore, we found that while some thermophilic fungi have had their genomes sequenced, many taxa still do not have barcode sequences of reference strains available in public databases. This lack of basic information is a limiting factor for the species identification of thermophilic fungi and for metagenomic studies in this field. Based on next-generation sequencing, such studies generate large amounts of data, which may reveal new species of thermophilic fungi in different substrates (composting systems, geothermal areas, piles of plant material). As discussed in this study, there are intrinsic problems associated with this method, considering the actual state of the taxonomy of thermophilic fungi. To overcome such difficulties, the taxonomic classification of this group should move towards standardizing the commonly used species names in industry and to assess the possibility of including new systems for describing species based on environmental sequences.

  3. Taxonomy, Physiology, and Natural Products of Actinobacteria

    OpenAIRE

    Barka, Essaid Ait; Vatsa, Parul; Sanchez, Lisa; Gaveau-Vaillant, Nathalie; Jacquard, Cedric; Klenk, Hans-Peter; Clément, Christophe; Ouhdouch, Yder; van Wezel, Gilles P.

    2015-01-01

    Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal c...

  4. Pragmatic Strategies and Linguistic Structures in Making ‘Suggestions’: Towards Comprehensive Taxonomies

    Directory of Open Access Journals (Sweden)

    Hossein Abolfathiasl

    2013-11-01

    Full Text Available This paper analyses and upgrades taxonomies of strategies and structures for the speech act of suggesting based on existing taxonomies and classifications in the pragmatics research literature. Previous studies have focused mainly on linguistic structures used to perform the speech act of suggesting. Thus, there seems to be a need to provide a more comprehensive set of taxonomies for structures as well as strategies that can be used in EFL/ESL classrooms and for research on the speech act of suggesting. To this end, the speech act of suggesting is defined first and the features of this speech act are discussed. Second, the most recent classifications proposed for structures and linguistic realization strategies for suggestions were analysed and contrasted and a more comprehensive taxonomy of structures and linguistic realization strategies is provided, based on previous taxonomies. Finally, taxonomy of politeness strategies in making suggestions are provided, based on recent studies in cross-cultural pragmatics research.

  5. Computation and analysis of the transverse current autocorrelation function, Ct(k,t), for small wave vectors: A molecular-dynamics study for a Lennard-Jones fluid

    Science.gov (United States)

    Vogelsang, R.; Hoheisel, C.

    1987-02-01

    Molecular-dynamics (MD) calculations are reported for three thermodynamic states of a Lennard-Jones fluid. Systems of 2048 particles and 105 integration steps were used. The transverse current autocorrelation function, Ct(k,t), has been determined for wave vectors of the range 0.5viscosities which showed a systematic behavior as a function of k. Extrapolation to the hydrodynamic region at k=0 gave shear viscosity coefficients in good agreement with direct Green-Kubo results obtained in previous work. The two-exponential model fit for the memory function proposed by other authors does not provide a reasonable description of the MD results, as the fit parameters show no systematic wave-vector dependence, although the Ct(k,t) functions are somewhat better fitted. Similarly, the semiempirical interpolation formula for the decay time based on the viscoelastic concept proposed by Akcasu and Daniels fails to reproduce the correct k dependence for the wavelength range investigated herein.

  6. Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Cristiane C. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Amaral, Gilda R. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Campeão, Mariana [Univ. of Rio de Janeiro (UFRJ) (Brazil); Edwards, Robert A. [Univ. of Rio de Janeiro (UFRJ) (Brazil); San Diego State Univ., CA (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Polz, Martin F. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Dutilh, Bas E. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Radbould Univ., Nijmegen (Netherlands); Ussery, David W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sawabe, Tomoo [Hokkaido Univ., Hakodate (Japan); Swings, Jean [Univ. of Rio de Janeiro (UFRJ) (Brazil); Ghent Univ. (Belgium); Thompson, Fabiano L. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Advanced Systems Laboratory Production Management COPPE / UFRJ, Rio de Janeiro (Brazil)

    2014-12-23

    Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. We re-evaluated the prokaryote species twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. We will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

  7. Technology and Bloom's Taxonomy: Tools to Facilitate Higher-Level Learning in Chemistry

    National Research Council Canada - National Science Library

    Morgan, Matthew

    1997-01-01

    This research project ties together chemistry data acquisition technology, introductory chemistry laboratory experiments, and Bloom's Taxonomy of Educational Objectives into a unified learning model...

  8. Orobanche lutea Baumg. (Orobanchaceae in Poland: revised distribution, taxonomy, phytocoenological and host relations

    Directory of Open Access Journals (Sweden)

    Piwowarczyk Renata

    2014-06-01

    Full Text Available The paper presents current distribution of Orobanche lutea Baumg. in Poland based on a critical revision of herbarium and literature data as well as results of field investigations conducted between 1999-2014. Majority of localities are centred around the Silesia-Cracow, Małopolska and Lublin-Lviv Uplands. The greatest density of sites with probably the most abundant populations in Europe is in the central part of Silesia-Cracow Upland, which, by several hundred years, was heavily exploited for calamine mining (rich in zinc, lead and silver. This resulted in the formation of large areas of gangue containing toxic heavy metals. Since limestone, dolomite, marl and postglacial calcareous clay and sands occur there in most places, the soil is often strongly calcareous. Populations of O. lutea contain here many thousands of shoots. The distribution of the species in Poland is mapped. The taxonomy, biology, ecology and threats are also discussed.

  9. Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp.) in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry

    Science.gov (United States)

    Cunha, Haydée A.; de Castro, Rocio Loizaga; Secchi, Eduardo R.; Crespo, Enrique A.; Lailson-Brito, José; Azevedo, Alexandre F.; Lazoski, Cristiano; Solé-Cava, Antonio M.

    2015-01-01

    The taxonomy of common dolphins (Delphinus sp.) has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758). Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution. PMID:26559411

  10. Molecular and Morphological Differentiation of Common Dolphins (Delphinus sp. in the Southwestern Atlantic: Testing the Two Species Hypothesis in Sympatry.

    Directory of Open Access Journals (Sweden)

    Haydée A Cunha

    Full Text Available The taxonomy of common dolphins (Delphinus sp. has always been controversial, with over twenty described species since the original description of the type species of the genus (Delphinus delphis Linnaeus, 1758. Two species and four subspecies are currently accepted, but recent molecular data have challenged this view. In this study we investigated the molecular taxonomy of common dolphins through analyses of cytochrome b sequences of 297 individuals from most of their distribution. We included 37 novel sequences from the Southwestern Atlantic Ocean, a region where the short- and long-beaked morphotypes occur in sympatry, but which had not been well sampled before. Skulls of individuals from the Southwestern Atlantic were measured to test the validity of the rostral index as a diagnostic character and confirmed the presence of the two morphotypes in our genetic sample. Our genetic results show that all common dolphins in the Atlantic Ocean belong to a single species, Delphinus delphis. According to genetic data, the species Delphinus capensis is invalid. Long-beaked common dolphins from the Northeastern Pacific Ocean may constitute a different species. Our conclusions prompt the need for revision of currently accepted common dolphin species and subspecies and of Delphinus delphis distribution.

  11. Taxonomy, Physiology, and Natural Products of Actinobacteria.

    Science.gov (United States)

    Barka, Essaid Ait; Vatsa, Parul; Sanchez, Lisa; Gaveau-Vaillant, Nathalie; Jacquard, Cedric; Meier-Kolthoff, Jan P; Klenk, Hans-Peter; Clément, Christophe; Ouhdouch, Yder; van Wezel, Gilles P

    2016-03-01

    Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  12. Molecular Diagnostics

    OpenAIRE

    Choe, Hyonmin; Deirmengian, Carl A.; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.

    2015-01-01

    Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid...

  13. Scientific teaching: defining a taxonomy of observable practices.

    Science.gov (United States)

    Couch, Brian A; Brown, Tanya L; Schelpat, Tyler J; Graham, Mark J; Knight, Jennifer K

    2015-03-02

    Over the past several decades, numerous reports have been published advocating for changes to undergraduate science education. These national calls inspired the formation of the National Academies Summer Institutes on Undergraduate Education in Biology (SI), a group of regional workshops to help faculty members learn and implement interactive teaching methods. The SI curriculum promotes a pedagogical framework called Scientific Teaching (ST), which aims to bring the vitality of modern research into the classroom by engaging students in the scientific discovery process and using student data to inform the ongoing development of teaching methods. With the spread of ST, the need emerges to systematically define its components in order to establish a common description for education researchers and practitioners. We describe the development of a taxonomy detailing ST's core elements and provide data from classroom observations and faculty surveys in support of its applicability within undergraduate science courses. The final taxonomy consists of 15 pedagogical goals and 37 supporting practices, specifying observable behaviors, artifacts, and features associated with ST. This taxonomy will support future educational efforts by providing a framework for researchers studying the processes and outcomes of ST-based course transformations as well as a concise guide for faculty members developing classes. © 2015 B. A. Couch et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  14. Fast reactor knowledge preservation system: Taxonomy and basic requirements

    International Nuclear Information System (INIS)

    2008-01-01

    The IAEA has taken the initiative to coordinate efforts of Member States in the preservation of knowledge in the area of fast reactors. In the framework of this initiative, the IAEA intends to create an international database compiling information from different Member States on fast reactors through a web portal. Other activities related to this initiative are being designed to accumulate and exchange information on the fast reactor area, to facilitate access to this information by users in different countries and to assist Member States in preserving the experience gained in their countries. The purpose of this publication is to develop a taxonomy of the Fast Reactor Knowledge Preservation System (FRKPS) that will facilitate the preservation of the world's fast reactor knowledge base, to identify basic requirements of this taxonomy on the basis of the experience gained in the fast reactor area, as well as results of previous IAEA activities on fast reactor knowledge preservation. The need for such taxonomy arises from the fact that during the past 15 years there has been stagnation in the development of fast reactors in the industrialized countries that were involved, earlier, in intensive development of this area. All studies on fast reactors have been stopped in countries such as Germany, Italy, the United Kingdom and the United States of America and the only work being carried out is related to the decommissioning of fast reactors. Many specialists who were involved in the studies and development work in this area in these countries have already retired or are close to retirement. In countries such as France, Japan and the Russian Federation that are still actively pursuing the evolution of fast reactor technology, the situation is aggravated by the lack of young scientists and engineers moving into this branch of nuclear power

  15. Thermal and single frequency counter-current ultrasound pretreatments of sodium caseinate: enzymolysis kinetics and thermodynamics, amino acids composition, molecular weight distribution and antioxidant peptides.

    Science.gov (United States)

    Abdualrahman, Mohammed Adam Y; Ma, Haile; Zhou, Cunshan; Yagoub, Abu ElGasim A; Hu, Jiali; Yang, Xue

    2016-12-01

    Due to the disadvantages of traditional enzymolysis, pretreatments are crucial to enhance protein enzymolysis. Enzymolysis kinetics and thermodynamics, amino acids composition, molecular weight distribution, fluorescence spectroscopy and antioxidant activity of thermal (HT) and single frequency counter-current ultrasound (SCFU) pretreated sodium caseinate (NaCas) were studied. Enzymolysis of untreated NaCas (control) improved significantly (P < 0.05) by SFCU and followed by HT. Values of the Michaelis-Menten constant (K M ) of SFCU and HT were 0.0212 and 0.0250, respectively. HT and SFCU increased (P < 0.05) the reaction rate constant (k) by 38.64 and 90.91%, respectively at 298 K. k values decreased with increasing temperature. The initial activation energy (46.39 kJ mol -1 ) reduced (P < 0.05) by HT (39.66 kJ mol -1 ) and further by SFCU (33.42 kJ mol -1 ). SFCU-pretreated NaCas hydrolysates had the highest contents of hydrophobic, aromatic, positively and negatively charged amino acids. Medium-sized peptides (5000-1000 Da) are higher in SFCU (78.11%) than HT and the control. SFCU induced molecular unfolding of NaCas proteins. Accordingly, SFCU-pretreated NaCas hydrolysate exhibited the highest scavenging activity on DPPH and hydroxyl radicals, reducing power, and iron chelating ability. SFCU pretreatment would be a useful tool for production of bioactive peptides from NaCas hydrolysate. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  16. Penetration Testing Professional Ethics: a conceptual model and taxonomy

    Directory of Open Access Journals (Sweden)

    Justin Pierce

    2006-05-01

    Full Text Available In an environment where commercial software is continually patched to correct security flaws, penetration testing can provide organisations with a realistic assessment of their security posture. Penetration testing uses the same principles as criminal hackers to penetrate corporate networks and thereby verify the presence of software vulnerabilities. Network administrators can use the results of a penetration test to correct flaws and improve overall security. The use of hacking techniques, however, raises several ethical questions that centre on the integrity of the tester to maintain professional distance and uphold the profession. This paper discusses the ethics of penetration testing and presents our conceptual model and revised taxonomy.

  17. License - Taxonomy Icon | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Taxonomy Icon License License to Use This Database Last updated : 2013/3/21 You may use this database...the license terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attribut...ion 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: Taxon...ative Commons Attribution 2.1 Japan is found here . With regard to this database,

  18. A taxonomy for user-healthcare robot interaction.

    Science.gov (United States)

    Bzura, Conrad; Im, Hosung; Liu, Tammy; Malehorn, Kevin; Padir, Taskin; Tulu, Bengisu

    2012-01-01

    This paper evaluates existing taxonomies aimed at characterizing the interaction between robots and their users and modifies them for health care applications. The modifications are based on existing robot technologies and user acceptance of robotics. Characterization of the user, or in this case the patient, is a primary focus of the paper, as they present a unique new role as robot users. While therapeutic and monitoring-related applications for robots are still relatively uncommon, we believe they will begin to grow and thus it is important that the spurring relationship between robot and patient is well understood.

  19. Taxonomy and antifungal susceptibility of clinically important Rasamsonia species

    DEFF Research Database (Denmark)

    Houbraken, J.; Giraud, S.; Meijer, M.

    2013-01-01

    In recent years, Geosmithia argillacea has been increasingly reported in humans and animals and can be considered an emerging pathogen. The taxonomy of Geosmithia was recently studied, and Geosmithia argillacea and related species were transferred to the new genus Rasamsonia. The diversity among...... reported clinical isolates from animal or human patients. Susceptibility tests showed that the antifungal susceptibility profiles of the four members of the R. argillacea complex are similar, and caspofungin showed significant activity in vitro, followed by amphotericin B and posaconazole. Voriconazole...

  20. Taxonomy of interstate conflicts: is South America a peaceful region?

    Directory of Open Access Journals (Sweden)

    Tássio Franchi

    2017-08-01

    Full Text Available This article revisits theoretical efforts to classify interstate conflicts. It analyses South America and discuss the adequacy of influential interpretations about the intensity of interstate conflicts in the region as compared to global or other regions ones. The literature takes for granted that South America is a peaceful region. Such interpretation results from the indicators adopted. We argue that traditional indicators do not fully capture latent tensions and the actual level of conflicts in the region. The article suggests an alternative taxonomy that better fits the South America context and argues that a research agenda on the extent and nature of interstate conflics is needed.

  1. Unpacking the Revised Bloom's Taxonomy: Developing Case-Based Learning Activities

    Science.gov (United States)

    Nkhoma, Mathews Zanda; Lam, Tri Khai; Sriratanaviriyakul, Narumon; Richardson, Joan; Kam, Booi; Lau, Kwok Hung

    2017-01-01

    Purpose: The purpose of this paper is to propose the use of case studies in teaching an undergraduate course of Internet for Business in class, based on the revised Bloom's taxonomy. The study provides the empirical evidence about the effect of case-based teaching method integrated the revised Bloom's taxonomy on students' incremental learning,…

  2. Interpersonal lexicon : Structural evidence from two independently constructed verb-based taxonomies

    NARCIS (Netherlands)

    De Raad, B.

    1999-01-01

    In this study the structure of interpersonal behavior is investigated according to the principles of the so-called psycholexical approach. As bases for this study, we used the data from a taxonomy of interpersonal behavior verbs and a subset of data from a taxonomy of interpersonal tl-nir verbs. The

  3. A Taxonomy for In-depth Evaluation of Normalization for User Generated Content

    NARCIS (Netherlands)

    van der Goot, Rob; van Noord, Rik; van Noord, Gertjan

    2018-01-01

    In this work we present a taxonomy of error categories for lexical normalization, which is the task of translating user generated content to canonical language. We annotate a recent normalization dataset to test the practical use of the taxonomy and read a near-perfect agreement. This annotated

  4. A Taxonomy of Latent Structure Assumptions for Probability Matrix Decomposition Models.

    Science.gov (United States)

    Meulders, Michel; De Boeck, Paul; Van Mechelen, Iven

    2003-01-01

    Proposed a taxonomy of latent structure assumptions for probability matrix decomposition (PMD) that includes the original PMD model and a three-way extension of the multiple classification latent class model. Simulation study results show the usefulness of the taxonomy. (SLD)

  5. Developing a taxonomy of coordination behaviours in nuclear power plant control rooms during emergencies.

    Science.gov (United States)

    Wang, Dunxing; Gao, Qin; Li, Zhizhong; Song, Fei; Ma, Liang

    2017-12-01

    This study aims to develop a taxonomy of coordination behaviours during emergencies in nuclear power plants (NPPs). We summarised basic coordination behaviours from literature in aviation, health care and nuclear field and identified coordination behaviours specific to the nuclear domain by interviewing and surveying control crew operators. The established taxonomy includes 7 workflow stages and 24 basic coordination behaviours. To evaluate the reliability and feasibility of the taxonomy, we analysed 12 videos of operators' training sessions by coding coordination behaviours with the taxonomy and the inter-rater reliability was acceptable. Further analysis of the frequency, the duration and the direction of the coordination behaviours revealed four coordination problems. This taxonomy provides a foundation of systematic observation of coordination behaviours among NPP crews, advances researchers' understanding of the coordination mechanism during emergencies in NPPs and facilitate the possibility to deepen the understanding of the relationships between coordination behaviours and team performance. Practitioner Summary: A taxonomy of coordination behaviours during emergencies in nuclear power plants was developed. Reliability and feasibility of the taxonomy was verified through the analysis of 12 training sessions. The taxonomy can serve as an observation system for analysis of coordination behaviours and help to identify coordination problems of control crews.

  6. Taxonomy in biomedical resources of the Exclusive Economic Zone of India

    Digital Repository Service at National Institute of Oceanography (India)

    Parulekar, A.H.

    stream_size 9 stream_content_type text/plain stream_name Taxonomy_Environ_Biol_1990_49.pdf.txt stream_source_info Taxonomy_Environ_Biol_1990_49.pdf.txt Content-Encoding ISO-8859-1 Content-Type text/plain; charset=ISO-8859-1 ...

  7. Taxonomy for Education and Training in Clinical Neuropsychology: past, present, and future.

    Science.gov (United States)

    Sperling, Scott A; Cimino, Cynthia R; Stricker, Nikki H; Heffelfinger, Amy K; Gess, Jennifer L; Osborn, Katie E; Roper, Brad L

    2017-07-01

    Historically, the clinical neuropsychology training community has not clearly or consistently defined education or training opportunities. The lack of consistency has limited students' and trainees' ability to accurately assess and compare the intensity of neuropsychology-specific training provided by programs. To address these issues and produce greater 'truth in advertising' across programs, CNS, with SCN's Education Advisory Committee (EAC), ADECN, AITCN, and APPCN constructed a specialty-specific taxonomy, namely, the Taxonomy for Education and Training in Clinical Neuropsychology. The taxonomy provides consensus in the description of training offered by doctoral, internship, and postdoctoral programs, as well as at the post-licensure stage. Although the CNS approved the taxonomy in February 2015, many programs have not adopted its language. Increased awareness of the taxonomy and the reasons behind its development and structure, as well as its potential benefits, are warranted. In 2016, a working group of clinical neuropsychologists from the EAC and APPCN, all authors of this manuscript, was created and tasked with disseminating information about the taxonomy. Group members held regular conference calls, leading to the generation of this manuscript. This manuscript is the primary byproduct of the working group. Its purpose is to (1) outline the history behind the development of the taxonomy, (2) detail its structure and utility, (3) address the expected impact of its adoption, and (4) call for its adoption across training programs. This manuscript outlines the development and structure of the clinical neuropsychology taxonomy and addresses the need for its adoption across training programs.

  8. A Faceted Taxonomy for Rating Student Bibliographies in an Online Information Literacy Game

    Science.gov (United States)

    Leeder, Chris; Markey, Karen; Yakel, Elizabeth

    2012-01-01

    This study measured the quality of student bibliographies through creation of a faceted taxonomy flexible and fine-grained enough to encompass the variety of online sources cited by today's students. The taxonomy was developed via interviews with faculty, iterative refinement of categories and scoring, and testing on example student…

  9. A Preliminary Bloom's Taxonomy Assessment of End-of-Chapter Problems in Business School Textbooks

    Science.gov (United States)

    Marshall, Jennings B.; Carson, Charles M.

    2008-01-01

    This article examines textbook problems used in a sampling of some of the most common core courses found in schools of business to ascertain what level of learning, as defined by Bloom's Taxonomy, is required to provide a correct answer. A set of working definitions based on Bloom's Taxonomy (Bloom & Krathwohl, 1956) was developed for the six…

  10. Climbing Bloom's Taxonomy Pyramid: Lessons from a Graduate Histology Course

    Science.gov (United States)

    Zaidi, Nikki B.; Hwang, Charles; Scott, Sara; Stallard, Stefanie; Purkiss, Joel; Hortsch, Michael

    2017-01-01

    Bloom's taxonomy was adopted to create a subject-specific scoring tool for histology multiple-choice questions (MCQs). This Bloom's Taxonomy Histology Tool (BTHT) was used to analyze teacher- and student-generated quiz and examination questions from a graduate level histology course. Multiple-choice questions using histological images were…

  11. Biome specificity of distinct genetic lineages within the four-striped mouse Rhabdomys pumilio (Rodentia: Muridae) from southern Africa with implications for taxonomy.

    Science.gov (United States)

    du Toit, Nina; van Vuuren, Bettine Jansen; Matthee, Sonja; Matthee, Conrad A

    2012-10-01

    Within southern Africa, a link between past climatic changes and faunal diversification has been hypothesized for a diversity of taxa. To test the hypothesis that evolutionary divergences may be correlated to vegetation changes (induced by changes in climate), we selected the widely distributed four-striped mouse, Rhabdomys, as a model. Two species are currently recognized, the mesic-adapted R. dilectus and arid-adapted R. pumilio. However, the morphology-based taxonomy and the distribution boundaries of previously described subspecies remain poorly defined. The current study, which spans seven biomes, focuses on the spatial genetic structure of the arid-adapted R. pumilio (521 specimens from 31 localities), but also includes limited sampling of the mesic-adapted R. dilectus (33 specimens from 10 localities) to act as a reference for interspecific variation within the genus. The mitochondrial COI gene and four nuclear introns (Eef1a1, MGF, SPTBN1, Bfib7) were used for the construction of gene trees. Mitochondrial DNA analyses indicate that Rhabdomys consists of four reciprocally monophyletic, geographically structured clades, with three distinct lineages present within the arid-adapted R. pumilio. These monophyletic lineages differ by at least 7.9% (±0.3) and these results are partly confirmed by a multilocus network of the combined nuclear intron dataset. Ecological niche modeling in MaxEnt supports a strong correlation between regional biomes and the distribution of distinct evolutionary lineages of Rhabdomys. A Bayesian relaxed molecular clock suggests that the geographic clades diverged between 3.09 and 4.30Ma, supporting the hypothesis that the radiation within the genus coincides with paleoclimatic changes (and the establishment of the biomes) characterizing the Miocene-Pliocene boundary. Marked genetic divergence at the mitochondrial DNA level, coupled with strong nuclear and mtDNA signals of non-monophyly of R. pumilio, support the notion that a taxonomic

  12. Towards a taxonomy of common factors in psychotherapy-results of an expert survey.

    Science.gov (United States)

    Tschacher, Wolfgang; Junghan, Ulrich Martin; Pfammatter, Mario

    2014-01-01

    How change comes about is hotly debated in psychotherapy research. One camp considers 'non-specific' or 'common factors', shared by different therapy approaches, as essential, whereas researchers of the other camp consider specific techniques as the essential ingredients of change. This controversy, however, suffers from unclear terminology and logical inconsistencies. The Taxonomy Project therefore aims at contributing to the definition and conceptualization of common factors of psychotherapy by analyzing their differential associations to standard techniques. A review identified 22 common factors discussed in psychotherapy research literature. We conducted a survey, in which 68 psychotherapy experts assessed how common factors are implemented by specific techniques. Using hierarchical linear models, we predicted each common factor by techniques and by experts' age, gender and allegiance to a therapy orientation. Common factors differed largely in their relevance for technique implementation. Patient engagement, Affective experiencing and Therapeutic alliance were judged most relevant. Common factors also differed with respect to how well they could be explained by the set of techniques. We present detailed profiles of all common factors by the (positively or negatively) associated techniques. There were indications of a biased taxonomy not covering the embodiment of psychotherapy (expressed by body-centred techniques such as progressive muscle relaxation, biofeedback training and hypnosis). Likewise, common factors did not adequately represent effective psychodynamic and systemic techniques. This taxonomic endeavour is a step towards a clarification of important core constructs of psychotherapy. This article relates standard techniques of psychotherapy (well known to practising therapists) to the change factors/change mechanisms discussed in psychotherapy theory. It gives a short review of the current debate on the mechanisms by which psychotherapy works. We

  13. The ACTTION-APS-AAPM Pain Taxonomy (AAAPT) Multidimensional Approach to Classifying Acute Pain Conditions

    DEFF Research Database (Denmark)

    Kent, Michael L; Tighe, Patrick J; Belfer, Inna

    2017-01-01

    the Analgesic, Anesthetic, and Addiction Clinical Trial Translations, Innovations, Opportunities, and Networks (ACTTION), American Pain Society (APS), and American Academy of Pain Medicine (AAPM). METHODS: As a complement to a taxonomy recently developed for chronic pain, the ACTTION public-private partnership...... with the US Food and Drug Administration, the APS, and the AAPM convened a consensus meeting of experts to develop an acute pain taxonomy using prevailing evidence. Key issues pertaining to the distinct nature of acute pain are presented followed by the agreed-upon taxonomy. The ACTTION-APS-AAPM Acute Pain...... Taxonomy will include the following dimensions: 1) core criteria, 2) common features, 3) modulating factors, 4) impact/functional consequences, and 5) putative pathophysiologic pain mechanisms. Future efforts will consist of working groups utilizing this taxonomy to develop diagnostic criteria...

  14. Adaptability in the workplace: development of a taxonomy of adaptive performance.

    Science.gov (United States)

    Pulakos, E D; Arad, S; Donovan, M A; Plamondon, K E

    2000-08-01

    The purpose of this research was to develop a taxonomy of adaptive job performance and examine the implications of this taxonomy for understanding, predicting, and training adaptive behavior in work settings. Two studies were conducted to address this issue. In Study 1, over 1,000 critical incidents from 21 different jobs were content analyzed to identify an 8-dimension taxonomy of adaptive performance. Study 2 reports the development and administration of an instrument, the Job Adaptability Inventory, that was used to empirically examine the proposed taxonomy in 24 different jobs. Exploratory factor analyses using data from 1,619 respondents supported the proposed 8-dimension taxonomy from Study 1. Subsequent confirmatory factor analyses on the remainder of the sample (n = 1,715) indicated a good fit for the 8-factor model. Results and implications are discussed.

  15. Toward A Unifying Taxonomy and Definition for Meditation

    Directory of Open Access Journals (Sweden)

    Jonathan David Nash

    2013-11-01

    Full Text Available One of the well-documented concerns confronting scholarly discourse about meditation is the plethora of semantic constructs and the lack of a unified definition and taxonomy. In recent years there have been several notable attempts to formulate new lexicons in order to define and categorize meditation methods. While these constructs have been useful and have encountered varying degrees of acceptance, they have also been subject to misinterpretation and debate, leaving the field devoid of a consensual paradigm. This paper attempts to influence this ongoing discussion by proposing two new models which hold the potential for enhanced scientific reliability and acceptance. Regarding the quest for a universally acceptable taxonomy, we suggest a paradigm shift away from the fabrication of categories based exclusively on first-person perspectives. As an alternative, we propose a new taxonomic system based on a third-person paradigm borrowed, in part, from the psychological and cognitive sciences. With regard to the elusive definitional problem, we propose a model of meditation as a dynamic process composed of several related but distinct stages. The overall goal is to provide researchers with a reliable nomenclature with which to categorize and classify diverse meditation methods, and a conceptual framework which can provide direction for their research and a theoretical basis for their findings.

  16. Threat and error management for anesthesiologists: a predictive risk taxonomy

    Science.gov (United States)

    Ruskin, Keith J.; Stiegler, Marjorie P.; Park, Kellie; Guffey, Patrick; Kurup, Viji; Chidester, Thomas

    2015-01-01

    Purpose of review Patient care in the operating room is a dynamic interaction that requires cooperation among team members and reliance upon sophisticated technology. Most human factors research in medicine has been focused on analyzing errors and implementing system-wide changes to prevent them from recurring. We describe a set of techniques that has been used successfully by the aviation industry to analyze errors and adverse events and explain how these techniques can be applied to patient care. Recent findings Threat and error management (TEM) describes adverse events in terms of risks or challenges that are present in an operational environment (threats) and the actions of specific personnel that potentiate or exacerbate those threats (errors). TEM is a technique widely used in aviation, and can be adapted for the use in a medical setting to predict high-risk situations and prevent errors in the perioperative period. A threat taxonomy is a novel way of classifying and predicting the hazards that can occur in the operating room. TEM can be used to identify error-producing situations, analyze adverse events, and design training scenarios. Summary TEM offers a multifaceted strategy for identifying hazards, reducing errors, and training physicians. A threat taxonomy may improve analysis of critical events with subsequent development of specific interventions, and may also serve as a framework for training programs in risk mitigation. PMID:24113268

  17. SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

    Science.gov (United States)

    Velankar, Sameer; Dana, José M.; Jacobsen, Julius; van Ginkel, Glen; Gane, Paul J.; Luo, Jie; Oldfield, Thomas J.; O’Donovan, Claire; Martin, Maria-Jesus; Kleywegt, Gerard J.

    2013-01-01

    The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information. PMID:23203869

  18. Taxonomy of Rhagoletis population associated with wild plums in Chile

    International Nuclear Information System (INIS)

    Frias, Daniel; Alvina, Andres

    2000-01-01

    In South America, there are about fifteen Rhagoletis species that live in association with wild and cultivated Solanaceae host plants (Foote 1981, Frias 1992). The principal information on taxonomy for these species is the morphology of adults. Thus, in the genus Rhagoletis, in general, there is little information about immature stages especially on first and second larva instars (Steck et al. 1990, Carrol and Wharton 1989, Steck and Wharton 1988, Persson 1963, White and Elson-Harris 1992, Hernandez-Ortiz 1992, 1993, Frias et al. 1993). Presently, in Chile, there are 4 species associated with Solanaceae host plants. R. tomatis Foote and R. nova (Schiner) are associated with cultivated Solanaceae Lycopersicum esculentum Miller or cultivated tomatoes and Solanum muricatum Aiton or sweet cucumber respectively. R. conversa Bethes has two Solanum host plants, S. nigrum L. and S. tomatillo (Remy) Phil. F. (Frias et al. 1984). The host for R. penela Foote is unknown. Moreover, in the last few years, a population on wild plums of the Myrobalan variety (Rosaceae) was detected (Gonzalez 1989). At present, there is no information about the origin and taxonomy of this population. In this work, we have studied the morphology of eggs, three instar larvae, pupae and adults of this population associated with wild plums as well as aspects of its geographical distribution in Chile

  19. Toward a unifying taxonomy and definition for meditation

    Science.gov (United States)

    Nash, Jonathan D.; Newberg, Andrew

    2013-01-01

    One of the well-documented concerns confronting scholarly discourse about meditation is the plethora of semantic constructs and the lack of a unified definition and taxonomy. In recent years there have been several notable attempts to formulate new lexicons in order to define and categorize meditation methods. While these constructs have been useful and have encountered varying degrees of acceptance, they have also been subject to misinterpretation and debate, leaving the field devoid of a consensual paradigm. This paper attempts to influence this ongoing discussion by proposing two new models which hold the potential for enhanced scientific reliability and acceptance. Regarding the quest for a universally acceptable taxonomy, we suggest a paradigm shift away from the norm of fabricatIng new terminology from a first-person perspective. As an alternative, we propose a new taxonomic system based on the historically well-established and commonly accepted third-person paradigm of Affect and Cognition, borrowed, in part, from the psychological and cognitive sciences. With regard to the elusive definitional problem, we propose a model of meditation which clearly distinguishes “method” from “state” and is conceptualized as a dynamic process which is inclusive of six related but distinct stages. The overall goal is to provide researchers with a reliable nomenclature with which to categorize and classify diverse meditation methods, and a conceptual framework which can provide direction for their research and a theoretical basis for their findings. PMID:24312060

  20. A taxonomy of accountable care organizations for policy and practice.

    Science.gov (United States)

    Shortell, Stephen M; Wu, Frances M; Lewis, Valerie A; Colla, Carrie H; Fisher, Elliott S

    2014-12-01

    To develop an exploratory taxonomy of Accountable Care Organizations (ACOs) to describe and understand early ACO development and to provide a basis for technical assistance and future evaluation of performance. Data from the National Survey of Accountable Care Organizations, fielded between October 2012 and May 2013, of 173 Medicare, Medicaid, and commercial payer ACOs. Drawing on resource dependence and institutional theory, we develop measures of eight attributes of ACOs such as size, scope of services offered, and the use of performance accountability mechanisms. Data are analyzed using a two-step cluster analysis approach that accounts for both continuous and categorical data. We identified a reliable and internally valid three-cluster solution: larger, integrated systems that offer a broad scope of services and frequently include one or more postacute facilities; smaller, physician-led practices, centered in primary care, and that possess a relatively high degree of physician performance management; and moderately sized, joint hospital-physician and coalition-led groups that offer a moderately broad scope of services with some involvement of postacute facilities. ACOs can be characterized into three distinct clusters. The taxonomy provides a framework for assessing performance, for targeting technical assistance, and for diagnosing potential antitrust violations. © Health Research and Educational Trust.

  1. A taxonomy for disease management: a scientific statement from the American Heart Association Disease Management Taxonomy Writing Group.

    Science.gov (United States)

    Krumholz, Harlan M; Currie, Peter M; Riegel, Barbara; Phillips, Christopher O; Peterson, Eric D; Smith, Renee; Yancy, Clyde W; Faxon, David P

    2006-09-26

    Disease management has shown great promise as a means of reorganizing chronic care and optimizing patient outcomes. Nevertheless, disease management programs are widely heterogeneous and lack a shared definition of disease management, which limits our ability to compare and evaluate different programs. To address this problem, the American Heart Association's Disease Management Taxonomy Writing Group developed a system of classification that can be used both to categorize and compare disease management programs and to inform efforts to identify specific factors associated with effectiveness. The AHA Writing Group began with a conceptual model of disease management and its components and subsequently validated this model over a wide range of disease management programs. A systematic MEDLINE search was performed on the terms heart failure, diabetes, and depression, together with disease management, case management, and care management. The search encompassed articles published in English between 1987 and 2005. We then selected studies that incorporated (1) interventions designed to improve outcomes and/or reduce medical resource utilization in patients with heart failure, diabetes, or depression and (2) clearly defined protocols with at least 2 prespecified components traditionally associated with disease management. We analyzed the study protocols and used qualitative research methods to develop a disease management taxonomy with our conceptual model as the organizing framework. The final taxonomy includes the following 8 domains: (1) Patient population is characterized by risk status, demographic profile, and level of comorbidity. (2) Intervention recipient describes the primary targets of disease management intervention and includes patients and caregivers, physicians and allied healthcare providers, and healthcare delivery systems. (3) Intervention content delineates individual components, such as patient education, medication management, peer support, or some

  2. A taxonomy and discussion of software attack technologies

    Science.gov (United States)

    Banks, Sheila B.; Stytz, Martin R.

    2005-03-01

    Software is a complex thing. It is not an engineering artifact that springs forth from a design by simply following software coding rules; creativity and the human element are at the heart of the process. Software development is part science, part art, and part craft. Design, architecture, and coding are equally important activities and in each of these activities, errors may be introduced that lead to security vulnerabilities. Therefore, inevitably, errors enter into the code. Some of these errors are discovered during testing; however, some are not. The best way to find security errors, whether they are introduced as part of the architecture development effort or coding effort, is to automate the security testing process to the maximum extent possible and add this class of tools to the tools available, which aids in the compilation process, testing, test analysis, and software distribution. Recent technological advances, improvements in computer-generated forces (CGFs), and results in research in information assurance and software protection indicate that we can build a semi-intelligent software security testing tool. However, before we can undertake the security testing automation effort, we must understand the scope of the required testing, the security failures that need to be uncovered during testing, and the characteristics of the failures. Therefore, we undertook the research reported in the paper, which is the development of a taxonomy and a discussion of software attacks generated from the point of view of the security tester with the goal of using the taxonomy to guide the development of the knowledge base for the automated security testing tool. The representation for attacks and threat cases yielded by this research captures the strategies, tactics, and other considerations that come into play during the planning and execution of attacks upon application software. The paper is organized as follows. Section one contains an introduction to our research

  3. Integrative taxonomy for continental-scale terrestrial insect observations.

    Directory of Open Access Journals (Sweden)

    Cara M Gibson

    Full Text Available Although 21(st century ecology uses unprecedented technology at the largest spatio-temporal scales in history, the data remain reliant on sound taxonomic practices that derive from 18(th century science. The importance of accurate species identifications has been assessed repeatedly and in instances where inappropriate assignments have been made there have been costly consequences. The National Ecological Observatory Network (NEON will use a standardized system based upon an integrative taxonomic foundation to conduct observations of the focal terrestrial insect taxa, ground beetles and mosquitoes, at the continental scale for a 30 year monitoring program. The use of molecular data for continental-scale, multi-decadal research conducted by a geographically widely distributed set of researchers has not been evaluated until this point. The current paper addresses the development of a reference library for verifying species identifications at NEON and the key ways in which this resource will enhance a variety of user communities.

  4. Integrative Taxonomy for Continental-Scale Terrestrial Insect Observations

    Science.gov (United States)

    Gibson, Cara M.; Kao, Rebecca H.; Blevins, Kali K.; Travers, Patrick D.

    2012-01-01

    Although 21st century ecology uses unprecedented technology at the largest spatio-temporal scales in history, the data remain reliant on sound taxonomic practices that derive from 18th century science. The importance of accurate species identifications has been assessed repeatedly and in instances where inappropriate assignments have been made there have been costly consequences. The National Ecological Observatory Network (NEON) will use a standardized system based upon an integrative taxonomic foundation to conduct observations of the focal terrestrial insect taxa, ground beetles and mosquitoes, at the continental scale for a 30 year monitoring program. The use of molecular data for continental-scale, multi-decadal research conducted by a geographically widely distributed set of researchers has not been evaluated until this point. The current paper addresses the development of a reference library for verifying species identifications at NEON and the key ways in which this resource will enhance a variety of user communities. PMID:22666362

  5. Integrative taxonomy of the genus Onchidium Buchannan, 1800 (Mollusca, Gastropoda, Pulmonata, Onchidiidae

    Directory of Open Access Journals (Sweden)

    Benoît Dayrat

    2016-11-01

    Full Text Available In an effort to clarify the species diversity of onchidiid slugs, the taxonomy of the genus Onchidium Buchannan, 1800 is revised using an integrative approach. New, fresh specimens were collected in a large number of places, including type localities. The genus Onchidium is redefined here as a clade including only three species which are strongly supported by both morphological and molecular data. All three species were already named: the type species O. typhae Buchannan, 1800, O. stuxbergi (Westerlund, 1883, and O. reevesii (J.E. Gray, 1850. With the exception of a re-description of O. typhae published in 1869, all three species are re-described here for the first time. First-hand observations on the color variation of live animals in their natural habitat are provided. The anatomy of each species is described. Important nomenclatural issues are addressed. In particular, Labella Starobogatov, 1976 is regarded as a junior synonym of Onchidium and Labella ajuthiae (Labbé, 1935 and O. nigrum (Plate, 1893 are regarded as junior synonyms of O. stuxbergi. The nomenclatural status of several other species names is discussed as well. Many new records are provided across South-East Asia and precise ranges of geographic distributions are provided for the genus Onchidium and its three species. Distinctive features that help distinguish the genus Onchidium from other onchidiids are provided, as well as an identification key for the three species.

  6. Diversity and taxonomy of endophytic xylariaceous fungi from medicinal plants of Dendrobium (Orchidaceae).

    Science.gov (United States)

    Chen, Juan; Zhang, Li-Chun; Xing, Yong-Mei; Wang, Yun-Qiang; Xing, Xiao-Ke; Zhang, Da-Wei; Liang, Han-Qiao; Guo, Shun-Xing

    2013-01-01

    Dendrobium spp. are traditional Chinese medicinal plants, and the main effective ingredients (polysaccharides and alkaloids) have pharmacologic effects on gastritis infection, cancer, and anti-aging. Previously, we confirmed endophytic xylariaceous fungi as the dominant fungi in several Dendrobium species of tropical regions from China. In the present study, the diversity, taxonomy, and distribution of culturable endophytic xylariaceous fungi associated with seven medicinal species of Dendrobium (Orchidaceae) were investigated. Among the 961 endophytes newly isolated, 217 xylariaceous fungi (morphotaxa) were identified using morphological and molecular methods. The phylogenetic tree constructed using nuclear ribosomal internal transcribed spacer (ITS), large subunit of ribosomal DNA (LSU), and beta-tubulin sequences divided these anamorphic xylariaceous isolates into at least 18 operational taxonomic units (OTUs). The diversity of the endophytic xylariaceous fungi in these seven Dendrobium species was estimated using Shannon and evenness indices, with the results indicating that the dominant Xylariaceae taxa in each Dendrobium species were greatly different, though common xylariaceous fungi were found in several Dendrobium species. These findings implied that different host plants in the same habitats exhibit a preference and selectivity for their fungal partners. Using culture-dependent approaches, these xylariaceous isolates may be important sources for the future screening of new natural products and drug discovery.

  7. A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies.

    Science.gov (United States)

    Ramos, Vitor; Morais, João; Vasconcelos, Vitor M

    2017-04-25

    The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.

  8. The status of taxonomy and venom in sea snakes

    DEFF Research Database (Denmark)

    Redsted Rasmussen, Arne; Sanders, Kate L.

    2017-01-01

    The status of taxonomy and venom in sea snakesArne R Rasmussen1, Kate L Sanders21 The Royal Danish Academy of Fine Arts, School of Architecture, Design & Conservation, Copenhagen, Denmark2 School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5000, AustraliaSea...... snakes form two aquatic groups of snakes with a flat vertically paddle-form tail (sea kraits and viviparous sea snakes). Sea snakes belong to the same family Elapidae, which also includes the terrestrial mambas, cobra, kraits, taipan and brown snake. All elapids are characterized by the anterior position...... of the poison-fangs on the maxillary bone (proteroglyphous). Globally there are some 70 species of sea snake found in the tropical and subtropical waters of the Indian Ocean and the Pacific Ocean. Most species are found in the Indo-Malayan Archipelago, the China Sea, Indonesia, and the Australian region...

  9. The status of taxonomy and venom in sea snakes

    DEFF Research Database (Denmark)

    Redsted Rasmussen, Arne; Sanders, Kate L.

    2017-01-01

    The status of taxonomy and venom in sea snakesArne R Rasmussen1, Kate L Sanders21 The Royal Danish Academy of Fine Arts, School of Architecture, Design & Conservation, Copenhagen, Denmark2 School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5000, Australia......, the Aipysurus group was separated from the other viviparous sea snakes at around 5.8 million years before present and in the Hydrophis lineage the Hydrophis group was separated from the three semi-marine lineages at around 4.4 million years before present. The venoms of sea snakes are rather simple, typically...... containing a-neurotoxins and phospholipases A2 (PLA2s), and in terms of lethality are known to be more potent than the venoms from terrestrial snakes....

  10. Smart farming technologies - description, taxonomy and economic impact

    DEFF Research Database (Denmark)

    Balafoutis, Athanasios T.; Beck, Bert; Tsiropoulos, Zisis

    2017-01-01

    Precision Agriculture is a cyclic optimization process where data have to be collected from the field, analysed and evaluated and finally used for decision making for site-specific management of the field. Smart farming technologies (SFT ) cover all these aspects of precision agriculture and can...... comprise the delineation of management zones, decision support systems and farm management information system s. Finally, precision application technologies embrace variable-rate application technologies, precision irrigation and weeding and machine guidance. In this chapter, the reader can find...... a technical description of the technologies included in each category accompanied by a taxonomy of all SFT in terms of farming system type, cropping system, availability, level of investment and farmers’ motives to adopt them. Finally, the economic impact that each SFT has compared to conventional...

  11. A Taxonomy for Differentiating Entrepreneurship Education Across Disciplines

    DEFF Research Database (Denmark)

    Warhuus, Jan P.; Blenker, Per

    of courses and curricula. At the core of this framework is a taxonomy for discipline-specific entrepreneurship education content and learning goals—different educations have varying inherent strengths and weakness vis-à-vis entrepreneurship, and thus have different pathways and barriers to develop......Entrepreneurship education (E-Ed) is maturing—from debate about whether or not it can be done, to how it should be done (Katz, 2003; Kuratko, 2005); from business schools teaching start-ups through a business plan format, toward converging upon a broader attitudechanging framework (Mwasalwiba, 2010......, and the need for a tailored, discipline-specific approach to E-Ed is becoming rapidly apparent. As a first step toward differentiating E-Ed across disciplines, we propose the establishment of an E-Ed framework that can guide and align stakeholders, program designers, and educators in the construction...

  12. Molecular and phenotypic characterization of anamorphic fungi

    OpenAIRE

    Madrid Lorca, Hugo

    2011-01-01

    Anamorphic fungi (those reproducing asexually) are a big part of kingdom Fungi. Most of them occur as saprobes in nature, but numerous species are pathogenic to plants and animals including man. With the aim of contributing to the knowledge of the diversity and distribution of anamorphic fungi, we performed a phenotypic and molecular characterization of environmental and clinical isolates of these fungi. Based on a polyphasic taxonomy approach which included morphology, physiology and DNA seq...

  13. Revisiting the genus Photobacterium: taxonomy, ecology and pathogenesis.

    Science.gov (United States)

    Labella, Alejandro M; Arahal, David R; Castro, Dolores; Lemos, Manuel L; Borrego, Juan J

    2017-03-01

    The genus Photobacterium, one of the eight genera included in the family Vibrionaceae, contains 27 species with valid names and it has received attention because of the bioluminescence and pathogenesis mechanisms that some of its species exhibit. However, the taxonomy and phylogeny of this genus are not completely elucidated; for example, P. logei and P. fischeri are now considered members of the genus Aliivibrio, and previously were included in the genus Vibrio. In addition, P. damselae subsp. piscicida was formed as a new combination for former Vibrio damsela and Pasteurella piscicida. Moreover, P. damselae subsp. damselae is an earlier heterotypic synonym of P. histaminum. To avoid these incovenences draft and complete genomic sequences of members of Photobacterium are increasingly becoming available and their use is now routine for many research laboratories to address diverse goals: species delineation with overall genomic indexes, phylogenetic analyses, comparative genomics, and phenotypic inference. The habitats and isolation source of the Photobacterium species include seawater, sea sediments, saline lake waters, and a variety of marine organisms with which the photobacteria establish different relationships, from symbiosis to pathogenic interactions. Several species of this genus contain bioluminescent strains in symbiosis with marine fish and cephalopods; in addition, other species enhance its growth at pressures above 1 atmosphere, by means of several high-pressure adaptation mechanisms and for this, they may be considered as piezophilic (former barophilic) bacteria. Until now, only P. jeanii, P. rosenbergii, P. sanctipauli, and the two subspecies of P. damselae have been reported as responsible agents of several pathologies on animal hosts, such as corals, sponges, fish and homeothermic animals. In this review we have revised and updated the taxonomy, ecology and pathogenicity of several members of this genus. [Int Microbiol 20(1): 1-10 (2017

  14. Physiology and taxonomy of lactobacilli surviving radurization of meat

    International Nuclear Information System (INIS)

    Hastings, J.W.

    1986-02-01

    The aim of this study was to isolate radiation-resistant lacto-bacilli from radurized (5 kGy) vacuum-packaged meat and subject them to biochemical, metabolic and physiological testing in order to gain a clearer understanding of the taxonomy of this group as well as determine characteristics which may be of technological significance. All 113 of the lactobacilli isolated were homofermentative, aciduric and were allocated to the sub-genus Streptobacterium. Numerical taxonomy by unweighted pair-group average linkage analysis revealed the existence of 5 clusters of the isolates. The same 113 isolates were classified using a purely classical taxonomic approach where the isolates were divided into 4 groups according to species designation. The basis upon which they were identified as a particular species was mainly their carbohydrate fermentation pattern. Several of the 113 isolates were selected for tests to determine characteristics of technological importance. All L.sake isolates exhibited the phenomenon of being more resistant to irradiation in the logarithmic phase than in the stationary phase of their growth cycle. This phenomenon was not characteristic of all the bacteria and was not always related to high radiation-resistance. Four L. sake isolates and three authentic strains were subjected to radiation-sensitivity testing in a natural food system where the bacteria were irradiated in minced meat packaged under four different conditions. The organisms exhibited the highest death rates under CO 2 packaging but resistance seemed to increase under N 2 -packaging. The radiation-resistance of the isolates was greater than that of the reference strains and all strains were approximately twice as resistant in the meat microenvironment than in a synthetic medium

  15. Application of the ultrametric distance to portfolio taxonomy. Critical approach and comparison with other methods

    Science.gov (United States)

    Skórnik-Pokarowska, Urszula; Orłowski, Arkadiusz

    2004-12-01

    We calculate the ultrametric distance between the pairs of stocks that belong to the same portfolio. The ultrametric distance allows us to distinguish groups of shares that are related. In this way, we can construct a portfolio taxonomy that can be used for constructing an efficient portfolio. We also construct a portfolio taxonomy based not only on stock prices but also on economic indices such as liquidity ratio, debt ratio and sales profitability ratio. We show that a good investment strategy can be obtained by applying to the portfolio chosen by the taxonomy method the so-called Constant Rebalanced Portfolio.

  16. The Effects of Bloom’s Revised Taxonomy on Measurement and Evaluation in Education

    Directory of Open Access Journals (Sweden)

    İrfan Yurdabakan

    2012-12-01

    Full Text Available The aim of this study is to discuss the revision of the original version of Bloom’s taxonomy of educational objectives under the leadership of Krathwohl and Anderson and its reflections on testing and assessment in education. Fort his purpose, international database was scanned to analyze the publications on “Bloom’s revised taxonomy and relationships between the revised taxonomy and testing and assessment”. The reasons for revision, the results that emerged following the revision and the reflections of those results on measurement and evaluation in education are described within the scope of those publications obtained

  17. The New Cannabis Policy Taxonomy on APIS: Making Sense of the Cannabis Policy Universe.

    Science.gov (United States)

    Klitzner, Michael D; Thomas, Sue; Schuler, Jonathan; Hilton, Michael; Mosher, James

    2017-06-01

    The National Institute on Alcohol Abuse and Alcoholism's Alcohol Policy Information System (APIS) is, for the first time, adding legal data pertaining to recreational cannabis use to its current offerings on alcohol policy. Now that Colorado, Washington, Oregon, Alaska, and the District of Columbia have legalized aspects of recreational cannabis, and more states are considering it, there is an urgency to provide high-quality, multi-dimensional legal data to the public health community. This article introduces the Cannabis Policy Taxonomy recently posted on APIS, and explores its theoretical and empirical contributions to the substance abuse literature and its potential for use in policy research. We also present results of interviews with public health experts in alcohol and cannabis policy, which sought to determine the most important variables to address in the initial release of cannabis policy data. From this process, we found that pricing controls emerged as the variable singled out by the largest number of experts. This analysis points to a host of vital policies that are of increasing importance to public health policy scholars and their current and future research.

  18. Toward genetics-based virus taxonomy: comparative analysis of a genetics-based classification and the taxonomy of picornaviruses.

    Science.gov (United States)

    Lauber, Chris; Gorbalenya, Alexander E

    2012-04-01

    Virus taxonomy has received little attention from the research community despite its broad relevance. In an accompanying paper (C. Lauber and A. E. Gorbalenya, J. Virol. 86:3890-3904, 2012), we have introduced a quantitative approach to hierarchically classify viruses of a family using pairwise evolutionary distances (PEDs) as a measure of genetic divergence. When applied to the six most conserved proteins of the Picornaviridae, it clustered 1,234 genome sequences in groups at three hierarchical levels (to which we refer as the "GENETIC classification"). In this study, we compare the GENETIC classification with the expert-based picornavirus taxonomy and outline differences in the underlying frameworks regarding the relation of virus groups and genetic diversity that represent, respectively, the structure and content of a classification. To facilitate the analysis, we introduce two novel diagrams. The first connects the genetic diversity of taxa to both the PED distribution and the phylogeny of picornaviruses. The second depicts a classification and the accommodated genetic diversity in a standardized manner. Generally, we found striking agreement between the two classifications on species and genus taxa. A few disagreements concern the species Human rhinovirus A and Human rhinovirus C and the genus Aphthovirus, which were split in the GENETIC classification. Furthermore, we propose a new supergenus level and universal, level-specific PED thresholds, not reached yet by many taxa. Since the species threshold is approached mostly by taxa with large sampling sizes and those infecting multiple hosts, it may represent an upper limit on divergence, beyond which homologous recombination in the six most conserved genes between two picornaviruses might not give viable progeny.

  19. New distribution records for four mammal species, with notes on their taxonomy and ecology

    Directory of Open Access Journals (Sweden)

    G.N. Bronner

    1990-09-01

    Full Text Available New distribution records for four small mammal species (Georychus capensis, Galerella pulverulenta, Rhinolophus swinnyi and Amblysomus julianae are presented, along with relevant notes on the taxonomy, karyology and ecology of these species.

  20. An Evidence-based Forensic Taxonomy of Windows Phone Dating Apps.

    Science.gov (United States)

    Cahyani, Niken Dwi Wahyu; Choo, Kim-Kwang Raymond; Ab Rahman, Nurul Hidayah; Ashman, Helen

    2018-05-21

    Advances in technologies including development of smartphone features have contributed to the growth of mobile applications, including dating apps. However, online dating services can be misused. To support law enforcement investigations, a forensic taxonomy that provides a systematic classification of forensic artifacts from Windows Phone 8 (WP8) dating apps is presented in this study. The taxonomy has three categories, namely: Apps Categories, Artifacts Categories, and Data Partition Categories. This taxonomy is built based on the findings from a case study of 28 mobile dating apps, using mobile forensic tools. The dating app taxonomy can be used to inform future studies of dating and related apps, such as those from Android and iOS platforms. © 2018 American Academy of Forensic Sciences.