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Sample records for taxonomic analysis establishes

  1. Polyphasic taxonomic analysis establishes Mycobacterium indicus pranii as a distinct species.

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    Vikram Saini

    necessitated further analysis of MIP with more sensitive and segregating parameters to ascertain its precise taxonomic position as a new species. The analysis of MIP and its comparison with other mycobacterial reference strains based on cellular and biochemical features, growth characteristics and chemotaxonomic studies like FAME profiling confirmed that MIP is uniquely endowed with diverse metabolic attributes that effectively distinguishes it from all the closely related mycobacteria including M. intracellulare and M. chimaera. CONCLUSION: The results presented in this study coupled with the non-pathogenic nature and different biochemical and immunomodulatory properties of MIP affirm it as a distinct species belonging to M. avium complex (MAC. It is further proposed to use an earlier suggested name Mycobacterium indicus pranii for this newly established mycobacterial species. This study also exemplifies the growing need for a uniform, consensus based broader polyphasic frame work for the purpose of taxonomy and speciation, particularly in the genus Mycobacterium.

  2. FANTOM: Functional and taxonomic analysis of metagenomes

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    Sanli Kemal

    2013-02-01

    Full Text Available Abstract Background Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context. Results Here we introduce FANTOM, a tool that allows for exploratory and comparative analysis of metagenomics abundance data integrated with metadata information and biological databases. Importantly, FANTOM can make use of any hierarchical database and it comes supplied with NCBI taxonomic hierarchies as well as KEGG Orthology, COG, PFAM and TIGRFAM databases. Conclusions The software is implemented in Python, is platform independent, and is available at http://www.sysbio.se/Fantom.

  3. Established and Emerging Decision Constructs – A Taxonomic Perspective

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    Chris Barry

    2016-06-01

    Full Text Available One might assume information systems (IS are developed so systems enhance the user experience and facilitate a satisfying, productive interaction. From prior research, the authors established this assumption was not safe and certain design features amongst some online retailers were atypical of ‘good’ design elsewhere. It was apparent the transactional process was being used to present consumers with optional extras (and other decisions that not only slowed the process down, but also stressed and agitated users. The research identified some new and unusual decision constructs such as the ‘must-opt’. The objective of the research presented herein is two-fold: to make an incremental contribution in first theorising and then identifying and categorising into a taxonomy some new decision constructs alongside established ones encountered throughout on-line Business-to-Consumer (B2C transactional processes followed by a preliminary study confirming their existence and examining their clarity.

  4. Taxonomical analysis of the Cancer cluster of galaxies

    International Nuclear Information System (INIS)

    Perea, J.; Olmo, A. del; Moles, M.

    1986-01-01

    A description is presented of the Cancer cluster of galaxies, based on a taxonomical analysis in (α,delta, Vsub(r)) space. Earlier results by previous authors on the lack of dynamical entity of the cluster are confirmed. The present analysis points out the existence of a binary structure in the most populated region of the complex. (author)

  5. Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species.

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    Natasha R Serrao

    Full Text Available Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway

  6. Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae

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    Simone Policena Rosa

    2014-01-01

    Full Text Available A phylogeny based on male morphological characters and taxonomic revision of the Physodactylinae genera are presented. The phylogenetic analysis based on 66 male characters resulted in the polyphyly of Physodactylinae which comprises four independent lineages. Oligostethius and Idiotropia from Africa were found to be sister groups. Teslasena from Brazil was corroborated as belonging to Cardiophorinae clade. The South American genera Physodactylus and Dactylophysus were found to be sister groups and phylogenetically related to Heterocrepidius species. The Oriental Toxognathus resulted as sister group of that clade plus (Dicrepidius ramicornis (Lissomus sp, Physorhynus erythrocephalus. Taxonomic revisions include diagnoses and redescriptions of genera and distributional records and illustrations of species. Key to species of Teslasena, Toxognathus, Dactylophysus and Physodactylus are also provided. Teslasena lucasi is synonymized with T. femoralis. A new species of Dactylophysus is described, D. hirtus sp. nov., and lectotypes are designated to non-conspecific D. mendax sensu Fleutiaux and Heterocrepidius mendax Candèze. Physodactylus niger is removed from synonymy under P. oberthuri; P. carreti is synonymized with P. niger; P. obesus and P. testaceus are synonymized with P. sulcatus. Nine new species are described in Physodactylus: P. asper sp. nov., P. brunneus sp. nov., P. chassaini sp. nov., P. flavifrons sp. nov., P. girardi sp. nov., P. gounellei sp. nov., P. latithorax sp. nov., P. patens sp. nov. and P. tuberculatus sp. nov.

  7. Memory systems, processes, and tasks: taxonomic clarification via factor analysis.

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    Bruss, Peter J; Mitchell, David B

    2009-01-01

    The nature of various memory systems was examined using factor analysis. We reanalyzed data from 11 memory tasks previously reported in Mitchell and Bruss (2003). Four well-defined factors emerged, closely resembling episodic and semantic memory and conceptual and perceptual implicit memory, in line with both memory systems and transfer-appropriate processing accounts. To explore taxonomic issues, we ran separate analyses on the implicit tasks. Using a cross-format manipulation (pictures vs. words), we identified 3 prototypical tasks. Word fragment completion and picture fragment identification tasks were "factor pure," tapping perceptual processes uniquely. Category exemplar generation revealed its conceptual nature, yielding both cross-format priming and a picture superiority effect. In contrast, word stem completion and picture naming were more complex, revealing attributes of both processes.

  8. Flora of the city of Podgorica, Montenegro: Taxonomic analysis

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    Stešević Danijela

    2008-01-01

    Full Text Available In this paper we present the taxonomic segment of a floristic study undertaken in the city of Podgorica in the period of 2002-2007. The check-list of spontaneously growing vascular plants includes 1227 species and subspecies belonging to 545 genera and 118 families. The dominant families are Poaceae (11.7%, asteraceae (11.2% and Fabaceae (9.2%. The most abundant genera are Trifolium (2.1%, Euphorbia (1.5%, Carex (1.5%, Bromus (1.3% and Vicia (1.2%. Analysis of the flora of Podgorica in comparison with some other european cities showed that the flora of Podgorica is most similar to that of Rome (Q/S= 0,7.

  9. Systematics of the Austral-Pacific Family Goodeniaceae - Establishing a Taxonomic and Evolutionary Framework

    DEFF Research Database (Denmark)

    Jabaily, Rachel S.; Gustafsson, Mats; Shepherd, K. A.

    2012-01-01

    The Goodeniaceae, close relatives of the Asteraceae, are a conspicuous part of the flora of Australia and many islands in the Pacific. A comprehensive molecular phylogenetic analysis of the family using cpDNA regions trnL-F and matK is presented, including representatives of all genera and nearly...

  10. Taxonomical analysis of the suspended bacterial fraction in the ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-30

    Nov 30, 2011 ... hundred individuals representative of the rumen bacterial community. A preliminary analysis ... sterile plastic syringes from eviscerated animals. The fluid was .... engaged in the active degradation of the substrate to which as a ...

  11. ToF-SIMS studies of Bacillus using multivariate analysis with possible identification and taxonomic applications

    International Nuclear Information System (INIS)

    Thompson, C.E.; Ellis, J.; Fletcher, J.S.; Goodacre, R.; Henderson, A.; Lockyer, N.P.; Vickerman, J.C.

    2006-01-01

    In this paper we discuss the application of ToF-SIMS with an Au 3 + primary ion beam, combined with principal components analysis (PCA) and discriminant function analysis (DFA) for the identification of individual strains of two Bacillus species. The ToF-SIMS PC-DFA methodology is capable of distinguishing bacteria at the strain level based on analysis of surface chemical species. By classifying the data using hierarchical cluster analysis (HCA) we are able to show quantitative separation of species and of these strains. This has taxonomic implications in the areas of rapid identification of pathogenic microbes isolated from the clinic, food and environment

  12. Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity.

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    Buckley, Thomas R; James, Sam; Allwood, Julia; Bartlam, Scott; Howitt, Robyn; Prada, Diana

    2011-01-01

    We have constructed the first ever phylogeny for the New Zealand earthworm fauna (Megascolecinae and Acanthodrilinae) including representatives from other major continental regions. Bayesian and maximum likelihood phylogenetic trees were constructed from 427 base pairs from the mitochondrial large subunit (16S) rRNA gene and 661 base pairs from the nuclear large subunit (28S) rRNA gene. Within the Acanthodrilinae we were able to identify a number of well-supported clades that were restricted to continental landmasses. Estimates of nodal support for these major clades were generally high, but relationships among clades were poorly resolved. The phylogenetic analyses revealed several independent lineages in New Zealand, some of which had a comparable phylogenetic depth to monophyletic groups sampled from Madagascar, Africa, North America and Australia. These results are consistent with at least some of these clades having inhabited New Zealand since rifting from Gondwana in the Late Cretaceous. Within the New Zealand Acanthodrilinae, major clades tended to be restricted to specific regions of New Zealand, with the central North Island and Cook Strait representing major biogeographic boundaries. Our field surveys of New Zealand and subsequent identification has also revealed extensive cryptic taxonomic diversity with approximately 48 new species sampled in addition to the 199 species recognized by previous authors. Our results indicate that further survey and taxonomic work is required to establish a foundation for future biogeographic and ecological research on this vitally important component of the New Zealand biota. Copyright © 2010 Elsevier Inc. All rights reserved.

  13. Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis.

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    Luo, Gang; Fotidis, Ioannis A; Angelidaki, Irini

    2016-01-01

    Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure. The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors. The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

  14. Taxonomic minimalism.

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    Beattle, A J; Oliver, I

    1994-12-01

    Biological surveys are in increasing demand while taxonomic resources continue to decline. How much formal taxonomy is required to get the job done? The answer depends on the kind of job but it is possible that taxonomic minimalism, especially (1) the use of higher taxonomic ranks, (2) the use of morphospecies rather than species (as identified by Latin binomials), and (3) the involvement of taxonomic specialists only for training and verification, may offer advantages for biodiversity assessment, environmental monitoring and ecological research. As such, formal taxonomy remains central to the process of biological inventory and survey but resources may be allocated more efficiently. For example, if formal Identification is not required, resources may be concentrated on replication and increasing sample sizes. Taxonomic minimalism may also facilitate the inclusion in these activities of important but neglected groups, especially among the invertebrates, and perhaps even microorganisms. Copyright © 1994. Published by Elsevier Ltd.

  15. Risk analysis in radiation treatment: Application of a new taxonomic structure

    International Nuclear Information System (INIS)

    Ekaette, Edidiong U.; Lee, Robert C.; Cooke, David L.; Kelly, Karie-Lynn; Dunscombe, Peter B.

    2006-01-01

    Background and purpose: Radiation treatment (RT) for cancer is susceptible to clinical incidents resulting from human errors and equipment failures. A systematic approach to collecting and processing incidents is required to manage patient risks. We describe the application of a new taxonomic structure for RT that supports risk analysis and organizational learning. Materials and methods: A systematic analysis of the RT process identified five process domains. Within each domain we defined incident type groups. We then constructed a database reflecting this taxonomic structure and populated it with incidents from publicly available sources. Querying this database provides insights into the nature and relative frequency of incidents in RT. Results: There are relatively few reports of incidents in the Prescription domain compared with the Preparation and Treatment domains. There are also fewer reports of systematic and infrastructure incidents in comparison to sporadic and process incidents. Infrastructure incidents are mainly systematic in nature, while process incidents are more likely to be sporadic. Conclusions: The lack of a standard, systems-oriented framework for incident reporting makes it difficult to learn from existing incident report sources. A clear understanding of the potential consequences and relationships between different incident types will guide incident reporting, resource allocation, and risk management efforts

  16. Habitats as surrogates of taxonomic and functional fish assemblages in coral reef ecosystems: a critical analysis of factors driving effectiveness.

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    Simon Van Wynsberge

    Full Text Available Species check-lists are helpful to establish Marine Protected Areas (MPAs and protect local richness, endemicity, rarity, and biodiversity in general. However, such exhaustive taxonomic lists (i.e., true surrogate of biodiversity require extensive and expensive censuses, and the use of estimator surrogates (e.g., habitats is an appealing alternative. In truth, surrogate effectiveness appears from the literature highly variable both in marine and terrestrial ecosystems, making it difficult to provide practical recommendations for managers. Here, we evaluate how the biodiversity reference data set and its inherent bias can influence effectiveness. Specifically, we defined habitats by geomorphology, rugosity, and benthic cover and architecture criteria, and mapped them with satellite images for a New-Caledonian site. Fish taxonomic and functional lists were elaborated from Underwater Visual Censuses, stratified according to geomorphology and exposure. We then tested if MPA networks designed to maximize habitat richness, diversity and rarity could also effectively maximize fish richness, diversity, and rarity. Effectiveness appeared highly sensitive to the fish census design itself, in relation to the type of habitat map used and the scale of analysis. Spatial distribution of habitats (estimator surrogate's distribution, quantity and location of fish census stations (target surrogate's sampling, and random processes in the MPA design all affected effectiveness to the point that one small change in the data set could lead to opposite conclusions. We suggest that previous conclusions on surrogacy effectiveness, either positive or negative, marine or terrestrial, should be considered with caution, except in instances where very dense data sets were used without pseudo-replication. Although this does not rule out the validity of using surrogates of species lists for conservation planning, the critical joint examination of both target and estimator

  17. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

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    Jiang Tao

    2011-10-01

    Full Text Available Abstract Background Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Results Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Conclusions Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  18. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences.

    Science.gov (United States)

    Ruegger, Paul M; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

    2011-10-10

    Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint) to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  19. Taxonomic analysis of extremely halophilic archaea isolated from 56-years-old dead sea brine samples.

    Science.gov (United States)

    Arahal, D R; Gutiérrez, M C; Volcani, B E; Ventosa, A

    2000-10-01

    A taxonomic study comprising both phenotypic and genotypic characterization, has been carried out on a total of 158 extremely halophilic aerobic archaeal strains. These strains were isolated from enrichments prepared from Dead Sea water samples dating from 1936 that were collected by B. E. Volcani for the demonstration of microbial life in the Dead Sea. The isolates were examined for 126 morphological, physiological, biochemical and nutritional tests. Numerical analysis of the data, by using the S(J) coefficient and UPGMA clustering method, showed that the isolates clustered into six phenons. Twenty-two out of the 158 strains used in this study were characterized previously (ARAHAL et al., 1996) and were placed into five phenotypic groups. The genotypic study included both the determination of the guanineplus-cytosine content of the DNA and DNA-DNA hybridization studies. For this purpose, representative strains from the six phenons were chosen. These groups were found to represent some members of three different genera - Haloarcula (phenons A, B, and C), Haloferax (phenons D and E) and Halobacterium (phenon F) - of the family Halobacteriaceae, some of them never reported to occur in the Dead Sea, such as Haloarcula hispanica, while Haloferax volcanii (phenons D and E) was described in the Dead Sea by studies carried out several decades later than Volcani's work.

  20. Transcriptome analysis of Phytophthora litchii reveals pathogenicity arsenals and confirms taxonomic status.

    Science.gov (United States)

    Sun, Jinhua; Gao, Zhaoyin; Zhang, Xinchun; Zou, Xiaoxiao; Cao, Lulu; Wang, Jiabao

    2017-01-01

    Litchi downy blight, caused by Peronophythora litchii, is one of the major diseases of litchi and has caused severe economic losses. P. litchii has the unique ability to produce downy mildew like sporangiophores under artificial culture. The pathogen had been placed in a new family Peronophytophthoraceae by some authors. In this study, the whole transcriptome of P. litchii from mycelia, sporangia, and zoospores was sequenced for the first time. A set of 23637 transcripts with an average length of 1284 bp was assembled. Using six open reading frame (ORF) predictors, 19267 representative ORFs were identified and were annotated by searching against several public databases. There were 4666 conserved gene families and various sets of lineage-specific genes among P. litchii and other four closely related oomycetes. In silico analyses revealed 490 pathogen-related proteins including 128 RXLR and 22 CRN effector candidates. Based on the phylogenetic analysis of 164 single copy orthologs from 22 species, it is validated that P. litchii is in the genus Phytophthora. Our work provides valuable data to elucidate the pathogenicity basis and ascertain the taxonomic status of P. litchii.

  1. MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.

    Science.gov (United States)

    Piro, Vitor C; Matschkowski, Marcel; Renard, Bernhard Y

    2017-08-14

    Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations. All this variation creates a complicated scenario to researchers to decide which methods to use. Installation, configuration and execution can also be difficult especially when dealing with multiple datasets and tools. We propose MetaMeta: a pipeline to execute and integrate results from metagenome analysis tools. MetaMeta provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. MetaMeta includes a database generation, pre-processing, execution, and integration steps, allowing easy execution and parallelization. The integration relies on the co-occurrence of organisms from different methods as the main feature to improve community profiling while accounting for differences in their databases. In a controlled case with simulated and real data, we show that the integrated profiles of MetaMeta overcome the best single profile. Using the same input data, it provides more sensitive and reliable results with the presence of each organism being supported by several methods. MetaMeta uses Snakemake and has six pre-configured tools, all available at BioConda channel for easy installation (conda install -c bioconda metameta). The MetaMeta pipeline is open-source and can be downloaded at: https://gitlab.com/rki_bioinformatics .

  2. Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos

    DEFF Research Database (Denmark)

    Sinniger, Frédéric; Pawlowski, Jan; Harii, Saki

    2016-01-01

    in 39 deep-sea sediment samples from bathyal and abyssal depths worldwide. The eDNA dataset was dominated by meiobenthic taxa and we identified all animal phyla commonly found in the deep-sea benthos; yet, the diversity within these phyla remains largely unknown. The large numbers of taxonomically...... for pure and applied deep-sea environmental research but also emphasizes the necessity to integrate such new approaches with traditional morphology-based examination of deep-sea organisms....

  3. Taxonomic Analysis of Voivodships Development in Terms of ICT Usage in Enterprises

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    Kaczmarczyk Paweł

    2017-12-01

    Full Text Available The aim of this paper is to analyse the development of voivodships in terms of ICT usage in enterprises by means of taxonomic methods. The theoretical part of the paper has been devoted to the role of modern information and communication technologies in post-industrial enterprises, in particular to the meaning of these technologies for new management concepts (e-business, online marketing, CRM, network management, X-engineering. The research methodology has been carried out, with special attention being paid to the agglomerative clustering method and optimization clustering method.

  4. Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

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    Margarita Gomila

    2017-12-01

    Full Text Available The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies.

  5. Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling.

    Science.gov (United States)

    Hill, Robert V

    2005-08-01

    Several mutually exclusive hypotheses have been advanced to explain the phylogenetic position of turtles among amniotes. Traditional morphology-based analyses place turtles among extinct anapsids (reptiles with a solid skull roof), whereas more recent studies of both morphological and molecular data support an origin of turtles from within Diapsida (reptiles with a doubly fenestrated skull roof). Evaluation of these conflicting hypotheses has been hampered by nonoverlapping taxonomic samples and the exclusion of significant taxa from published analyses. Furthermore, although data from soft tissues and anatomical systems such as the integument may be particularly relevant to this problem, they are often excluded from large-scale analyses of morphological systematics. Here, conflicting hypotheses of turtle relationships are tested by (1) combining published data into a supermatrix of morphological characters to address issues of character conflict and missing data; (2) increasing taxonomic sampling by more than doubling the number of operational taxonomic units to test internal relationships within suprageneric ingroup taxa; and (3) increasing character sampling by approximately 25% by adding new data on the osteology and histology of the integument, an anatomical system that has been historically underrepresented in morphological systematics. The morphological data set assembled here represents the largest yet compiled for Amniota. Reevaluation of character data from prior studies of amniote phylogeny favors the hypothesis that turtles indeed have diapsid affinities. Addition of new ingroup taxa alone leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of a

  6. MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data.

    Science.gov (United States)

    Riffle, Michael; May, Damon H; Timmins-Schiffman, Emma; Mikan, Molly P; Jaschob, Daniel; Noble, William Stafford; Nunn, Brook L

    2017-12-27

    Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the proteins that perform those functions? However, traditional protein-centric functional analysis is greatly complicated by the large size, redundancy, and lack of biological annotations for the protein sequences in the database used to search the data. To help address these issues, we have developed an algorithm and web application (dubbed "MetaGOmics") that automates the quantitative functional (using Gene Ontology) and taxonomic analysis of metaproteomics data and subsequent visualization of the results. MetaGOmics is designed to overcome the shortcomings of traditional proteomics analysis when used with metaproteomics data. It is easy to use, requires minimal input, and fully automates most steps of the analysis-including comparing the functional makeup between samples. MetaGOmics is freely available at https://www.yeastrc.org/metagomics/.

  7. Asteroid taxonomic classifications

    International Nuclear Information System (INIS)

    Tholen, D.J.

    1989-01-01

    This paper reports on three taxonomic classification schemes developed and applied to the body of available color and albedo data. Asteroid taxonomic classifications according to two of these schemes are reproduced

  8. MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data

    Directory of Open Access Journals (Sweden)

    Michael Riffle

    2017-12-01

    Full Text Available Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil to microbiome data from multicellular organisms (such as the human gut. Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the proteins that perform those functions? However, traditional protein-centric functional analysis is greatly complicated by the large size, redundancy, and lack of biological annotations for the protein sequences in the database used to search the data. To help address these issues, we have developed an algorithm and web application (dubbed “MetaGOmics” that automates the quantitative functional (using Gene Ontology and taxonomic analysis of metaproteomics data and subsequent visualization of the results. MetaGOmics is designed to overcome the shortcomings of traditional proteomics analysis when used with metaproteomics data. It is easy to use, requires minimal input, and fully automates most steps of the analysis—including comparing the functional makeup between samples. MetaGOmics is freely available at https://www.yeastrc.org/metagomics/.

  9. Exploring historical trends using taxonomic name metadata

    Directory of Open Access Journals (Sweden)

    Schenk Ryan

    2008-05-01

    Full Text Available Abstract Background Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy. Results From the over 10.7 million taxonomic names that are part of the uBio system 4, approximately 3 million names were identified to have taxonomic authority information from the years 1750 to 2004. A pipe-delimited file was then generated, organized according to a Linnaean hierarchy and by years from 1750 to 2004, and imported into an Excel workbook. A series of macros were developed to create an Excel-based tool and a complementary Web site to explore the taxonomic data. A cursory and speculative analysis of the data reveals observable trends that may be attributable to significant events that are of both taxonomic (e.g., publishing of key monographs and societal importance (e.g., world wars. The findings also help quantify the number of taxonomic descriptions that may be made available through digitization initiatives. Conclusion Temporal organization of taxonomic data can be used to identify interesting biological epochs relative to historically significant events and ongoing efforts. We have developed an Excel workbook and complementary Web site that enables one to explore taxonomic trends for Linnaean taxonomic groupings, from Kingdoms to Families.

  10. Evaluation of diffuse hepatic diseases by integrated image, SPECT and numerical taxonomic analysis

    Energy Technology Data Exchange (ETDEWEB)

    Kobayashi, Shin

    1987-02-01

    In 135 patients with various hepatic diseases, cardiopulmonary circulation and hepatic accumulation of the activity were collected for 100 sec after bolus injection of 111-222 MBq (3 - 6 mci) of /sup 99m/Tc-phytate, and then integrated as a single image. Anterior, right lateral and posterior planar images, and hepatosplenic SPECT images were obtained thereafter. Lung to liver count ratio (P/L) was estimated by the integrated image. Liver volume (HV), spleen volume (SV) and liver to spleen count ratio (MHC/MSC) were calculated using the data obtained by SPECT. P/L was useful as an index of effective hepatic blood flow. MHC/MSC was closely correlated with the grade of portal hypertension. HV or SV alone shows low clinical value in discriminating liver diseases. Principal component analysis was applied to the 4 above-mentioned radinuclide data and the following 11 laboratory data ; total serum protein, serum albumine, glutamate oxaloacetate transaminase (GOT), glutamate pyruvate transaminase (GPT), lactic dehydrogenase (LDH), alkaline phosphatase (AL-P), zink sulfateturbidity test (ZTT), thymol turbidity test (TTT), r-glutamyl transpeptidase (r-GTP), cholinesterase (Ch-E), and total bilirubin (T-Bil). These fifteen data were condensed to 5 principal components. And then cluster analysis was carried out among 135 patients. The subjects were classified in 7 small groups. In group (G) I to GIII, frequency of liver cirrhosis was high, while on the contrary in GIV to GVII, the frequency of normal cases increased gradually. From the above results, cluster analysis seemed to reflect the pathophysiological state and the grade of the disease. This method might be useful for estimation of the grade of damage in diffuse hepatic disease and a good objective evaluation method in follow-up studies. (J.P.N.).

  11. Analysis of mitochondrial DNA: taxonomic and phylogenetic relationships in two fish taxa (Pisces: Mugilidae and Cyprinidae).

    Science.gov (United States)

    Semina, A V; Polyakova, N E; Brykov, Vl A

    2007-12-01

    To solve some systematic questions as well as to study genetic variability and evolutionary relationships in two groups of fish belonging to the Mugilid (Mugilidae) and Cyprinid (Cyprinidae) families, we have used restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction. The analysis of three mtDNA fragments of 7220 bp total length of six Mugilid species has shown that Mediterranean Liza aurata, L. ramada, L. saliens, and Chelon labrosus form a common cluster, L. aurata and C. labrosus being the closest relatives, whereas L. haematocheilus (syn. C. haematocheilus) of the Sea of Japan forms a sister group to the Mediterranean cluster. It was found that Chelon and Liza genera are paraphyletic, and therefore their division into two genera is unnatural and they should be synonymized. According to priority, Liza species should be ascribed to Chelon genus. Mugil cephalus is the most distant compared to the rest of the species studied. The level of genetic divergence between allopatric samples of M. cephalus from the Sea of Japan and the Mediterranean Sea has proved to be very high--4.5% of nucleotide substitutions. The analysis of four mtDNA fragments of 9340 bp total length of six Cyprinid species has shown that L. waleckii is the most genetically distant. Pseudaspius leptocephalus is a sister group to Tribolodon species. All Tribolodon species form a common cluster with T. sachalinensis as a root. The remaining species form two branches, one of which includes T. nakamurai and T. brandtii, another one combines T. hakonensis and a new form of Tribolodon revealed that is close to T. hakonensis by its mtDNA (2.4% of nucleotide substitutions). This new form might be an independent species.

  12. Isolation, taxonomic analysis, and phenotypic characterization of bacterial endophytes present in alfalfa (Medicago sativa) seeds.

    Science.gov (United States)

    López, José Luis; Alvarez, Florencia; Príncipe, Analía; Salas, María Eugenia; Lozano, Mauricio Javier; Draghi, Walter Omar; Jofré, Edgardo; Lagares, Antonio

    2018-02-10

    A growing body of evidence has reinforced the central role of microbiomes in the life of sound multicellular eukaryotes, thus more properly described as true holobionts. Though soil was considered a main source of plant microbiomes, seeds have been shown to be endophytically colonized by microorganisms thus representing natural carriers of a selected microbial inoculum to the young seedlings. In this work we have investigated the type of culturable endophytic bacteria that are carried within surface-sterilized alfalfa seeds. MALDI-TOF analysis revealed the presence of bacteria that belonged to 40 separate genera, distributed within four taxa (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes). Nonsymbiotic members of the Rhizobiaceae family were also found. The evaluation of nine different in-vitro biochemical activities demonstrated isolates with complex combinations of traits that, upon a Principal-Component-Analysis, could be classified into four phenotypic groups. That isolates from nearly half of the genera identified had been able to colonize alfalfa plants grown under axenic conditions was remarkable. Further analyses should be addressed to investigating the colonization mechanisms of the alfalfa seeds, the evolutionary significance of the alfalfa-seed endophytes, and also how after germination the seed microbiome competes with spermospheric and rhizospheric soil bacteria to colonize newly emerging seedlings. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Taxonomic analysis of perceived risk: modeling individual and group perceptions within homogeneous hazard domains

    International Nuclear Information System (INIS)

    Kraus, N.N.; Slovic, P.

    1988-01-01

    Previous studies of risk perception have typically focused on the mean judgments of a group of people regarding the riskiness (or safety) of a diverse set of hazardous activities, substances, and technologies. This paper reports the results of two studies that take a different path. Study 1 investigated whether models within a single technological domain were similar to previous models based on group means and diverse hazards. Study 2 created a group taxonomy of perceived risk for only one technological domain, railroads, and examined whether the structure of that taxonomy corresponded with taxonomies derived from prior studies of diverse hazards. Results from Study 1 indicated that the importance of various risk characteristics in determining perceived risk differed across individuals and across hazards, but not so much as to invalidate the results of earlier studies based on group means and diverse hazards. In Study 2, the detailed analysis of railroad hazards produced a structure that had both important similarities to, and dissimilarities from, the structure obtained in prior research with diverse hazard domains. The data also indicated that railroad hazards are really quite diverse, with some approaching nuclear reactors in their perceived seriousness. These results suggest that information about the diversity of perceptions within a single domain of hazards could provide valuable input to risk-management decisions

  14. Establishment of computer code system for nuclear reactor design - analysis

    International Nuclear Information System (INIS)

    Subki, I.R.; Santoso, B.; Syaukat, A.; Lee, S.M.

    1996-01-01

    Establishment of computer code system for nuclear reactor design analysis is given in this paper. This establishment is an effort to provide the capability in running various codes from nuclear data to reactor design and promote the capability for nuclear reactor design analysis particularly from neutronics and safety points. This establishment is also an effort to enhance the coordination of nuclear codes application and development existing in various research centre in Indonesia. Very prospective results have been obtained with the help of IAEA technical assistance. (author). 6 refs, 1 fig., 1 tab

  15. Analysis on Factors Affecting Seedling Establishment in Rice

    Directory of Open Access Journals (Sweden)

    Ju LUO

    2007-03-01

    Full Text Available Elongations of coleoptile and mesocotyl are related directly to rice seedling establishment in soil and height of plant is related to lodging in rice production. Twelve typical rice cultivars with different lengths of coleoptile and mesocotyl (long, medium and short were selected by screening the lengths of coleoptile and mesocotyl in 1500 accessions. The seedling establishments of these typical cultivars were compared under the combinations of different sowing depths and flooding durations, and two semi-dwarf varieties (G140, Zhong 96–21 with good seedling establishments and optimum mesocotyl lengths were found. The length of mesocotyl was completely fitted negative binomial distribution and the length of coleoptile was nearly fitted lognormal distribution. Analysis of the relationships among mesocotyl, coleoptile, seeding depth, flooding duration, and their interactions to seedling establishment percentage showed that there existed significant relations among mesocotyl, coleoptile, mesocotyl × coleoptile, seeding depth, flooding duration and mesocotyl × sowing depth in the experiment for seedling establishment.

  16. Establishment of Safety Analysis System and Technology for CANDU Reactors

    International Nuclear Information System (INIS)

    Min, Byung Joo; Kim, W. Y.; Kim, H. T.; Rhee, B. W.; Yoon, C.; Kang, H. S.; Yoo, K. J.

    2005-03-01

    To improve the CANDU design/operation safety analysis codes and the CANDU safety analysis methodology, the following works have been done. From the development of the lattice codes (WIMS/CANDU), the lattice model simulates the real core lattice geometry and the effect of the pressure tube creep to the core lattice parameter has been evaluated. From the development of the 3-dimensional thermal-hydraulic analysis model of the moderator behavior (CFX4-CAMO), validation of the model against STERN Lab experiment has been executed. The butterfly-shaped grid structure and the 3-dimensional flow resistance model for porous media were developed and applied to the moderator analysis for Wolsong units 2/3/4. The single fuel channel analysis codes for blowdown and post-blowdown were unified by CATHENA. The 3-dimensional fuel channel analysis model (CFX-CACH) has been developed for validation of CATHENA fuel channel analysis model. The interlinking analysis system (CANVAS) of the thermal-hydraulic safety analysis codes for the primary heat transport system and containment system has been executed. The database system of core physics and thermal-hydraulics experimental data for safety analysis has been established on the URL: http://CANTHIS.kaeri.re.kr. For documentation and Standardization of the general safety analysis procedure, the general safety analysis procedure is developed and applied to a large break LOCA. The present research results can be utilized for establishment of the independent safety analysis technology and acquisition of the optimal safety analysis technology

  17. Taxonomic revision and cladistic analysis of Avicularia Lamarck, 1818 (Araneae, Theraphosidae, Aviculariinae with description of three new aviculariine genera01

    Directory of Open Access Journals (Sweden)

    Caroline Sayuri Fukushima

    2017-03-01

    Full Text Available The genus Avicularia Lamarck, 1818 is revised and all species are rediagnosed. The type species, described as Aranea avicularia Linnaeus, 1758, is the oldest mygalomorph species described and its taxonomic history is extensive and confusing. Cladistic analyses using both equal and implied weights were carried out with a matrix of 46 taxa from seven theraphosid subfamilies, and 71 morphological and ecological characters. The optimal cladogram found with Piwe and concavity = 6 suggests Avicularia and Aviculariinae are monophyletic. Subfamily Aviculariinae includes Avicularia Lamarck, 1818, Typhochlaena C. L. Koch, 1850, Tapinauchenius Ausserer, 1871, Stromatopelma Karsch, 1881, Ephebopus Simon, 1892, Psalmopoeus Pocock, 1895, Heteroscodra Pocock, 1899, Iridopelma Pocock, 1901, Pachistopelma Pocock, 1901, Ybyrapora gen. n., Caribena gen. n., and Antillena gen. n. The clade is supported by well-developed scopulae on tarsi and metatarsi, greatly extended laterally. Avicularia synapomorphies are juveniles bearing black tarsi contrasting with other lighter articles; spermathecae with an accentuated outwards curvature medially, and male palpal bulb with embolus medial portion and tegulum’s margin form an acute angle in retrolateral view. Avicularia is composed of twelve species, including three new species: Avicularia avicularia (Linnaeus, 1818, Avicularia glauca Simon, 1891, Avicularia variegata (F. O. Pickard-Cambridge, 1896 stat. n., A. minatrix Pocock, 1903, Avicularia taunayi (Mello-Leitão, 1920, Avicularia juruensis Mello-Leitão, 1923, Avicularia rufa Schiapelli & Gerschman, 1945, Avicularia purpurea Kirk, 1990, A. hirschii Bullmer et al. 2006, Avicularia merianae sp. n., A. lynnae sp. n., and A. caei sp. n.. Avicularia species are distributed throughout Mexico, Costa Rica, Panama, Trinidad and Tobago, Venezuela, Guyana, Suriname, French Guiana, Colombia, Ecuador, Peru, Bolivia, and Brazil. Three new genera are erected to accommodate former

  18. Taxonomic revision and cladistic analysis of Avicularia Lamarck, 1818 (Araneae, Theraphosidae, Aviculariinae) with description of three new aviculariine genera.

    Science.gov (United States)

    Fukushima, Caroline Sayuri; Bertani, Rogério

    2017-01-01

    The genus Avicularia Lamarck, 1818 is revised and all species are rediagnosed. The type species, described as Aranea avicularia Linnaeus, 1758, is the oldest mygalomorph species described and its taxonomic history is extensive and confusing. Cladistic analyses using both equal and implied weights were carried out with a matrix of 46 taxa from seven theraphosid subfamilies, and 71 morphological and ecological characters. The optimal cladogram found with Piwe and concavity = 6 suggests Avicularia and Aviculariinae are monophyletic. Subfamily Aviculariinae includes Avicularia Lamarck, 1818, Typhochlaena C. L. Koch, 1850, Tapinauchenius Ausserer, 1871, Stromatopelma Karsch, 1881, Ephebopus Simon, 1892, Psalmopoeus Pocock, 1895, Heteroscodra Pocock, 1899, Iridopelma Pocock, 1901, Pachistopelma Pocock, 1901, Ybyrapora gen. n. , Caribena gen. n. , and Antillena gen. n. The clade is supported by well-developed scopulae on tarsi and metatarsi, greatly extended laterally. Avicularia synapomorphies are juveniles bearing black tarsi contrasting with other lighter articles; spermathecae with an accentuated outwards curvature medially, and male palpal bulb with embolus medial portion and tegulum's margin form an acute angle in retrolateral view. Avicularia is composed of twelve species, including three new species: Avicularia avicularia (Linnaeus, 1818), Avicularia glauca Simon, 1891, Avicularia variegata (F. O. Pickard-Cambridge, 1896) stat. n., Avicularia minatrix Pocock, 1903, Avicularia taunayi (Mello-Leitão, 1920), Avicularia juruensis Mello-Leitão, 1923, Avicularia rufa Schiapelli & Gerschman, 1945, Avicularia purpurea Kirk, 1990, Avicularia hirschii Bullmer et al. 2006, Avicularia merianae sp. n. , Avicularia lynnae sp. n. , and Avicularia caei sp. n. . Avicularia species are distributed throughout Mexico, Costa Rica, Panama, Trinidad and Tobago, Venezuela, Guyana, Suriname, French Guiana, Colombia, Ecuador, Peru, Bolivia, and Brazil. Three new genera are erected to

  19. Risk Analysis as Regulatory Science: Toward The Establishment of Standards.

    Science.gov (United States)

    Murakami, Michio

    2016-09-01

    Understanding how to establish standards is essential for risk communication and also provides perspectives for further study. In this paper, the concept of risk analysis as regulatory science for the establishment of standards is demonstrated through examples of standards for evacuation and provisional regulation values in foods and drinking water. Moreover, academic needs for further studies related to standards are extracted. The concepts of the traditional 'Standard I', which has a paternalistic orientation, and 'Standard II', established through stakeholder consensus, are then systemized by introducing the current status of the new standards-related movement that developed after the Fukushima nuclear power plant accident, and the perspectives of the standards are discussed. Preparation of standards on the basis of stakeholder consensus through intensive risk dialogue before a potential nuclear power plant accident is suggested to be a promising approach to ensure a safe society and enhance subjective well-being. © The Author 2016. Published by Oxford University Press.

  20. Molecular taxonomic analysis of the plant associations of adult pollen beetles (Nitidulidae: Meligethinae), and the population structure of Brassicogethes aeneus.

    Science.gov (United States)

    Ouvrard, Pierre; Hicks, Damien M; Mouland, Molly; Nicholls, James A; Baldock, Katherine C R; Goddard, Mark A; Kunin, William E; Potts, Simon G; Thieme, Thomas; Veromann, Eve; Stone, Graham N

    2016-12-01

    Pollen beetles (Nitidulidae: Meligethinae) are among the most abundant flower-visiting insects in Europe. While some species damage millions of hectares of crops annually, the biology of many species is little known. We assessed the utility of a 797 base pair fragment of the cytochrome oxidase 1 gene to resolve molecular operational taxonomic units (MOTUs) in 750 adult pollen beetles sampled from flowers of 63 plant species sampled across the UK and continental Europe. We used the same locus to analyse region-scale patterns in population structure and demography in an economically important pest, Brassicogethes aeneus. We identified 44 Meligethinae at ∼2% divergence, 35 of which contained published sequences. A few specimens could not be identified because the MOTUs containing them included published sequences for multiple Linnaean species, suggesting either retention of ancestral haplotype polymorphism or identification errors in published sequences. Over 90% of UK specimens were identifiable as B. aeneus. Plant associations of adult B. aeneus were found to be far wider taxonomically than for their larvae. UK B. aeneus populations showed contrasting affiliations between the north (most similar to Scandinavia and the Baltic) and south (most similar to western continental Europe), with strong signatures of population growth in the south.

  1. Establishment of Safety Analysis System and Technology for CANDU Reactors

    International Nuclear Information System (INIS)

    Park, Joo Hwan; Rhee, B. W.; Min, B. J.; Kim, H. T.; Kim, W. Y.; Yoon, C.; Chun, J. S.; Cho, M. S.; Jeong, J. Y.; Kang, H. S.

    2007-06-01

    The following 4 research items have been studied to establish a CANDU safety analysis system and to develop the relevant elementary technology for CANDU reactors. First, to improve and validate the CANDU design and operational safety analysis codes, the CANDU physics cell code WIMS-CANDU was improved, and validated, and an analysis of the moderator subcooling and pressure tube integrity has been performed for the large break LOCAs without ECCS. Also a CATHENA model and a CFD model for a post-blowdown fuel channel analysis have been developed and validated against two high temperature thermal-chemical experiments, CS28-1 and 2. Second, to improve the integrated operating system of the CANDU safety analysis codes, an extension has been made to them to include the core and fuel accident analyses, and a web-based CANDU database, CANTHIS version 2.0 was completed. Third, to assess the applicability of the ACR-7 safety analysis methodology to CANDU-6 the ACR-7 safety analysis methods were reviewed and the safety analysis methods of ACR-7 applicable to CANDU-6 were recommended. Last, to supplement and improve the existing CANDU safety analysis procedures, detailed analysis procedures have been prepared for individual accident scenarios. The results of this study can be used to resolve the CANDU safety issues, to improve the current design and operational safety analysis codes, and to technically support the Wolsong site to resolve their problems

  2. Analysis of differential lipofection efficiency in primary and established myoblasts.

    Science.gov (United States)

    Pampinella, Francesca; Lechardeur, Delphine; Zanetti, Elena; MacLachlan, Ian; Benharouga, Mohammed; Lukacs, Gergely L; Vitiello, Libero

    2002-02-01

    In this study we have compared the process of lipid-mediated transfection in primary and established myoblasts, in an attempt to elucidate the mechanisms responsible for the scarce transfectability of the former. We determined the metabolic stability of cytoplasmically injected and lipofected DNA in primary and established myoblasts and carried out a comparative time course analysis of luciferase reporter-gene expression and DNA stability. The efficiency of the transcription-translation machinery of the two cell types was compared by intranuclear injection of naked plasmid DNA encoding luciferase. Subcellular colocalization of fluorescein-labeled lipopolyplexes with specific endosomal and lysosomal markers was performed by confocal microscopy to monitor the intracellular trafficking of plasmid DNA during transfection. The metabolic stability of plasmid DNA was similar in primary and established myoblasts after both lipofection and cytoplasmic injection. In both cell types, lipofection had no detectable effect on the rate of cell proliferation. Confocal analysis showed that nuclear translocation of transfected DNA coincided with localization in a compartment devoid of endosome- or lysosome-specific marker proteins. The residency time of plasmid DNA in this compartment differed for primary and established myoblasts. Our findings suggest that the lower transfectability of primary myoblasts is mostly due to a difference in the intracellular delivery pathway that correlates with more rapid delivery of internalized complex to the lysosomal compartment.

  3. Establishment of analysis method for methane detection by gas chromatography

    Science.gov (United States)

    Liu, Xinyuan; Yang, Jie; Ye, Tianyi; Han, Zeyu

    2018-02-01

    The study focused on the establishment of analysis method for methane determination by gas chromatography. Methane was detected by hydrogen flame ionization detector, and the quantitative relationship was determined by working curve of y=2041.2x+2187 with correlation coefficient of 0.9979. The relative standard deviation of 2.60-6.33% and the recovery rate of 96.36%∼105.89% were obtained during the parallel determination of standard gas. This method was not quite suitable for biogas content analysis because methane content in biogas would be over the measurement range in this method.

  4. Establishment of ultra trace nuclear material analysis system

    International Nuclear Information System (INIS)

    Song, Kyuseok; Jee, Kwangyong; Lee, Changheon

    2012-05-01

    Highly accurate and precise analysis of ultra trace nuclear materials contained in swipe samples and environmental samples is required to improve the national nuclear transparency and the international nuclear security. The objectives of the first stage of this project are to develop the techniques for bulk analysis of environmental samples and the elemental techniques for particle analysis using FT-TIMS. To accomplish the objectives, state-of-the-art analytical instruments were set up followed by the development of the techniques for screening of nuclear materials, chemical treatement, particle handling, isotopic measurements using TIMS and ICP-MS, and fabrication of uranium microparticles. The verifications of the developed techniques were carried out by measurement of reference materials, and by participation to interlaboratory comparison programs. In additon, the establishement of a quality management system and the performance of the analysis of QC samples for IAEA-NWAL qualification were carried out to obtain the international accreditation for the related analytical system. In this report, the results of research and developments, and the achievements to obtain the international accreditation were summarized

  5. Bovine teat microbiome analysis revealed reduced alpha diversity and significant changes in taxonomic profiles in quarters with a history of mastitis

    Directory of Open Access Journals (Sweden)

    Helene eFalentin

    2016-04-01

    Full Text Available Mastitis is a mammary gland inflammatory disease often due to bacterial infections. Like many other infections, it used to be considered as a host-pathogen interaction driven by host and bacterial determinants. Until now, the involvement of the bovine mammary gland microbiota in the host-pathogen interaction has been poorly investigated, and mainly during the infectious episode. In this study, the bovine teat microbiome was investigated in 31 quarters corresponding to 27 animals, which were all free of inflammation at sampling time but which had different histories regarding mastitis: from no episode of mastitis on all the previous lactations (Healthy quarter, Hq to one or several clinical mastitis events (Mastitic quarter, Mq. Several quarters whose status was unclear (possible history of subclinical mastitis were classified as NDq. Total bacterial DNA was extracted from foremilk samples and swab samples of the teat canal. Taxonomic profiles were determined by pyrosequencing on 16s amplicons of the V3-4 region. Hq quarters showed a higher diversity compared to Mq ones (Shannon index: ~8 and 6, respectively. Clustering of the quarters based on their bacterial composition made it possible to separate Mq and Hq quarters into two separate clusters (C1 and C2, respectively. Discriminant analysis of taxonomic profiles between these clusters revealed several differences and allowed the identification of taxonomic markers in relation to mastitis history. C2 quarters were associated with a higher proportion of the Clostridia class (including genera such as Ruminococcus, Oscillospira, Roseburia, Dorea, etc., the Bacteroidetes phylum (Prevotella, Bacteroides, Paludibacter, etc., and the Bifidobacteriales order (Bifidobacterium, whereas C1 quarters showed a higher proportion of the Bacilli class (Staphylococcus and Chlamydiia class. These results indicate that microbiota is altered in udders which have already developed mastitis, even far from the

  6. Feasibility Study Analysis of Establishing Archery Sports Special Place

    Science.gov (United States)

    Tarigan, U. P. P.; Mardhatillah, A.; Budiman, I.; Sembiring, A. C.; Ramadhan, M. S.

    2018-04-01

    This study essentially discusses the basic concepts related to the decision and process of selecting a sports archery business project in order to provide economic and social benefits over time. Archery sports is a sport that requires special skills, both accuracy, coordination mental training and improves the physical condition of the prime. In Medan, it's still a bit of practice archery, but many people love this sport. From the data collected, there are three locations where archery in the city of the field of the Sunggal Knights is located at Jl Tunggul Hitam no.1A, Kec. Medan Sunggal, Avros Educational Park Aval address at Avros Street No.60 Medan, and the Knights of Johor Archery Club which is located at Jl. The work of Darma Gg. Ujung Family, Medan Johor. Therefore a feasibility study was undertaken in establishing an archery sports place in the field. The aspects to be considered in making feasibility studies are market and marketing aspects, technical and equipment aspects, management aspects, legal aspects, economic and social aspects, and financial aspects. Financial analysis using own capital got Payback Period 3 years 5,8 months, Net Present Value Rp 11.684.026 and obtained Internal Rate of Return of 17%.

  7. mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences.

    Science.gov (United States)

    Links, Matthew G; Chaban, Bonnie; Hemmingsen, Sean M; Muirhead, Kevin; Hill, Janet E

    2013-08-15

    Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.

  8. Charting taxonomic knowledge through ontologies and ranking algorithms

    Science.gov (United States)

    Huber, Robert; Klump, Jens

    2009-04-01

    Since the inception of geology as a modern science, paleontologists have described a large number of fossil species. This makes fossilized organisms an important tool in the study of stratigraphy and past environments. Since taxonomic classifications of organisms, and thereby their names, change frequently, the correct application of this tool requires taxonomic expertise in finding correct synonyms for a given species name. Much of this taxonomic information has already been published in journals and books where it is compiled in carefully prepared synonymy lists. Because this information is scattered throughout the paleontological literature, it is difficult to find and sometimes not accessible. Also, taxonomic information in the literature is often difficult to interpret for non-taxonomists looking for taxonomic synonymies as part of their research. The highly formalized structure makes Open Nomenclature synonymy lists ideally suited for computer aided identification of taxonomic synonyms. Because a synonymy list is a list of citations related to a taxon name, its bibliographic nature allows the application of bibliometric techniques to calculate the impact of synonymies and taxonomic concepts. TaxonRank is a ranking algorithm based on bibliometric analysis and Internet page ranking algorithms. TaxonRank uses published synonymy list data stored in TaxonConcept, a taxonomic information system. The basic ranking algorithm has been modified to include a measure of confidence on species identification based on the Open Nomenclature notation used in synonymy list, as well as other synonymy specific criteria. The results of our experiments show that the output of the proposed ranking algorithm gives a good estimate of the impact a published taxonomic concept has on the taxonomic opinions in the geological community. Also, our results show that treating taxonomic synonymies as part of on an ontology is a way to record and manage taxonomic knowledge, and thus contribute

  9. Taxonomic evaluation of putative Streptomyces scabiei strains held in the ARS (NRRL) Culture Collection using multi-locus sequence analysis

    Science.gov (United States)

    Multi-locus sequence analysis has been demonstrated to be a useful tool for identification of Streptomyces species and was previously applied to phylogenetically differentiate the type strains of species pathogenic on potatoes (Solanum tuberosum L.). The ARS Culture Collection (NRRL) contains 43 str...

  10. Analysis of Drop Call Probability in Well Established Cellular ...

    African Journals Online (AJOL)

    Technology in Africa has increased over the past decade. The increase in modern cellular networks requires stringent quality of service (QoS). Drop call probability is one of the most important indices of QoS evaluation in a large scale well-established cellular network. In this work we started from an accurate statistical ...

  11. Identification, in vitro establishment and preliminary phytochemical analysis of wild yam (Dioscorea spp. used for medicinal purposes

    Directory of Open Access Journals (Sweden)

    Víctor Andrés Ramos Duarte

    2015-01-01

    Full Text Available Wild tubers of the genus Dioscorea sold for medicinal use were collected for the purpose of achieving its establishment under in vitro conditions. First we taxonomically identified the species and through phytochemical analysis demonstrated pharmaceutical potential. The material collected was identified as Dioscorea coriacea, D. lehmannii, D. meridensis, D. polygonoides and the edible species D. trifida. Tubers collected from wholesale distributors and from the field were washed, disinfected, sprayed with Gibberellic Acid (GA3 and planted in substrate BM-2®, in a greenhouse at 18 ° C during the day and 10 ° C overnight. Whole tubers or sections thereof were stored in sealed bags at room temperature. Subsequently plant material of the species D. coriacea, D. lehmannii, D. meridensis and D. polygonoides was disinfected and healthy buds (D. coriacea / laboratory were selected for in vitro establishment. Three different culture media were evaluated for establishment; that which presented the best results was the Murashige & Skoog (1962 medium, supplemented with BAP 1 mL / L, GA3 1 mL / L and Putrescin 2 mL / L. For the collection and analysis of secondary metabolites, tubers of D. coriacea, D. lehmannii and D. polygonoides were used, using methanol as the extraction solvent. The highest concentration of plant extract, 54%, was found in D. coriacea, a higher value than that of D. polygonoides, which had been reported previously; the presence of saponins was confirmed by thin layer chromatography (TLC. These results will enable more advanced analysis of the present compounds and enhance their mass propagation under in vitro conditions.

  12. A Data Analysis Expert System For Large Established Distributed Databases

    Science.gov (United States)

    Gnacek, Anne-Marie; An, Y. Kim; Ryan, J. Patrick

    1987-05-01

    The purpose of this work is to analyze the applicability of artificial intelligence techniques for developing a user-friendly, parallel interface to large isolated, incompatible NASA databases for the purpose of assisting the management decision process. To carry out this work, a survey was conducted to establish the data access requirements of several key NASA user groups. In addition, current NASA database access methods were evaluated. The results of this work are presented in the form of a design for a natural language database interface system, called the Deductively Augmented NASA Management Decision Support System (DANMDS). This design is feasible principally because of recently announced commercial hardware and software product developments which allow cross-vendor compatibility. The goal of the DANMDS system is commensurate with the central dilemma confronting most large companies and institutions in America, the retrieval of information from large, established, incompatible database systems. The DANMDS system implementation would represent a significant first step toward this problem's resolution.

  13. Contribution to a Taxonomic Revision of the Sicilian Helichrysum Taxa by PCA Analysis of Their Essential-Oil Compositions.

    Science.gov (United States)

    Maggio, Antonella; Bruno, Maurizio; Guarino, Riccardo; Senatore, Felice; Ilardi, Vincenzo

    2016-02-01

    The chemical profile of the essential oils in ten populations of the genus Helichrysum Mill. (Asteraceae), collected in the loci classici of the nomenclatural types of the taxa endemic to Sicily, were analyzed. Our results confirm that the analysis of secondary metabolites can be used to fingerprint wild populations of Helichrysum, the chemical profiles being coherent with the systematic arrangement of the investigated populations in three main clusters, referring to the aggregates of H. stoechas, H. rupestre, and H. italicum, all belonging to the section Stoechadina. The correct nomenclatural designation of the investigated populations is discussed and the following two new combinations are proposed: Helichrysum preslianum subsp. compactum (Guss.) Maggio, Bruno, Guarino, Senatore & Ilardi and Helichrysum panormitanum subsp. latifolium Maggio, Bruno, Guarino, Senatore & Ilardi. Copyright © 2016 Verlag Helvetica Chimica Acta AG, Zürich.

  14. A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution

    Science.gov (United States)

    Heinz, Eva; Lithgow, Trevor

    2014-01-01

    Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins. PMID:25101071

  15. New Eocene Coleoid (Cephalopoda Diversity from Statolith Remains: Taxonomic Assignation, Fossil Record Analysis, and New Data for Calibrating Molecular Phylogenies.

    Directory of Open Access Journals (Sweden)

    Pascal Neige

    Full Text Available New coleoid cephalopods are described from statolith remains from the Middle Eocene (Middle Lutetian of the Paris Basin. Fifteen fossil statoliths are identified and assigned to the Sepiidae (Sepia boletzkyi sp. nov.,? Sepia pira sp. nov., Loliginidae (Loligo clarkei sp. nov., and Ommastrephidae (genus indet. families. The sediments containing these fossils indicate permanent aquatic settings in the infralittoral domain. These sediments range in age from 46 Mya to 43 Mya. Analysis of the fossil record of statoliths (from findings described here, together with a review of previously published data indicates marked biases in our knowledge. Fossil statoliths are known from as far back as the Early Jurassic (199.3 to 190.8 Mya but surprisingly, to the best of our knowledge, no record occurs in the Cretaceous. This is a "knowledge bias" and clearly calls for further studies. Finally, we attempt to compare findings described here with fossils previously used to constrain divergence and/or diversification ages of some coleoid subclades in molecular phylogenies. This comparison clearly indicates that the new records detailed here will challenge some estimated divergence times of coleoid cephalopod subclades.

  16. New Eocene Coleoid (Cephalopoda) Diversity from Statolith Remains: Taxonomic Assignation, Fossil Record Analysis, and New Data for Calibrating Molecular Phylogenies.

    Science.gov (United States)

    Neige, Pascal; Lapierre, Hervé; Merle, Didier

    2016-01-01

    New coleoid cephalopods are described from statolith remains from the Middle Eocene (Middle Lutetian) of the Paris Basin. Fifteen fossil statoliths are identified and assigned to the Sepiidae (Sepia boletzkyi sp. nov.,? Sepia pira sp. nov.), Loliginidae (Loligo clarkei sp. nov.), and Ommastrephidae (genus indet.) families. The sediments containing these fossils indicate permanent aquatic settings in the infralittoral domain. These sediments range in age from 46 Mya to 43 Mya. Analysis of the fossil record of statoliths (from findings described here, together with a review of previously published data) indicates marked biases in our knowledge. Fossil statoliths are known from as far back as the Early Jurassic (199.3 to 190.8 Mya) but surprisingly, to the best of our knowledge, no record occurs in the Cretaceous. This is a "knowledge bias" and clearly calls for further studies. Finally, we attempt to compare findings described here with fossils previously used to constrain divergence and/or diversification ages of some coleoid subclades in molecular phylogenies. This comparison clearly indicates that the new records detailed here will challenge some estimated divergence times of coleoid cephalopod subclades.

  17. A Taxonomic Search Engine: Federating taxonomic databases using web services

    Directory of Open Access Journals (Sweden)

    Page Roderic DM

    2005-03-01

    Full Text Available Abstract Background The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results The Taxonomic Search Engine (TSE is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata for each name. Conclusion The Taxonomic Search Engine is available at http://darwin.zoology.gla.ac.uk/~rpage/portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.

  18. A Taxonomic Search Engine: federating taxonomic databases using web services.

    Science.gov (United States)

    Page, Roderic D M

    2005-03-09

    The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. The Taxonomic Search Engine is available at http://darwin.zoology.gla.ac.uk/~rpage/portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.

  19. Radiochemical analysis in the nuclear research establishment (KFA) Juelich, FRG

    International Nuclear Information System (INIS)

    Anon.

    1975-01-01

    KFA Juelich is one of the two great nuclear research centres of the Federal Republic of Germany. About 3700 employees including about 700 scientists are engaged in a great number of programs and projects belonging to six main fields of research and development: high temperature reactor and energy techniques; nuclear fusion; properties of materials; materials research; life and environment; methods. In the article the radiochemical analysis work of the former Central Institute of Analytical Chemistry and its two successors is described: activation analysis, application of tracer techniques, fission product analysis. Further on the irradiation facilities are described, a short survey is given on the instrumentation, and the future work is outlined. (T.G.)

  20. A data analysis expert system for large established distributed databases

    Science.gov (United States)

    Gnacek, Anne-Marie; An, Y. Kim; Ryan, J. Patrick

    1987-01-01

    A design for a natural language database interface system, called the Deductively Augmented NASA Management Decision support System (DANMDS), is presented. The DANMDS system components have been chosen on the basis of the following considerations: maximal employment of the existing NASA IBM-PC computers and supporting software; local structuring and storing of external data via the entity-relationship model; a natural easy-to-use error-free database query language; user ability to alter query language vocabulary and data analysis heuristic; and significant artificial intelligence data analysis heuristic techniques that allow the system to become progressively and automatically more useful.

  1. Neutron activation analysis as an element of sculpture provenance establishing

    International Nuclear Information System (INIS)

    Panczyk, E.; Rowinska, L.; Walis, L.; Ligeza, M.; Nalepa, B.

    1998-01-01

    Investigation was carried out on the subject named ''Madonna Jackowa'' (XV cent.). The investigation object was to answer whether ''Madonna Jackowa'' was made of a native alabaster. Alabaster derived from five carious mines situated at the Cracow - Lvov line and ''Madonna Jackowa'' were analysed and the trace elements contents were compared. Instrumental neutron activation method was used for analysis of the trace. (author)

  2. Establishing a framework for comparative analysis of genome sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bansal, A.K.

    1995-06-01

    This paper describes a framework and a high-level language toolkit for comparative analysis of genome sequence alignment The framework integrates the information derived from multiple sequence alignment and phylogenetic tree (hypothetical tree of evolution) to derive new properties about sequences. Multiple sequence alignments are treated as an abstract data type. Abstract operations have been described to manipulate a multiple sequence alignment and to derive mutation related information from a phylogenetic tree by superimposing parsimonious analysis. The framework has been applied on protein alignments to derive constrained columns (in a multiple sequence alignment) that exhibit evolutionary pressure to preserve a common property in a column despite mutation. A Prolog toolkit based on the framework has been implemented and demonstrated on alignments containing 3000 sequences and 3904 columns.

  3. The Pareto Analysis for Establishing Content Criteria in Surgical Training.

    Science.gov (United States)

    Kramp, Kelvin H; van Det, Marc J; Veeger, Nic J G M; Pierie, Jean-Pierre E N

    2016-01-01

    Current surgical training is still highly dependent on expensive operating room (OR) experience. Although there have been many attempts to transfer more training to the skills laboratory, little research is focused on which technical behaviors can lead to the highest profit when they are trained outside the OR. The Pareto principle states that in any population that contributes to a common effect, a few account for the bulk of the effect. This principle has been widely used in business management to increase company profits. This study uses the Pareto principle for establishing content criteria for more efficient surgical training. A retrospective study was conducted to assess verbal guidance provided by 9 supervising surgeons to 12 trainees performing 64 laparoscopic cholecystectomies in the OR. The verbal corrections were documented, tallied, and clustered according to the aimed change in novice behavior. The corrections were rank ordered, and a cumulative distribution curve was used to calculate which corrections accounted for 80% of the total number of verbal corrections. In total, 253 different verbal corrections were uttered 1587 times and were categorized into 40 different clusters of aimed changes in novice behaviors. The 35 highest-ranking verbal corrections (14%) and the 11 highest-ranking clusters (28%) accounted for 80% of the total number of given verbal corrections. Following the Pareto principle, we were able to identify the aspects of trainee behavior that account for most corrections given by supervisors during a laparoscopic cholecystectomy on humans. This strategy can be used for the development of new training programs to prepare the trainee in advance for the challenges encountered in the clinical setting in an OR. Copyright © 2016 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

  4. Establishment of a Policy Analysis Capability in Romania

    Directory of Open Access Journals (Sweden)

    Carole M.P. NEVES

    2000-01-01

    Full Text Available The Romanian government, like other governments of former communist countries, emerged from the collapsed Soviet Union ill prepared to confront the complex challenges of governing under a democratic, free market system. At the core of governments that formulate sound public policies, successfully implement programs, and respond effectively to rapidly changing situations is the capacity to carry out independent, high quality research and analysis that results in improved decision making. During the 21st century, the need and acceptance of the incorporation of policy analysis courses in public administration curricula in Romania is expected to grow. In time, educational programs are expected to result in the following consequences: _ Formation of a body of strong independent policy researchers employed by the national and local governments as well as by universities and non-profit institutions _ Utilization of analytical outcomes as tools of political, social and economic improvement by the executive, legislative and judicial branches and by non-profit and private sectors _ Greater public understanding of and participation in public policy processes.

  5. Establishment of analysis procedure for control rod reactivity worth

    Energy Technology Data Exchange (ETDEWEB)

    Song, Hoon; Kim, Young Il; Kim, Sang Ji; Kim, Young In

    2001-03-01

    As to the calculation method of control rod reactivity relating to hexagonal assembly, which are used generally in fast reactor, we have investigated the calculation method, the problems to rise during calculation, the degrees of calculation and the enhancement of calculation modeling so on, and estimated the application of calculation method through comparison and analysis of calculation result using the effective cross section generation system, TRANSX/TWODANT, and neutron flux calculation system, diffusion theory code DIF-3D, which are belonged to K-CORE System, and determined the basic calculation method, and extracted the present calculation problem in case of application in K-CORE System and the future improvement items so on.

  6. Establishment of analysis procedure for control rod reactivity worth

    International Nuclear Information System (INIS)

    Song, Hoon; Kim, Young Il; Kim, Sang Ji; Kim, Young In

    2001-03-01

    As to the calculation method of control rod reactivity relating to hexagonal assembly, which are used generally in fast reactor, we have investigated the calculation method, the problems to rise during calculation, the degrees of calculation and the enhancement of calculation modeling so on, and estimated the application of calculation method through comparison and analysis of calculation result using the effective cross section generation system, TRANSX/TWODANT, and neutron flux calculation system, diffusion theory code DIF-3D, which are belonged to K-CORE System, and determined the basic calculation method, and extracted the present calculation problem in case of application in K-CORE System and the future improvement items so on

  7. Establishing working standards of chromosome aberrations analysis for biological dosimetry

    International Nuclear Information System (INIS)

    Bui Thi Kim Luyen; Tran Que; Pham Ngoc Duy; Nguyen Thi Kim Anh; Ha Thi Ngoc Lien

    2015-01-01

    Biological dosimetry is an dose assessment method using specify bio markers of radiation. IAEA (International Atomic Energy Agency) and ISO (International Organization for Standardization) defined that dicentric chromosome is specify for radiation, it is a gold standard for biodosimetry. Along with the documents published by IAEA, WHO, ISO and OECD, our results of study on the chromosome aberrations induced by radiation were organized systematically in nine standards that dealing with chromosome aberration test and micronucleus test in human peripheral blood lymphocytes in vitro. This standard addresses: the reference dose-effect for dose estimation, the minimum detection levels, cell culture, slide preparation, scoring procedure for chromosome aberrations use for biodosimetry, the criteria for converting aberration frequency into absorbed dose, reporting of results. Following these standards, the automatic analysis devices were calibrated for improving biological dosimetry method. This standard will be used to acquire and maintain accreditation of the Biological Dosimetry laboratory in Nuclear Research Institute. (author)

  8. Elemental analysis of artefacts - establishing external beam PIXE

    International Nuclear Information System (INIS)

    Alves, A.; Johnston, P.; Short, R.; Bubb, I.

    1999-01-01

    The development of an external PIXE facility on the 1 MV Tandetron accelerator at RMIT has led to a wide range of research possibilities. A proton beam, generated inside a vacuum is brought into air via an Au coated Kapton foil exit window (thickness 8μm, diameter 0.35mm). Monitoring of the beam intensity is achieved by detecting backscattered protons from the inside Au coating on the window. Artefacts, which may be too large to be placed inside the vacuum, are positioned in the beamline opposite the exit window. An optical system consisting of a CCD camera, alignment laser and two mirrors allows viewing of a region of the target 10mm x 10mm. This technique provides quantitative analysis of elements in the pigments used in paintings and on ceramics, which is a valuable tool in art conservation and authentication. Application of the technique to a ceramic sample from the historic house 'Viewbank' is described

  9. Diesel engine coolant analysis, new application for established instrumentation

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, D P; Lukas, M; Lynch, B K [Spectro Incorporated, Littleton, MA (United States)

    1998-12-31

    Rotating disk electrode (RDE) arc emission spectrometers are user` many commercial, industrial and military laboratories throughout the world to analyze millions of oil and fuel samples each year. In fact, RDE spectrometers have been used exclusively for oil and fuel analysis for so long that it has nearly been forgotten by most practitioners that when RDE spectrometers were first introduced more than 40 years ago, they were routinely used for aqueous samples as well. This presentation reviews early methods of aqueous sample analysis using RDE technology. This presentation also describes recent work to calibrate an RDE spectrometer for both water samples and for engine coolant samples which are a mixture of approximately 50 % water and 50 % ethylene or propylene glycol. Limits of detection determined for aqueous standards are comparable to limits of detection for oil standards. Repeatability of aqueous samples is comparable to the repeatability achieved for oil samples. A comparison of results for coolant samples measured by both inductively coupled plasma (ICP) and rotating disk electrode (RDE) spectrometers is presented. Not surprisingly, RDE results are significantly higher for samples containing particles larger than a few micrometers. Although limits of detection for aqueous samples are not as low as can be achieved using the more modern ICP spectrometric method or the more cumbersome atomic absorption (AA) method, this presentation suggests that RDE spectrometers may be appropriate for certain types of aqueous samples in situations where the more sensitive ICP or AA spectrometers and the laboratory environment and skilled personnel needed for them to operate are not conveniently available. (orig.) 4 refs.

  10. Diesel engine coolant analysis, new application for established instrumentation

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, D.P.; Lukas, M.; Lynch, B.K. [Spectro Incorporated, Littleton, MA (United States)

    1997-12-31

    Rotating disk electrode (RDE) arc emission spectrometers are user` many commercial, industrial and military laboratories throughout the world to analyze millions of oil and fuel samples each year. In fact, RDE spectrometers have been used exclusively for oil and fuel analysis for so long that it has nearly been forgotten by most practitioners that when RDE spectrometers were first introduced more than 40 years ago, they were routinely used for aqueous samples as well. This presentation reviews early methods of aqueous sample analysis using RDE technology. This presentation also describes recent work to calibrate an RDE spectrometer for both water samples and for engine coolant samples which are a mixture of approximately 50 % water and 50 % ethylene or propylene glycol. Limits of detection determined for aqueous standards are comparable to limits of detection for oil standards. Repeatability of aqueous samples is comparable to the repeatability achieved for oil samples. A comparison of results for coolant samples measured by both inductively coupled plasma (ICP) and rotating disk electrode (RDE) spectrometers is presented. Not surprisingly, RDE results are significantly higher for samples containing particles larger than a few micrometers. Although limits of detection for aqueous samples are not as low as can be achieved using the more modern ICP spectrometric method or the more cumbersome atomic absorption (AA) method, this presentation suggests that RDE spectrometers may be appropriate for certain types of aqueous samples in situations where the more sensitive ICP or AA spectrometers and the laboratory environment and skilled personnel needed for them to operate are not conveniently available. (orig.) 4 refs.

  11. CANDU safety analysis system establishment; development of trip coverage and multi-dimensional hydrogen analysis methodology

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jong Ho; Ohn, M. Y.; Cho, C. H. [KOPEC, Taejon (Korea)

    2002-03-01

    The trip coverage analysis model requires the geometry network for primary and secondary circuit as well as the plant control system to simulate all the possible plant operating conditions throughout the plant life. The model was validated for the power maneuvering and the Wolsong 4 commissioning test. The trip coverage map was produced for the large break loss of coolant accident and the complete loss of class IV power event. The reliable multi-dimensional hydrogen analysis requires the high capability for thermal hydraulic modelling. To acquire such a basic capability and verify the applicability of GOTHIC code, the assessment of heat transfer model, hydrogen mixing and combustion model was performed. Also, the assessment methodology for flame acceleration and deflagration-to-detonation transition is established. 22 refs., 120 figs., 31 tabs. (Author)

  12. Generalizing human error rates: A taxonomic approach

    International Nuclear Information System (INIS)

    Buffardi, L.; Fleishman, E.; Allen, J.

    1989-01-01

    It is well established that human error plays a major role in malfunctioning of complex, technological systems and in accidents associated with their operation. Estimates of the rate of human error in the nuclear industry range from 20-65% of all system failures. In response to this, the Nuclear Regulatory Commission has developed a variety of techniques for estimating human error probabilities for nuclear power plant personnel. Most of these techniques require the specification of the range of human error probabilities for various tasks. Unfortunately, very little objective performance data on error probabilities exist for nuclear environments. Thus, when human reliability estimates are required, for example in computer simulation modeling of system reliability, only subjective estimates (usually based on experts' best guesses) can be provided. The objective of the current research is to provide guidelines for the selection of human error probabilities based on actual performance data taken in other complex environments and applying them to nuclear settings. A key feature of this research is the application of a comprehensive taxonomic approach to nuclear and non-nuclear tasks to evaluate their similarities and differences, thus providing a basis for generalizing human error estimates across tasks. In recent years significant developments have occurred in classifying and describing tasks. Initial goals of the current research are to: (1) identify alternative taxonomic schemes that can be applied to tasks, and (2) describe nuclear tasks in terms of these schemes. Three standardized taxonomic schemes (Ability Requirements Approach, Generalized Information-Processing Approach, Task Characteristics Approach) are identified, modified, and evaluated for their suitability in comparing nuclear and non-nuclear power plant tasks. An agenda for future research and its relevance to nuclear power plant safety is also discussed

  13. Performance, labour flexibility and migrant workers in hotels: An establishment and departmental level analysis

    OpenAIRE

    Yaduma, N; Williams, A; Lockwood, A; Park, S

    2015-01-01

    © 2015. This paper analyses flexible working, and the employment of migrants, as determinants of performance in hotels, utilising a highly disaggregated data set of actual hours worked and outputs, on a monthly basis, over an 8 year period for 25 establishments within a single firm. It examines not only inter-establishment, but also intra-establishment (departmental) variations in performance. The analysis also systematically compares the findings based on financial versus physical measures, ...

  14. TaxMan: a taxonomic database manager

    Directory of Open Access Journals (Sweden)

    Blaxter Mark

    2006-12-01

    Full Text Available Abstract Background Phylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic problems. Supermatrices (concatenated multiple sequence alignments of multiple genes can yield more phylogenetic signal than individual genes. However, manually assembling such datasets for a large taxonomic group is time-consuming and error-prone. Additionally, sequence curation, alignment and assessment of the results of phylogenetic analysis are made particularly difficult by the potential for a given gene in a given species to be unrepresented, or to be represented by multiple or partial sequences. We have developed a software package, TaxMan, that largely automates the processes of sequence acquisition, consensus building, alignment and taxon selection to facilitate this type of phylogenetic study. Results TaxMan uses freely available tools to allow rapid assembly, storage and analysis of large, aligned DNA and protein sequence datasets for user-defined sets of species and genes. The user provides GenBank format files and a list of gene names and synonyms for the loci to analyse. Sequences are extracted from the GenBank files on the basis of annotation and sequence similarity. Consensus sequences are built automatically. Alignment is carried out (where possible, at the protein level and aligned sequences are stored in a database. TaxMan can automatically determine the best subset of taxa to examine phylogeny at a given taxonomic level. By using the stored aligned sequences, large concatenated multiple sequence alignments can be generated rapidly for a subset and output in analysis-ready file formats. Trees resulting from phylogenetic analysis can be stored and compared with a reference taxonomy. Conclusion TaxMan allows rapid automated assembly of a multigene datasets of aligned sequences for large taxonomic groups. By extracting sequences on the basis of

  15. Using HABIT to Establish the Chemicals Analysis Methodology for Maanshan Nuclear Power Plant

    OpenAIRE

    J. R. Wang; S. W. Chen; Y. Chiang; W. S. Hsu; J. H. Yang; Y. S. Tseng; C. Shih

    2017-01-01

    In this research, the HABIT analysis methodology was established for Maanshan nuclear power plant (NPP). The Final Safety Analysis Report (FSAR), reports, and other data were used in this study. To evaluate the control room habitability under the CO2 storage burst, the HABIT methodology was used to perform this analysis. The HABIT result was below the R.G. 1.78 failure criteria. This indicates that Maanshan NPP habitability can be maintained. Additionally, the sensitivity study of the paramet...

  16. Designing and conducting in silico analysis for identifying of Echinococcus spp. with discrimination of novel haplotypes: an approach to better understanding of parasite taxonomic.

    Science.gov (United States)

    Spotin, Adel; Gholami, Shirzad; Nasab, Abbas Najafi; Fallah, Esmaeil; Oskouei, Mahmoud Mahami; Semnani, Vahid; Shariatzadeh, Seyyed Ali; Shahbazi, Abbas

    2015-04-01

    The definitive identification of Echinococcus species is currently carried out by sequencing and phylogenetic strategies. However, the application of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns is not broadly used as a result of heterogeneity traits of Echinococcus genome in different regions of the world. Therefore, designing and conducting a standardized pattern should indigenously be considered in under-studied areas. In this investigation, an in silico mapping was designed and developed for eight Echinococcus spp. on the basis of regional sequences in Iran and the world. The numbers of 60 Echinococcus isolates were collected from the liver and lungs of 15 human, 15 sheep, 15 cattle, and 15 camel cases in Semnan province, Central Iran. DNA samples were extracted and examined by polymerase chain reaction of ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) and PCR-RFLP via Rsa1 endonuclease enzyme. Moreover, 15 amplicons of cytochrome oxidase 1 (Cox1) were directly sequenced in order to identify the strains/haplotypes. PCR-RFLP and phylogenetic analyses revealed firmly the presence of the G1 and G6 genotypes with heterogeneity (three novel haplotypes) of Cox1 gene although no other expected genotypes were found in the region. Finding shows that the identification of novel haplotypes along with discrimination of Echinococcus spp. through regional patterns can unambiguously illustrate the real taxonomic status of parasite in Central Iran.

  17. PESI - a taxonomic backbone for Europe

    Science.gov (United States)

    Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D.; Boegh, Phillip S.; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M.; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M.J.C.; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M. de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A.; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

    2015-01-01

    Abstract Background Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. PMID:26491393

  18. Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri

    Science.gov (United States)

    TANIZAWA, Yasuhiro; KOBAYASHI, Hisami; KAMINUMA, Eli; SAKAMOTO, Mitsuo; OHKUMA, Moriya; NAKAMURA, Yasukazu; ARITA, Masanori; TOHNO, Masanori

    2017-01-01

    Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573T to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L. parakefiri in functional foods such as kefir grains. PMID:28748134

  19. The taxlist package: managing plant taxonomic lists in R

    Directory of Open Access Journals (Sweden)

    Miguel Alvarez

    2018-05-01

    Full Text Available Taxonomic lists are crucial elements of vegetation-plot databases and provide the links between original entries, reference taxon views and different taxon concepts. We introduce the R package taxlist in the context of object-oriented modelling for taxonomic lists. This package provides a data structure based on species lists in Turboveg, which is a software broadly used for the storage of vegetation-plot databases and implements functions for importing and handling them prior to statistical analysis. We also present a schema for relational databases, compatible with taxlist objects and recommend its use for handling diversity records.

  20. Floristic composition and taxonomic distribution of plants in the ...

    African Journals Online (AJOL)

    Floristic composition and taxonomic distribution of plants in the dryland of Northwestern Nigeria. ... Analysis of abundance and rarity of species reveals that 10% and 90% of the encountered species were abundant and rare respectively in the study area. These finding poses serious ecological concerns in the study area, ...

  1. Strategic analysis on establishing a natural gas trading hub in China

    Directory of Open Access Journals (Sweden)

    Xiaoguang Tong

    2014-12-01

    Full Text Available Since 2010, the LNG importing price premium in the Asia–Pacific markets has become increasingly high, generating great effects on the economic development in China. In addition, the natural gas dependence degree is expanding continuously, making it extremely urgent to establish a natural gas trading hub in China, with the aim to ensure national energy security, to gain the pricing power, and to build the regional benchmark prices. Through a comparative analysis of internal strength/weakness and external competitiveness, we concluded that with intensively-issued supporting policies on the natural gas sector, the initiation of spot and futures markets, the rapid growth of gas production and highly-improved infrastructures, as well as Shanghai's advantageous location, China has more advantages in establishing an Asian Natural Gas Trading Hub than other counties like Singapore, Japan and Malaysia. Moreover, based on the SWOT (strength, weakness, opportunity and threat and the marketization process analysis, the following strategies were presented: to impel the establishment of a natural gas trading hub depending on the gas supply condition, to follow the policies to complete the gas storage system, to form regional communities by taking comparative advantages, and to reinforce the marketization reform and regulation system establishment with foreign experiences for reference. This study rationalized the necessity and practicality of establishing a natural gas trading hub in China and will help China make a proper decision and find a periodical strategic path in this sector.

  2. Population density and efficiency in energy consumption: An empirical analysis of service establishments

    International Nuclear Information System (INIS)

    Morikawa, Masayuki

    2012-01-01

    This study, using novel establishment-level microdata from the Energy Consumption Statistics, empirically analyzes the effect of urban density on energy intensity in the service sector. According to the analysis, the efficiency of energy consumption in service establishments is higher for densely populated cities. Quantitatively, after controlling for differences among industries, energy efficiency increases by approximately 12% when the density in a municipality population doubles. This result suggests that, given a structural transformation toward the service economy, deregulation of excessive restrictions hindering urban agglomeration, and investment in infrastructure in city centers would contribute to environmentally friendly economic growth.

  3. Establishment of analytical methods for analysis of pesticides and organic chlorides by hplc

    International Nuclear Information System (INIS)

    Ghaffar, A.; Mashiatullah, A.; Javed, T.

    2012-01-01

    Methods for the analysis of organic chlorides and pesticides like dichlorophenol (DCP), DDT, Chlorpyrifos, Cypermethrin, Melathion, Diazinon and Pendimathalin by HPLC equipped with UV detector were established. The methods were optimized by applying different wavelengths and by changing the composition of mobile phase and flow rates. A series of analysis were performed to optimize the solvent composition, flow rate and wave length for analysis. The standard solutions with different concentration were prepared and run on HPLC. The calibration curves constructed from the peak area versus concentrations were linear (r = 0. 99). Efficiency of the developed methods was tested by taking known quantities of compounds in sample media by spiking separate portions of samples and repeating the analysis. The accuracy of the established methods was checked by interference and spiking the samples with the standard solution. The sample was analyzed and spiked with equal volume of standard solution. The calculated and actual analyzed concentrations were compared for the accuracy of method. The recoveries of samples ranged between 96-98 %, which prove the accuracy of the established methods. (orig./A.B.)

  4. [Taxonomic theory for non-classical systematics].

    Science.gov (United States)

    Pavlinov, I Ia

    2012-01-01

    Outlined briefly are basic principles of construing general taxonomic theory for biological systematics considered in the context of non-classical scientific paradigm. The necessity of such kind of theory is substantiated, and some key points of its elaboration are exposed: its interpretation as a framework concept for the partial taxonomic theories in various schools of systematics; elaboration of idea of cognitive situation including three interrelated components, namely subject, object, and epistemic ones; its construing as a content-wisely interpreted quasi-axiomatics, with strong structuring of its conceptual space including demarcation between axioms and inferring rules; its construing as a "conceptual pyramid" of concepts of various levels of generality; inclusion of a basic model into definition of the taxonomic system (classification) regulating its content. Two problems are indicated as fundamental: definition of taxonomic diversity as a subject domain for the systematics as a whole; definition of onto-epistemological status of taxonomic system (classification) in general and of taxa in particular.

  5. A Study on the Development of Building Energy Analysis Program and the Establishment of BEPS

    Energy Technology Data Exchange (ETDEWEB)

    Kong, S.R.; Kwon, K.J.; Yoo, Y.H.; Cho, Y.K.; Kijm, Y.D.; Han, S.W. [Korea Electric Power Corp. (KEPCO), Taejon (Korea, Republic of). Research Center; Kim, M.H.; Kim, K.W.; Cho, K.H.; Lee, H.W.; Lee, Y.H.; Kim, S.J.; Song, K.S.; Heon, C.T.; Choi, J.M.; Kim, Y.I.; Suk, H.T.; Kang, J.S.; Kim, Y.D.; Kang, K.T.; Lee, J.E.; Kwark, H.S. [Seoul National Univ. (Korea, Republic of)

    1994-12-31

    The amount of energy consumption in building covers the 30% of the total energy consumption and that of electricity is much the same. Because of the improvement of the living quality, energy consumption in building part is increasing and the rate is much higher than that of other parts. So, KEPCO, one of the major domestic energy suppliers and consumers, needs to develop reliable computerized building energy analysis program and to establish building energy performance standards for the reasonable energy management and the efficient execution of energy budget and the improvement of working condition of the corp`s buildings. So the study aims to the development of computerized building energy analysis program, and the establishment energy budget level and building energy performance standards for the corp`s buildings.

  6. Establishment of Grain Farmers' Supply Response Model and Empirical Analysis under Minimum Grain Purchase Price Policy

    OpenAIRE

    Zhang, Shuang

    2012-01-01

    Based on farmers' supply behavior theory and price expectations theory, this paper establishes grain farmers' supply response model of two major grain varieties (early indica rice and mixed wheat) in the major producing areas, to test whether the minimum grain purchase price policy can have price-oriented effect on grain production and supply in the major producing areas. Empirical analysis shows that the minimum purchase price published annually by the government has significant positive imp...

  7. Antipyretic therapy in critically ill patients with established sepsis: a trial sequential analysis.

    Directory of Open Access Journals (Sweden)

    Zhongheng Zhang

    Full Text Available antipyretic therapy for patients with sepsis has long been debated. The present study aimed to explore the beneficial effect of antipyretic therapy for ICU patients with sepsis.systematic review and trial sequential analysis of randomized controlled trials.Pubmed, Scopus, EBSCO and EMBASE were searched from inception to August 5, 2014.Mortality was dichotomized as binary outcome variable and odds ratio (OR was chosen to be the summary statistic. Pooled OR was calculated by using DerSimonian and Laird method. Statistical heterogeneity was assessed by using the statistic I2. Trial sequential analysis was performed to account for the small number of trials and patients.A total of 6 randomized controlled trials including 819 patients were included into final analysis. Overall, there was no beneficial effect of antipyretic therapy on mortality risk in patients with established sepsis (OR: 1.02, 95% CI: 0.50-2.05. The required information size (IS was 2582 and our analysis has not yet reached half of the IS. The Z-curve did not cross the O'Brien-Fleming α-spending boundary or reach the futility, indicating that the non-significant result was probably due to lack of statistical power.our study fails to identify any beneficial effect of antipyretic therapy on ICU patients with established diagnosis of sepsis. Due to limited number of total participants, more studies are needed to make a conclusive and reliable analysis.

  8. Developing green supply chain management strategies: A taxonomic approach

    Directory of Open Access Journals (Sweden)

    Michael Mutingi

    2013-06-01

    Full Text Available Purpose: The objective of this research is to explore the empirical green supply chain activities found in literature, and to develop a taxonomic framework that can be used for formulating appropriate strategies for green supply chains, based on characteristic dimensions for the green supply chain. Design/methodology/approach: The taxonomic framework is developed through (i analysis of green supply chain activities found in existing empirical work or case studies recorded in literature, (ii identification of key dimensions that influence green supply chain management strategies, and (iii development of a taxonomic scheme for selecting or developing green strategies. Findings: The paper finds that this study yielded: a set of three characteristic dimensions that influence strategic green supply chain management, and a guided structured approach selecting appropriate green strategies, providing managerial insights. Research limitations/implications: This paper shows that future work includes development of specific performance management indices according to the taxonomy of green strategies developed in this study. Practical implications: This research provided a practical guided approach that enhances appropriate formulation of green strategies for green supply chain management, while providing sound managerial insights for the supply chain decision maker. The choice of supply chain strategy directly impacts the overall environmental, economic and operations performance of the supply chain. Originality/value: This study presents to supply chain decision makers a new taxonomic framework that simplifies and enhances the formulation of green strategies, and to researchers a comparative understanding of various strategies applicable to green supply chains.

  9. Large sample neutron activation analysis: establishment at CDTN/CNEN, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Menezes, Maria Angela de B.C., E-mail: menezes@cdtn.b [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil); Jacimovic, Radojko, E-mail: radojko.jacimovic@ijs.s [Jozef Stefan Institute, Ljubljana (Slovenia). Dept. of Environmental Sciences. Group for Radiochemistry and Radioecology

    2011-07-01

    In order to improve the application of the neutron activation technique at CDTN/CNEN, the large sample instrumental neutron activation analysis is being established, IAEA BRA 14798 and FAPEMIG APQ-01259-09 projects. This procedure, LS-INAA, usually requires special facilities for the activation as well as for the detection. However, the TRIGA Mark I IPR R1, CDTN/CNEN has not been adapted for the irradiation and the usual gamma spectrometry has being carried out. To start the establishment of the LS-INAA, a 5g sample - IAEA/Soil 7 reference material was analyzed by k{sub 0}-standardized method. This paper is about the detector efficiency over the volume source using KayWin v2.23 and ANGLE V3.0 software. (author)

  10. Establishment of an ASEAN Ion Beam Analysis Centre for Material Characterizations at Chiang Mai University

    International Nuclear Information System (INIS)

    Kamwanna, T.; Junphong, P.; Yu, L.D.; Singkarat, S.; Intarasiri, S.; Suwannakachorn, D.

    2015-01-01

    A comprehensive ion beam analysis centre unique in the ASEAN (Association of Southeast Asian Nations) region has been established at Chiang Mai University, Thailand. The centre is equipped with a 1.7 MV Tandetron tandem accelerator and a 300 kV medium energy ion beam accelerator for ion beam analysis. The Tandetron accelerator employs two ion sources, a duoplasmatron ion source and a sputter ion source, capable of producing ion beams of both light species (hydrogen and helium) and heavy species. The beamline is currently able to perform ion beam analysis techniques, such as Rutherford backscattering spectrometry (RBS), RBS/channelling, elastic backscattering (EBS), particle induced x ray emission (PIXE) and ionoluminescence (IL) with the assistance of commercial and self-developed software. The medium energy ion accelerator features an ns pulsed beam so that time of flight (ToF) RBS analysis using medium energy ion beams is available for detailed analysis of materials. Ion beam analysis experiments and applications have been vigorously developed for the real time characterization of various materials. Examples are presented and qualities of the ion beam analysis techniques are discussed. (author)

  11. Taxonomic names, metadata, and the Semantic Web

    Directory of Open Access Journals (Sweden)

    Roderic D. M. Page

    2006-01-01

    Full Text Available Life Science Identifiers (LSIDs offer an attractive solution to the problem of globally unique identifiers for digital objects in biology. However, I suggest that in the context of taxonomic names, the most compelling benefit of adopting these identifiers comes from the metadata associated with each LSID. By using existing vocabularies wherever possible, and using a simple vocabulary for taxonomy-specific concepts we can quickly capture the essential information about a taxonomic name in the Resource Description Framework (RDF format. This opens up the prospect of using technologies developed for the Semantic Web to add ``taxonomic intelligence" to biodiversity databases. This essay explores some of these ideas in the context of providing a taxonomic framework for the phylogenetic database TreeBASE.

  12. A nutritional risk screening model for patients with liver cirrhosis established using discriminant analysis

    Directory of Open Access Journals (Sweden)

    ZHU Binghua

    2017-06-01

    Full Text Available ObjectiveTo establish a nutritional risk screening model for patients with liver cirrhosis using discriminant analysis. MethodsThe clinical data of 273 patients with liver cirrhosis who were admitted to Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine from August 2015 to March 2016 were collected. Body height, body weight, upper arm circumference, triceps skinfold thickness, subscapular skinfold thickness, and hand grip strength were measured and recorded, and then body mass index (BMI and upper arm muscle circumference were calculated. Laboratory markers including liver function parameters, renal function parameters, and vitamins were measured. The patients were asked to complete Nutritional Risk Screening 2002 and Malnutrition Universal Screening Tool (MUST, and a self-developed nutritional risk screening pathway was used for nutritional risk classification. Observation scales of the four diagnostic methods in traditional Chinese medicine were used to collect patients′ symptoms and signs. Continuous data were expressed as mean±SD (x±s; an analysis of variance was used for comparison between multiple groups, and the least significant difference t-test was used for further comparison between two groups. Discriminant analysis was used for model establishment, and cross validation was used for model verification. ResultsThe nutritional risk screening pathway for patients with liver cirrhosis was used for the screening of respondents, and there were 49 patients (17.95% in non-risk group, 49 (17.95% in possible-risk group, and 175 (64.10% in risk group. The distance criterion function was used to establish the nutritional risk screening model for patients with liver cirrhosis: D1=-11.885+0.310×BMI+0150×MAC+0.005×P-Alb-0.001×Vit B12+0.103×Vit D-0.89×ascites-0.404×weakness-0.560×hypochondriac pain+0035×dysphoria with feverish sensation (note: if a patient has ascites, weakness, hypochondriac pain

  13. [Etiological analysis and establishment of a discriminant model for lower respiratory tract infections in hospitalized patients].

    Science.gov (United States)

    Chen, Y S; Lin, X H; Li, H R; Hua, Z D; Lin, M Q; Huang, W S; Yu, T; Lyu, H Y; Mao, W P; Liang, Y Q; Peng, X R; Chen, S J; Zheng, H; Lian, S Q; Hu, X L; Yao, X Q

    2017-12-12

    Objective: To analyze the pathogens of lower respiratory tract infection(LRTI) including bacterial, viral and mixed infection, and to establish a discriminant model based on clinical features in order to predict the pathogens. Methods: A total of 243 hospitalized patients with lower respiratory tract infections were enrolled in Fujian Provincial Hospital from April 2012 to September 2015. The clinical data and airway (sputum and/or bronchoalveolar lavage) samples were collected. Microbes were identified by traditional culture (for bacteria), loop-mediated isothermal amplification(LAMP) and gene sequencing (for bacteria and atypical pathogen), or Real-time quantitative polymerase chain reaction (Real-time PCR)for viruses. Finally, a discriminant model was established by using the discriminant analysis methods to help to predict bacterial, viral and mixed infections. Results: Pathogens were detected in 53.9% (131/243) of the 243 cases.Bacteria accounted for 23.5%(57/243, of which 17 cases with the virus, 1 case with Mycoplasma pneumoniae and virus), mainly Pseudomonas Aeruginosa and Klebsiella Pneumonia. Atypical pathogens for 4.9% (12/243, of which 3 cases with the virus, 1 case of bacteria and viruses), all were mycoplasma pneumonia. Viruses for 34.6% (84/243, of which 17 cases of bacteria, 3 cases with Mycoplasma pneumoniae, 1 case with Mycoplasma pneumoniae and bacteria) of the cases, mainly Influenza A virus and Human Cytomegalovirus, and other virus like adenovirus, human parainfluenza virus, respiratory syncytial virus, human metapneumovirus, human boca virus were also detected fewly. Seven parameters including mental status, using antibiotics prior to admission, complications, abnormal breath sounds, neutrophil alkaline phosphatase (NAP) score, pneumonia severity index (PSI) score and CRUB-65 score were enrolled after univariate analysis, and discriminant analysis was used to establish the discriminant model by applying the identified pathogens as the

  14. Establishment of joint application system of safety analysis codes between Korea and Vietnam

    International Nuclear Information System (INIS)

    Chung, Bub Dong; Kim, Kyung Doo; Park, Cheol; Bae, Sung Won; Baek, Won Pil; Song, Cheol hwa; Jeong, Jae Jun; Lee, Seung Wook; Hwang, Moon Kyu; Lee, Chang Sup

    2011-04-01

    The following KAERI-VAEI collaboration works have been performed during the 2 year project ('09.4∼'11.4). 1) On the job training of Vietnam code users(1st training for 4 VAEI staff-3 months. 2nd training for 3 VAEI staff- 3 month), 2) Lecture of nuclear safety analysis (30 hrs basic course and 30 hrs advanced course), 3) Review of safety analysis method (IAEA safety concept and requirements), 4) Collaborative assessment of safety analysis code MARS (13 conceptual problem, 2 separate effect test problem, 1 integral effect test problem), 5) Input deck preparation of standard PWR (Preparation of APR1400 input deck and safety analysis of DBA). VAEI staffs have been familiarized to Korean PWR safety assessment technology through the collaboration assessment work using a computer code developed in Korea. The lectures for Vietnamese research will be contributed to the utilization and cultivation of Korean safety technology. The collaborated assessment works will be used for the establishment of MARS based safety analysis system which is independent from US safety assessment system

  15. Instability risk analysis and risk assessment system establishment of underground storage caverns in bedded salt rock

    Science.gov (United States)

    Jing, Wenjun; Zhao, Yan

    2018-02-01

    Stability is an important part of geotechnical engineering research. The operating experiences of underground storage caverns in salt rock all around the world show that the stability of the caverns is the key problem of safe operation. Currently, the combination of theoretical analysis and numerical simulation are the mainly adopts method of reserve stability analysis. This paper introduces the concept of risk into the stability analysis of underground geotechnical structure, and studies the instability of underground storage cavern in salt rock from the perspective of risk analysis. Firstly, the definition and classification of cavern instability risk is proposed, and the damage mechanism is analyzed from the mechanical angle. Then the main stability evaluating indicators of cavern instability risk are proposed, and an evaluation method of cavern instability risk is put forward. Finally, the established cavern instability risk assessment system is applied to the analysis and prediction of cavern instability risk after 30 years of operation in a proposed storage cavern group in the Huai’an salt mine. This research can provide a useful theoretical base for the safe operation and management of underground storage caverns in salt rock.

  16. Establishment of joint application system of safety analysis codes between Korea and Vietnam

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Bub Dong; Kim, Kyung Doo; Park, Cheol; Bae, Sung Won; Baek, Won Pil; Song, Cheol hwa; Jeong, Jae Jun; Lee, Seung Wook; Hwang, Moon Kyu; Lee, Chang Sup [KAERI, Daejeon (Korea, Republic of)

    2011-04-15

    The following KAERI-VAEI collaboration works have been performed during the 2 year project ('09.4{approx}'11.4). 1) On the job training of Vietnam code users(1st training for 4 VAEI staff-3 months. 2nd training for 3 VAEI staff- 3 month), 2) Lecture of nuclear safety analysis (30 hrs basic course and 30 hrs advanced course), 3) Review of safety analysis method (IAEA safety concept and requirements), 4) Collaborative assessment of safety analysis code MARS (13 conceptual problem, 2 separate effect test problem, 1 integral effect test problem), 5) Input deck preparation of standard PWR (Preparation of APR1400 input deck and safety analysis of DBA). VAEI staffs have been familiarized to Korean PWR safety assessment technology through the collaboration assessment work using a computer code developed in Korea. The lectures for Vietnamese research will be contributed to the utilization and cultivation of Korean safety technology. The collaborated assessment works will be used for the establishment of MARS based safety analysis system which is independent from US safety assessment system

  17. Contextual Factors for Establishing Nursing Regulation in Iran: A Qualitative Content Analysis.

    Science.gov (United States)

    Nejatian, Ahmad; Joulaei, Hassan

    2018-04-01

    Professional regulation is one of the strategies of the governments which protect the public's right. Nursing practice is not an exception; hence, it is regulated to protect the public against nursing services' adverse effects. Although modern nursing in Iran started from 100 years ago, documents show that there was no regulation mechanism for nursing in Iran till 2016. Hence, this study was conducted to illuminate the contextual factors affecting the nursing regulation process in Iran. To explore the contextual elements of late establishment of nursing registration as an important part of nursing regulation, we applied directed qualitative content analysis. For this purpose, all the historical events and related materials including articles published in scientific journals, gray literature, statements, news articles, and interviews in the period of 2006-2016 were reviewed and analyzed by expert panel and categorized in predetermined groups. Pooled analysis data showed four contributing elements that affected the emerging nursing regulation in Iran. These elements include 1) cultural determinants, 2) structural determinants, 3) situational determinants, and 4) international or exogenous determinants. Nursing regulation is an important health policy issue in Iran which needs to be facilitated by contextual factors. These factors are complicated and country-specific. Political willingness should be accompanied by nursing association willingness to establish and improve nursing regulation. Other researches are recommended to explore actors and process and content of nursing regulation policy in Iran.

  18. Taxonomic, biogeographic, and taphonomic reassessment of a large extinct species of paca from the Quaternary of Brazil

    Directory of Open Access Journals (Sweden)

    Elver Luiz Mayer

    2016-12-01

    Full Text Available The taxonomy of extinct species of Cuniculus (Caviomorpha, Rodentia, Mammalia is confusing and poorly studied. Here we provide a taxonomic review of extinct cuniculids, and discuss the taxonomic, biogeographic, taphonomic and chronologic aspects of new remains of an extinct large cuniculid from Brazilian Quaternary Gruta Cuvieri cave deposits. Our taxonomic review suggests that Cuniculus rugiceps (Lund, 1837 is the valid taxon to include all available occurrences of extinct cuniculids. The most evident features of this taxon are its larger size and the stronger and more densely distributed rugosities on the skull external surface when compared to the extant species. At present, the distribution of C. rugiceps is restricted to the tropical region of Brazil. Regarding the new remains, taphonomic analysis of the specimens from Cuvieri Cave suggests our sample is represented by at least seven individuals that accumulated within the cave deposit by pitfall entrapment. The biostratinomy of the specimens was characterized by prolonged surface exposure inside the pit with fragmentation and displacement caused mostly by falling and subsequent trampling by individuals of the same and/or other species. The stratigraphically controlled excavations and chronological data allowed the establishment of a Late Pleistocene minimum age for these specimens.

  19. Establishment of a clean laboratory for ultra trace analysis of nuclear materials in safeguards environmental samples

    International Nuclear Information System (INIS)

    Hanzawa, Yukiko; Magara, Masaaki; Watanabe, Kazuo

    2003-01-01

    The Japan Atomic Energy Research Institute has established a cleanroom facility with cleanliness of ISO Class 5: the Clean Laboratory for Environmental Analysis and Research (CLEAR). It was designed to be used for the analysis of nuclear materials in environmental samples mainly for the safeguards, in addition to the Comprehensive Nuclear-Test-Ban Treaty verification and research on environmental sciences. The CLEAR facility was designed to meet conflicting requirements of a cleanroom and for handling of nuclear materials according to Japanese regulations, i.e., to avoid contamination from outside and to contain nuclear materials inside the facility. This facility has been intended to be used for wet chemical treatment, instrumental analysis and particle handling. A fume-hood to provide a clean work surface for handling of nuclear materials was specially designed. Much attention was paid to the selection of construction materials for use to corrosive acids. The performance of the cleanroom and analytical background in the laboratory are discussed. This facility has satisfactory specification required for joining the International Atomic Energy Agency Network of Analytical Laboratories. It can be concluded that the CLEAR facility enables analysis of ultra trace amounts of nuclear materials at sub-pictogram level in environmental samples. (author)

  20. Ion Torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity.

    Directory of Open Access Journals (Sweden)

    Martin Kemler

    Full Text Available The Kingdom Fungi adds substantially to the diversity of life, but due to their cryptic morphology and lifestyle, tremendous diversity, paucity of formally described specimens, and the difficulty in isolating environmental strains into culture, fungal communities are difficult to characterize. This is especially true for endophytic communities of fungi living in healthy plant tissue. The developments in next generation sequencing technologies are, however, starting to reveal the true extent of fungal diversity. One of the promising new technologies, namely semiconductor sequencing, has thus far not been used in fungal diversity assessments. In this study we sequenced the internal transcribed spacer 1 (ITS1 nuclear encoded ribosomal RNA of the endophytic community of the economically important tree, Eucalyptus grandis, from South Africa using the Ion Torrent Personal Genome Machine (PGM. We determined the impact of various analysis parameters on the interpretation of the results, namely different sequence quality parameter settings, different sequence similarity cutoffs for clustering and filtering of databases for removal of sequences with incomplete taxonomy. Sequence similarity cutoff values only had a marginal effect on the identified family numbers, whereas different sequence quality filters had a large effect (89 vs. 48 families between least and most stringent filters. Database filtering had a small, but statistically significant, effect on the assignment of sequences to reference sequences. The community was dominated by Ascomycota, and particularly by families in the Dothidiomycetes that harbor well-known plant pathogens. The study demonstrates that semiconductor sequencing is an ideal strategy for environmental sequencing of fungal communities. It also highlights some potential pitfalls in subsequent data analyses when using a technology with relatively short read lengths.

  1. Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

    Directory of Open Access Journals (Sweden)

    Jonas Zimmermann

    Full Text Available DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.

  2. Utilizing job/task analysis to establish content validity in the design of training programs

    Energy Technology Data Exchange (ETDEWEB)

    Nay, W.E.

    1988-01-01

    The decade of the 1980's has been a turbulent time for the Department of Energy. With concern mounting about the terrorist threat, a wave of congressional inquiries and internal inspections crossed the nation and engulfed many of the nuclear laboratories and facilities operated by DOE contractors. A typical finding was the need to improve, and increase, the training of the protective force. The immediate reaction resulted in a wide variety of responses, with most contractors feeling safer with too much, rather than not enough training. As soon as the initial pressures to upgrade subsided, a task force was established to evaluate the overall training needs. Representatives from the contractor facilities worked together to conduct a job analysis of the protective force. A generic task inventory was established, and validated at the different sites. This list has been invaluable for determining the tasks, conditions, and standards needed to develop well stated learning objectives. The enhanced training programs are being refined to ensure job content validity based on the data collected.

  3. Establishment of a clean chemistry laboratory at JAERI. Clean laboratory for environmental analysis and research (CLEAR)

    Energy Technology Data Exchange (ETDEWEB)

    Hanzawa, Yukiko; Magara, Masaaki; Watanabe, Kazuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; and others

    2003-02-01

    The JAERI has established a facility with a cleanroom: the Clean Laboratory for Environmental Analysis and Research (CLEAR). This report is an overview of the design, construction and performance evaluation of the CLEAR in the initial stage of the laboratory operation in June 2001. The CLEAR is a facility to be used for analyses of ultra trace amounts of nuclear materials in environmental samples for the safeguards, for the CTBT verification and for researches on environmental sciences. One of the special features of the CLEAR is that it meets double requirements of a cleanroom and for handling of nuclear materials. As another feature of the CLEAR, much attention was paid to the construction materials of the cleanroom for trace analysis of metal elements using considerable amounts of corrosive acids. The air conditioning and purification system, specially designed experimental equipment to provide clean work surfaces, utilities and safety systems are also demonstrated. The potential contamination from the completed cleanroom atmosphere during the analytical procedure was evaluated. It can be concluded that the CLEAR has provided a suitable condition for reliable analysis of ultra trace amounts of nuclear materials and other heavy elements in environmental samples. (author)

  4. A framework for establishing the technical efficiency of Electricity Distribution Counties (EDCs) using Data Envelopment Analysis

    International Nuclear Information System (INIS)

    Mullarkey, Shane; Caulfield, Brian; McCormack, Sarah; Basu, Biswajit

    2015-01-01

    Highlights: • Six models are employed to establish the technical efficiency of Electricity Distribution Counties. • A diagnostic parameter is incorporated to account for differences across Electricity Distribution Counties. • The amalgamation of Electricity Distribution Counties leads to improved efficiency in the production of energy. - Abstract: European Energy market liberalization has entailed the restructuring of electricity power markets through the unbundling of electricity generation, transmission and distribution, supply activities and introducing competition into electricity generation. Under these new electricity market regimes, it is important to have an evaluation tool that is capable of examining the impacts of these market changes. The adoption of Data Envelopment Analysis as a form of benchmarking for electricity distribution regulation is one method to conduct this analysis. This paper applies a Data Envelopment Analysis framework to the electricity distribution network in Ireland to explore the merits of using this approach, to determine the technical efficiency and the potential scope for efficiency improvements through reorganizing and the amalgamation of the distribution network in Ireland. The results presented show that overall grid efficiency is improved through this restructuring. A diagnostic parameter is defined and pursued to account for aberrations across Electricity Distribution Counties as opposed to the traditionally employed environmental variables. The adoption of this diagnostic parameter leads to a more intuitive understanding of Electricity Distribution Counties

  5. Matrix Methods and Models of Economic Analysis in the Marketing Activity of Higher Educational Establishments

    Directory of Open Access Journals (Sweden)

    Natalia Stebliuk

    2018-05-01

    Full Text Available On the present stage of the development of educational environment, it is necessary to use the scientific tools for understanding the market patterns of the interaction of demand and supply of educational services, which will allow not only to navigate the consumer preferences but also to form them. It is in these circumstances that it is extremely important to study changes in the volume of demand for educational services in order to adapt them to the system of higher education. The aim of the article is to substantiate the theoretical positions and develop practical recommendations for the definition of the competitive marketing strategy of higher education organizations in the market of educational services with the help of modern approaches and methods of economic-mathematical modeling. The practical significance of the obtained results is the introduction of methodological provisions for forecasting the demand and supply of educational services for higher educational establishments. The complexity and interdependence of managerial problems in the system of higher education require new ideas and approaches, which necessitates the search for new definite solutions, namely: the research paper offers the method of optimal distribution of budgetary places of the university by means of practical application of the theory of system constraints and the theory of fuzzy sets. Along with that, the calculation of the optimal number of students of the corresponding specialty with the help of cluster analysis has been carried out. In addition, an important place for improvement and development is taken by the economics and mathematical methods and methods of linear programming, they are effective means of identifying the most influential factors in achieving the goals of a higher educational establishment and justifying the marketing strategy of its development in modern conditions. To predict the quantitative values of social and economic indicators

  6. Converting Taxonomic Descriptions to New Digital Formats

    Directory of Open Access Journals (Sweden)

    Hong Cui

    2008-01-01

    Full Text Available Abstract.--The majority of taxonomic descriptions is currently in print format. The majority of digital descriptions are in formats such as DOC, HTML, or PDF and for human readers. These formats do not convey rich semantics in taxonomic descriptions for computer-aided process. Newer digital formats such as XML and RDF accommodate semantic annotations that allow computers to process the rich semantics on human's behalf, thus open up opportunities for a wide range of innovative usages of taxonomic descriptions, such as searching in more precise and flexible ways, integrating with gnomic and geographic information, generating taxonomic keys automatically, and text data mining and information visualization etc. This paper discusses the challenges in automated conversion of multiple collections of descriptions to XML format and reports an automated system, MARTT. MARTT is a machine-learning system that makes use of training examples to tag new descriptions into XML format. A number of utilities are implemented as solutions to the challenges. The utilities are used to reduce the effort for training example preparation, to facilitate the creation of a comprehensive schema, and to predict system performance on a new collection of descriptions. The system has been tested with several plant and alga taxonomic publications including Flora of China and Flora of North America.

  7. Landslide Monitoring Network Establishment within Unified Datum and Stability Analysis in the Three Gorges Reservoir Area

    Directory of Open Access Journals (Sweden)

    Shengxiang Huang

    2017-01-01

    Full Text Available A landslide monitoring network construction within unified datum which combined fiducial points, working reference points, and monitoring points was intensively studied in the Three Gorges Reservoir area. With special long and narrow geographical location in the area, designing and building monitoring network was vital to the realization of landslide monitoring. To build such a network with high precision, this paper mainly focused on the following four aspects: (1 method of using multiple GPS reference stations to build a unified datum network and subnet adjustment, (2 GPS data processing algorithm with millimeter level, (3 analysis of influence on the adjustment resulting from systematic error of time evolution datum from different GPS observations, and (4 establishment and stability analysis of unified datum. Then, using global test and trial-and-error method to analyze the datum based on the GPS observations (2008~2011 of landslide monitoring network in the area, we concluded that there were moved reference points during the three years of high water impoundment, and the horizontal displacement of moved reference points was more than 4 cm, even up to 79.4 cm. The displacement direction of unstable reference points was inspected with geographical environment at sites, which revealed congruency between them.

  8. Current Taxonomical Situation of Streptococcus suis.

    Science.gov (United States)

    Okura, Masatoshi; Osaki, Makoto; Nomoto, Ryohei; Arai, Sakura; Osawa, Ro; Sekizaki, Tsutomu; Takamatsu, Daisuke

    2016-06-24

    Streptococcus suis, a major porcine pathogen and an important zoonotic agent, is considered to be composed of phenotypically and genetically diverse strains. However, recent studies reported several "S. suis-like strains" that were identified as S. suis by commonly used methods for the identification of this bacterium, but were regarded as distinct species from S. suis according to the standards of several taxonomic analyses. Furthermore, it has been suggested that some S. suis-like strains can be assigned to several novel species. In this review, we discuss the current taxonomical situation of S. suis with a focus on (1) the classification history of the taxon of S. suis; (2) S. suis-like strains revealed by taxonomic analyses; (3) methods for detecting and identifying this species, including a novel method that can distinguish S. suis isolates from S. suis-like strains; and (4) current topics on the reclassification of S. suis-like strains.

  9. Global hotspots and correlates of alien species richness across taxonomic groups

    Science.gov (United States)

    Dawson, Wayne; Moser, Dietmar; van Kleunen, Mark; Kreft, Holger; Pergl, Jan; Pysek, Petr; Weigelt, Patrick; Winter, Marten; Lenzner, Bernd; Blackburn, Tim M.; Dyer, Ellie; Cassey, Phillip; Scrivens, Sally-Louise; Economo, Evan P.; Guenard, Benoit; Capinha, Cesar; Seebens, Hanno; Garcia-Diaz, Pablo; Nentwig, Wolfgang; Garcia-Berthou, Emili; Casal, Christine; Mandrak, Nicholas E.; Fuller, Pam; Meyer, Carsten; Essl, Franz

    2017-01-01

    Human-mediated transport beyond biogeographic barriers has led to the introduction and establishment of alien species in new regions worldwide. However, we lack a global picture of established alien species richness for multiple taxonomic groups. Here, we assess global patterns and potential drivers of established alien species richness across eight taxonomic groups (amphibians, ants, birds, freshwater fishes, mammals, vascular plants, reptiles and spiders) for 186 islands and 423 mainland regions. Hotspots of established alien species richness are predominantly island and coastal mainland regions. Regions with greater gross domestic product per capita, human population density, and area have higher established alien richness, with strongest effects emerging for islands. Ants and reptiles, birds and mammals, and vascular plants and spiders form pairs of taxonomic groups with the highest spatial congruence in established alien richness, but drivers explaining richness differ between the taxa in each pair. Across all taxonomic groups, our results highlight the need to prioritize prevention of further alien species introductions to island and coastal mainland regions globally.

  10. Establishing community-based integrated care for elderly patients through interprofessional teamwork: a qualitative analysis

    Directory of Open Access Journals (Sweden)

    Asakawa T

    2017-10-01

    Full Text Available Tomohiro Asakawa,1 Hidenobu Kawabata,1 Kengo Kisa,2 Takayoshi Terashita,3 Manabu Murakami,4 Junji Otaki1 1Department of Medical Education and General Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, 2Kutchan-Kosei General Hospital, Kutchan, Hokkaido, 3Graduate School of Radiological Technology Gunma Prefectural College of Health Sciences, Kamioki-machi, Maebashi, Gunma, 4International Relations Office, Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan Background: Working in multidisciplinary teams is indispensable for ensuring high-quality care for elderly people in Japan’s rapidly aging society. However, health professionals often experience difficulty collaborating in practice because of their different educational backgrounds, ideas, and the roles of each profession. In this qualitative descriptive study, we reveal how to build interdisciplinary collaboration in multidisciplinary teams. Methods: Semi-structured interviews were conducted with a total of 26 medical professionals, including physicians, nurses, public health nurses, medical social workers, and clerical personnel. Each participant worked as a team member of community-based integrated care. The central topic of the interviews was what the participants needed to establish collaboration during the care of elderly residents. Each interview lasted for about 60 minutes. All the interviews were recorded, transcribed verbatim, and subjected to content analysis. Results: The analysis yielded the following three categories concerning the necessary elements of building collaboration: 1 two types of meeting configuration; 2 building good communication; and 3 effective leadership. The two meetings described in the first category – “community care meetings” and “individual care meetings” – were aimed at bringing together the disciplines and discussing individual cases, respectively. Building good communication referred to the activities

  11. Establishment of screening technique for mutant cell and analysis of base sequence in the mutation

    International Nuclear Information System (INIS)

    Sofuni, Toshio; Nomi, Takehiko; Yamada, Masami; Masumura, Kenichi

    2000-01-01

    This research project aimed to establish an easy and quick detection method for radiation-induced mutation using molecular-biological techniques and an effective analyzing method for the molecular changes in base sequence. In this year, Spi mutants derived from γ-radiation exposed mouse were analyzed by PCR method and DNA sequence method. Male transgenic mice were exposed to γ-ray at 5,10, 50 Gy and the transgene was taken out from the genome DNA from the spleen in vivo packaging method. Spi mutant plaques were obtained by infecting the recovered phage to E. coli. Sequence analysis for the mutants was made using ALFred DNA sequencer and SequiTherm TM Long-Red Cycle sequencing kit. Sequence analysis was carried out for 41 of 50 independent Spi mutants obtained. The deletions were classified into 4 groups; Group 1 included 15 mutants that were characterized with a large deletion (43 bp-10 kb) with a short homologous sequence. Group 2 included 11 mutants of a large deletion having no homologous sequence at the connecting region. Group 3 included 11 mutants having a short deletion of less than 20 bp, which occurred in the non-repetitive sequence of gam gene and possibly caused by oxidative breakage of DNA or recombination of DNA fragment produced by the breakage. Group 4 included 4 mutants having deletions as short as 20 bp or less in the repetitive sequence of gam gene, resulting in an alteration of the reading frame. Thus, the synthesis of Gam protein was terminated by the appearance of TGA between code 13 and 14 of redB gene, leading to inactivation of gam gene and redBA gene. These results indicated that most of Spi mutants had a deletion in red/gam region and the deletions in more than half mutants occurred in homologous sequences as short as 8 bp. (M.N.)

  12. ANALYSIS OF THE POSSIBILITY FOR ESTABLISHING PROJECT MANAGEMENT OFFICE (PMO IN COMPANIES IN SERBIA

    Directory of Open Access Journals (Sweden)

    Dragana Milin

    2012-09-01

    Full Text Available Project Management Office (PMO is an organizational unit established to help project managers, project teams and the various levels of management in carrying out the principles of project management. The research was carried out in Serbia, in 2011, with the aim to establish which methodologies and techniques are used for project m anagement, and which of them are used the most frequently. Furthermore, the need for establishment of PMOs in Serbia is discussed. These offices should help in establishing a standardized methodology (at the organization level and thus overcome the obviou s poor use of any project management methodology at all.

  13. A taxonomic revision of Lamium (Lamiaceae)

    NARCIS (Netherlands)

    Mennema, J.

    1989-01-01

    The present study deals with the systematics and taxonomy of the genus Lamium (Lamiaceae). The taxonomic revision is mainly based on the study of herbarium collections, and to a smaller degree on field observations and abstracts from literature. The research was done at the Rijksherbarium, Leyden,

  14. Seasonality, distribution and taxonomic status of avian ...

    African Journals Online (AJOL)

    Description of a new species is based upon morphology of gametocyte development in the peripheral blood of the avian host. This does not distinguish between morphologically identical gametocytes from different avian host families, nor is species or family level a valid taxonomic character. Thus, Haemoproteus and ...

  15. Taxonomic Challenges and Distribution of Gracilarioid Algae ...

    African Journals Online (AJOL)

    This paper reviews the taxonomical literature of the gracilarioid algae from Tanzania, and provides information about their ecology and distribution based on an intensive regime of local collection. Its aim was to provide names, even if on a preliminary basis, for local gracilarioid taxa. Our revision shows that species ...

  16. Taxonomic novelties in African Dracaena (Dracaenaceae)

    NARCIS (Netherlands)

    Damen, T.H.J.; Burg, van der W.J.; Wiland-Szymańska, J.; Sosef, M.S.M.

    2018-01-01

    In preparing the treatment of Dracaena for Flore du Gabon and Flore d’Afrique centrale, a relatively high number of taxonomic and nomenclatural novelties were discovered; these are presented here. Within Dracaena five species and one forma are described as new, D. bushii, D. haemanthoides, D.

  17. Polyphasic taxonomic characterization of lactic acid bacteria ...

    African Journals Online (AJOL)

    The results of these analyses showed that ting fermentation involved at least three different species of LAB, i.e. Lactobacillus fermentum, L. plantarum and L. rhamnosus. To our knowledge, this is the first report of polyphasic taxonomic characterization of LAB from this food. This research forms an essential first step towards ...

  18. A Framework for Establishing Standard Reference Scale of Texture by Multivariate Statistical Analysis Based on Instrumental Measurement and Sensory Evaluation.

    Science.gov (United States)

    Zhi, Ruicong; Zhao, Lei; Xie, Nan; Wang, Houyin; Shi, Bolin; Shi, Jingye

    2016-01-13

    A framework of establishing standard reference scale (texture) is proposed by multivariate statistical analysis according to instrumental measurement and sensory evaluation. Multivariate statistical analysis is conducted to rapidly select typical reference samples with characteristics of universality, representativeness, stability, substitutability, and traceability. The reasonableness of the framework method is verified by establishing standard reference scale of texture attribute (hardness) with Chinese well-known food. More than 100 food products in 16 categories were tested using instrumental measurement (TPA test), and the result was analyzed with clustering analysis, principal component analysis, relative standard deviation, and analysis of variance. As a result, nine kinds of foods were determined to construct the hardness standard reference scale. The results indicate that the regression coefficient between the estimated sensory value and the instrumentally measured value is significant (R(2) = 0.9765), which fits well with Stevens's theory. The research provides reliable a theoretical basis and practical guide for quantitative standard reference scale establishment on food texture characteristics.

  19. Scaling Analysis Techniques to Establish Experimental Infrastructure for Component, Subsystem, and Integrated System Testing

    Energy Technology Data Exchange (ETDEWEB)

    Sabharwall, Piyush [Idaho National Laboratory (INL), Idaho Falls, ID (United States); O' Brien, James E. [Idaho National Laboratory (INL), Idaho Falls, ID (United States); McKellar, Michael G. [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Housley, Gregory K. [Idaho National Laboratory (INL), Idaho Falls, ID (United States); Bragg-Sitton, Shannon M. [Idaho National Laboratory (INL), Idaho Falls, ID (United States)

    2015-03-01

    Hybrid energy system research has the potential to expand the application for nuclear reactor technology beyond electricity. The purpose of this research is to reduce both technical and economic risks associated with energy systems of the future. Nuclear hybrid energy systems (NHES) mitigate the variability of renewable energy sources, provide opportunities to produce revenue from different product streams, and avoid capital inefficiencies by matching electrical output to demand by using excess generation capacity for other purposes when it is available. An essential step in the commercialization and deployment of this advanced technology is scaled testing to demonstrate integrated dynamic performance of advanced systems and components when risks cannot be mitigated adequately by analysis or simulation. Further testing in a prototypical environment is needed for validation and higher confidence. This research supports the development of advanced nuclear reactor technology and NHES, and their adaptation to commercial industrial applications that will potentially advance U.S. energy security, economy, and reliability and further reduce carbon emissions. Experimental infrastructure development for testing and feasibility studies of coupled systems can similarly support other projects having similar developmental needs and can generate data required for validation of models in thermal energy storage and transport, energy, and conversion process development. Experiments performed in the Systems Integration Laboratory will acquire performance data, identify scalability issues, and quantify technology gaps and needs for various hybrid or other energy systems. This report discusses detailed scaling (component and integrated system) and heat transfer figures of merit that will establish the experimental infrastructure for component, subsystem, and integrated system testing to advance the technology readiness of components and systems to the level required for commercial

  20. Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

    Directory of Open Access Journals (Sweden)

    Weis Patrick

    2010-01-01

    Full Text Available Abstract Background The newt Notophthalmus viridescens possesses the remarkable ability to respond to cardiac damage by formation of new myocardial tissue. Surprisingly little is known about changes in gene activities that occur during the course of regeneration. To begin to decipher the molecular processes, that underlie restoration of functional cardiac tissue, we generated an EST database from regenerating newt hearts and compared the transcriptional profile of selected candidates with genes deregulated during zebrafish heart regeneration. Results A cDNA library of 100,000 cDNA clones was generated from newt hearts 14 days after ventricular injury. Sequencing of 11520 cDNA clones resulted in 2894 assembled contigs. BLAST searches revealed 1695 sequences with potential homology to sequences from the NCBI database. BLAST searches to TrEMBL and Swiss-Prot databases assigned 1116 proteins to Gene Ontology terms. We also identified a relatively large set of 174 ORFs, which are likely to be unique for urodele amphibians. Expression analysis of newt-zebrafish homologues confirmed the deregulation of selected genes during heart regeneration. Sequences, BLAST results and GO annotations were visualized in a relational web based database followed by grouping of identified proteins into clusters of GO Terms. Comparison of data from regenerating zebrafish hearts identified biological processes, which were uniformly overrepresented during cardiac regeneration in newt and zebrafish. Conclusion We concluded that heart regeneration in newts and zebrafish led to the activation of similar sets of genes, which suggests that heart regeneration in both species might follow similar principles. The design of the newly established newt EST database allows identification of molecular pathways important for heart regeneration.

  1. Cost-benefit analysis of establishing and operating radiation oncology services in Fiji.

    Science.gov (United States)

    Kim, Eunkyoung; Cho, Yoon-Min; Kwon, Soonman; Park, Kunhee

    2017-10-01

    Rising demand for services of cancer patients has been recognised by the Government of Fiji as a national health priority. Increasing attention has been paid to the lack of service of radiation therapy or radiotherapy in Fiji. This study aims to estimate and compare the costs and benefits of introducing radiation oncology services in Fiji from the societal perspective. Time horizon for cost-benefit analysis (CBA) was 15 years from 2021 to 2035. The benefits and costs were converted to the present values of 2016. Estimates for the CBA model were taken from previous studies and expert opinions and data obtained from field visits to Fiji in January 2016. Sensitivity analyses with changing assumptions were undertaken. The estimated net benefit, applying the national minimum wage (NMW) to measure monetary value for life-year gained, was -31,624,421 FJD with 0.69 of benefit-cost (B/C) ratio. If gross national income (GNI) per capita was used for the value of life years, net benefit was 3,975,684 FJD (B/C ratio: 1.04). With a pessimistic scenario, establishing the center appeared to be not cost-beneficial, and the net benefit was -53,634,682 FJD (B/C ratio: 0.46); net benefit with an optimistic scenario was estimated 23,178,189 FJD (B/C ratio: 1.20). Based on the CBA results from using GNI per capita instead of the NMW, this project would be cost-beneficial. Introducing a radiation oncology center in Fiji would have potential impacts on financial sustainability, financial protection, and accessibility and equity of the health system. Copyright © 2017 World Health Organization. Published by Elsevier Ltd.. All rights reserved.

  2. Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.

    Directory of Open Access Journals (Sweden)

    Vineet K Sharma

    Full Text Available Taxonomic assignment of sequence reads is a challenging task in metagenomic data analysis, for which the present methods mainly use either composition- or homology-based approaches. Though the homology-based methods are more sensitive and accurate, they suffer primarily due to the time needed to generate the Blast alignments. We developed the MetaBin program and web server for better homology-based taxonomic assignments using an ORF-based approach. By implementing Blat as the faster alignment method in place of Blastx, the analysis time has been reduced by severalfold. It is benchmarked using both simulated and real metagenomic datasets, and can be used for both single and paired-end sequence reads of varying lengths (≥45 bp. To our knowledge, MetaBin is the only available program that can be used for the taxonomic binning of short reads (<100 bp with high accuracy and high sensitivity using a homology-based approach. The MetaBin web server can be used to carry out the taxonomic analysis, by either submitting reads or Blastx output. It provides several options including construction of taxonomic trees, creation of a composition chart, functional analysis using COGs, and comparative analysis of multiple metagenomic datasets. MetaBin web server and a standalone version for high-throughput analysis are available freely at http://metabin.riken.jp/.

  3. Toward an accurate taxonomic interpretation of Carex fossil fruits (Cyperaceae): a case study in section Phacocystis in the Western Palearctic.

    Science.gov (United States)

    Jiménez-Mejías, Pedro; Martinetto, Edoardo

    2013-08-01

    Despite growing interest in the systematics and evolution of the hyperdiverse genus Carex, few studies have focused on its evolution using an absolute time framework. This is partly due to the limited knowledge of the fossil record. However, Carex fruits are not rare in certain sediments. We analyzed carpological features of modern materials from Carex sect. Phacocystis to characterize the fossil record taxonomically. We studied 374 achenes from modern materials (18 extant species), as well as representatives from related groups, to establish the main traits within and among species. We also studied 99 achenes from sediments of living populations to assess their modification process after decay. Additionally, we characterized 145 fossil achenes from 10 different locations (from 4-0.02 mya), whose taxonomic assignment we discuss. Five main characters were identified for establishing morphological groups of species (epidermis morphology, achene-utricle attachment, achene base, style robustness, and pericarp section). Eleven additional characters allowed the discrimination at species level of most of the taxa. Fossil samples were assigned to two extant species and one unknown, possibly extinct species. The analysis of fruit characters allows the distinction of groups, even up to species level. Carpology is revealed as an accurate tool in Carex paleotaxonomy, which could allow the characterization of Carex fossil fruits and assign them to subgeneric or sectional categories, or to certain species. Our conclusions could be crucial for including a temporal framework in the study of the evolution of Carex.

  4. Establishing a Link Between Prescription Drug Abuse and Illicit Online Pharmacies: Analysis of Twitter Data.

    Science.gov (United States)

    Katsuki, Takeo; Mackey, Tim Ken; Cuomo, Raphael

    2015-12-16

    Youth and adolescent non-medical use of prescription medications (NUPM) has become a national epidemic. However, little is known about the association between promotion of NUPM behavior and access via the popular social media microblogging site, Twitter, which is currently used by a third of all teens. In order to better assess NUPM behavior online, this study conducts surveillance and analysis of Twitter data to characterize the frequency of NUPM-related tweets and also identifies illegal access to drugs of abuse via online pharmacies. Tweets were collected over a 2-week period from April 1-14, 2015, by applying NUPM keyword filters for both generic/chemical and street names associated with drugs of abuse using the Twitter public streaming application programming interface. Tweets were then analyzed for relevance to NUPM and whether they promoted illegal online access to prescription drugs using a protocol of content coding and supervised machine learning. A total of 2,417,662 tweets were collected and analyzed for this study. Tweets filtered for generic drugs names comprised 232,108 tweets, including 22,174 unique associated uniform resource locators (URLs), and 2,185,554 tweets (376,304 unique URLs) filtered for street names. Applying an iterative process of manual content coding and supervised machine learning, 81.72% of the generic and 12.28% of the street NUPM datasets were predicted as having content relevant to NUPM respectively. By examining hyperlinks associated with NUPM relevant content for the generic Twitter dataset, we discovered that 75.72% of the tweets with URLs included a hyperlink to an online marketing affiliate that directly linked to an illicit online pharmacy advertising the sale of Valium without a prescription. This study examined the association between Twitter content, NUPM behavior promotion, and online access to drugs using a broad set of prescription drug keywords. Initial results are concerning, as our study found over 45,000 tweets

  5. Analyses of the stability and core taxonomic memberships of the human microbiome.

    Directory of Open Access Journals (Sweden)

    Kelvin Li

    Full Text Available Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa ("core", versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH sponsored Human Microbiome Project (HMP has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool, and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat's microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of "minor" oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region.

  6. Environmental regulations and plant exit: A logit analysis based on established panel data

    Energy Technology Data Exchange (ETDEWEB)

    Bioern, E; Golombek, R; Raknerud, A

    1995-12-01

    This publication uses a model to study the relationship between environmental regulations and plant exit. It has the main characteristics of a multinomial qualitative response model of the logit type, but also has elements of a Markov chain model. The model uses Norwegian panel data for establishments in three manufacturing sectors with high shares of units which have been under strict environmental regulations. In two of the sectors, the exit probability of non-regulated establishments is about three times higher than for regulated ones. It is also found that the probability of changing regulation status from non-regulated to regulated depends significantly on economic factors. In particular, establishments with weak profitability are the most likely to become subject to environmental regulation. 12 refs., 2 figs., 6 tabs.

  7. Partitioning taxonomic diversity of aquatic insect assemblages ...

    Science.gov (United States)

    Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feeding groups (FFG) in Neotropical Savanna (southeastern Brazilian Cerrado) streams. To do so, we considered three diversity components: stream site (α), among stream sites (β1), and among hydrologic units (β2). We also evaluated the association of EPT genera composition with heterogeneity in land use, instream physical habitat structure, and instream water quality variables. The percent of EPT taxonomic α diversity (20.7%) was lower than the β1 and β2 diversities (53.1% and 26.2%, respectively). The EPT FFG α diversity (26.5%) was lower than the β1 diversity (55.8%) and higher than the β2 (17.7%) diversity. The collector-gatherer FFG was predominant and had the greatest β diversity among stream sites (β1, 55.8%). Our findings support the need for implementing regional scale conservation strategies in the Cerrado biome, which has been degraded by anthropogenic activities. Using adaptations of the US EPA’s National Aquatic Resource Survey (NARS) designs and methods, Ferreira and colleagues examined the distribution of taxonomic and functional diversity of aquatic insects among basins, stream sites within basins, and within stream sample reaches. They sampled 160 low-order stre

  8. Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae

    Directory of Open Access Journals (Sweden)

    Jessica Nayara Carvalho Francisco

    2018-01-01

    Full Text Available Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae. The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera, which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised.

  9. Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae).

    Science.gov (United States)

    Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G

    2018-01-01

    Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae). The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera , which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised.

  10. Taxonomic and functional responses to fire and post-fire management of a Mediterranean hymenoptera community.

    Science.gov (United States)

    Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

    2011-11-01

    Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

  11. Taxonomic and Functional Responses to Fire and Post-Fire Management of a Mediterranean Hymenoptera Community

    Science.gov (United States)

    Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

    2011-11-01

    Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

  12. Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment

    NARCIS (Netherlands)

    Veneault-Fourrey, Claire; Commun, Carine; Kohler, Annegret; Morin, Emmanuelle; Balestrini, Raffaella; Plett, Jonathan; Danchin, Etienne; Coutinho, Pedro; Wiebenga, A.; de Vries, Ronald P; Henrissat, Bernard; Martin, Francis; van den Brink, J.

    2014-01-01

    Ectomycorrhizal fungi, living in soil forests, are required microorganisms to sustain tree growth and productivity. The establishment of mutualistic interaction with roots to form ectomycorrhiza (ECM) is not well known at the molecular level. In particular, how fungal and plant cell walls are

  13. A Molecular Analysis of Training Multiple versus Single Manipulations to Establish a Generalized Manipulative Imitation Repertoire

    Science.gov (United States)

    Hartley, Breanne K.

    2009-01-01

    This study evaluates the necessity of training multiple versus single manipulative-imitations per object in order to establish generalized manipulative-imitation. Training took place in Croyden Avenue School's Early Childhood Developmental Delay preschool classroom in Kalamazoo, MI. Two groups of 3 children each were trained to imitate in order to…

  14. Does global warning increase establishment rates of invasive alien species? A centurial time series analysis

    Science.gov (United States)

    Dingcheng Huang; Robert A. Haack; Runzhi. Zhang

    2011-01-01

    The establishment rate of invasive alien insect species has been increasing worldwide during the past century. This trend has been widely attributed to increased rates of international trade and associated species introductions, but rarely linked to environmental change. To better understand and manage the bioinvasion process, it is crucial to understand the...

  15. An Analysis of the Gaps in the Newly Established South African ...

    African Journals Online (AJOL)

    The South African Department of Defence and Military Veterans can be commended for having taken a bold step in an endeavour to establish an independent entity capable of conducting oversight of its military through the introduction of the Military Ombud Act. However, said Act seems not to adequately address pertinent ...

  16. Taxonomic revision of Eoalligator (Crocodylia, Brevirostres and the paleogeographic origins of the Chinese alligatoroids

    Directory of Open Access Journals (Sweden)

    Yan-yin Wang

    2016-08-01

    Full Text Available Background. The primarily Neotropical distribution of living alligatoroids raises questions as to when and how the ancestors of Alligator sinensis migrated to China. As phylogeny provides a necessary framework for historical biogeographic issues, determining the phylogenetic positions of the Chinese alligatoroids is a crucial step towards understanding global alligatoroid paleobiogeography. Besides the unnamed alligatoroids from the Eocene of Guangdong Province, three Chinese fossil taxa have been referred to Alligatoroidea: Alligator luicus, Eoalligator chunyii and Eoalligator huiningensis. However, none of these fossil taxa has been included in a phylogenetic analysis. The genus Eoalligator was established to accommodate E. chunyii from Guangdong Province. E. huiningensis from Anhui Province was later erected as a second species, despite no distinctive similarities with E. chunyii. By contrast, the putative crocodyline Asiatosuchus nanlingensis was established based on material from Guangdong Province, close to the E. chunyii specimens geographically and stratigraphically. Furthermore, specimens of A. nanlingensis and E. chunyii share four distinctive characters, but display no evident differences. As a result, the taxonomic relationships of these three species require restudy. Methods. In this paper, all specimens of E. chunyii and E. huiningensis are reassessed in detail, and compared to specimens of A. nanlingensis. Detailed re-descriptions and revised diagnoses are provided, and a cladistic analysis is carried out to assess the phylogenetic positions of E. chunyii, E. huiningensis and A. nanlingensis. Results. The analysis recovers E. chunyii and A. nanlingensis as sister taxa among basal Crocodylidae, while P. huiningensis is posited as an alligatoroid. Two key characters support the monophyly E. chunyii + A. nanlingensis: sulcus within surangular, and anteroposteriorly oriented surangular-articular suture. The former character is unique

  17. Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

    Science.gov (United States)

    Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

    2014-04-01

    Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

  18. Species delimitation in taxonomically difficult fungi: the case of Hymenogaster.

    Directory of Open Access Journals (Sweden)

    Benjamin Stielow

    2011-01-01

    Full Text Available False truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions.In this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software.Among distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season. In particular, taxa described in the 19(th century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general.

  19. Analysis of the Economic and Welfare Impacts of Establishing Irrigation Water Market in Qazvin Province

    Directory of Open Access Journals (Sweden)

    2014-03-01

    Full Text Available In this study economic and welfare impacts of establishing irrigation water market in Qazvin province as well as potentiality of irrigation water transfer under stress irrigation conditions in the cities of Qazvin province were analyzed. To achieve the above objectives, Positive Mathematical Programming model and State Wide Agricultural Production functions were used. To achieve applicable results, the production function with a constant elasticity of substitution and cost function with an exponential form were included into the Positive Mathematical Programming model was imported. The study data for the year 2011-2012 was collected by asking the relevant offices in each city of Qazvin province. The proposed model was solved in six successive stages using the GAMS software. After solving the model, amount changes in the area of irrigated crops, farmer's gross profit and labor surplus under the two conditions of “existence of water market” and “lack of water market “at the regional level were calculated. The results showed that establishing irrigation water market increases total irrigated lands for 1/2 percent, total farmer’s gross profit for 1/86 percent and total labor force employed in agriculture for 1/8 percent in the province. Ultimately, considering the supportive and constructive role of regional water markets, it is recommended to provide necessary conditions and tools to establish an optimal use of such a mechanism associated with the type of market in Qazvin province.

  20. Analysis of ISO/IEC 17025 for establishment of KOLAS (Korea Laboratory Accreditation Scheme) quality assurance system

    International Nuclear Information System (INIS)

    Nam, Ji Hee

    2000-12-01

    Besides one existent accredited lab, radioactive material chemical analysis lab, five test laboratories and two calibration labs are under plan to acquire the accreditation from KOLAS. But the current Quality Manual was developed according to ISO Guide 25 that was superceded by ISO/IEC 17025. Since it is tailored to the radioactive material chemical analysis lab, a number of requirements of the Manual are not applicable to the labs other than radioactive material chemical analysis lab. Through the analysis of ISO/IEC 17025, a model of quality system was established which is not only consistent with ISO/IEC 17025 but reflective of the KAERI's situation

  1. Economic Analysis for the Establishment of a Dry Dates Irradiation Facility at El Wadi - El Gedid Governorate

    International Nuclear Information System (INIS)

    El Gameel, E.A.

    2011-01-01

    The present study discus the economic analysis of the establishing dry dates irradiation facility at El Wadi El Gadid governorate. This study was divided into three sections the first section includes the arrangement of the equation of simple regression foretelling the future production for dry dates and radiation source activity , the second section was studied the financial analysis for the project. The third section includes the suitable commodities mix to full off the capacity

  2. Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment.

    Science.gov (United States)

    Veneault-Fourrey, Claire; Commun, Carine; Kohler, Annegret; Morin, Emmanuelle; Balestrini, Raffaella; Plett, Jonathan; Danchin, Etienne; Coutinho, Pedro; Wiebenga, Ad; de Vries, Ronald P; Henrissat, Bernard; Martin, Francis

    2014-11-01

    Ectomycorrhizal fungi, living in soil forests, are required microorganisms to sustain tree growth and productivity. The establishment of mutualistic interaction with roots to form ectomycorrhiza (ECM) is not well known at the molecular level. In particular, how fungal and plant cell walls are rearranged to establish a fully functional ectomycorrhiza is poorly understood. Nevertheless, it is likely that Carbohydrate Active enZymes (CAZyme) produced by the fungus participate in this process. Genome-wide transcriptome profiling during ECM development was used to examine how the CAZome of Laccaria bicolor is regulated during symbiosis establishment. CAZymes active on fungal cell wall were upregulated during ECM development in particular after 4weeks of contact when the hyphae are surrounding the root cells and start to colonize the apoplast. We demonstrated that one expansin-like protein, whose expression is specific to symbiotic tissues, localizes within fungal cell wall. Whereas L. bicolor genome contained a constricted repertoire of CAZymes active on cellulose and hemicellulose, these CAZymes were expressed during the first steps of root cells colonization. L. bicolor retained the ability to use homogalacturonan, a pectin-derived substrate, as carbon source. CAZymes likely involved in pectin hydrolysis were mainly expressed at the stage of a fully mature ECM. All together, our data suggest an active remodelling of fungal cell wall with a possible involvement of expansin during ECM development. By contrast, a soft remodelling of the plant cell wall likely occurs through the loosening of the cellulose microfibrils by AA9 or GH12 CAZymes and middle lamella smooth remodelling through pectin (homogalacturonan) hydrolysis likely by GH28, GH12 CAZymes. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Building a Taxonomic Data Editor: ITIS Taxonomic Workbench 6.0

    OpenAIRE

    Mitchell,David; Bowman,Lisa; Brockmeier,Christopher

    2017-01-01

    The Integrated Taxonomic Information System (ITIS - www.itis.gov) provides a regularly updated global database that currently contains over 840,000 scientific names and their hierarchy. A new rich Internet application for adding and editing ITIS data, Taxonomic Workbench 6.0, is being developed using the AngularJS framework. AngularJS is designed to take advantage of many features that are fairly recent to the web platform, facilitates a well-structured product that is easier to maintain, and...

  4. Taxonomic novelties within the genus Columnea (Gesneriaceae)

    International Nuclear Information System (INIS)

    Amaya Marquez, Marisol

    2010-01-01

    A new species of Columnea and a new variety of Columnea lanata (Seem.) Kuntze belonging to section Collandra (Gesneriaceae) are described and illustrated. The new species was found in the Pacific slopes of the Cordillera Occidental in the Department of Choco in Colombia; the new variety comes from the Pacific slopes of the Cordillera Occidental, in the region of Murri located at the North West of the Department of Antioquia . A taxonomic key to distinguish the new species from the morphologically closer species is presented.

  5. Degradation mode analysis: An approach to establish effective predictive maintenance tasks

    International Nuclear Information System (INIS)

    Sonnett, D.E.; Douglass, P.T.; Barnard, D.D.

    1991-01-01

    A significant number of nuclear generating stations have been employing Reliability Centered Maintenance methodology to arrive at applicable and effective maintenance tasks for their plant equipment. The resultant endpoint of most programs has been an increased emphasis on predictive maintenance as the task of choice for monitoring and trending plant equipment condition to address failure mechanisms of the analyses. Many of these plants have spent several years conducting reliability centered analysis before they seriously begin implementing predictive program improvements. In this paper we present another methodology, entitled Degradation Mode Analysis, which provides a more direct method to quickly and economically achieve the major benefit of reliability centered analysis, namely predictive maintenance. (author)

  6. Can You Trust Your Data? Establishing the Need for a Measurement and Analysis Infrastructure Diagnostic

    National Research Council Canada - National Science Library

    Kasunic, Mark; McCurley, James; Zubrow, David

    2008-01-01

    ... or determine how to begin improving their data This report describes common errors in measurement and analysis and the need for a criterion-based assessment method that will allow organizations to evaluate...

  7. A strategic analysis of future growth options for an established process control company

    OpenAIRE

    Levesque, Sheila Lynne

    2007-01-01

    This project speaks to the prevailing business environment presently encountered at WESTCOAST Controls Ltd (WESTCOAST), a leading process control company in British Columbia, Canada. The scope of the project covers topics such as company overview, external industry analysis, and internal company analysis including strategic tools such as Porter's 5 Forces. The project concludes with a recommendation for the restructuring of the control systems & solutions division for improved performan...

  8. Variance Component Selection With Applications to Microbiome Taxonomic Data

    Directory of Open Access Journals (Sweden)

    Jing Zhai

    2018-03-01

    Full Text Available High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Microbiome data are summarized as counts or composition of the bacterial taxa at different taxonomic levels. An important problem is to identify the bacterial taxa that are associated with a response. One method is to test the association of specific taxon with phenotypes in a linear mixed effect model, which incorporates phylogenetic information among bacterial communities. Another type of approaches consider all taxa in a joint model and achieves selection via penalization method, which ignores phylogenetic information. In this paper, we consider regression analysis by treating bacterial taxa at different level as multiple random effects. For each taxon, a kernel matrix is calculated based on distance measures in the phylogenetic tree and acts as one variance component in the joint model. Then taxonomic selection is achieved by the lasso (least absolute shrinkage and selection operator penalty on variance components. Our method integrates biological information into the variable selection problem and greatly improves selection accuracies. Simulation studies demonstrate the superiority of our methods versus existing methods, for example, group-lasso. Finally, we apply our method to a longitudinal microbiome study of Human Immunodeficiency Virus (HIV infected patients. We implement our method using the high performance computing language Julia. Software and detailed documentation are freely available at https://github.com/JingZhai63/VCselection.

  9. Taxonomic revision and phylogenetic analyses of rubber powdery mildew fungi.

    Science.gov (United States)

    Liyanage, K K; Khan, Sehroon; Brooks, Siraprapa; Mortimer, Peter E; Karunarathna, Samantha C; Xu, Jianchu; Hyde, Kevin D

    2017-04-01

    Powdery mildew is a fungal disease that infects a wide range of plants, including rubber trees, which results in a reduction of latex yields of up to 45%. The causal agent of powdery mildew of rubber was first described as Oidium heveae, but later morpho-molecular research suggested that in the past, O. heveae has been confused with Erysiphe quercicola. However, it is still under debate whether the causal agent should be classified as a species of the genus Erysiphe emend. or Golovinomyces and Podosphaera, respectively. Therefore, the aim of this study was to undertake the morpho-molecular characterization of powdery mildew species associated with rubber trees, thus resolving these taxonomic issues. Morphological observation under light and scanning electron microscopes (SEM) clearly identified two morphotypes of the rubber powdery mildew. With the support of morphological and phylogenetic data, one of the two morphotypes was identified as the asexual morph of E. quercicola, while the second morphotype is still insufficiently known and according to the morphological results obtained we assume that it might belong to the genus Golovinomyces. More collections and additional molecular data are required for final conclusions regarding the exact taxonomic position of the second morphotype of rubber powdery mildew and its relation to the name O. heveae. The haplotype analysis identified eight haplotype groups of E. quercicola indicating the high genetic diversity of the species. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Communication component of rehabilitation establishments in Ukraine: issues of methodology of analysis

    Directory of Open Access Journals (Sweden)

    S. Y. Nedoboi

    2017-08-01

    As a result, there is a number of specific features in communication component of rehabilitation establishments. Firstly, a rehabilitation program is the first step in rehabilitation process. Effectiveness of its drafting and implementation is defined by an ability to make a contact and communication between doctor and patient. Secondly, communication and interaction between doctor and patient should continue from the beginning of treatment and even after person’s return to home life. Thirdly, a phenomenon of «therapeutic alliance» and a principle of «peer to peer» become meaningful in mentioned institutions as well as a growing role of practical nurses and other professionals in rehabilitation process.

  11. Use of benefit-cost analysis in establishing Federal radiation protection standards: a review

    Energy Technology Data Exchange (ETDEWEB)

    Erickson, L.E.

    1979-10-01

    This paper complements other work which has evaluated the cost impacts of radiation standards on the nuclear industry. It focuses on the approaches to valuation of the health and safety benefits of radiation standards and the actual and appropriate processes of benefit-cost comparison. A brief historical review of the rationale(s) for the levels of radiation standards prior to 1970 is given. The Nuclear Regulatory Commission (NRC) established numerical design objectives for light water reactors (LWRs). The process of establishing these numerical design criteria below the radiation protection standards set in 10 CFR 20 is reviewed. EPA's 40 CFR 190 environmental standards for the uranium fuel cycle have lower values than NRC's radiation protection standards in 10 CFR 20. The task of allocating EPA's 40 CFR 190 standards to the various portions of the fuel cycle was left to the implementing agency, NRC. So whether or not EPA's standards for the uranium fuel cycle are more stringent for LWRs than NRC's numerical design objectives depends on how EPA's standards are implemented by NRC. In setting the numerical levels in Appendix I to 10 CFR 50 and 40 CFR 190 NRC and EPA, respectively, focused on the costs of compliance with various levels of radiation control. A major portion of the paper is devoted to a review and critique of the available methods for valuing health and safety benefits. All current approaches try to estimate a constant value of life and use this to vaue the expected number of lives saved. This paper argues that it is more appropriate to seek a value of a reduction in risks to health and life that varies with the extent of these risks. Additional research to do this is recommended. (DC)

  12. Establishment of Orthotopic Xuanwei Lung Cancer SCID Mouse Model 
and Analysis of Biological Properties

    Directory of Open Access Journals (Sweden)

    Yongchun ZHOU

    2012-08-01

    Full Text Available Background and objective The incidence of Xuanwei lung cancer ranks first in China, and its pathogenesis requires in-depth investigation. This study aims to establish an orthotopic Xuanwei lung cancer severe combined immunodeficiency (SCID mouse model and to provide a basic experimental platform for further study. Methods The Xuanwei lung cancer cell line XWLC-05 was inoculated into the lung tissue of SCID mice in high and low doses. The tumor formation rates, tumor characteristics, spontaneous metastases, and survival times of the mice were observed, taking a subcutaneously transplanted tumor as control. Results The tumor formation rates of the orthotopic transplantation of lung cancer cells in high and low doses were 81% and 83%, respectively, among which mice in the high-dose group appeared cachectic on day 13. Extensive invasion and adhesion were observed in the contralateral lung and thoracic cavity, but no distant metastasis was exhibited. Mice with low-dose cells in the orthotopic transplantation group appeared cachectic and distant metastasis occurred on day 25. The tumor formation rates in the subcutaneous inoculation group by the high and low doses of cells were 100% and 94.5%, respectively, and no distant metastasis was observed. The rate of metastasis within the orthotopic transplantation group and between the orthotopic and subcutaneous inoculation groups showed a significant difference (P<0.05. A significant difference was indicated by the survival rate within and between the groups (P<0.001. Conclusion We successfully established an orthotopic XWLC SCID mouse model, which lays the foundation for a more in-depth study.

  13. COST ANALYSIS OF LONG ESTABLISHED AND NEWER ORAL ANTIEPILEPTIC DRUGS AVAILABLE IN THE INDIAN MARKET

    Directory of Open Access Journals (Sweden)

    Phatak Abhishek M, Hotwani Jitendra H, Deshmukhkiran R, Panchal Sagar S, Naik Madhura S

    2015-10-01

    Full Text Available Background: Large number of pharmaceutical companies manufactures antiepileptic drugs in India. The price variations among the marketed drugs are wide. Aims: The present study was aimed to find the cost of different oral antiepileptic drugs available in Indian market as monotherapy, combination therapy and number of manufacturing companies for each, to evaluate difference in cost of different brands of same dosage of same active drug by calculating percentage variation of cost. Methods and Materials: Cost of a drug being manufactured by different companies, in the same strength and dosage forms was obtained from “Indian Drug Review” Vol. XXI, Issue No.4, 2014 and “Current Index of Medical Specialties” July-October 2014. The difference in the maximum and minimum price of the same drug manufactured by different pharmaceutical companies and percentage variation in price was calculated. Results: The percentage price variation noted of long-established drugs was – Phenytoin (50mg: 140%, Carbamazepine (100mg: 1033%, Phenobarbital (30mg : 730%, Valproic acid (300mg : 420%. Newer drugs –Levetiracetam (250mg: 75%, Lamotrigine (25mg: 66%, Topiramate (50mg: 108%, Zonisamide (100mg: 19%. Combination drugs – Phenobarbital + Phenytoin (30+100 mg: 354.55%. Conclusion: The percentage price variation of different brands of the same commonly used long-established oral antiepileptic drug manufactured in India is very wide. The formulation or brand of Antiepileptic drugs (AED’s should preferably not be changed since variations in bioavailability or different pharmacokinetic profiles may increase the potential for reduced effect or excessive side effects. Hence, manufacturing companies should aim to decrease the price variation while maintaining the therapeutic efficacy.

  14. Establishment of animal model for the analysis of cancer cell metastasis during radiotherapy

    International Nuclear Information System (INIS)

    Park, Jong Kuk; Jang, Su Jin; Kang, Sung Wook; Park, Sunhoo; Hwang, Sang-Gu; Kim, Wun-Jae; Kang, Joo Hyun; Um, Hong-Duck

    2012-01-01

    Γ-Ionizing radiation (IR) therapy is one of major therapeutic tools in cancer treatment. Nevertheless, γ-IR therapy failed due to occurrence of metastasis, which constitutes a significant obstacle in cancer treatment. The main aim of this investigation was to construct animal model which present metastasis during radiotherapy in a mouse system in vivo and establishes the molecular mechanisms involved. The C6L transfectant cell line expressing firefly luciferase (fLuc) was treated with γ-IR, followed by immunoblotting, zymography and invasion assay in vitro. We additionally employed the C6L transfectant cell line to construct xenografts in nude mice, which were irradiated with γ-IR. Irradiated xenograft-containing mice were analyzed via survival curves, measurement of tumor size, and bioluminescence imaging in vivo and ex vivo. Metastatic lesions in organs of mice were further assessed using RT-PCR, H & E staining and immunohistochemistry. γ-IR treatment of C6L cells induced epithelial-mesenchymal transition (EMT) and increased cell invasion. In irradiated xenograft-containing mice, tumor sizes were decreased dramatically and survival rates extended. Almost all non-irradiated xenograft-containing control mice had died within 4 weeks. However, we also observed luminescence signals in about 22.5% of γ-IR-treated mice. Intestines or lungs of mice displaying luminescence signals contained several lesions, which expressed the fLuc gene and presented histological features of cancer tissues as well as expression of EMT markers. These findings collectively indicate that occurrences of metastases during γ-IR treatment accompanied induction of EMT markers, including increased MMP activity. Establishment of a murine metastasis model during γ-IR treatment should aid in drug development against cancer metastasis and increase our understanding of the mechanisms underlying the metastatic process

  15. Use of benefit-cost analysis in establishing Federal radiation protection standards: a review

    International Nuclear Information System (INIS)

    Erickson, L.E.

    1979-10-01

    This paper complements other work which has evaluated the cost impacts of radiation standards on the nuclear industry. It focuses on the approaches to valuation of the health and safety benefits of radiation standards and the actual and appropriate processes of benefit-cost comparison. A brief historical review of the rationale(s) for the levels of radiation standards prior to 1970 is given. The Nuclear Regulatory Commission (NRC) established numerical design objectives for light water reactors (LWRs). The process of establishing these numerical design criteria below the radiation protection standards set in 10 CFR 20 is reviewed. EPA's 40 CFR 190 environmental standards for the uranium fuel cycle have lower values than NRC's radiation protection standards in 10 CFR 20. The task of allocating EPA's 40 CFR 190 standards to the various portions of the fuel cycle was left to the implementing agency, NRC. So whether or not EPA's standards for the uranium fuel cycle are more stringent for LWRs than NRC's numerical design objectives depends on how EPA's standards are implemented by NRC. In setting the numerical levels in Appendix I to 10 CFR 50 and 40 CFR 190 NRC and EPA, respectively, focused on the costs of compliance with various levels of radiation control. A major portion of the paper is devoted to a review and critique of the available methods for valuing health and safety benefits. All current approaches try to estimate a constant value of life and use this to vaue the expected number of lives saved. This paper argues that it is more appropriate to seek a value of a reduction in risks to health and life that varies with the extent of these risks. Additional research to do this is recommended

  16. Intra- and interpopulation relationships and taxonomic status of Pinus nigra Arnold in Croatia according to morphology and anatomy of needles

    Directory of Open Access Journals (Sweden)

    Zlatko Liber

    2014-01-01

    Full Text Available Intra- and interpopulational relationships and taxonomic status of six natural black pine populations (Pinus nigra Arnold from Croatia were analyzed. Special attention in this research was paid to the establishment of taxonomic status and distribution of stenoendemic Dalmatian black pine (Pinus nigra Arnold subsp. dalmatica (Vis. Franco. Three morphological and twenty-one anatomical traits of needles were used as well as analysis by the methods of multivariate statistics. Most of the researched individuals showed strong population affiliation, whereas a clinal transition of morphological and anatomical traits of needles was determined among the populations. The opinion of the existence of three subspecies of black pine on the territory of Republic of Croatia (Pinus nigra Arnold subsp. nigra, Pinus nigra Arnold subsp. dalmatica (Vis. Franco and Pinus nigra Arnold subsp. illyrica (Vid. Fukarek was confirmed. For each of the three subspecies new ranges were represented. Four Croatian populations were included in the stenoendemic subspecies of the Dalmatian black pine (Brač, Hvar, Grobnik and Pelješac, and a new distribution, broken in two, was suggested. Since the Dalmatian black pine has been reduced to several populations only, and there are some signs of continuous diminishing of its range, this research points out the need of making an action plan to preserve all natural populations of this subspecies.

  17. CRAB3: Establishing a new generation of services for distributed analysis at CMS

    International Nuclear Information System (INIS)

    Cinquilli, M; Spiga, D; Konstantinov, P; Mascheroni, M; Grandi, C; Hernàndez, J M; Riahi, H; Vaandering, E

    2012-01-01

    In CMS Computing the highest priorities for analysis tools are the improvement of the end users’ ability to produce and publish reliable samples and analysis results as well as a transition to a sustainable development and operations model. To achieve these goals CMS decided to incorporate analysis processing into the same framework as data and simulation processing. This strategy foresees that all workload tools (TierO, Tier1, production, analysis) share a common core with long term maintainability as well as the standardization of the operator interfaces. The re-engineered analysis workload manager, called CRAB3, makes use of newer technologies, such as RESTFul based web services and NoSQL Databases, aiming to increase the scalability and reliability of the system. As opposed to CRAB2, in CRAB3 all work is centrally injected and managed in a global queue. A pool of agents, which can be geographically distributed, consumes work from the central services serving the user tasks. The new architecture of CRAB substantially changes the deployment model and operations activities. In this paper we present the implementation of CRAB3, emphasizing how the new architecture improves the workflow automation and simplifies maintainability. In particular, we will highlight the impact of the new design on daily operations.

  18. CRAB3: Establishing a new generation of services for distributed analysis at CMS

    Science.gov (United States)

    Cinquilli, M.; Spiga, D.; Grandi, C.; Hernàndez, J. M.; Konstantinov, P.; Mascheroni, M.; Riahi, H.; Vaandering, E.

    2012-12-01

    In CMS Computing the highest priorities for analysis tools are the improvement of the end users’ ability to produce and publish reliable samples and analysis results as well as a transition to a sustainable development and operations model. To achieve these goals CMS decided to incorporate analysis processing into the same framework as data and simulation processing. This strategy foresees that all workload tools (TierO, Tier1, production, analysis) share a common core with long term maintainability as well as the standardization of the operator interfaces. The re-engineered analysis workload manager, called CRAB3, makes use of newer technologies, such as RESTFul based web services and NoSQL Databases, aiming to increase the scalability and reliability of the system. As opposed to CRAB2, in CRAB3 all work is centrally injected and managed in a global queue. A pool of agents, which can be geographically distributed, consumes work from the central services serving the user tasks. The new architecture of CRAB substantially changes the deployment model and operations activities. In this paper we present the implementation of CRAB3, emphasizing how the new architecture improves the workflow automation and simplifies maintainability. In particular, we will highlight the impact of the new design on daily operations.

  19. Establishing guidance for the review of human reliability analysis in PSA

    International Nuclear Information System (INIS)

    Reer, B.; Dang, V.N.; Hirschberg, S.; Meyer, P.

    2000-01-01

    PSI was commissioned to develop Guidelines for the Regulatory Review of the Human Reliability Analysis (HRA) within Probabilistic Safety Assessments (PSAs) for nuclear power plants. In the Guidelines, HRA quality is addressed in terms of 97 indicators. Each indicator is formulated as a question, described as a specific feature of the analysis, and then explained in detail. Two analysis stages are distinguished: the selection of the human errors to be modelled, and their quantification to determine their impact on the core damage frequency. Review findings are grouped under two headings: transparency and adequacy. An analysis is 'transparent' if an externally qualified person is able to reproduce the analysis results, and 'adequate' if such results reflect the plant-specific conditions related to safety. To allocate resources efficiently, the review is structured in two phases: (1) The Quick Review, which clarifies whether the HRA has a fundamental deficiency and, furthermore, if it points to information needs and areas of emphasis for the detailed review, and (2) The Detailed Review, which results in well-grounded findings, based on extended examinations and close-plant contacts. (authors)

  20. CRAB3: Establishing a new generation of services for distributed analysis at CMS

    Energy Technology Data Exchange (ETDEWEB)

    Cinquilli, M. [CERN; Spiga, D. [CERN; Grandi, C. [INFN, Bologna; Hernandez, J. M. [Madrid, CIEMAT; Konstantinov, P. [CERN; Mascheroni, M. [CERN; Riahi, H. [INFN, Perugia; Vaandering, E. [Fermilab

    2012-01-01

    In CMS Computing the highest priorities for analysis tools are the improvement of the end users ability to produce and publish reliable samples and analysis results as well as a transition to a sustainable development and operations model. To achieve these goals CMS decided to incorporate analysis processing into the same framework as data and simulation processing. This strategy foresees that all workload tools (TierO, Tier1, production, analysis) share a common core with long term maintainability as well as the standardization of the operator interfaces. The re-engineered analysis workload manager, called CRAB3, makes use of newer technologies, such as RESTFul based web services and NoSQL Databases, aiming to increase the scalability and reliability of the system. As opposed to CRAB2, in CRAB3 all work is centrally injected and managed in a global queue. A pool of agents, which can be geographically distributed, consumes work from the central services serving the user tasks. The new architecture of CRAB substantially changes the deployment model and operations activities. In this paper we present the implementation of CRAB3, emphasizing how the new architecture improves the workflow automation and simplifies maintainability. In particular, we will highlight the impact of the new design on daily operations.

  1. Establishing Equivalence: Methodological Progress in Group-Matching Design and Analysis

    Science.gov (United States)

    Kover, Sara T.; Atwood, Amy K.

    2013-01-01

    This methodological review draws attention to the challenges faced by intellectual and developmental disabilities researchers in the appropriate design and analysis of group comparison studies. We provide a brief overview of matching methodologies in the field, emphasizing group-matching designs used in behavioral research on cognition and…

  2. Establishing a Common Vocabulary of Key Concepts for the Effective Implementation of Applied Behavior Analysis

    Science.gov (United States)

    Cihon, Traci M.; Cihon, Joseph H.; Bedient, Guy M.

    2016-01-01

    The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case…

  3. Analysis, Reconstruction and Establishment Tourist Destination in Toba Samosir, North Sumatera, Indonesia

    Directory of Open Access Journals (Sweden)

    Menara Simanjuntak

    2012-09-01

    Full Text Available This study aimed to provide inputs for local government of Toba Samosir (Tobasa in preparing strategic development plan of tourist destinations in District Tobasa. This study is a qualitative approach through in-depth interviews and feedback from forum discussion groups with participants representing community leaders, indigenous peoples, governments and travel business. Total participants are 15 people collected on June 1, 2012 at Balige government office. Discussion forums formulated nine locations of tourist destination spread in Toba Samosir. As result this research, we formulated four strategic plans with tactical plans; (1 specifying and establish the location of tourist destinations in the District Tobasa; (2 submitting plans to the government budget or through the budget of Tobasa district in five years starting in 2014 to follow; (3 conducting government financing for infrastructure development and tourism industry participation; (4 doing tourism and cultural promotion. We found limitations for the plan. Some of them were: the low budget provided by the District government so that we expected supports from domestic investors to accelerate tourism development in the area. Most activities were proposed under the action plan of both Tobasa District government and North Sumatra Government.

  4. Analysis of human protein replacement stable cell lines established using snoMEN-PR vector.

    Directory of Open Access Journals (Sweden)

    Motoharu Ono

    Full Text Available The study of the function of many human proteins is often hampered by technical limitations, such as cytotoxicity and phenotypes that result from overexpression of the protein of interest together with the endogenous version. Here we present the snoMEN (snoRNA Modulator of gene ExpressioN vector technology for generating stable cell lines where expression of the endogenous protein can be reduced and replaced by an exogenous protein, such as a fluorescent protein (FP-tagged version. SnoMEN are snoRNAs engineered to contain complementary sequences that can promote knock-down of targeted RNAs. We have established and characterised two such partial protein replacement human cell lines (snoMEN-PR. Quantitative mass spectrometry was used to analyse the specificity of knock-down and replacement at the protein level and also showed an increased pull-down efficiency of protein complexes containing exogenous, tagged proteins in the protein replacement cell lines, as compared with conventional co-expression strategies. The snoMEN approach facilitates the study of mammalian proteins, particularly those that have so far been difficult to investigate by exogenous expression and has wide applications in basic and applied gene-expression research.

  5. Establishing a Common Vocabulary of Key Concepts for the Effective Implementation of Applied Behavior Analysis

    OpenAIRE

    Traci M. CIHON; Joseph H. CIHON; Guy M. BEDIENT

    2016-01-01

    The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case example of the development of a shared vocabulary, using plain English when possible, among supervisors and supervisees at a large public school distric...

  6. Establishing a protocol for element determination in human nail clippings by neutron activation analysis

    International Nuclear Information System (INIS)

    Sanches, Thalita Pinheiro; Saiki, Mitiko

    2011-01-01

    Human nail samples have been analyzed to evaluate occupational exposure, nutritional status and to diagnose certain diseases. However, sampling and washing protocols for nail analyses vary from study to study not allowing comparisons between studies. One of the difficulties in analyzing nail samples is to eliminate only surface contamination without removing elements of interest in this tissue. In the present study, a protocol was defined in order to obtain reliable results of element concentrations in human nail clippings. Nail clippings collected from all 10 fingers or toes were previously pre cleaned using an ethyl alcohol solution to eliminate microbes. Then, the clippings were cut in small pieces and submitted to different reagents for washing by shaking. Neutron activation analysis (NAA) was applied for nail samples analysis which consisted of irradiating aliquots of samples together with synthetic elemental standards in the IEA-R1 nuclear research reactor followed by gamma ray spectrometry. Comparisons made between the results obtained for nails submitted to different reagents for cleaning indicated that the procedure using acetone and Triton X100 solution is more effective than that of nitric acid solution. Analyses in triplicates of a nail sample indicated results with relative standard deviations lower than 15% for most of elements, showing the homogeneity of the prepared sample. Qualitative analyses of different nail polishes showed that the presence of elements determined in the present study is negligible in these products. Quality control of the analytical results indicated that the applied NAA procedure is adequate for human nail analysis. (author)

  7. Provenance Establishment of Stingless Bee Honey Using Multi-element Analysis in Combination with Chemometrics Techniques.

    Science.gov (United States)

    Shadan, Aidil Fahmi; Mahat, Naji A; Wan Ibrahim, Wan Aini; Ariffin, Zaiton; Ismail, Dzulkiflee

    2018-01-01

    As consumption of stingless bee honey has been gaining popularity in many countries including Malaysia, ability to identify accurately its geographical origin proves pertinent for investigating fraudulent activities for consumer protection. Because a chemical signature can be location-specific, multi-element distribution patterns may prove useful for provenancing such product. Using the inductively coupled-plasma optical emission spectrometer as well as principal component analysis (PCA) and linear discriminant analysis (LDA), the distributions of multi-elements in stingless bee honey collected at four different geographical locations (North, West, East, and South) in Johor, Malaysia, were investigated. While cross-validation using PCA demonstrated 87.0% correct classification rate, the same was improved (96.2%) with the use of LDA, indicating that discrimination was possible for the different geographical regions. Therefore, utilization of multi-element analysis coupled with chemometrics techniques for assigning the provenance of stingless bee honeys for forensic applications is supported. © 2017 American Academy of Forensic Sciences.

  8. Phytoliths as Emerging Taxonomic Tools for Identification of Plants: An Overview

    Directory of Open Access Journals (Sweden)

    Sheikh Abdul Shakoor

    2014-01-01

    Full Text Available In the recent advancements in identification of plant species, phytoliths have found an immense role in the identification of plants at different levels of taxonomic hierarchy. Many plant groups are known to accumulate silica in solid form in and between the cells and tissues and hence create the structures commonly known as phytoliths. These phytoliths create replicas of the structures where they are deposited. The shapes of phytolith replicas, their size dimensions (morphometric parameters, surface features (ornamentation, distribution, and orientation pattern in epidermal layers of vegetative and reproductive structures as well as their frequency are highly important for characterization of species. Monocotyledonous families particularly the family Poaceae (Gramineae are known to produce diverse phytolith types that can serve as diagnostic markers for characterization of different taxa at different levels of taxonomic hierarchy. The present paper highlights the importance of phytoliths in taxonomic analysis of plants particularly in the family Poaceae.

  9. Establishment and validation of a dose-effect curve for γ-rays by cytogenetic analysis

    International Nuclear Information System (INIS)

    Barquinero, Joan F.; Caballin, Maria Rosa; Barrios, Leonardo; Ribas, Montserrat; Miro, Rosa; Egozcue, Josep

    1995-01-01

    A dose-effect curve obtained by analysis of dicentric chromosomes after irradiation of peripheral blood samples, from one donor, at 11 different doses of γ-rays is presented. For the elaboration of this curve, more than 18,000 first division metaphases have been analyzed. The results fit very well to the linear-quadratic model. To validate the curve, samples from six individuals (three controls and three occupationally exposed persons) were irradiated at 2 Gy. The results obtained, when compared with the curve, showed that in all cases the 95% confidence interval included the 2 Gy dose, with estimated dose ranges from 1.82 to 2.19 Gy

  10. Establishing a Common Vocabulary of Key Concepts for the Effective Implementation of Applied Behavior Analysis

    Directory of Open Access Journals (Sweden)

    Traci M. CIHON

    2016-12-01

    Full Text Available The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case example of the development of a shared vocabulary, using plain English when possible, among supervisors and supervisees at a large public school district in which behavior analytic services were provided for children diagnosed with autism spectrum disorders. A list of terms and definitions are provided as well as suggestions on how to develop shared vocabularies within the readers’ own service provision context.

  11. Statistical analysis of the established salary in small and medium enterprises

    Directory of Open Access Journals (Sweden)

    Yu. S. Pin’kovetskaya

    2017-01-01

    Full Text Available The aim of the study was to analyze the present regularities, specific to the employees’ salaries of aggregates of small and medium enterprises related to the three dimensional categories and located in different regions of Russia. The following tasks were solved: the indexes, characterizing average monthly salary of employees based on the mentioned enterprises were assessed, belonging to different size categories and located in each of the regions; the relations were established between the average monthly salaries of employees of aggregates of small and medium enterprises and the cost of living in all regions of the country.Preliminary results of stopwatch reading of small and medium business activities in 2015 were used as initial data. The research was based on the comparison of indexes for the entrepreneurial sector and the full range of enterprises and organizations.Modeling differentiation of salaries’ values of small and medium enterprises aggregations, as well as its relationship to the values of the subsistence level was based on the development of the density function of normal distribution. The quality of the developed models was checked according to the Kolmogorov-Smirnov, Pearson and Shapiro-Wilk criteria.The obtained results have some theoretical significance, in particular, when conducting research related to the justification of the proposed wage of employees of enterprises different in number, the formation of measures for increasing efficiency of the entrepreneurial sector activity. Density functions of normal distribution given in the paper can be used in the justification of concepts, plans and programs of developing small and medium entrepreneurship in regions and municipalities. The practical importance of research results connected with the possibility of their use by entrepreneurs directly (especially by beginners when assessing the potential of enterprise creation and definition of employees’ proposed salaries. In

  12. Establishing the date of Maori environmental impact in New Zealand through pollen analysis and radiocarbon dating

    Energy Technology Data Exchange (ETDEWEB)

    McGlone, M.S.; Wilmshurst, J.M. [Landcare Research, Lincoln, (New Zealand)

    1997-12-31

    Full text: Over the last decade there has been an intense debate about whether New Zealand prehistory is long ( > 1500 years) or short ( < 800 years). Pollen and charcoal analyses have played a key role in this debate by helping to pinpoint the transition from relatively undisturbed environments to those deforested by anthropogenic fires. Problems with in situ contamination, reworking of sediments, confusion of natural with anthropogenic impacts, and different theoretical expectations of growth, spread and impact of early Maori populations have led to disparate conclusions. We review pollen based studies carried out on a variety of fossil sites, including peat bogs, swamps, estuaries and lakes, and contribute new results. Different sedimentary environments show varying susceptibilities to contamination and have resulted in a wide spread of ages for initial Maori impact. Datable materials least susceptible to contamination by old or young carbon are pure peat and macrofossils, whereas lake, swamp and silty sediments are most susceptible. Analysis of the radiocarbon ages obtained for the start of Maori deforestation show that ages falling in the `long` prehistory period are exclusively derived from lake sediments and swamps. In contrast, the bulk of the ages falling in the `short` prehistory period are from pure peat and selected plant fragments. We conclude from our analysis of radiocarbon ages for pollen based deforestation that the first evidence of Maori environmental impact began about 700-550 calendar years BP (1250-1400 AD). Finer age resolution is limited by dating techniques, site limitations and the uncertainty associated with identifying the first signs of human impact. The period we have identified corresponds with the oldest dated archaeological sites and supports the short prehistory hypothesis. We discuss how to distinguish reliable fossil sites from those that have a high risk of giving misleading results.

  13. Establishing the date of Maori environmental impact in New Zealand through pollen analysis and radiocarbon dating

    International Nuclear Information System (INIS)

    McGlone, M.S.; Wilmshurst, J.M.

    1997-01-01

    Full text: Over the last decade there has been an intense debate about whether New Zealand prehistory is long ( > 1500 years) or short ( < 800 years). Pollen and charcoal analyses have played a key role in this debate by helping to pinpoint the transition from relatively undisturbed environments to those deforested by anthropogenic fires. Problems with in situ contamination, reworking of sediments, confusion of natural with anthropogenic impacts, and different theoretical expectations of growth, spread and impact of early Maori populations have led to disparate conclusions. We review pollen based studies carried out on a variety of fossil sites, including peat bogs, swamps, estuaries and lakes, and contribute new results. Different sedimentary environments show varying susceptibilities to contamination and have resulted in a wide spread of ages for initial Maori impact. Datable materials least susceptible to contamination by old or young carbon are pure peat and macrofossils, whereas lake, swamp and silty sediments are most susceptible. Analysis of the radiocarbon ages obtained for the start of Maori deforestation show that ages falling in the 'long' prehistory period are exclusively derived from lake sediments and swamps. In contrast, the bulk of the ages falling in the 'short' prehistory period are from pure peat and selected plant fragments. We conclude from our analysis of radiocarbon ages for pollen based deforestation that the first evidence of Maori environmental impact began about 700-550 calendar years BP (1250-1400 AD). Finer age resolution is limited by dating techniques, site limitations and the uncertainty associated with identifying the first signs of human impact. The period we have identified corresponds with the oldest dated archaeological sites and supports the short prehistory hypothesis. We discuss how to distinguish reliable fossil sites from those that have a high risk of giving misleading results

  14. A taxonomic, phylogenetic and biogeographic study of the genus Acanthophora (Rhodomelaceae, Rhodophyta)

    NARCIS (Netherlands)

    Jong, de Yde S.D.M.; Hitipeuw, Creusa; Prud’homme van Reine, Willem F.

    1999-01-01

    A cladistic analysis, based on a taxonomic revision is carried out for 7 Acanthophora species using 19 characters. Hypotheses on species affinities are based primarily on morphological characters. Because most species show only few distinctive characters, emphasis was placed on features of spine

  15. The Analysis of the Relationship between Communication Skills and the Establishment of Clark's Management Network among Sport Managers

    Directory of Open Access Journals (Sweden)

    Rasool NAZARI

    2016-03-01

    Full Text Available The purpose of this study was to analyze the relationship between communication skills and the establishment of Clark's Management Network among sport managers. This applied research is a kind of correlational – survey study. Statistical population consist ed of 140 sport managers working for sport organizations in Isfahan Province, which have been selected by stratified random sampling. Measurement tools included two questionnaires of Communication Skill (91% and Establishment of Clark's Management Network (87%. Descriptive and inferential statistical methods applied for statistical analysis using SPSS software. Results show that there is a relationship between communication skills and the establishment of Clark's Management Network among sport managers. I n addition, the feedback component has greater contribution to prediction of Clark's management network (p 0.05. In general, it can acknowledge that the communication skills are effective in the establishment of Clark's management network and cause to i mprove the management process of sport organizations' managers and to achieve to the organizational goals with high level of productivity.

  16. Taxonomic etymology – in search of inspiration

    Directory of Open Access Journals (Sweden)

    Piotr Jozwiak

    2015-07-01

    Full Text Available We present a review of the etymology of zoological taxonomic names with emphasis on the most unusual examples. The names were divided into several categories, starting from the most common – given after morphological features – through inspiration from mythology, legends, and classic literature but also from fictional and nonfictional pop-culture characters (e.g., music, movies or cartoons, science, and politics. A separate category includes zoological names created using word-play and figures of speech such as tautonyms, acronyms, anagrams, and palindromes. Our intention was to give an overview of possibilities of how and where taxonomists can find the inspirations that will be consistent with the ICZN rules and generate more detail afterthought about the naming process itself, the meaningful character of naming, as well as the recognition and understanding of names.

  17. Flexible taxonomic assignment of ambiguous sequencing reads

    Directory of Open Access Journals (Sweden)

    Jansson Jesper

    2011-01-01

    Full Text Available Abstract Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results.

  18. Global taxonomic diversity of living reptiles.

    Science.gov (United States)

    Pincheira-Donoso, Daniel; Bauer, Aaron M; Meiri, Shai; Uetz, Peter

    2013-01-01

    Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world's diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of

  19. Global Taxonomic Diversity of Living Reptiles

    Science.gov (United States)

    Pincheira-Donoso, Daniel; Bauer, Aaron M.; Meiri, Shai; Uetz, Peter

    2013-01-01

    Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world’s diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of

  20. Global taxonomic diversity of living reptiles.

    Directory of Open Access Journals (Sweden)

    Daniel Pincheira-Donoso

    Full Text Available Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world's diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3% is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians. In strong contrast, turtles (3.4%, crocodilians (0.3%, and tuataras (0.01% are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera containing few lineages (monophyletic genera and species, respectively, while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus. Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant. We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012, the

  1. Establishment of design and performance requirements using cost and systems analysis

    International Nuclear Information System (INIS)

    Waganer, L.M.; Carosella, L.A.; Defreece, D.A.

    1977-01-01

    The current uncertainty in design approach and performance requirements for a commercial fusion power plant poses a problem for the designer in configuring the plant and for the utilities in analyzing the attractiveness of a future fusion power plant. To provide direction and insight in this area, a systems analysis model was constructed at McDonnell Douglas, utilizing fusion subsystem algorithms with subsystem cost estimating relationships into a self-consistent computerized model for several fusion reactor concepts. Cost estimating data has been compiled by utilizing McDonnell Douglas' experience in fabricating large, complex metal assemblies and soliciting the accumulated store of knowledge in existing power plants and new emerging technologies such as the Clinch River Breeder Reactor. Using the computer model, sensitivities to plasma, reactor and plant parameters are a few of the options that have been evaluated to yield recommended concepts/techniques/solutions. This is a very beneficial tool in assessing the impact of the fusion reactor on the electrical power community and charting the optimum developmental approach

  2. Are Australians concerned about nanoparticles? A comparative analysis with established and emerging environmental health issues.

    Science.gov (United States)

    Capon, Adam; Rolfe, Margaret; Gillespie, James; Smith, Wayne

    2015-02-01

    Introducing new technologies into society raises considerable public concern. We determine the public concern about nanoparticles, and compare this concern to other environmental health issues such as wind farms and coal seam gas production. A repeat cross sectional survey examining views on environmental health issues, risk, chemicals and trust was undertaken in more than 1,300 Australian residents in 2000 and 2013. Logistic regression and principal component analysis was used to investigate predictors of nanoparticle concern and identify a component structure for environmental health issues that could explain a trend of future nanoparticle concern. Australians have a relatively low level of concern about the risks of nanoparticles to health when compared to their concerns about other environmental health issues. Items associated with concern included gender, a general wish to avoid chemicals and possibly trust in politicians. Concern over nanoparticles clustered with similar views on technological risks. Current public concern over the risks of nanoparticles is low. However, a reframing of the issue towards 'chemicals' is likely to have a negative effect on risk perceptions. This paper raises questions about appropriate channels for the effective communication of risk. © 2015 Public Health Association of Australia.

  3. Cost analysis of establishing a relationship between a surgical program in the US and Vietnam.

    Science.gov (United States)

    Chu, Quyen D; Nguyen, Thu; Nguyen, Phuong; Ho, Hung S

    2012-01-01

    "Twinning" refers to a constructive partnership between hospitals in developed and developing nations. Such an effort may contribute immensely to capacity building for the developing nation, but one of the reasons given for the lack of sustainability is cost. We share a detailed operating cost analysis of our recent experience with an institution in Vietnam. We were awarded a 1-year $54,000 grant from the Vietnam Education Foundation (VEF) to conduct a live tele-video conferencing course on the "Fundamentals of Clinical Surgery" with Thai Binh Medical University (TBMU). In-country lectures as well as an assessment of the needs at TBMU were performed. Total financial assistance and expenditures were tabulated to assess up-front infrastructure investment and annual cost required to sustain the program. The total amount of direct money ($66,686) and in-kind services ($70,276) was $136,962. The initial infrastructure cost was $41,085, which represented 62% of the direct money received. The annual cost to sustain the program was approximately $11,948. We concluded that the annual cost to maintain a "twinning" program was relatively low, and the efforts to sustain a "twinning" program were financially feasible and worthwhile endeavors. "Twinning" should be a critical part of the surgical humanitarian volunteerism effort.

  4. Analysis of the key issues in establishing the Russian-based high technological companies

    Directory of Open Access Journals (Sweden)

    V. G. Zinov

    2016-01-01

    Full Text Available The article analyses the reasons that prevent a competitive export-oriented Russian domestic development of the robot surgical complex from being industrially prototyped and serially released for the domestic and global market. The development is completed within the framework of a «priority project» which was also highlighted as of significant importance in the Forecast analysis of the scientific-technological development of Russia for the period of up until 2030 and in the road maps of the National technological initiative and other strategic documents. The project was financed by nearly all development funds and institutes in Russia. A conclusion is drawn that the key reason behind the significant increase in a life span of a high-tech market product is the absence of a target setting and a programme of coordinated actions from committed ministries and governmental agencies, as well as the lack of a large high tech company in Russia, capable of producing in industrial volumes the export-oriented products and ensure their global sales.

  5. XML schemas and mark-up practices of taxonomic literature.

    Science.gov (United States)

    Penev, Lyubomir; Lyal, Christopher Hc; Weitzman, Anna; Morse, David R; King, David; Sautter, Guido; Georgiev, Teodor; Morris, Robert A; Catapano, Terry; Agosti, Donat

    2011-01-01

    We review the three most widely used XML schemas used to mark-up taxonomic texts, TaxonX, TaxPub and taXMLit. These are described from the viewpoint of their development history, current status, implementation, and use cases. The concept of "taxon treatment" from the viewpoint of taxonomy mark-up into XML is discussed. TaxonX and taXMLit are primarily designed for legacy literature, the former being more lightweight and with a focus on recovery of taxon treatments, the latter providing a much more detailed set of tags to facilitate data extraction and analysis. TaxPub is an extension of the National Library of Medicine Document Type Definition (NLM DTD) for taxonomy focussed on layout and recovery and, as such, is best suited for mark-up of new publications and their archiving in PubMedCentral. All three schemas have their advantages and shortcomings and can be used for different purposes.

  6. A Falsification of the Citation Impediment in the Taxonomic Literature.

    Science.gov (United States)

    Steiner, Florian M; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C

    2015-09-01

    Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009-2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could

  7. Fossil struthionid eggshells from Laetoli, Tanzania: Taxonomic and biostratigraphic significance

    Science.gov (United States)

    Harrison, Terry; Msuya, Charles P.

    2005-04-01

    Recent paleontological investigations at Laetoli and neighboring localities in northern Tanzania have produced a large collection of fossil ostrich eggshells from the Pliocene-aged Laetolil Beds (˜3.5-4.5 Ma) and Ndolanya Beds (˜2.6-2.7 Ma). A detailed analysis of the morphology of the eggshells and their taxonomic affinities indicates that two different species of Struthio are represented. In the Lower Laetolil Beds and in the Upper Laetolil Beds below Tuff 3 a new species is recognized— Struthio kakesiensis. This is replaced in the Upper Laetolil Beds by Struthio camelus, the modern species of ostrich. Since radiometric age determinations are available for the stratigraphic sequence at Laetoli, it is possible to precisely date the first appearance of S. camelus at ˜3.6-3.8 Ma. Comparisons of the Laetoli material with specimens from the well-dated sequences at Lothagam and Kanapoi in northern Kenya, allow the taxonomic and biochronological analysis to be extended back in time to the late Miocene. At about 6.5 Ma, Diamantornis and elephant birds were replaced in East Africa by ostriches belonging to the genus Struthio. Three time-successive species of ostriches are identified in the fossil record of East Africa, beginning with Struthio. cf. karingarabensis (˜6.5-4.2 Ma), followed by S. kakesiensis (˜4.5-3.6 Ma) and then S. camelus (˜3.8 Ma onwards). A similar sequence of taxa has previously been recorded from localities in Namibia, but at these sites there is no possibility to precisely calibrate the ages of the different species using radiometric dating. Nevertheless, the broadly similar evolutionary sequence and the close correspondence in inferred ages for the succession of species in East Africa and Namibia suggest that ostrich eggshells are a very useful tool for biochronological correlation of paleontological sites in sub-Saharan Africa.

  8. Taxonomic separation of hippocampal networks: principal cell populations and adult neurogenesis

    Directory of Open Access Journals (Sweden)

    Roelof Maarten evan Dijk

    2016-03-01

    Full Text Available While many differences in hippocampal anatomy have been described between species, it is typically not clear if they are specific to a particular species and related to functional requirements or if they are shared by species of larger taxonomic units. Without such information, it is difficult to infer how anatomical differences may impact on hippocampal function, because multiple taxonomic levels need to be considered to associate behavioral and anatomical changes. To provide information on anatomical changes within and across taxonomic ranks, we present a quantitative assessment of hippocampal principal cell populations in 20 species or strain groups, with emphasis on rodents, the taxonomic group that provides most animals used in laboratory research. Of special interest is the importance of adult hippocampal neurogenesis in species-specific adaptations relative to other cell populations. Correspondence analysis of cell numbers shows that across taxonomic units, phylogenetically related species cluster together, sharing similar proportions of principal cell populations. CA3 and hilus are strong separators that place rodent species into a tight cluster based on their relatively large CA3 and small hilus while non-rodent species (including humans and non-human primates are placed on the opposite side of the spectrum. Hilus and CA3 are also separators within rodents, with a very large CA3 and rather small hilar cell populations separating mole-rats from other rodents that, in turn, are separated from each other by smaller changes in the proportions of CA1 and granule cells. When adult neurogenesis is included, the relatively small populations of young neurons, proliferating cells and hilar neurons become main drivers of taxonomic separation within rodents. The observations provide challenges to the computational modeling of hippocampal function, suggest differences in the organization of hippocampal information streams in rodent and non

  9. Guidance for establishment and implementation of field sample management programs in support of EM environmental sampling and analysis activities

    International Nuclear Information System (INIS)

    1994-01-01

    The role of the National Sample Management Program (NSMP) proposed by the Department of Energy's Office of Environmental Management (EM) is to be a resource for EM programs and for local Field Sample Management Programs (FSMPs). It will be a source of information on sample analysis and data collection within the DOE complex. The purpose of this document is to establish the suggested scope of the FSMP activities to be performed under each Operations Office, list the drivers under which the program will operate, define terms and list references. This guidance will apply only to EM sampling and analysis activities associated with project planning, contracting, laboratory selection, sample collection, sample transportation, laboratory analysis and data management

  10. The application of DEA (Data Envelopment Analysis) window analysis in the assessment of influence on operational efficiencies after the establishment of branched hospitals.

    Science.gov (United States)

    Jia, Tongying; Yuan, Huiyun

    2017-04-12

    Many large-scaled public hospitals have established branched hospitals in China. This study is to provide evidence for strategy making on the management and development of multi-branched hospitals by evaluating and comparing the operational efficiencies of different hospitals before and after their establishment of branched hospitals. DEA (Data Envelopment Analysis) window analysis was performed on a 7-year data pool from five public hospitals provided by health authorities and institutional surveys. The operational efficiencies of sample hospitals measured in this study (including technical efficiency, pure technical efficiency and scale efficiency) had overall trends towards increase during this 7-year period of time, however, a temporary downturn occurred shortly after the establishment of branched hospitals; pure technical efficiency contributed more to the improvement of technical efficiency compared to scale efficiency. The establishment of branched-hospitals did not lead to a long-term negative effect on hospital operational efficiencies. Our data indicated the importance of improving scale efficiency via the optimization of organizational management, as well as the advantage of a different form of branch-establishment, merging and reorganization. This study brought an insight into the practical application of DEA window analysis on the assessment of hospital operational efficiencies.

  11. Chemical analysis of Zam Zam water of Saudi Arabia and drinking water supplies of Atomic Energy Research Establishment, Bangladesh

    International Nuclear Information System (INIS)

    Khan, M.A.; Sharif, A.K.M.; Idriss A, K.M.; Alamgir, M.

    1991-01-01

    The quality of water plays an important role to the living beings. Chemical analysis have been performed on Zam Zam water of Saudi Arabia and drinking water of the Atomic Energy Research Establishment, Bangladesh. Quantitative measurements of some essential elements (Ca, Mg, Na, K, Fe, Cu, Zn, Co and Ni) and toxic elements (Pb and Cd) were carried out using atomic absorption spectrometric method. Tests indicate that all three samples (Zam Zam, tap and solar pump water) are drinkable and palatable. pH measurements show that Zam Zam water is alkaline whereas both tap and solar pump water are slightly acidic

  12. Developing the Coach Analysis and Intervention System (CAIS): establishing validity and reliability of a computerised systematic observation instrument.

    Science.gov (United States)

    Cushion, Christopher; Harvey, Stephen; Muir, Bob; Nelson, Lee

    2012-01-01

    We outline the evolution of a computerised systematic observation tool and describe the process for establishing the validity and reliability of this new instrument. The Coach Analysis and Interventions System (CAIS) has 23 primary behaviours related to physical behaviour, feedback/reinforcement, instruction, verbal/non-verbal, questioning and management. The instrument also analyses secondary coach behaviour related to performance states, recipient, timing, content and questioning/silence. The CAIS is a multi-dimensional and multi-level mechanism able to provide detailed and contextualised data about specific coaching behaviours occurring in complex and nuanced coaching interventions and environments that can be applied to both practice sessions and competition.

  13. Taxonomic composition of phytoplankton in the Vakh River (Western Siberia)

    Science.gov (United States)

    Skorobogatova, O. N.

    2018-03-01

    This paper provides data on the hydrological and hydrochemical parameters of the Vakh River in the Middle Ob region. In 2005-2008 we have identified 404 taxonomic units represented by 463 species, types and forms of algae, belonging to 140 genera, 52 families, 13 classes and 7 divisions. 386 species were identified for the first time, 141 taxa were identified as rare and 22 taxa as new for Western Siberia. Leading divisions, Bacillariophyta and Chlorophyta, make up for 78.9% of total phytoplankton diversity. Cyanobacteria, Chrysophyta and Euglenophyta form a community of 88 taxonomic units having a rank lower than genus level, and represent 19.0% of the total number. The floral role of Xanthophyta and Dinophyta is insignificant (2.1%). The main structure-forming species are 14: vegetating throughout the year (Aulacoseira italica, Asterionella formosa), summer taxa (Microcystis aeruginosa, Melosira varians, Aulacoseira granulata, Pandorina morum, Pediastrum boryanum, P. duplex, Lacunastrum gracillimum, Scenedesmus quadricauda) and summer-autumn (Microcystis pulverea, Tabellaria fenestrata, T. flocculosa, Mucidosphaerium pulchellum). The Vakh River demonstrates specific characteristics of boreal flowing waterways. The northern composition is represented in a big rate of families (44.2%) and genera (109 77.9) with one to three species. The richest genera Closterium (31 taxa), Eunotia (27 taxa), Pinnularia (22 taxa), Desmidium (11 taxa) and the family Desmidiaceae (45 taxa) ensure diversity of phytoplankton. Ecological and geographical analysis demonstrates predominance of cosmopolitan algae (56.6%). Plankton represents 44.7% of all algae, oligogalobs - 78.8% and indifferent algae – 36.7%. Water meets the requirements for β-mezosaprobian pollution zone, class of satisfactory purity (III class).

  14. An edit script for taxonomic classifications

    Directory of Open Access Journals (Sweden)

    Valiente Gabriel

    2005-08-01

    Full Text Available Abstract Background The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification. Results In this paper, we present a solution to the problem of generating modifications of the NCBI taxonomy, based on the computation of an edit script that summarises the differences between two classification trees. Our algorithms find the shortest possible edit script based on the identification of all shared subtrees, and only take time quasi linear in the size of the trees because classification trees have unique node labels. Conclusion These algorithms have been recently implemented, and the software is freely available for download from http://darwin.zoology.gla.ac.uk/~rpage/forest/.

  15. Elaiophores: their taxonomic distribution, morphology and functions

    Directory of Open Access Journals (Sweden)

    Clivia Carolina Fiorilo Possobom

    Full Text Available ABSTRACT Elaiophores are floral glands that secrete non-volatile oils as a reward for their pollinators. Their secretions mediate a specialized interaction between oil-producing plants and a few species of oil-collecting bees - Apidae and Melittidae. The present review focuses on the morphological and functional aspects of these secretory structures. We also provide information on their chemistry and pollination ecology. Our survey is organized taxonomically among the plant families for which elaiophore occurrence has been confirmed -for the monocots, Iridaceae and Orchidaceae, and for the eudicots, Calceolariaceae, Cucurbitaceae, Krameriaceae, Malpighiaceae, Plantaginaceae, Primulaceae, Scrophulariaceae, Solanaceae and Stilbaceae. Most oil flowers are zygomorphic, bisexual, nectarless and present their elaiophores on the protective whorls or on the androecium. Trichomal elaiophores are reported in all of these families except Krameriaceae and Malpighiaceae, and they vary in the density and morphology of the trichomes. Epithelial elaiophores occur in some monocot representatives and in Krameriaceae and Malpighiaceae, and are similar among species. An intermediate type of elaiophore is reported in some species of Orchidaceae. Regardless of elaiophore type, these glands have similar subcellular features and secretion-release mechanisms. Finally, we note the dearth of information on elaiophore ultrastructure and functioning for several plant families.

  16. Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal

    Directory of Open Access Journals (Sweden)

    Nico Franz

    2016-09-01

    Full Text Available Overview. Taxonomic names are imperfect identifiers of specific and sometimes conflicting taxonomic perspectives in aggregated biodiversity data environments. The inherent ambiguities of names can be mitigated using syntactic and semantic conventions developed under the taxonomic concept approach. These include: (1 representation of taxonomic concept labels (TCLs: name sec. source to precisely identify name usages and meanings, (2 use of parent/child relationships to assemble separate taxonomic perspectives, and (3 expert provision of Region Connection Calculus articulations (RCC–5: congruence, [inverse] inclusion, overlap, exclusion that specify how data identified to different-sourced TCLs can be integrated. Application of these conventions greatly increases trust in biodiversity data networks, most of which promote unitary taxonomic 'syntheses' that obscure the actual diversity of expert-held views. Better design solutions allow users to control the taxonomic variable and thereby assess the robustness of their biological inferences under different perspectives. A unique constellation of prior efforts – including the powerful Symbiota collections software platform, the Euler/X multi-taxonomy alignment toolkit, and the "Weakley Flora" which entails 7,000 concepts and more than 75,000 RCC–5 articulations – provides the opportunity to build a first full-scale concept resolution service for SERNEC, the SouthEast Regional Network of Expertise and Collections, currently with 60 member herbaria and 2 million occurrence records. Intellectual merit. We have developed a multi-dimensional, step-wise plan to transition SERNEC's data culture from name- to concept-based practices. (1 We will engage SERNEC experts through annual, regional workshops and follow-up interactions that will foster buy-in and ultimately the completion of 12 community-identified use cases. (2. We will leverage RCC–5 data from the Weakley Flora and further development of

  17. Establishment of a protocol for the gene expression analysis of laser microdissected rat kidney samples with affymetrix genechips

    International Nuclear Information System (INIS)

    Stemmer, Kerstin; Ellinger-Ziegelbauer, Heidrun; Lotz, Kerstin; Ahr, Hans-J.; Dietrich, Daniel R.

    2006-01-01

    Laser microdissection in conjunction with microarray technology allows selective isolation and analysis of specific cell populations, e.g., preneoplastic renal lesions. To date, only limited information is available on sample preparation and preservation techniques that result in both optimal histomorphological preservation of sections and high-quality RNA for microarray analysis. Furthermore, amplification of minute amounts of RNA from microdissected renal samples allowing analysis with genechips has only scantily been addressed to date. The objective of this study was therefore to establish a reliable and reproducible protocol for laser microdissection in conjunction with microarray technology using kidney tissue from Eker rats p.o. treated for 7 days and 6 months with 10 and 1 mg Aristolochic acid/kg bw, respectively. Kidney tissues were preserved in RNAlater or snap frozen. Cryosections were cut and stained with either H and E or cresyl violet for subsequent morphological and RNA quality assessment and laser microdissection. RNA quality was comparable in snap frozen and RNAlater-preserved samples, however, the histomorphological preservation of renal sections was much better following cryopreservation. Moreover, the different staining techniques in combination with sample processing time at room temperature can have an influence on RNA quality. Different RNA amplification protocols were shown to have an impact on gene expression profiles as demonstrated with Affymetrix Rat Genome 230 2 .0 arrays. Considering all the parameters analyzed in this study, a protocol for RNA isolation from laser microdissected samples with subsequent Affymetrix chip hybridization was established that was also successfully applied to preneoplastic lesions laser microdissected from Aristolochic acid-treated rats

  18. Taxonomic chauvinism revisited: insight from parental care research.

    Directory of Open Access Journals (Sweden)

    Zachary R Stahlschmidt

    Full Text Available Parental care (any non-genetic contribution by a parent that appears likely to increase the fitness of its offspring is a widespread trait exhibited by a broad range of animal taxa. In addition to influencing the fitness of parent(s and offspring, parental care may be inextricably involved in other evolutionary processes, such as sexual selection and the evolution of endothermy. Yet, recent work has demonstrated that bias related to taxonomy is prevalent across many biological disciplines, and research in parental care may be similarly burdened. Thus, I used parental care articles published in six leading journals of fundamental behavioral sciences (Animal Behaviour, Behavioral Ecology, Behavioral Ecology and Sociobiology, Ethology, Hormones and Behavior, and Physiology & Behavior from 2001-2010 (n = 712 to examine the year-to-year dynamics of two types of bias related to taxonomy across animals: (1 taxonomic bias, which exists when research output is not proportional to the frequency of organisms in nature, and (2 taxonomic citation bias, which is a proxy for the breadth of a given article-specifically, the proportion of articles cited that refer solely to the studied taxon. I demonstrate that research on birds likely represents a disproportionate amount of parental care research and, thus, exhibits taxonomic bias. Parental care research on birds and mammals also refers to a relatively narrow range of taxonomic groups when discussing its context and, thus, exhibits taxonomic citation bias. Further, the levels of taxonomic bias and taxonomic citation bias have not declined over the past decade despite cautionary messages about similar bias in related disciplines--in fact, taxonomic bias may have increased. As in Bonnet et al. (2002, my results should not be interpreted as evidence of an 'ornithological Mafia' conspiring to suppress other taxonomic groups. Rather, I generate several rational hypotheses to determine why bias persists and to

  19. Taxonomic chauvinism revisited: insight from parental care research.

    Science.gov (United States)

    Stahlschmidt, Zachary R

    2011-01-01

    Parental care (any non-genetic contribution by a parent that appears likely to increase the fitness of its offspring) is a widespread trait exhibited by a broad range of animal taxa. In addition to influencing the fitness of parent(s) and offspring, parental care may be inextricably involved in other evolutionary processes, such as sexual selection and the evolution of endothermy. Yet, recent work has demonstrated that bias related to taxonomy is prevalent across many biological disciplines, and research in parental care may be similarly burdened. Thus, I used parental care articles published in six leading journals of fundamental behavioral sciences (Animal Behaviour, Behavioral Ecology, Behavioral Ecology and Sociobiology, Ethology, Hormones and Behavior, and Physiology & Behavior) from 2001-2010 (n = 712) to examine the year-to-year dynamics of two types of bias related to taxonomy across animals: (1) taxonomic bias, which exists when research output is not proportional to the frequency of organisms in nature, and (2) taxonomic citation bias, which is a proxy for the breadth of a given article-specifically, the proportion of articles cited that refer solely to the studied taxon. I demonstrate that research on birds likely represents a disproportionate amount of parental care research and, thus, exhibits taxonomic bias. Parental care research on birds and mammals also refers to a relatively narrow range of taxonomic groups when discussing its context and, thus, exhibits taxonomic citation bias. Further, the levels of taxonomic bias and taxonomic citation bias have not declined over the past decade despite cautionary messages about similar bias in related disciplines--in fact, taxonomic bias may have increased. As in Bonnet et al. (2002), my results should not be interpreted as evidence of an 'ornithological Mafia' conspiring to suppress other taxonomic groups. Rather, I generate several rational hypotheses to determine why bias persists and to guide future

  20. A global analysis of alternative tillage and crop establishment practices for economically and environmentally efficient rice production.

    Science.gov (United States)

    Chakraborty, Debashis; Ladha, Jagdish Kumar; Rana, Dharamvir Singh; Jat, Mangi Lal; Gathala, Mahesh Kumar; Yadav, Sudhir; Rao, Adusumilli Narayana; Ramesha, Mugadoli S; Raman, Anitha

    2017-08-24

    Alternative tillage and rice establishment options should aim at less water and labor to produce similar or improved yields compared with traditional puddled-transplanted rice cultivation. The relative performance of these practices in terms of yield, water input, and economics varies across rice-growing regions. A global meta and mixed model analysis was performed, using a dataset involving 323 on-station and 9 on-farm studies (a total of 3878 paired data), to evaluate the yield, water input, greenhouse gas emissions, and cost and net return with five major tillage/crop establishment options. Shifting from transplanting to direct-seeding was advantageous but the change from conventional to zero or reduced tillage reduced yields. Direct-seeded rice under wet tillage was the best alternative with yield advantages of 1.3-4.7% (p Direct-seeding under zero tillage was another potential alternative with high savings in water input and cost of cultivation, with no yield penalty. The alternative practices reduced methane emissions but increased nitrous oxide emissions. Soil texture plays a key role in relative yield advantages, and therefore refinement of the practice to suit a specific agro-ecosystem is needed.

  1. Analysis of time in establishing synchronization radio communication system with expanded spectrum conditions for communication with mobile robots

    Science.gov (United States)

    Latinovic, T. S.; Kalabic, S. B.; Barz, C. R.; Petrica, P. Paul; Pop-Vădean, A.

    2018-01-01

    This paper analyzes the influence of the Doppler Effect on the length of time to establish synchronization pseudorandom sequences in radio communications systems with an expanded spectrum. Also, this paper explores the possibility of using secure wireless communication for modular robots. Wireless communication could be used for local and global communication. We analyzed a radio communication system integrator, including the two effects of the Doppler signal on the duration of establishing synchronization of the received and locally generated pseudorandom sequence. The effects of the impact of the variability of the phase were analyzed between the said sequences and correspondence of the phases of these signals with the interval of time of acquisition of received sequences. An analysis of these impacts is essential in the transmission of signal and protection of the transfer of information in the communication systems with an expanded range (telecommunications, mobile telephony, Global Navigation Satellite System GNSS, and wireless communication). Results show that wireless communication can provide a safety approach for communication with mobile robots.

  2. Stable isotope analysis of a newly established macrofaunal food web 1.5 years after the Hebei Spirit oil spill

    International Nuclear Information System (INIS)

    Han, Eunah; Park, Hyun Je; Bergamino, Leandro; Choi, Kwang-Sik; Choy, Eun Jung; Yu, Ok Hwan; Lee, Tae Won; Park, Heung-Sik; Shim, Won Joon; Kang, Chang-Keun

    2015-01-01

    Highlights: • We examined trophic structure in a newly established community after an oil spill. • This is the most extensive in situ isotopic analysis on an oiled benthic community. • Consumer-food source δ 13 C and δ 15 N rejected influx of petroleum into the community. • A novel circular statistics rejected trophic niche change of major feeding guilds. • Prevalence of omnivory and trophic plasticity may promote the recovery process. - Abstract: We examined trophic relationships in a newly established community 1.5 years after the Hebei Spirit oil spill on the west coast of Korea. Carbon and nitrogen stable isotope ratios in consumers and their potential food sources were compared between the oil-spill site and reference site, located 13.5 km from the oil-spill spot. The isotopic mixing model and a novel circular statistics rejected the influx of petrogenic carbon into the community and identified spatial consistencies such as the high contributions of microphytobenthos, food-chain length, and the isotopic niche of each feeding guild between sites. We suggested that high level of trophic plasticity and the prevalence of omnivory of consumers may promote the robustness of food web against the oil contamination. Furthermore, we highlighted the need of holistic approaches including different functional groups to quantify changes in the food web structure and assess the influence of different perturbations including oil spill

  3. Measurement and Analysis of Olfactory Responses with the Aim of Establishing an Objective Diagnostic Method for Central Olfactory Disorders

    Science.gov (United States)

    Uno, Tominori; Wang, Li-Qun; Miwakeichi, Fumikazu; Tonoike, Mitsuo; Kaneda, Teruo

    In order to establish a new diagnostic method for central olfactory disorders and to identify objective indicators, we measured and analyzed brain activities in the parahippocampal gyrus and uncus, region of responsibility for central olfactory disorders. The relationship between olfactory stimulation and brain response at region of responsibility can be examined in terms of fitted responses (FR). FR in these regions may be individual indicators of changes in brain olfactory responses. In the present study, in order to non-invasively and objectively measure olfactory responses, an odor oddball task was conducted on four healthy volunteers using functional magnetic resonance imaging (fMRI) and a odorant stimulator with blast-method. The results showed favorable FR and activation in the parahippocampal gyrus or uncus in all subjects. In some subjects, both the parahippocampal gyrus and uncus were activated. Furthermore, activation was also confirmed in the cingulate gyrus, middle frontal gyrus, precentral gyrus, postcentral gyrus, superior temporal gyrus and insula. The hippocampus and uncus are known to be involved in the olfactory disorders associated with early-stage Alzheimer's disease and other olfactory disorders. In the future, it will be necessary to further develop the present measurement and analysis method to clarify the relationship between central olfactory disorders and brain activities and establish objective indicators that are useful for diagnosis.

  4. Taxonomic reappraisal of Antithamnion sparsum Tokida (Ceramiaceae, Rhodophyta).

    Science.gov (United States)

    Kim, Gwang Hoon; Han, He Kyong; Lim, Kook Jin

    2008-07-01

    The taxonomic criterion of Antithamnion sparsum was reappraised in comparison with A. densum and A. defectum based on crossing experiments, morphological observation, chromosome study and Random Amplified Polymorphic DNA (RAPD) analysis. These species had a very similar morphology but were sexually isolated. The chromosome number was n = ca. 24 for A. densum, n = ca. 21 for A. defectum, and n = ca. 44 for A. sparsum. All isolates of A. sparsum and A. densum showed polysiphonia-type life history Asexual reproduction was induced by favorable environmental conditions. In A. sparsum, 1-2% of male plants developed mitotic tetrasporangia together with spermatangia. In A. densum, 5-10% of tetraspores developed into asexual tetrasporophytes. Phylogenetic relationships between these species were examined using RAPD analysis, and A. glanduliferum was used as an outgroup. A total of 167 polymorphic RAPD markers amplified from 15 different primers were analyzed. Results suggested that these species were closely related, with A. defectum placed in the middle of A. sparsum and A. densum. Chromosome study and RAPD analysis implied that A. sparsum first separated from A. defectum through polyploidization and later A. densum evolved. These species may present another example of the narrow species concept in the genus Antithamnion.

  5. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    Energy Technology Data Exchange (ETDEWEB)

    Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  6. New-doses limits introduction analysis for the design and operation of teletherapy facilities established by IAEA

    International Nuclear Information System (INIS)

    Castaneda M, A.; Jimenez C, I.; Ramirez M, J.C.; Sanchez V, H.F.

    1996-01-01

    A design of a typical teletherapy facility was made considering a Co-60 rotating unit and using critical parameters, taking into account as a design base the dose limits established in the Safety Series No. 9 (1), and Safety Series No.115-I (2), shielding thickness when the dose limits were changed. An increment in the required thickness of 1,35 CHR for controlled areas and 2,37 CHR for non-controlled areas were found. This work considered the selection of four different types of teletherapy facilities using Co-60 sources, with different design and type of used unit. An analysis of thickness was made taking into account both the original values for the design and the real operation values in each facility. In order to determine the necessary changes for the wall thicknesses when the new recommendations are applied. (authors). 4 refs., 3 tabs

  7. The Bland-Altman analysis: Does it have a role in assessing radiation dosimeter performance relative to an established standard?

    International Nuclear Information System (INIS)

    Hill, R.F.; Tofts, P.S.; Baldock, C.

    2010-01-01

    Bland-Altman analysis is used to compare two different methods of measurement and to determine whether a new method of measurement may replace an existing accepted 'gold standard' method. In this work, Bland-Altman analysis has been applied to radiation dosimetry to compare the PTW Markus and Roos parallel plate ionisation chambers and a PTW PinPoint chamber against a Farmer type ionisation chamber which is accepted as the gold standard for radiation dosimetry in the clinic. Depth doses for low energy x-rays beams with energies of 50, 75 and 100 kVp were measured using each of the ionisation chambers. Depth doses were also calculated by interpolation of the data in the British Journal of Radiology (BJR) Report 25. From the Bland-Altman analysis, the mean dose difference between the two parallel plate chambers and the Farmer chambers was 1% over the range of depths measured. The PinPoint chamber gave significant dose differences compared to the Farmer chamber. There were also differences of up to 12% between the BJR Report 25 depth doses and the measured data. For the Bland-Altman plots, the lines representing the limits of agreement were selected to be a particular percentage agreement e.g. 1 or 2%, instead of being based on the standard deviation (σ) of the differences. The Bland-Altman statistical analysis is a powerful tool for making comparisons of ionisation chambers with an ionisation chamber that has been accepted as a 'gold standard'. Therefore we conclude that Bland-Altman analysis does have a role in assessing radiation dosimeter performance relative to an established standard.

  8. The Establishment of Object Selection Criteria for Effect Analysis of Electromagnetic Pulse (EMP) in Operating Nuclear Power Plants

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Song Hae; Ryu, Hosun; Kim, Minyi; Lee, Euijong [KHNP CRI, Daejeon (Korea, Republic of)

    2016-10-15

    The electromagnetic pulse (EMP) can be used as a strategic weapon by inducing damaging voltage and currents that the electrical circuits are not designed to withstand. EMPs are lethal to electronic systems. All EMP events have three common components: a source, coupling path, and receptor. It can also travel across power grids, destroying electronics as it passes in less than a second. There have been no research studies on the effect analysis for EMP in domestic nuclear power plants and power grids. To ensure the safety of operating nuclear power plants in this environment, the emission of EMP is needed for the effect analysis and safety measures against EMPs. Actually, it is difficult and inefficient to conduct the effect analysis of EMP with all the equipment and systems in nuclear power plants (NPPs). Therefore, this paper presents the results of establishing the object selection criteria for the effect analysis of EMP in operating nuclear power plants through reviewing previous research in the US and the safety related design concepts in domestic NPPs. It is not necessary to ensure the continued operation of the plant in intense multiple EMP environments. The most probable effect of EMP on a modern nuclear power plant is an unscheduled shutdown. EMP may also cause an extended shutdown by the unnecessary activation of some safety related systems. In general, EMP can be considered a nuisance to nuclear plants, but it is not considered a serious threat to plant safety. The results of EMP effect analysis show less possibility of failure in the tested individual equipment. It was also confirmed that there is no possibility of simultaneous failure for devices in charge of the safety shutdown in the NPP.

  9. Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks.

    Directory of Open Access Journals (Sweden)

    Laurel S Burall

    Full Text Available In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra analysis plots standardized (z-score tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2. This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993-1994 and a single case from 2011 as well as

  10. Taxonomic and phylogenetic utility of variation in advertising calls of ...

    African Journals Online (AJOL)

    Taxonomic and phylogenetic utility of variation in advertising calls of francolins and spurfowls (Galliformes: Phasianidae). Tshifhiwa G. Mandiwana-Neudani, Rauri C.K. Bowie, Martine Hausberger, Laurence Henry, Timothy M. Crowe ...

  11. Deliberate teaching tools for clinical teaching encounters: A critical scoping review and thematic analysis to establish definitional clarity.

    Science.gov (United States)

    Sidhu, Navdeep S; Edwards, Morgan

    2018-04-27

    We conducted a scoping review of tools designed to add structure to clinical teaching, with a thematic analysis to establish definitional clarity. Six thousand and forty nine citations were screened, 434 reviewed for eligibility, and 230 identified as meeting study inclusion criteria. Eighty-nine names and 51 definitions were identified. Based on a post facto thematic analysis, we propose that these tools be named "deliberate teaching tools" (DTTs) and defined as "frameworks that enable clinicians to have a purposeful and considered approach to teaching encounters by incorporating elements identified with good teaching practice." We identified 46 DTTs in the literature, with 38 (82.6%) originally described for the medical setting. Forty justification articles consisted of 16 feedback surveys, 13 controlled trials, seven pre-post intervention studies with no control group, and four observation studies. Current evidence of efficacy is not entirely conclusive, and many studies contain methodology flaws. Forty-nine clarification articles comprised 12 systematic reviews and 37 narrative reviews. The most number of DTTs described by any review was four. A common design theme was identified in approximately three-quarters of DTTs. Applicability of DTTs to specific alternate settings should be considered in context, and appropriately designed justification studies are warranted to demonstrate efficacy.

  12. Taxonomic colouring of phylogenetic trees of protein sequences

    Directory of Open Access Journals (Sweden)

    Andrade-Navarro Miguel A

    2006-02-01

    Full Text Available Abstract Background Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common. Results We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree. Conclusion PhyloView can be used at http://www.ogic.ca/projects/phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address.

  13. Establishment of Exposure to Organophosphorus Warfare Agents by Means of SPME-GSMS Analysis of Bodily Fluids

    International Nuclear Information System (INIS)

    Saveleva, E. I.; Koryagina, N. L.; Radilov, A. S.; Khlebnikova, N. S.; Khrustaleva, V. S.; Feld, V. E.

    2007-01-01

    Reliable chemical analytical procedures for revealing an exposure to toxic chemicals, identifying the active substance, and assessing the degree of exposure are necessary as a component of medical and forensic activities in cases of the possible use of highly toxic chemicals in war conflicts and terrorism acts, as well as emergency situations in chemical industry, specifically at chemical weapons storage and destruction facilities. According to Chemical Weapons Convention, Part XI, Appendix 4, e-17, 'samples of importance in the investigation of alleged use include biomedical samples from human or animal sources (blood, urine, excreta, tissue etc.)'. Urinary metabolites, O-alkyl esters of methylphosphic acid, offer one of the simplest means of confirming an exposure to organophosphorus warfare agents (OPWA). Urine, unlike blood or tissues, does not require invasive collection demanding in terms of sterility. Excretion with urine is the major route of elimination of OPWA from an organism. According to published data, 90% of OPWA metabolites are excreted within 48-72 h after intoxication. We developed an SPME-GCMS procedure for the determination of O-alkyl esters methylphosphonic acid in urine, with the following detection limits,: isopropyl and isobutyl esters 5 ng/ml and pinacolyl ester 1 ng/ml. The procedure involves derivatization of the target compounds directly on the microfiber. The total analysis time is 1-1.5 h. In animal experiments in vivo we could establish the exposure to OPWA at a half-LD50 level within no less than 48 h after intoxication. In principle, OPWA metabolites could be detected in urine within two weeks after intoxication but at higher doses. Retrospective analysis of urinary metabolites in cases of the exposure to low doses of OPWA requires lower detection limits (0.1-1 ng/ml). Optimal objects for the retrospective analysis of OPWA in an organism are long-lived blood protein adducts. We developed a procedure for revealing an exposure to

  14. Automatic identification of optimal marker genes for phenotypic and taxonomic groups of microorganisms.

    Directory of Open Access Journals (Sweden)

    Elad Segev

    Full Text Available Finding optimal markers for microorganisms important in the medical, agricultural, environmental or ecological fields is of great importance. Thousands of complete microbial genomes now available allow us, for the first time, to exhaustively identify marker proteins for groups of microbial organisms. In this work, we model the biological task as the well-known mathematical "hitting set" problem, solving it based on both greedy and randomized approximation algorithms. We identify unique markers for 17 phenotypic and taxonomic microbial groups, including proteins related to the nitrite reductase enzyme as markers for the non-anammox nitrifying bacteria group, and two transcription regulation proteins, nusG and yhiF, as markers for the Archaea and Escherichia/Shigella taxonomic groups, respectively. Additionally, we identify marker proteins for three subtypes of pathogenic E. coli, which previously had no known optimal markers. Practically, depending on the completeness of the database this algorithm can be used for identification of marker genes for any microbial group, these marker genes may be prime candidates for the understanding of the genetic basis of the group's phenotype or to help discover novel functions which are uniquely shared among a group of microbes. We show that our method is both theoretically and practically efficient, while establishing an upper bound on its time complexity and approximation ratio; thus, it promises to remain efficient and permit the identification of marker proteins that are specific to phenotypic or taxonomic groups, even as more and more bacterial genomes are being sequenced.

  15. Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program

    Science.gov (United States)

    Walsh, Stephen Joseph; Meador, Michael R.

    1998-01-01

    Fish community structure is characterized by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of a perennial, multidisciplinary approach to evaluating the physical, chemical, and biological conditions of the Nation's water resources. The objective of quality assurance and quality control of fish taxonomic data that are collected as part of the NAWQA Program is to establish uniform guidelines and protocols for the identification, processing, and archiving of fish specimens to ensure that accurate and reliable data are collected. Study unit biologists, collaborating with regional biologists and fish taxonomic specialists, prepare a pre-sampling study plan that includes a preliminary faunal list and identification of an ichthyological curation center for receiving preserved fish specimens. Problematic taxonomic issues and protected taxa also are identified in the study plan, and collecting permits are obtained in advance of sampling activities. Taxonomic specialists are selected to identify fish specimens in the field and to assist in determining what fish specimens should be sacrificed, fixed, and preserved for laboratory identification, independent taxonomic verification, and long-term storage in reference or voucher collections. Quantitative and qualitative sampling of fishes follows standard methods previously established for the NAWQA Program. Common ichthyological techniques are used to process samples in the field and prepare fish specimens to be returned to the laboratory or sent to an institutional repository. Taxonomic identifications are reported by using a standardized list of scientific names that provides nomenclatural consistency and uniformity across study units.

  16. The Use of the Position Analysis Questionnaire (PAQ) for Establishing the Job Component Validity of Tests. Report No. 5. Final Report.

    Science.gov (United States)

    McCormick, Ernest J.; And Others

    The Position Analysis Questionnaire (PAQ), a structured job analysis questionnaire that provides for the analysis of individual jobs in terms of each of 187 job elements, was used to establish the job component validity of certain commercially-available vocational aptitude tests. Prior to the general analyses reported here, a statistical analysis…

  17. How do habitat filtering and niche conservatism affect community composition at different taxonomic resolutions?

    Science.gov (United States)

    Munoz, François; Ramesh, B R; Couteron, Pierre

    2014-08-01

    Understanding how local species assembly depends on the regional biogeographic and environmental context is a challenging task in community ecology. In spatially implicit neutral models, a single immigration parameter, I(k), represents the flux of immigrants from a regional pool that compete with local offspring for establishment in communities. This flux counterbalances the effect of local stochastic extinctions to maintain local species diversity. If some species within the regional pool are not adapted to the local environment (habitat filtering), the migrant flux is reduced beyond that of the neutral model, such that habitat filtering influences the value of I(k) in non-neutral situations. Here, we propose a novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism). Using both analytical reasoning and simulations, we demonstrate that I(k) is expected to be constant when estimated based on the community composition at several taxonomic levels, not only under neutral assumptions, but also when habitat filtering occurs, unless there is substantial niche conservatism. In the latter case, I(k) is expected to decrease when estimated based on the composition at species to genus and family levels, thus allowing a signature of niche conservatism to be detected by simply comparing I(k) estimates across taxonomic levels. We applied this approach to three rain forest data sets from South India and Central America and found no significant signature of niche conservatism when I(k) was compared across taxonomic levels, except at the family level in South India. We further observed more limited immigration in South Indian forests, supporting the hypothesis of a greater impact of habitat filtering and heterogeneity there than in Central America. Our results highlight the relevance of studying variations of I

  18. Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions

    Science.gov (United States)

    Conte-Grand, Cecilia; Britz, Ralf; Dahanukar, Neelesh; Raghavan, Rajeev; Pethiyagoda, Rohan; Tan, Heok Hui; Hadiaty, Renny K.; Yaakob, Norsham S.

    2017-01-01

    Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group. PMID

  19. Taxonomic and chemical assessment of exceptionally abundant rock mine biofilm

    Directory of Open Access Journals (Sweden)

    Karolina Tomczyk-Żak

    2017-08-01

    Full Text Available Background An exceptionally thick biofilm covers walls of ancient gold and arsenic Złoty Stok mine (Poland in the apparent absence of organic sources of energy. Methods and Results We have characterized this microbial community using culture-dependent and independent methods. We sequenced amplicons of the 16S rRNA gene obtained using generic primers and additional primers targeted at Archaea and Actinobacteria separately. Also, we have cultured numerous isolates from the biofilm on different media under aerobic and anaerobic conditions. We discovered very high biodiversity, and no single taxonomic group was dominant. The majority of almost 4,000 OTUs were classified above genus level indicating presence of novel species. Elemental analysis, performed using SEM-EDS and X-ray, of biofilm samples showed that carbon, sulphur and oxygen were not evenly distributed in the biofilm and that their presence is highly correlated. However, the distribution of arsenic and iron was more flat, and numerous intrusions of elemental silver and platinum were noted, indicating that microorganisms play a key role in releasing these elements from the rock. Conclusions Altogether, the picture obtained throughout this study shows a very rich, complex and interdependent system of rock biofilm. The chemical heterogeneity of biofilm is a likely explanation as to why this oligotrophic environment is capable of supporting such high microbial diversity.

  20. Taxonomic status of the Columbia duskysnail (Truncatelloidea, Amnicolidae, Colligyrus).

    Science.gov (United States)

    Liu, Hsiu-Ping; Hershler, Robert; Rossel, Christopher S

    2015-01-01

    Undescribed freshwater snails (Amnicolidae: Colligyrus) from the Mount Hood region (northwestern United States) identified as a new species (commonly known as the Columbia duskysnail) in grey literature have been provided federal protection under the "survey and manage" provisions of the Northwest Forest Plan and have been placed on conservation watch lists. However, there are no published studies of the identity of these snails aside from a molecular phylogenetic analysis which delineated a close relationship between the single sampled population and Colligyrusgreggi, which is distributed more than 750 km to the east of the Mount Hood area. Here we examine the taxonomic status of the Columbia duskysnail based on additional molecular sampling of mitochondrial DNA sequences (COI) and morphological evidence. We found that the Columbia duskysnail is not a monophyletic group and forms a strongly supported clade with Colligyrusgreggi. The COI divergence between these broadly disjunct groups (2.1%) was somewhat larger than that within Colligyrusgreggi (1.0%) but considerably less than that among the three currently recognized species of Colligyrus (8.7-12.1%). Additionally we found that the Columbia duskysnail and Colligyrusgreggi cannot be consistently differentiated by previously reported diagnostic characters (size and shape of shell spire, pigmentation of body and penis) and are closely similar in other aspects of morphology. Based on these results we conclude that the Columbia duskysnail is conspecific with Colligyrusgreggi.

  1. Taxonomic status of the Columbia duskysnail (Truncatelloidea, Amnicolidae, Colligyrus

    Directory of Open Access Journals (Sweden)

    Hsiu-Ping Liu

    2015-07-01

    Full Text Available Undescribed freshwater snails (Amnicolidae: Colligyrus from the Mount Hood region (northwestern United States identified as a new species (commonly known as the Columbia duskysnail in grey literature have been provided federal protection under the “survey and manage” provisions of the Northwest Forest Plan and have been placed on conservation watch lists. However, there are no published studies of the identity of these snails aside from a molecular phylogenetic analysis which delineated a close relationship between the single sampled population and C. greggi, which is distributed more than 750 km to the east of the Mount Hood area. Here we examine the taxonomic status of the Columbia duskysnail based on additional molecular sampling of mitochondrial DNA sequences (COI and morphological evidence. We found that the Columbia duskysnail is not a monophyletic group and forms a strongly supported clade with C. greggi. The COI divergence between these broadly disjunct groups (2.1% was somewhat larger than that within C. greggi (1.0% but considerably less than that among the three currently recognized species of Colligyrus (8.7–12.1%. Additionally we found that the Columbia duskysnail and C. greggi cannot be consistently differentiated by previously reported diagnostic characters (size and shape of shell spire, pigmentation of body and penis and are closely similar in other aspects of morphology. Based on these results we conclude that the Columbia duskysnail is conspecific with C. greggi.

  2. Establishment of a maintenance plan based on quantitative analysis in the context of RCM in a JIT production scenario

    International Nuclear Information System (INIS)

    Alebrant Mendes, Angélica; Duarte Ribeiro, José Luis

    2014-01-01

    This paper presents a quantitative method for supporting the preparation or review of an equipment maintenance plan in a Just-in-time production scenario. The proposed method includes the following steps: (i) identifying the parts that influence reliability; (ii) surveying the failure rates and times to repair the parts; (iii) classification of parts according to the effect of their failures; (iv) surveying the line occupation parameters; (v) identifying the probability distributions for time to failure, time to repair, and line occupation; (vi) simulating the production and maintenance using the Monte Carlo approach; (vii) conducting a sensitivity analysis concerning variations in demand, MTTF, and MTTR; and (viii) establishing optimized intervals for preventive maintenance. The method is illustrated through an application in a labeling and filling gallons line at a paints and dyes production company. This method allowed the identification of critical parts as it relates to the productive scenario in question. The results can support companies in their decision making regarding the need and/or type of maintenance investment that would best fit an expected demand scenario

  3. Establishment and in-house validation of stem-loop RT PCR method for MicroRNA398 expression analysis

    Directory of Open Access Journals (Sweden)

    Timotijević Gordana S.

    2015-01-01

    Full Text Available MicroRNAs (miRNAs belong to the class of small non-coding RNAs which have important roles throughout development as well as in plant response to diverse environmental stresses. Some of plant miRNAs are essential for regulation and maintenance of nutritive homeostasis when nutrients are in excess or shortage comparing to optimal concentration for certain plant species. Better understanding of miRNAs functions implies development of efficient technology for profiling their gene expression. We set out to establish validate the methodology for miRNA gene expression analysis in cucumber grown under suboptimal mineral nutrient regimes, including iron deficiency. Reverse transcription by “stem-loop” primers in combination with Real time PCR method is one of potential approaches for quantification of miRNA gene expression. In this paper we presented a method for “stem loop” primer design specific for miR398, as well as reaction optimization and determination of Real time PCR efficiency. Proving the accuracy of this method was imperative as “stem loop” RT which consider separate transcription of target and endogenous control. The method was verified by comparison of the obtained data with results of miR398 expression achieved using a commercial kit based on simultaneous conversion of all RNAs in cDNAs. [Projekat Ministarstva nauke Republike Srbije, br. 173005 i br. ON-173028

  4. Effect of Fructose on Established Lipid Targets: A Systematic Review and Meta-Analysis of Controlled Feeding Trials

    Science.gov (United States)

    Chiavaroli, Laura; de Souza, Russell J; Ha, Vanessa; Cozma, Adrian I; Mirrahimi, Arash; Wang, David D; Yu, Matthew; Carleton, Amanda J; Di Buono, Marco; Jenkins, Alexandra L; Leiter, Lawrence A; Wolever, Thomas M S; Beyene, Joseph; Kendall, Cyril W C; Jenkins, David J A; Sievenpiper, John L

    2015-01-01

    Background Debate over the role of fructose in mediating cardiovascular risk remains active. To update the evidence on the effect of fructose on established therapeutic lipid targets for cardiovascular disease (low-density lipoprotein cholesterol [LDL]-C, apolipoprotein B, non-high-density lipoprotein cholesterol [HDL-C]), and metabolic syndrome (triglycerides and HDL-C), we conducted a systematic review and meta-analysis of controlled feeding trials. Methods and Results MEDLINE, EMBASE, CINHAL, and the Cochrane Library were searched through July 7, 2015 for controlled feeding trials with follow-up ≥7 days, which investigated the effect of oral fructose compared to a control carbohydrate on lipids (LDL-C, apolipoprotein B, non-HDL-C, triglycerides, and HDL-C) in participants of all health backgrounds. Two independent reviewers extracted relevant data. Data were pooled using random effects models and expressed as mean difference with 95% CI. Interstudy heterogeneity was assessed (Cochran Q statistic) and quantified (I2 statistic). Eligibility criteria were met by 51 isocaloric trials (n=943), in which fructose was provided in isocaloric exchange for other carbohydrates, and 8 hypercaloric trials (n=125), in which fructose supplemented control diets with excess calories compared to the control diets alone without the excess calories. Fructose had no effect on LDL-C, non-HDL-C, apolipoprotein B, triglycerides, or HDL-C in isocaloric trials. However, in hypercaloric trials, fructose increased apolipoprotein B (n=2 trials; mean difference = 0.18 mmol/L; 95% CI: 0.05, 0.30; P=0.005) and triglycerides (n=8 trials; mean difference = 0.26 mmol/L; 95% CI: 0.11, 0.41; Peffect on established lipid targets when added to existing diets so as to provide excess calories (+21% to 35% energy). When isocalorically exchanged for other carbohydrates, fructose had no adverse effects on blood lipids. More trials that are larger, longer, and higher quality are required. Clinical

  5. Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR.

    Science.gov (United States)

    Oueslati, Amel; Ollitrault, Frederique; Baraket, Ghada; Salhi-Hannachi, Amel; Navarro, Luis; Ollitrault, Patrick

    2016-08-18

    Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the "true citrus" genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at

  6. Floral Volatiles in Parasitic Plants of the Orobanchaceae. Ecological and Taxonomic Implications

    Directory of Open Access Journals (Sweden)

    Peter eTóth

    2016-03-01

    Full Text Available The holoparasitic broomrapes, Orobanche spp. and Phelipanche spp. (Orobanchaceae, are root parasites that completely depend on a host plant for survival and reproduction. There is considerable controversy on the taxonomy of this biologically and agronomically important family. Flowers of over 25 parasitic Orobanchaceae and a number of close, parasitic and non-parasitic, relatives emitted a complex blend of volatile organic compounds (VOCs, consisting of over 130 VOCs per species. Floral VOC blend-based phylogeny supported the known taxonomy in internal taxonomic grouping of genus and eliminated the uncertainty in some taxonomical groups. Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial hosts, and for the annual hosts, into weedy and non-weedy broomrapes. We conclude that floral VOCs are a significant tool in species identification and possibly even in defining new species and can help to improve controversial taxonomy in the Orobanchaceae.

  7. Floral Volatiles in Parasitic Plants of the Orobanchaceae. Ecological and Taxonomic Implications

    Science.gov (United States)

    Tóth, Peter; Undas, Anna K.; Verstappen, Francel; Bouwmeester, Harro

    2016-01-01

    The holoparasitic broomrapes, Orobanche spp. and Phelipanche spp. (Orobanchaceae), are root parasites that completely depend on a host plant for survival and reproduction. There is considerable controversy on the taxonomy of this biologically and agronomically important family. Flowers of over 25 parasitic Orobanchaceae and a number of close, parasitic and non-parasitic, relatives emitted a complex blend of volatile organic compounds (VOCs), consisting of over 130 VOCs per species. Floral VOC blend-based phylogeny supported the known taxonomy in internal taxonomic grouping of genus and eliminated the uncertainty in some taxonomical groups. Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial hosts, and for the annual hosts, into weedy and non-weedy broomrapes. We conclude that floral VOCs are a significant tool in species identification and possibly even in defining new species and can help to improve controversial taxonomy in the Orobanchaceae. PMID:27014329

  8. Description of a taxonomically undefined Sclerotiniaceae strain from withered rotten-grapes.

    Science.gov (United States)

    Lorenzini, Marilinda; Zapparoli, Giacomo

    2016-02-01

    A necrotrophic member of the Sclerotiniaceae family (herewith named strain C10) isolated from withered rotten-grapes, is described. Interestingly, the fungus has no defined taxonomic position since it has been impossible to attribute it to an existing genus. Phylogenetic analysis of partial sequences of glyceraldehyde 3-phosphate dehydrogenase (G3PDH), heat shock protein 60 (HSP60) and DNA-directed RNA polymerase II subunit (RPB2), revealed that strain C10 is distantly related to Amphobotrys and Botrytis. This evidence clearly distinguishes this new Sclerotiniaceae member from other taxa of the family. Moreover, its morphological characteristics did not match those of Amphobotrys and Botrytis. Infectivity assays demonstrated that strain C10 could be a potential postharvest pathogen of withered grapes. This study revealed the taxonomic importance of this strain suggesting the existence of a possible new genus, a theory that requires further investigation.

  9. Taxonomic reassessment of two Indian shieldtail snakes in the Uropeltis ceylanicus species group (Reptilia: Uropeltidae

    Directory of Open Access Journals (Sweden)

    S.R. Ganesh

    2014-01-01

    Full Text Available Uropeltis is the most speciose of all shieldtail snake (uropeltid genera, particularly in India, and has been bedeviled by a complex and intricate taxonomic history, with several weakly established synonyms and widely disjunct geographic ranges. Our present work on two Indian Uropeltis species revealed greater species diversity than what is currently recognised. We elevate Uropeltis arcticeps madurensis to species level, and revive Silybura shorttii (in the combination Uropeltis shorttii from the subjective synonymy of U. ceylanicus. We provide differential diagnoses, descriptions of examined material and comparisons with similar species based on an examination of voucher specimens as well as fresh, uncollected topotypes documented in the field.

  10. Taxonomic relationships of some species of orobanche l. evidence from rapd-pcr and issr markers

    International Nuclear Information System (INIS)

    Sharawy, S.; Karakish, E.

    2015-01-01

    The taxonomic relationships among 25 samples representing nine species of Orobanche L. (Orobanchaceae) were determined by the analysis of morphological characters and molecular polymorphism using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR). In order to construct dendrogram elucidating the relationships among the examined taxa, the coded data were analyzed using the software package NTSYS-pc 2.1 based on the Neighbor-joining (NJ) tree building method based on a distance matrix. The aim of this study is to develop taxonomic relationship based on morphological and molecular data, in order to obtain a more reliable taxonomic relationship of Orobanche species under study. The dendrogram produced by the analysis of the molecular data (RAPD and ISSR) resembled that constructed by NJ dendrogram for the morphological variation. The studied taxa were separated in two groups, the first comprised of the five species of section Trionychon (O. purpurea, O.lavandulacea, O. ramosa, O. mutelii and O. aegyptiaca) and the second comprised of the four species of section Orobanche (O.cernua, O. crenata, O. minor and O. pubescens). High similarity was detected between O. pubescens and O. minor. The results confirmed the close relationship between O. ramosa and O. mutelii. Moreover, this study demonstrated the grouping of the studied taxa in most cases by geographically isolated population. (author)

  11. Taxonomic bias in biodiversity data and societal preferences.

    Science.gov (United States)

    Troudet, Julien; Grandcolas, Philippe; Blin, Amandine; Vignes-Lebbe, Régine; Legendre, Frédéric

    2017-08-22

    Studying and protecting each and every living species on Earth is a major challenge of the 21 st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.

  12. Taxonomic distinctness and richness of helminth parasite assemblages of freshwater fishes in Mexican hydrological basins.

    Science.gov (United States)

    Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

    2013-01-01

    In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra--host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern--nearctic and southern--neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance--decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis.

  13. Taxonomic distinctness and richness of helminth parasite assemblages of freshwater fishes in Mexican hydrological basins.

    Directory of Open Access Journals (Sweden)

    Benjamín Quiroz-Martínez

    Full Text Available In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra--host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern--nearctic and southern--neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance--decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis.

  14. The mutational profile and infiltration pattern of murine MLH1-/- tumors: concurrences, disparities and cell line establishment for functional analysis.

    Science.gov (United States)

    Maletzki, Claudia; Beyrich, Franziska; Hühns, Maja; Klar, Ernst; Linnebacher, Michael

    2016-08-16

    Mice lines homozygous negative for one of the four DNA mismatch repair (MMR) genes (MLH1, MSH2, PMS2, MSH6) were generated as models for MMR deficient (MMR-D) diseases. Clinically, hereditary forms of MMR-D include Lynch syndrome (characterized by a germline MMR gene defect) and constitutional MMR-D, the biallelic form. MMR-D knockout mice may be representative for both diseases. Here, we aimed at characterizing the MLH1-/- model focusing on tumor-immune microenvironment and identification of coding microsatellite mutations in lymphomas and gastrointestinal tumors (GIT).All tumors showed microsatellite instability (MSI) in non-coding mononucleotide markers. Mutational profiling of 26 coding loci in MSI+ GIT and lymphomas revealed instability in half of the microsatellites, two of them (Rfc3 and Rasal2) shared between both entities. MLH1-/- tumors of both entities displayed a similar phenotype (high CD71, FasL, PD-L1 and CTLA-4 expression). Additional immunofluorescence verified the tumors' natural immunosuppressive character (marked CD11b/CD200R infiltration). Vice versa, CD3+ T cells as well as immune checkpoints molecules were detectable, indicative for an active immune microenvironment. For functional analysis, a permanent cell line from an MLH1-/- GIT was established. The newly developed MLH1-/- A7450 cells exhibit stable in vitro growth, strong invasive potential and heterogeneous drug response. Moreover, four additional MSI target genes (Nktr1, C8a, Taf1b, and Lig4) not recognized in the primary were identified in this cell line.Summing up, molecular and immunological mechanisms of MLH1-/- driven carcinogenesis correlate well with clinical features of MMR-D. MLH1-/- knockout mice combine characteristics of Lynch syndrome and constitutional MMR-D, making them suitable models for preclinical research aiming at MMR-D related diseases.

  15. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

    DEFF Research Database (Denmark)

    Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic Antoine Alexandre

    2013-01-01

    -eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g-h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (. Scrophulariaceae......We use 2nd generation sequencing technology on sedimentary ancient DNA (. sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the results with those previously obtained from pollen and macrofossils in the same lake. Thirty...... and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650calyrBP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less...

  16. An Analysis of Second-Tier Arms Producing Countries' Offset Policies: Technology Transfer and Defense Industrial Base Establishment

    National Research Council Canada - National Science Library

    Confer, Brian S

    2008-01-01

    The purpose of this thesis is to determine if offsets are an effective means of second-tier countries acquiring technology and if offsets enhance their ability to establish and maintain an industrial...

  17. Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?

    Science.gov (United States)

    Souza, Renata Carolini; Mendes, Iêda Carvalho; Reis-Junior, Fábio Bueno; Carvalho, Fabíola Marques; Nogueira, Marco Antonio; Vasconcelos, Ana Tereza Ribeiro; Vicente, Vânia Aparecida; Hungria, Mariangela

    2016-03-16

    The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome. Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance. High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most

  18. Taxonomic perspective of plant species yielding vegetable oils used ...

    African Journals Online (AJOL)

    A search conducted to determine the plants yielding vegetable oils resulted in 78 plant species with potential use in cosmetics and skin care products. The taxonomic position of these plant species is described with a description of vegetable oils from these plants and their use in cosmetic and skin care products.

  19. Data composition and taxonomic resolution in macroinvertebrate stream typology

    NARCIS (Netherlands)

    Verdonschot, P.F.M.

    2006-01-01

    In the EU water framework directive (WFD) a typological framework is defined for assessing the ecological quality of water bodies in the future. The aim of this study was to test the effect of data composition and taxonomic resolution on this typology. The EU research projects AQEM and STAR provided

  20. Taxonomic status and conservation importance of the avifauna of ...

    African Journals Online (AJOL)

    Democratic Republic of Congo) focussed on the status of 56 taxa, to reveal a high endemism (14 species of a total of at least 642). In addition, 33 taxa were also revealed as possible south-central African endemics but need thorough taxonomic ...

  1. The taxonomic status of giant sengis ( genus Rhynchocyon ) in ...

    African Journals Online (AJOL)

    The sengis (elephant-shrews) of Mozambique are poorly known, especially the taxonomic status of the giant sengis, genus Rhynchocyon. Currently, Rhynchocyon from Mozambique are thought to be chequered sengis, R. cirnei with specimens from the central coastal areas being placed in the subspecies R. c. cirnei, while ...

  2. Taxonomic analysis of Paraguayan samples of Homonota fasciata Duméril & Bibron (1836 with the revalidation of Homonota horrida Burmeister (1861 (Reptilia: Squamata: Phyllodactylidae and the description of a new species

    Directory of Open Access Journals (Sweden)

    Pier Cacciali

    2017-08-01

    Full Text Available Homonota is a Neotropical genus of nocturnal lizards characterized by the following combination of characters: absence of femoral pores, infradigital lamellae not dilated, claws without sheath, inferior lamellae laterally not denticulate, and presence of a ceratobranchial groove. Currently the genus is composed of 10 species assembled in three groups: two groups with four species, and the fasciata group with only two species. Here, we analyzed genetic and morphologic data of samples of Homonota fasciata from Paraguay; according to Maximum Likelihood and Bayesian inference analyses, the Paraguay population represents an undescribed species. Additionally, morphological analysis of the holotype of H. fasciata (MNHN 6756 shows that it is morphologically different from the banded, large-scaled Homonota commonly referred to as “H. fasciata”. Given the inconsistency between morphological characters of the name-bearing type of H. fasciata and the species commonly referred to as H. fasciata, we consider them as different taxa. Thus, H. fasciata is a species inquirenda which needs further studies, and we resurrect the name H. horrida for the banded, large-scaled Homonota. The undescribed species from Paraguay is similar to H. horrida, but can be differentiated by the high position of the auditory meatus relative to the mouth commissure (vs. low position in H. horrida; and less developed tubercles on the sides of the head, including a narrow area between the orbit and the auditory meatus covered with small granular scales with or without few tubercles (vs. several big tubercles on the sides of the head even in the area between the orbit and the auditory meatus. The new species is distributed in the Dry Chaco in South America. With the formal description of this species, the actual diversity of the genus Homonota is increased to 12 species. Furthermore, we infer phylogenetic relationships for 11 of the 12 described species of the genus, based on 11

  3. Summary and statistical analysis of environmental monitoring data in the Oarai Research Establishment, Japan Atomic Energy Research Institute

    International Nuclear Information System (INIS)

    Tamura, Katsuhiro; Kitano, Kyoshiro; Sibanuma, Yukio; Takasaki, Koichi; Ohhata, Tsutomu

    1998-03-01

    In the Oarai Research Establishment, Japan Atomic Energy Research Institute (JAERI), the environmental monitoring has been conducted for about 29 years since April 1968. The results are discussed for evaluation of long-term and short-term fluctuation in the radiological conditions in the Oarai area. This report summarises the data of the environmental monitoring in Oarai, and statistical analyses were made of the data collected from 1985 through 1994. (author)

  4. Analysis of risk factors and the establishment of a risk model for peripherally inserted central catheter thrombosis

    OpenAIRE

    Fang Hu; Ruo-Nan Hao; Jie Zhang; Zhi-Cheng Ma

    2016-01-01

    Objective: To investigate the main risk factors of peripherally inserted central catheter (PICC) related upper extremity deep venous thrombosis and establish the risk predictive model of PICC-related upper extremity deep venous thrombosis. Methods: Patients with PICC who were hospitalized between January 2014 and July 2015 were studied retrospectively; they were divided into a thrombosis group (n = 52), with patients who had a venous thrombosis complication after PICC, and a no-thrombosis ...

  5. Establishment of a continuous culture system for Entamoeba muris and analysis of the small subunit rRNA gene

    OpenAIRE

    Kobayashi S.; Suzuki J.; Takeuchi T.

    2009-01-01

    We established a culture system for Entamoeba muris (MG-EM-01 strain isolated from a Mongolian gerbil) using a modified Balamuth’s egg yolk infusion medium supplemented with 4% adult bovine serum and Bacteroides fragilis cocultured with Escherichia coli. Further, encystation was observed in the culture medium. The morphological characteristics of E. muris are similar to those of Entamoeba coli (E. coli); moreover, the malic isoenzyme electrophoretic band, which shows species-specific electrop...

  6. Outcome Analysis following Operative Skeletal Stabilization in Established Non Unions of Malleolar Fractures ? A Series of 11 Cases

    OpenAIRE

    Balasubramanian, Navin; Babu, Ganesh; Prakasam, Sindhuja

    2015-01-01

    Introduction: Established non-unions pose a real nightmare for even the most accomplished surgeon. The variations in anatomy due to extensive fibrous tissue growth, soft tissue contractures around the fracture site and bony alterations like smoothening and sclerosis of the fracture ends must each be addressed as a whole if good outcome is to be expected. Case series: Here we present a series of 11 patients who had bimalleolar fracture of the ankle following which they had native splinting. Th...

  7. Outcome Analysis following Operative Skeletal Stabilization in Established Non Unions of Malleolar Fractures - A Series of 11 Cases.

    Science.gov (United States)

    Balasubramanian, Navin; Babu, Ganesh; Prakasam, Sindhuja

    2015-01-01

    Established non-unions pose a real nightmare for even the most accomplished surgeon. The variations in anatomy due to extensive fibrous tissue growth, soft tissue contractures around the fracture site and bony alterations like smoothening and sclerosis of the fracture ends must each be addressed as a whole if good outcome is to be expected. Here we present a series of 11 patients who had bimalleolar fracture of the ankle following which they had native splinting. These patients presented to us with established non-union. There were 7 males and 4 females in the study. The average age was 44.63 years. Ten out of the 11 patients went on to union (90.1%) following internal fixation with or without immobilization in a plaster cast at an average of 13.8 weeks (range 12-17 weeks). The remaining patient did not progress to union and was advised revision fixation but she refused. She was put on an ankle foot orthoses and mobilized with satisfactory results. There was no infection in any of the patients. Two patients had delayed wound healing with delayed suture removal at 18 days. Weight bearing was started at the end of 16 weeks in all the patients. All patients were assessed using the Karlsson and Peterson functional score for the ankle. Six patients had excellent outcome, 3 had good outcome, 2 had fair with one patient having poor functional result. We conclude that open reduction internal fixation +/- bone grafting provides excellent union rates and good functional results in even the most established non unions of bimalleolar fractures of the ankle.

  8. Expression profiling of human renal carcinomas with functional taxonomic analysis

    Science.gov (United States)

    2002-01-01

    Background Molecular characterization has contributed to the understanding of the inception, progression, treatment and prognosis of cancer. Nucleic acid array-based technologies extend molecular characterization of tumors to thousands of gene products. To effectively discriminate between tumor sub-types, reliable laboratory techniques and analytic methods are required. Results We derived mRNA expression profiles from 21 human tissue samples (eight normal kidneys and 13 kidney tumors) and two pooled samples using the Affymetrix GeneChip platform. A panel of ten clustering algorithms combined with four data pre-processing methods identified a consensus cluster dendrogram in 18 of 40 analyses and of these 16 used a logarithmic transformation. Within the consensus dendrogram the expression profiles of the samples grouped according to tissue type; clear cell and chromophobe carcinomas displayed distinctly different gene expression patterns. By using a rigorous statistical selection based method we identified 355 genes that showed significant (p Matrix Organization and Adhesion. Conclusions Affymetrix GeneChip profiling differentiated clear cell and chromophobe carcinomas from one another and from normal kidney cortex. Clustering methods that used logarithmic transformation of data sets produced dendrograms consistent with the sample biology. Functional taxonomy provided a practical approach to the interpretation of gene expression data. PMID:12356337

  9. Expression profiling of human renal carcinomas with functional taxonomic analysis

    Directory of Open Access Journals (Sweden)

    Madore Steven J

    2002-09-01

    Full Text Available Abstract Background Molecular characterization has contributed to the understanding of the inception, progression, treatment and prognosis of cancer. Nucleic acid array-based technologies extend molecular characterization of tumors to thousands of gene products. To effectively discriminate between tumor sub-types, reliable laboratory techniques and analytic methods are required. Results We derived mRNA expression profiles from 21 human tissue samples (eight normal kidneys and 13 kidney tumors and two pooled samples using the Affymetrix GeneChip platform. A panel of ten clustering algorithms combined with four data pre-processing methods identified a consensus cluster dendrogram in 18 of 40 analyses and of these 16 used a logarithmic transformation. Within the consensus dendrogram the expression profiles of the samples grouped according to tissue type; clear cell and chromophobe carcinomas displayed distinctly different gene expression patterns. By using a rigorous statistical selection based method we identified 355 genes that showed significant (p Conclusions Affymetrix GeneChip profiling differentiated clear cell and chromophobe carcinomas from one another and from normal kidney cortex. Clustering methods that used logarithmic transformation of data sets produced dendrograms consistent with the sample biology. Functional taxonomy provided a practical approach to the interpretation of gene expression data.

  10. Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

    Science.gov (United States)

    Alsop, Eric B; Raymond, Jason

    2013-01-01

    Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses) for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

  11. Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

    Directory of Open Access Journals (Sweden)

    Eric B Alsop

    Full Text Available Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

  12. Taxonomic Studies on the Genus Arnebia Forssk. (Boraginaceae in India

    Directory of Open Access Journals (Sweden)

    Kumar Ambrish

    2014-12-01

    Full Text Available The genus Arnebia Forssk. in India is taxonomically studied based on field surveys, collection of live plants, consultation of herbarium and literature. The genus is represented in India by 10 taxa including 8 species and 2 varieties viz., Arnebia bhattacharyyae K. Ambrish & S.K. Srivast., A. benthamii (Wall. ex G. Don I.M. Johnst., A. euchroma ( Royle I.M. Johnst., A. guttata Bunge, A. hispidissima (Sieber ex Lehm. A.DC., A. linearifolia A.DC., A. griffithii Boiss., A. nandadeviensis K. Chandra Sek. & R.S. Rawal , A. euchroma var. grandis (Bornm. Kazmi and A. guttata var. thomsonii (C.B. Clarke Kazmi, distributed in Jammu & Kashmir, Himachal Pradesh and Uttarakhand in North-West Himalaya to Uttar Pradesh, Punjab and Rajasthan in India. Dichotomous keys to all the species in India along with taxonomic description, distribution, illustrations and images of most of the species including type and their economic importance are provided.

  13. A taxonomic synopsis of Altingiaceae with nine new combinations

    Directory of Open Access Journals (Sweden)

    Stefanie Ickert-Bond

    2013-12-01

    Full Text Available A taxonomic synopsis of the Altingiaceae is presented, including the taxonomic enumeration and distribution of 15 recognized species based on studies of 1,500 specimens from 24 herbaria throughout the distributional range of the taxa. Previous phylogenetic analyses based on several molecular markers have shown that Altingia and Semiliquidambar are nested within Liquidambar. All Altingia and Semiliquidambar species are now formally transferred to Liquidambar, which has the nomenclatural priority. The following nine new combinations are herein made: Liquidambar cambodiana (Lecomte Ickert-Bond & J. Wen, L. caudata (H. T. Chang Ickert-Bond & J. Wen, L. chingii (Metcalf Ickert-Bond & J. Wen, L. gracilipes (Hemsl. Ickert-Bond & J. Wen, L. multinervis (Cheng Ickert-Bond & J. Wen, L. obovata (Merrill & Chun Ickert-Bond & J. Wen, L. poilanei (Tardieu Ickert-Bond & J. Wen, L. siamensis (Craib Ickert-Bond & J. Wen, and L. yunnanensis (Rehder & Wilson Ickert-Bond & J. Wen.

  14. Partial migration in fishes: definitions, methodologies and taxonomic distribution

    DEFF Research Database (Denmark)

    Chapman, B B; Skov, C; Hulthén, K

    2012-01-01

    published. In addition, previous work and synthesis has been hampered by a varied lexicon associated with this phenomenon in fishes. In this review, definitions and important concepts in partial migration research are discussed, and a classification system of the different forms of partial migration......Partial migration, where populations are composed of both migratory and resident individuals, is extremely widespread across the animal kingdom. Researchers studying fish movements have long recognized that many fishes are partial migrants, however, no detailed taxonomic review has ever been...... in fishes introduced. Next, a detailed taxonomic overview of partial migration in this group is considered. Finally, methodological approaches that ichthyologists can use to study this fascinating phenomenon are reviewed. Partial migration is more widespread amongst fishes than previously thought, and given...

  15. The preliminary analysis of establishing the cost control system of AP1000 for the Haiyang nuclear power project

    International Nuclear Information System (INIS)

    Li Jing; Li Xiaobing

    2012-01-01

    The AP1000 technology has been first applied to Nuclear Power Plant construction in China. Haiyang Project is the second plant which applies the new technology, and it is the key to the success of the project, that how to control the cost. The cost control of AP1000 is to manage and monitor all the cost of the project, including the cost of project management, design, procurement, construction, and startup/commissioning. For the Haiyang Project, the cost control system should be established to ensure that the evaluation of the procurement order should be covered in the original budget, and all potential commitments are evaluated and approved within the confinement of cost control, and reduce the risk of the first reactor and get the most profit. (authors)

  16. Standardizing metadata and taxonomic identification in metabarcoding studies.

    Science.gov (United States)

    Tedersoo, Leho; Ramirez, Kelly S; Nilsson, R Henrik; Kaljuvee, Aivi; Kõljalg, Urmas; Abarenkov, Kessy

    2015-01-01

    High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.

  17. Support Vector Machine Based Tool for Plant Species Taxonomic Classification

    OpenAIRE

    Manimekalai .K; Vijaya.MS

    2014-01-01

    Plant species are living things and are generally categorized in terms of Domain, Kingdom, Phylum, Class, Order, Family, Genus and name of Species in a hierarchical fashion. This paper formulates the taxonomic leaf categorization problem as the hierarchical classification task and provides a suitable solution using a supervised learning technique namely support vector machine. Features are extracted from scanned images of plant leaves and trained using SVM. Only class, order, family of plants...

  18. La confusa taxonomía de Cryptosporidium

    Directory of Open Access Journals (Sweden)

    Gregorio Pérez-Cordón

    2006-10-01

    Full Text Available Los últimos descubrimientos en la biología y filogenética de Cryptosporidium refuerzan la necesidad de una exhaustiva revisión del ciclo de vida y la taxonomía de este parásito. Tanto futuros estudios de cultivo in vitro e in vivo así como estudios moleculares y genéticos permitirán avanzar en el profundo conocimiento de este interesante parásito.

  19. A taxonomic revision of the genus Rafnia Thunb. (Fabaceae, Crotalarieae)

    OpenAIRE

    2012-01-01

    M.Sc. A taxonomic revision of the genus Rafnia Thunb. (= Oedmannia Thunb., Vascoa DC., Pelecynthis E. Mey), a relatively poorly known papilionoid legume genus, is presented. Rafnia (family Fabaceae, tribe Crotalarieae) is subendemic to the fynbos region of the Western and Eastern Cape Provinces of South Africa, with one species having a distribution area reaching into KwaZulu-Natal. The species delimitation has been unsatisfactory, and the relationships among the taxa uncertain. Rafnia is ...

  20. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

    Directory of Open Access Journals (Sweden)

    Cronn Richard

    2009-12-01

    Full Text Available Abstract Background Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels? Results We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2, highlighting their unusual evolutionary properties. Conclusion Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling

  1. High taxonomic variability despite stable functional structure across microbial communities.

    Science.gov (United States)

    Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

    2016-12-05

    Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

  2. Guidance for establishment and implementation of a national sample management program in support of EM environmental sampling and analysis activities

    International Nuclear Information System (INIS)

    1994-01-01

    The role of the National Sample Management Program (NSMP) proposed by the Department of Energy's Office of Environmental Management (EM) is to be a resource for EM programs and for local Field Sample Management Programs (FSMPs). It will be a source of information on sample analysis and data collection within the DOE complex. Therefore the NSMP's primary role is to coordinate and function as a central repository for information collected from the FSMPs. An additional role of the NSMP is to monitor trends in data collected from the FSMPs over time and across sites and laboratories. Tracking these trends will allow identification of potential problems in the sampling and analysis process

  3. Grey relevant analysis of sodium critical heat flux in annular channel and the establishing of grey model

    International Nuclear Information System (INIS)

    Zhou Tao; Su Guanghui; Liao Yixiang; Zhang Weizhong; Qiu Suizheng; Jia Dounan

    1999-12-01

    Using grey systems theory and experimental data obtained from sodium boiling test loop in China, grey mutual analysis is done to some parameters influencing sodium CHF. The results of CHF are predicted by using GM (1,1) model. The GM(1,h) model is made up for creating CHF model. The results are in good agreement with the experimental data

  4. 75 FR 58023 - Guidelines Establishing Test Procedures for the Analysis of Pollutants Under the Clean Water Act...

    Science.gov (United States)

    2010-09-23

    ... chemical and instrument setup as in EPA Method 351.2 in Table IB. The same chemical reaction is measured in.... There are slight modifications in the chemical reaction, but the molybdenum blue final analyte is the... CONTACT: Lemuel Walker, Engineering and Analysis Division (4303T), USEPA Office of Science and Technology...

  5. Establishment study of the in vivo imaging analysis with small animal imaging modalities for bio-durg development

    International Nuclear Information System (INIS)

    Jang, Beomsu; Park, Sanghyeon; Choi, Dae Seong; Park, Jeonghoon; Jung, Uhee; Lee, Yun Jong

    2012-01-01

    In this study, we established the image modalities (micro-PET, SPECT/CT) using the experimental animal (mouse) for the development of imaging assessment method for the bio-durg and extramural collaboration proposal. We examined the micro-SPECT/CT, PET imaging study using the Siemens Inveon micro-multimodality system (SPECT/CT) and imaging study using the Siemens Inveon micro-multimodality system (SPECT/CT) and micro-PET with 99m Tc tricarbonyl bifunctional chelators and 18 F-clotrimazole derivative. SPECT imaging studies were performed with 99m Tc tricarbonyl BFCs. PET imaging study was performed with 18 F-clotrimazole derivatives. We performed the PET image study of 18 F-clotrimazole derivatives using U87MG tumor bearing mice. Also we tested the intramural and extramural collaboration using small animal imaging modalities and prepared the draft of extramural R and D operation manual for small animal imaging modalities and the experimental animal imaging facility. These research results can be utilized as a basic image study protocols and data for the image assessment of drugs including biological drug

  6. Establishment of a continuous culture system for Entamoeba muris and analysis of the small subunit rRNA gene

    Directory of Open Access Journals (Sweden)

    Kobayashi S.

    2009-06-01

    Full Text Available We established a culture system for Entamoeba muris (MG-EM-01 strain isolated from a Mongolian gerbil using a modified Balamuth’s egg yolk infusion medium supplemented with 4% adult bovine serum and Bacteroides fragilis cocultured with Escherichia coli. Further, encystation was observed in the culture medium. The morphological characteristics of E. muris are similar to those of Entamoeba coli (E. coli; moreover, the malic isoenzyme electrophoretic band, which shows species-specific electrophoretic mobility, of E. muris had almost the same mobility as that observed with the malic isoenzyme electrophorectic band of E. coli (UZG-EC-01 strain isolated from a gorilla. We determined the small subunit rRNA (SSU-rRNA gene sequence of the MG-EM-01 strain, and this sequence was observed to show 82.7% homology with that of the UZG-EC-01 strain. Further, the resultant phylogenetic tree for molecular taxonomy based on the SSU-rRNA genes of the 21 strains of the intestinal parasitic amoeba species indicated that the MG-EM-01 strain was most closely related to E. coli.

  7. Establishing a common vocabulary of key concepts for the effective ımplementation of applied behavior analysis

    OpenAIRE

    Traci M Cihon; Joseph H Cihon; Guy M. Bedient

    2016-01-01

    The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case example of the development of a shared vocabulary, using plain English when possible, among supervisors and supervisees at a large public school distric...

  8. [Establishment and assessment of QA/QC method for sampling and analysis of atmosphere background CO2].

    Science.gov (United States)

    Liu, Li-xin; Zhou, Ling-xi; Xia, Ling-jun; Wang, Hong-yang; Fang, Shuang-xi

    2014-12-01

    To strengthen scientific management and sharing of greenhouse gas data obtained from atmospheric background stations in China, it is important to ensure the standardization of quality assurance and quality control method for background CO2 sampling and analysis. Based on the greenhouse gas sampling and observation experience of CMA, using portable sampling observation and WS-CRDS analysis technique as an example, the quality assurance measures for atmospheric CO,sampling and observation in the Waliguan station (Qinghai), the glass bottle quality assurance measures and the systematic quality control method during sample analysis, the correction method during data processing, as well as the data grading quality markers and data fitting interpolation method were systematically introduced. Finally, using this research method, the CO2 sampling and observation data at the atmospheric background stations in 3 typical regions were processed and the concentration variation characteristics were analyzed, indicating that this research method could well catch the influences of the regional and local environmental factors on the observation results, and reflect the characteristics of natural and human activities in an objective and accurate way.

  9. [Analysis of genetic polymorphism in randomized donor's HPA 1-16 antigens and establishment of typed platelet donor data bank].

    Science.gov (United States)

    Sun, Guo-Dong; Duan, Xian-Min; Zhang, Yan-Ping; Yin, Zhi-Zhu; Niu, Xiao-Li; Li, Yan-Feng; Niu, Hai-Jiang; Zhao, You-Liang

    2005-10-01

    To study the genetic polymorphism of HPA 1-16 platelet antigen alleles among unrelated volunteer donors and establish a typed platelet donor panel in Handan, typing was perfomed by polymerase chain reaction using sequence-specific primers (SSP-PCR); 148 random unrelated blood donors in Handan were genotyped for each of the HPA 1-16 antigen. The gene frequencies were analyzed and the genetype frequencies were determined by direct counting, and these data were compared with HPA distribution among various population by the chi-square test. The results indicated that HPA-1a, 2a, 4a-14a, 16a genes were found among the 16 HPAs in every sample tested. Monomorphic HPA-4a, 7a-14a, 16a were found in the samples. For HPA-1, 2, 5 and 6, a/a homozygosity was predominant with frequencies of 0.9595, 0.8108, 0.9865, 0.9797, respectively, and none of HPA b/b was found in the samples. HPA-1b, 2b, 5b, 6b were rarely found among subjects. HPA-15 had the greatest heterozygosity with a gene frequency of 0.2230, 0.5270, 0.2500 for HPA15a/15a, HPA15a/15b, HPA15b/15b, respectively. HPA-3 showed the second greatest heterozygosity with a gene frequency of 0.3851, 0.5135, 0.1014 for HPA3a/3a, HPA3a/3b, HPA3b/3b, respectively. HPA genotype frequencies showed a good fit to Hardy-Weinberg equilibrium. HPA1-5 gene frequencies for Chinese people in Handan were consistent with those of Chinese people in Shijiazhuang (P > 0.05). Among the HPA1-13, -15, the frequencies of HPA-1, -2, -6 for Chinese people in Handan differed appreciably from those for Chinese people in Taiwan (P Taiwan. Among the HPA 1 - 8, a similarity was noted between Chinese people in Handan and Koreans (P > 0.05), except for HPA-3. Frequencies of HPA-1, -2, -5 significantly were differed from those in African Americans, as compared with HPA 1-5 (P < 0.05). Comparison of gene frequencies from HPA-1 and -5 showed significant differences between Chinese people in Handan and people in UK (P < 0.05). It is concluded that HPA-2, -3, -5

  10. The Analysis of the Chest Tube Thoracostomies Performed in a Newly Established Hospital of a Medical School

    Directory of Open Access Journals (Sweden)

    Timucin Alar

    2014-03-01

    Full Text Available Aim: We have analyzed the chest tube thoracostomies (CTT performed in our Thoracic Surgery clinics of our newly established medical school hospital. Material and Method: The medical records of 130 patients to whom CTT were performed by the Thoracic Surgery Clinics of the Canakkale Onsekiz Mart University from December 2009 to July 2013 were retrospectively analyzed. Results: 102 patients (78% out of 130 were male and 28 (22% were women. Mean age of the patients were 58.9±20.4. 19% (n:25 of these patients were diagnosed at our clinics and the remaining 81% (n:105 were consultated from other clinics The most common indication of CTT was pleural effusion (35%, n:45. The mean fluid drainage of the patients with pleural effusions for various reasons (63%, n:84 were 1462.80±1054.46. The mean air drainage time for the patients with pneumothorax for various reasons (37%, n:46 were 5.8±3.1 days. There was only one complication (0,8% in these 130 patients which was the intraparanchymal drain placement. Discussion: As a procedure that is usually performed under emergency conditions CTT has a high potential for development of serious complications and thus increasing the importance of resident doctor training in Thoracic Surgery clinics. CTT has a low rate of complications when performed with the right indication, at the appropriate location and in devotion to the surgical principles; can increase the importance of the Thoracic Surgeons in the medical centers that they are working at and can also increase the relationship of the Thoracic Surgery clinics with the other clinics.

  11. Morphological variations caused by fixation techniques may lead to taxonomic confusion in Laeonereis (Polychaeta: Nereididae

    Directory of Open Access Journals (Sweden)

    Verônica M. Oliveira

    2010-02-01

    Full Text Available The nereidid polychaete Laeonereis acuta (Treadwell, 1923 is either considered to be a valid species, or a synonym of Laeonereis culveri (Webster, 1879. The species epithet, acuta, refers to the acuminate anterior region of the body followed by a widening that is visible up to the 10th setiger. The relative width of the anterior region of the body, however, has been reported in the taxonomic literature as variable for Laeonereis Hartman, 1945, a genus known from the eastern coast of North America to Patagonia (southern South America. To test whether variations in this character are real, or whether they correspond to an artifact, we analyzed morphological changes associated with different anesthesia and fixation techniques regularly used to prepare specimens of Laeonereis from southern Brazil (formerly reported as L. acuta. Six treatments, including combinations of anesthetics and fixative agents, and a control, were evaluated in groups of 25 adult animals. A simple model II regression analysis on living specimens showed that the growth is approximately isometric. One-way ANOVA was used to compare the treatment effect on the ratio of peristome width: setiger 6 width. This ratio was smaller in non-anesthetized individuals, especially when prepared in formalin and freshwater. When anesthetized with menthol and fixed in formalin with sea water, individuals retained a shape that was closest to their in vivo shape. Consequently, our results suggest that fixation without prior anesthesia is not recommended for morphological and taxonomical studies. Since morphology and morphometrics of the anterior region are consistently influenced by preparation techniques, it is likely that inadequate fixation routines have introduced several errors in the taxonomic and ecological literature of Laeonereis.

  12. Field-based detection of biological samples for forensic analysis: Established techniques, novel tools, and future innovations.

    Science.gov (United States)

    Morrison, Jack; Watts, Giles; Hobbs, Glyn; Dawnay, Nick

    2018-04-01

    Field based forensic tests commonly provide information on the presence and identity of biological stains and can also support the identification of species. Such information can support downstream processing of forensic samples and generate rapid intelligence. These approaches have traditionally used chemical and immunological techniques to elicit the result but some are known to suffer from a lack of specificity and sensitivity. The last 10 years has seen the development of field-based genetic profiling systems, with specific focus on moving the mainstay of forensic genetic analysis, namely STR profiling, out of the laboratory and into the hands of the non-laboratory user. In doing so it is now possible for enforcement officers to generate a crime scene DNA profile which can then be matched to a reference or database profile. The introduction of these novel genetic platforms also allows for further development of new molecular assays aimed at answering the more traditional questions relating to body fluid identity and species detection. The current drive for field-based molecular tools is in response to the needs of the criminal justice system and enforcement agencies, and promises a step-change in how forensic evidence is processed. However, the adoption of such systems by the law enforcement community does not represent a new strategy in the way forensic science has integrated previous novel approaches. Nor do they automatically represent a threat to the quality control and assurance practices that are central to the field. This review examines the historical need and subsequent research and developmental breakthroughs in field-based forensic analysis over the past two decades with particular focus on genetic methods Emerging technologies from a range of scientific fields that have potential applications in forensic analysis at the crime scene are identified and associated issues that arise from the shift from laboratory into operational field use are discussed

  13. Establishing normal values for pediatric nighttime sleep measured by actigraphy: a systematic review and meta-analysis.

    Science.gov (United States)

    Galland, Barbara C; Short, Michelle A; Terrill, Philip; Rigney, Gabrielle; Haszard, Jillian J; Coussens, Scott; Foster-Owens, Mistral; Biggs, Sarah N

    2018-04-01

    Despite the widespread use of actigraphy in pediatric sleep studies, there are currently no age-related normative data. To systematically review the literature, calculate pooled mean estimates of actigraphy-derived pediatric nighttime sleep variables and to examine the magnitude of change with age. A systematic search was performed across eight databases of studies that included at least one actigraphy sleep variable from healthy children aged 0-18 years. Data suitable for meta-analysis were confined to ages 3-18 years with seven actigraphy variables analyzed using random effects meta-analysis and meta-regression performed using age as a covariate. In total, 1334 articles did not meet inclusion criteria; 87 had data suitable for review and 79 were suitable for meta-analysis. Pooled mean estimates for overnight sleep duration declined from 9.68 hours (3-5 years age band) to 8.98, 8.85, 8.05, and 7.4 for age bands 6-8, 9-11, 12-14, and 15-18 years, respectively. For continuous data, the best-fit (R2 = 0.74) equation for hours over the 0-18 years age range was 9.02 - 1.04 × [(age/10)^2 - 0.83]. There was a significant curvilinear association between both sleep onset and offset with age (p < .001). Sleep latency was stable at 19.4 min per night. There were significant differences among the older age groups between weekday and weekend/nonschool days (18 studies). Total sleep time in 15-18 years old was 56 min longer, and sleep onset and offset almost 1 and 2 hours later, respectively, on weekend or nonschool days. These normative values have potential application to assist the interpretation of actigraphy measures from nighttime recordings across the pediatric age range, and aid future research.

  14. Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

    Directory of Open Access Journals (Sweden)

    Olivera Savic

    Full Text Available We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

  15. Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

    Science.gov (United States)

    Savic, Olivera; Savic, Andrej M; Kovic, Vanja

    2017-01-01

    We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

  16. Profiled Roller Stress/Fatigue Life Analysis Methodology and Establishment of an Appropriate Stress/Life Exponent

    Science.gov (United States)

    1997-01-01

    The objective of this work was to determine the three dimensional volumetric stress field, surface pressure distribution and actual contact area between a 0.50" square roller with different crown profiles and a flat raceway surface using Finite Element Analysis. The 3-dimensional stress field data was used in conjunction with several bearing fatigue life theories to extract appropriate values for stress-life exponents. Also, results of the FEA runs were used to evaluate the laminated roller model presently used for stress and life prediction.

  17. Establishing a common vocabulary of key concepts for the effective ımplementation of applied behavior analysis

    Directory of Open Access Journals (Sweden)

    Traci M Cihon

    2016-12-01

    Full Text Available The technical language of behavior analysis is arguably necessary to share ideas and research with precision among each other. However, it can hinder effective implementation of behavior analytic techniques when it prevents clear communication between the supervising behavior analyst and behavior technicians. The present paper provides a case example of the development of a shared vocabulary, using plain English when possible, among supervisors and supervisees at a large public school district in which behavior analytic services were provided for children diagnosed with autism spectrum disorders. A list of terms and definitions are provided as well as suggestions on how to develop shared vocabularies within the readers’ own service provision context.

  18. Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria.

    Science.gov (United States)

    Brown-Elliott, Barbara A; Wallace, Richard J

    2002-10-01

    The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing.

  19. An analysis of the proposed MITR-III core to establish thermal-hydraulic limits at 10 MW. Final report

    International Nuclear Information System (INIS)

    Harling, O.K.; Lanning, D.D.; Bernard, J.A.; Meyer, J.E.; Henry, A.F.

    1997-01-01

    The 5 MW Massachusetts Institute of Technology Research Reactor (MITR-II) is expected to operate under a new license beginning in 1999. Among the options being considered is an upgrade in the heat removal system to allow operation at 10 MW. The purpose of this study is to predict the Limiting Safety System Settings and Safety Limits for the upgraded reactor (MITR-III). The MITR Multi-Channel Analysis Code was written to analyze the response of the MITR system to a series of anticipated transients in order to determine the Limiting Safety System Settings and Safety Limits under various operating conditions. The MIT Multi-Channel Analysis Code models the primary and secondary systems, with special emphasis placed on analyzing the thermal-hydraulic conditions in the core. The code models each MITR fuel element explicitly in order to predict the behavior of the system during flow instabilities. The results of the code are compared to experimental data from MITR-II and other sources. New definitions are suggested for the Limiting Safety System Settings and Safety Limits. MITR Limit Diagrams are included for three different heat removal system configurations. It is concluded that safe, year-round operating at 10 MW is possible, given that the primary and secondary flow rates are both increased by approximately 40%

  20. A Study on establishing Top-Down model - development of Global CGE model for Kyoto mechanism analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Gyeong Lyeong [Korea Energy Economics Institute, Euiwang (Korea)

    1999-07-01

    In Korea, it is true that studies on the Convention on Climate Change is behind compared with the developed countries. As a result, a clear goal on negotiation and a reasonable alternative to persuade other countries were not prepared and a negative and passive attitude of negotiation was showed when entering into negotiations with other countries. However, fortunately, the Convention on Climate Change is not completely reached an agreement. It means that there still remains time to contrive for terms favorable to Korea. To do this, a precise negotiating strategy should be prepared based on a reasonable and systematic study and with diplomatic negotiating power to assist it. Also, it should prepare for a next stage after the negotiation through the analyses of several scenarios. Developing a model for a simulation analysis is absolutely needed to set a more systematic and reasonable negotiation strategy for the Convention on Climate Change. (author). 32 refs., 14 fig., 36 tabs.

  1. The establishment and analysis of TRACE model for ultimate response guideline of Chinshan nuclear power plant - 15448

    International Nuclear Information System (INIS)

    Huang, J.J.; Wang, J.R.; Shih, C.; Chen, S.W.; Liao, L.Y.; Lin, H.T.

    2015-01-01

    The purpose of this research is to use TRACE code to perform a simulation that executes the procedures of URG (Ultimate Response Guidelines) to deal with Fukushima-like accidents. TRACE is an advanced thermal hydraulic code that has been developed by the United States Nuclear Regulatory Commission for NPP safety analysis. In this work TRACE has been used to analyze the thermal hydraulic model for the URG of the Chinshan nuclear power plant that is composed of 2 BWR-type reactors. URG includes 2-stage depressurization, alternative water injection and removing decay heat through the ejection from containment. The 2-stage depressurization strategy includes controlled depressurization and emergency depressurization to replace traditional one-stage depressurization. Results show that by comparing with one-stage depressurization strategy, 2-stage depressurization strategy is able to reduce peak cladding temperature (PCT) effectively and needs much less minimum flow rate of alternative water injection in the accident

  2. Assessment of trophic ecomorphology in non-alligatoroid crocodylians and its adaptive and taxonomic implications.

    Science.gov (United States)

    Iijima, Masaya

    2017-08-01

    Although the establishment of trophic ecomorphology in living crocodylians can contribute to estimating feeding habits of extinct large aquatic reptiles, assessment of ecomorphological traits other than the snout shape has scarcely been conducted in crocodylians. Here, I tested the validity of the proposed trophic ecomorphological traits in crocodylians by examining the correlation between those traits and the snout shape (an established trophic ecomorphology), using 10 non-alligatoroid crocodylian species with a wide range of snout shape. I then compared the ontogenetic scaling of trophic ecomorphology to discuss its adaptive and taxonomic significance. The results demonstrated that degree of heterodonty, tooth spacing, size of supratemporal fenestra (STF), ventral extension of pterygoid flange and length of lower jaw symphysis are significantly correlated with snout shape by both non-phylogenetic and phylogenetic regression analyses. Gavialis gangeticus falls outside of 95% prediction intervals for the relationships of some traits and the snout shape, suggesting that piscivorous specialization involves the deviation from the typical transformation axis of skull characters. The comparative snout shape ontogeny revealed a universal trend of snout widening through growth in the sampled crocodylians, implying the existence of a shared size-dependent biomechanical constraint in non-alligatoroid crocodylians. Growth patterns of other traits indicated that G. gangeticus shows atypical trends for degree of heterodonty, size of STF, and symphysis length, whereas the same trends are shared for tooth spacing and ventral extension of pterygoid flange among non-alligatoroid crocodylians. These suggest that some characters are ontogenetically labile in response to prey preference shifts through growth, but other characters are in keeping with the conserved biomechanics among non-alligatoroid crocodylians. Some important taxonomic characters such as the occlusal pattern are

  3. Taxonomic and numerical sufficiency in a Lower and Middle Miocene molluscan metacommunity of the Central Paratethys

    Science.gov (United States)

    Zuschin, Martin; Nawrot, Rafal; Harzhauser, Mathias; Mandic, Oleg

    2015-04-01

    Among the most important questions in quantitative palaeoecology is how taxonomic and numerical resolution affect the analysis of community and metacommunity patterns. A species-abundance data set (10 localities, 213 bulk samples, 478 species, > 49,000 shells) from Burdigalian, Langhian and Serravallian benthic marine molluscan assemblages of the Central Paratethys was studied for this purpose. Assemblages are from two nearshore habitats (estuarine and marine intertidal) and three subtidal habitats (estuarine, fully marine sandy, and fully marine pelitic), which represent four biozones and four 3rd order depositional sequences over more than three million years, and are developed along the same depth-related environmental gradient. Double-standardized data subsampled to 19 samples per habitat, each with a minimum of 50 specimens, were used to calculate R²-values from PERMANOVA as a measure of differences between habitats at three taxonomic levels (species, genera and families) and at five levels of data transformation (raw abundances, percentages, square-root transformed percentages, fourth-root transformed percentages, presence-absence data). Species discriminate better between habitats than genera and families, but the differences between taxonomic levels are much stronger in the subtidal, where genera and families have more species than than in the intertidal. When all habitats are compared percentages and square-root transformed percentages discriminate equally well and perform better than higher levels of data transformation. Among nearshore and among subtidal habitats, however, the ability to discriminate between habitats increases with the level of data transformation (i.e., it is best for fourth-root transformed percentages and presence-absence data). The impact of decreasing taxonomic resolution is of minor importance in nearshore habitats, which are characterized by similar assemblages showing strong dominance of few widely distributed species, and many

  4. The location of midfacial landmarks according to the method of establishing the midsagittal reference plane in three-dimensional computed tomography analysis of facial asymmetry

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Min Sun; Lee, Eun Joo; Lee, Jae Seo; Kang, Byung Cheock; Yoon, Suk Ja [Dental Science Research Institute, Chonnam National University, Gwangju (Korea, Republic of); Song, In Ja [Dept. of Nursing, Kwangju Women' s University, Gwangju (Korea, Republic of)

    2015-12-15

    The purpose of this study was to evaluate the influence of methods of establishing the midsagittal reference plane (MRP) on the locations of midfacial landmarks in the three-dimensional computed tomography (CT) analysis of facial asymmetry. A total of 24 patients (12 male and 12 female; mean age, 22.5 years; age range, 18.2-29.7 years) with facial asymmetry were included in this study. The MRP was established using two different methods on each patient's CT image. The x-coordinates of four midfacial landmarks (the menton, nasion, upper incisor, and lower incisor) were obtained by measuring the distance and direction of the landmarks from the MRP, and the two methods were compared statistically. The direction of deviation and the severity of asymmetry found using each method were also compared. The x-coordinates of the four anatomic landmarks all showed a statistically significant difference between the two methods of establishing the MRP. For the nasion and lower incisor, six patients (25.0%) showed a change in the direction of deviation. The severity of asymmetry also changed in 16 patients (66.7%). The results of this study suggest that the locations of midfacial landmarks change significantly according to the method used to establish the MRP.

  5. Establishing a Mathematical Equations and Improving the Production of L-tert-Leucine by Uniform Design and Regression Analysis.

    Science.gov (United States)

    Jiang, Wei; Xu, Chao-Zhen; Jiang, Si-Zhi; Zhang, Tang-Duo; Wang, Shi-Zhen; Fang, Bai-Shan

    2017-04-01

    L-tert-Leucine (L-Tle) and its derivatives are extensively used as crucial building blocks for chiral auxiliaries, pharmaceutically active ingredients, and ligands. Combining with formate dehydrogenase (FDH) for regenerating the expensive coenzyme NADH, leucine dehydrogenase (LeuDH) is continually used for synthesizing L-Tle from α-keto acid. A multilevel factorial experimental design was executed for research of this system. In this work, an efficient optimization method for improving the productivity of L-Tle was developed. And the mathematical model between different fermentation conditions and L-Tle yield was also determined in the form of the equation by using uniform design and regression analysis. The multivariate regression equation was conveniently implemented in water, with a space time yield of 505.9 g L -1  day -1 and an enantiomeric excess value of >99 %. These results demonstrated that this method might become an ideal protocol for industrial production of chiral compounds and unnatural amino acids such as chiral drug intermediates.

  6. Language proficiency among immigrants and the establishment of interethnic relations: a comparative analysis of Bilbao, Lisbon and Rotterdam

    Directory of Open Access Journals (Sweden)

    Alina Esteves

    2014-03-01

    Full Text Available Despite the increasing interest in exploring language proficiency among immigrants as a quintessential element for their economic integration in the host country, less attention has been devoted to the social impacts that destination-language proficiency may have on enhancing interethnic contacts between immigrants and the native population. This research aims to shed light on this latter topic, discussing if being a native-speaker immigrant in the host country or, for those immigrants who are non-native speakers, having a stronger command of the destination-language may increase their likelihood of interacting with the native population. Moreover, we question if there are significant differences in the interaction patterns between these two groups and the natives, presenting the cities of Bilbao, Lisbon and Rotterdam as a territorial frame. The analysis is based on data gathered through the GEITONIES survey. The results obtained indicate that native-speaker immigrants generally tend to show more interaction with the natives. Nevertheless, for immigrants not sharing such cultural similarity, those with a higher level of second-language proficiency clearly show stronger bonds with the native population; in both cases this can also be related to individual, group or place related variables.

  7. Using a Six Sigma Fishbone Analysis Approach To Evaluate the Effect of Extreme Weather Events on Salmonella Positives in Young Chicken Slaughter Establishments.

    Science.gov (United States)

    Linville, John W; Schumann, Douglas; Aston, Christopher; Defibaugh-Chavez, Stephanie; Seebohm, Scott; Touhey, Lucy

    2016-12-01

    A six sigma fishbone analysis approach was used to develop a machine learning model in SAS, Version 9.4, by using stepwise linear regression. The model evaluated the effect of a wide variety of variables, including slaughter establishment operational measures, normal (30-year average) weather, and extreme weather events on the rate of Salmonella -positive carcasses in young chicken slaughter establishments. Food Safety and Inspection Service (FSIS) verification carcass sampling data, as well as corresponding data from the National Oceanographic and Atmospheric Administration and the Federal Emergency Management Agency, from September 2011 through April 2015, were included in the model. The results of the modeling show that in addition to basic establishment operations, normal weather patterns, differences from normal and disaster events, including time lag weather and disaster variables, played a role in explaining the Salmonella percent positive that varied by slaughter volume quartile. Findings show that weather and disaster events should be considered as explanatory variables when assessing pathogen-related prevalence analysis or research and slaughter operational controls. The apparent significance of time lag weather variables suggested that at least some of the impact on Salmonella rates occurred after the weather events, which may offer opportunities for FSIS or the poultry industry to implement interventions to mitigate those effects.

  8. Taxonomic and Thematic Organisation of Proper Name Conceptual Knowledge

    Directory of Open Access Journals (Sweden)

    Sebastian J. Crutch

    2011-01-01

    Full Text Available We report the investigation of the organisation of proper names in two aphasic patients (NBC and FBI. The performance of both patients on spoken word to written word matching tasks was inconsistent, affected by presentation rate and semantic relatedness of the competing responses, all hallmarks of a refractory semantic access dysphasia. In a series of experiments we explored the semantic relatedness effects within their proper name vocabulary, including brand names and person names. First we demonstrated the interaction between very fine grain organisation and personal experience, with one patient with a special interest in the cinema demonstrating higher error rates when identifying the names of actors working in a similar film genre (e.g. action movies: Arnold Schwarzenegger, Bruce Willis, Sylvester Stallone, Mel Gibson than those working in different genres (e.g. Arnold Schwarzenegger, Gregory Peck, Robin Williams, Gene Kelly. Second we compared directly two potential principles of semantic organisation – taxonomic and thematic. Furthermore we considered these principles of organisation in the context of the individuals' personal knowledge base. We selected topics matching the interests and experience of each patient, namely cinema and literature (NBC and naval history (FBI. The stimulus items were arranged in taxonomic arrays (e.g. Jane Austen, Emily Bronte, Agatha Christie, thematic arrays (e.g. Jane Austen, Pride and Prejudice, Mr Darcy, and unrelated arrays (e.g. Jane Austen, Wuthering Heights, Hercule Poirot. We documented that different patterns of taxonomic and thematic organisation were constrained by whether the individual has limited knowledge, moderate knowledge or detailed knowledge of a particular vocabulary. It is suggested that moderate proper name knowledge is primarily organised by taxonomy whereas extensive experience results in a more detailed knowledge base in which theme is a powerful organising principle.

  9. Taxonomic and thematic organisation of proper name conceptual knowledge.

    Science.gov (United States)

    Crutch, Sebastian J; Warrington, Elizabeth K

    2011-01-01

    We report the investigation of the organisation of proper names in two aphasic patients (NBC and FBI). The performance of both patients on spoken word to written word matching tasks was inconsistent, affected by presentation rate and semantic relatedness of the competing responses, all hallmarks of a refractory semantic access dysphasia. In a series of experiments we explored the semantic relatedness effects within their proper name vocabulary, including brand names and person names. First we demonstrated the interaction between very fine grain organisation and personal experience, with one patient with a special interest in the cinema demonstrating higher error rates when identifying the names of actors working in a similar film genre (e.g., action movies: Arnold Schwarzenegger, Bruce Willis, Sylvester Stallone, Mel Gibson) than those working in different genres (e.g., Arnold Schwarzenegger, Gregory Peck, Robin Williams, Gene Kelly). Second we compared directly two potential principles of semantic organisation - taxonomic and thematic. Furthermore we considered these principles of organisation in the context of the individuals' personal knowledge base. We selected topics matching the interests and experience of each patient, namely cinema and literature (NBC) and naval history (FBI). The stimulus items were arranged in taxonomic arrays (e.g., Jane Austen, Emily Bronte, Agatha Christie), thematic arrays (e.g., Jane Austen, Pride and Prejudice, Mr Darcy), and unrelated arrays (e.g., Jane Austen, Wuthering Heights, Hercule Poirot). We documented that different patterns of taxonomic and thematic organisation were constrained by whether the individual has limited knowledge, moderate knowledge or detailed knowledge of a particular vocabulary. It is suggested that moderate proper name knowledge is primarily organised by taxonomy whereas extensive experience results in a more detailed knowledge base in which theme is a powerful organising principle.

  10. Trend analysis of GIMMS and MODIS NDVI time series for establishing a land degradation neutrality national baseline

    Science.gov (United States)

    Gichenje, Helene; Godinho, Sergio

    2017-04-01

    Land degradation is a key global environment and development problem that is recognized as a priority by the international development community. The Sustainable Development Goals (SDGs) were adopted by the global community in 2015, and include a goal related to land degradation and the accompanying target to achieve a land degradation-neutral (LDN) world by 2030. The LDN concept encompasses two joint actions of reducing the rate of degradation and increasing the rate of restoration. Using Kenya as the study area, this study aims to develop and test a spatially explicit methodology for assessing and monitoring the operationalization of a land degradation neutrality scheme at the national level. Time series analysis is applied to Normalized Difference Vegetation Index (NDVI) satellite data records, based on the hypothesis that the resulting NDVI residual trend would enable successful detection of changes in vegetation photosynthetic capacity and thus serve as a proxy for land degradation and regeneration processes. Two NDVI data sets are used to identify the spatial and temporal distribution of degraded and regenerated areas: the long term coarse resolution (8km, 1982-2015) third generation Global Inventory Modeling and Mapping Studies (GIMMS) NDVI3g data record; and the shorter-term finer resolution (250m, 2001-2015) Moderate Resolution Imaging Spectroradiometer (MODIS) derived NDVI data record. Climate data (rainfall, temperature and soil moisture) are used to separate areas of human-induced vegetation productivity decline from those driven by climate dynamics. Further, weekly vegetation health (VH) indexes (4km, 1982-2015) developed by National Oceanic and Atmospheric Administration (NOAA), are assessed as indicators for early detection and monitoring of land degradation by estimating vegetation stress (moisture, thermal and combined conditions).

  11. Taxonomic revision of Asian genus Glyptopetalum Thwaites (Celastraceae R. Br.

    Directory of Open Access Journals (Sweden)

    Ivan A. Savinov

    2014-12-01

    Full Text Available Taxonomic survey of Asian genus Glyptopetalum Thwaites (Celastraceae R. Br. is presented. Thirty five species taxa of Glyptopetalum are accepted, including one new species, G.  vidalii I. Savinov (Laos, Thailand, a new record for China, G. tonkinense Pitard (SE Yunnan and a new record for Cambodia,               G. quadrangulare Prain ex King, a new record for Indonesia – G. euonymoides Merr. and a new record for Philippines, Mindanao island – G. loheri Merr. 

  12. Pollen morphology of some asiatic species of genus salsola (chenopodiaceae) and its taxonomic relationships

    International Nuclear Information System (INIS)

    Toderich, K.N.; Shuyskaya, E.V.; Ozturk, M

    2010-01-01

    Comparative studies on the pollen grain morphology of 27 Asiatic species of the genus Salsola were conducted by using scanning electron microscope (SEM analysis) in order to assess the taxonomic value of pollen traits. The pollen are radially symmetrical isopolar, pantopolyporate, spherical or subspheroid. The pollen characters like size, pore number, chord (C/D ratio), pore diameter, exine thickness, level of sinking of pore, convexness of mesoporial exine, spinule and minute-hole densities and number of spines on pore membrane appeared to be useful characters in distinguishing the species. Interesting intraspecific variations in pollen grain morphology were recorded for the C/D ratio. This parameter is highly specific, supporting the delimitation of Salsola species, and appears to be more conservative than some flower and fruit characters. The numerical value of form index comprising the ratio between the length of polar axis and diameter (P/E) also was an informative trait for delimitation of the species investigated here. Three pollen types were recognized. Euclidean distance was used to compute the dissimilarity matrix and a cladogram prepared. The quantitative characters of pollen morphology allowed clustering of groups and ordination analyses of species from different sections/subsections within genus Salsola. These features indicated that overall pollen traits reflect the current taxonomic boundaries, except for the Salsola species allocated to Climacoptera and Halothamnus, which should be accepted as separate genera. (author)

  13. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.

    Directory of Open Access Journals (Sweden)

    Zachary S L Foster

    2017-02-01

    Full Text Available Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.

  14. Epicuticular chemistry reinforces the new taxonomic classification of the Bactrocera dorsalis species complex (Diptera: Tephritidae, Dacinae)

    Science.gov (United States)

    Vaníčková, Lucie; Nagy, Radka; Pompeiano, Antonio

    2017-01-01

    Bactrocera invadens Drew, Tsuruta & White, Bactrocera papayae Drew & Hancock, and Bactrocera philippinensis Drew & Hancock, key pest species within the Bactrocera dorsalis species complex, have been recently synonymized under the name Bactrocera dorsalis (Hendel). The closely related Bactrocera carambolae Drew & Hancock remains as a discrete taxonomic entity. Although the synonymizations have been accepted by most researchers, debate about the species limits remains. Because of the economic importance of this group of taxa, any new information available to support or deny the synonymizations is valuable. We investigated the chemical epicuticle composition of males and females of B. dorsalis, B. invadens, B. papayae, B. philippinensis, and B. carambolae by means of one- and two-dimensional gas chromatography–mass spectrometry, followed by multiple factor analyses and principal component analysis. Clear segregation of complex cuticule profiles of both B. carambolae sexes from B. dorsalis (Hendel) was observed. In addition to cuticular hydrocarbons, abundant complex mixtures of sex-specific oxygenated lipids (three fatty acids and 22 fatty acid esters) with so far unknown function were identified in epicuticle extracts from females of all species. The data obtained supports both taxonomic synonymization of B. invadens, B. papayae, and B. philippinensis with B. dorsalis, as well as the exclusion of B. carambolae from B. dorsalis. PMID:28873446

  15. Strengthening cost-effectiveness analysis in Thailand through the establishment of the health intervention and technology assessment program.

    Science.gov (United States)

    Tantivess, Sripen; Teerawattananon, Yot; Mills, Anne

    2009-01-01

    Capacity is limited in the developing world to conduct cost-effectiveness analysis (CEA) of health interventions. In Thailand, there have been concerted efforts to promote evidence-based policy making, including the introduction of economic appraisals within health technology assessment (HTA). This paper reviews the experience of this lower middle-income country, with an emphasis on the creation of the Health Intervention and Technology Assessment Program (HITAP), including its mission, management structures and activities. Over the past 3 decades, several HTA programmes were implemented in Thailand but not sustained or developed further into a national institute. As a response to increasing demands for HTA evidence including CEA information, the HITAP was created in 2007 as an affiliate unit of a semi-autonomous research arm of the Ministry of Public Health. An advantage of this HTA programme over previous initiatives was that it was hosted by a research institute with long-term experience in conducting health systems and policy research and capacity building of its research staff, and excellent research and policy networks. To deal with existing impediments to conducting health economics research, the main strategies of the HITAP were carefully devised to include not only capacity strengthening of its researchers and administrative staff, but also the development of essential elements for the country's health economic evaluation methodology. These included, for example, methodological guidelines, standard protocols and benchmarks for resource allocation, many of which have been adopted by national policy-making bodies including the three major public health insurance plans. Networks and collaborations with domestic and foreign institutes have been sought as a means of resource mobilization and exchange. Although the HITAP is well financed by a number of government agencies and international organizations, the programme is vulnerable to shortages of qualified

  16. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

    Science.gov (United States)

    Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic; Olsen, Jesper; Andersen, Kenneth; Holm, Jakob; Funder, Svend; Willerslev, Eske; Kjær, Kurt H.

    2013-09-01

    We use 2nd generation sequencing technology on sedimentary ancient DNA (sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the results with those previously obtained from pollen and macrofossils in the same lake. Thirty-eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g-h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (Scrophulariaceae and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650 cal yr BP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less detailed than pollen and macrofossil analyses can be a complementary tool for establishing the composition of both terrestrial and aquatic local plant communities and a method for identifying additional taxa.

  17. Una taxonomía de modelos de desarrollo sustentable

    Directory of Open Access Journals (Sweden)

    Darcy Tetreault

    2004-01-01

    Full Text Available Este ensayo pretende ayudar a desenmarañar una parte del discurso sobre desarrollo sustentable mediante la construcción de una taxonomía de modelos de desarrollo sustentable. La misma taxonomía se basa en una revisión literaria extensiva que en cierta medida privilegia la experiencia mexicana. De este modo, el ensayo presenta y compara tanto modelos normativos como positivos. Los modelos incluidos son el modelo dominante, el cual corresponde con la estrategia esbozada en el Informe Bruntland y Agenda 21; la ecología política, un modelo desarrollado por el economista francés Alain Lipietz; el modelo comunitario de desarrollo sustentable, cuyas raíces se encuentran en una escuela de pensamiento de la década de los setenta conocida como el “otro desarrollo”; el comercio justo, una experiencia cuyas raíces se encuentran en las comunidades indígenas de Oaxaca; la producción forestal industrial comunitaria, que ha sido puesta en práctica por varias comunidades forestales en el sur y el centro del país; el activismo ambiental, sobre todo respecto a los con- fl ictos locales que giran en torno al control de los recursos naturales; y la conservación basada en la comunidad, cuya manifestación principal es la reserva de la biosfera

  18. Taxonomic and ad hoc categorization within the two cerebral hemispheres.

    Science.gov (United States)

    Shen, Yeshayahu; Aharoni, Bat-El; Mashal, Nira

    2015-01-01

    A typicality effect refers to categorization which is performed more quickly or more accurately for typical than for atypical members of a given category. Previous studies reported a typicality effect for category members presented in the left visual field/right hemisphere (RH), suggesting that the RH applies a similarity-based categorization strategy. However, findings regarding the typicality effect within the left hemisphere (LH) are less conclusive. The current study tested the pattern of typicality effects within each hemisphere for both taxonomic and ad hoc categories, using words presented to the left or right visual fields. Experiment 1 tested typical and atypical members of taxonomic categories as well as non-members, and Experiment 2 tested typical and atypical members of ad hoc categories as well as non-members. The results revealed a typicality effect in both hemispheres and in both types of categories. Furthermore, the RH categorized atypical stimuli more accurately than did the LH. Our findings suggest that both hemispheres rely on a similarity-based categorization strategy, but the coarse semantic coding of the RH seems to facilitate the categorization of atypical members.

  19. Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria.

    Science.gov (United States)

    Hamedi, Javad; Mohammadipanah, Fatemeh

    2015-02-01

    Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.

  20. Habitat connectivity and local conditions shape taxonomic and functional diversity of arthropods on green roofs.

    Science.gov (United States)

    Braaker, Sonja; Obrist, Martin Karl; Ghazoul, Jaboury; Moretti, Marco

    2017-05-01

    Increasing development of urban environments creates high pressure on green spaces with potential negative impacts on biodiversity and ecosystem services. There is growing evidence that green roofs - rooftops covered with vegetation - can contribute mitigate the loss of urban green spaces by providing new habitats for numerous arthropod species. Whether green roofs can contribute to enhance taxonomic and functional diversity and increase connectivity across urbanized areas remains, however, largely unknown. Furthermore, only limited information is available on how environmental conditions shape green roof arthropod communities. We investigated the community composition of arthropods (Apidae, Curculionidae, Araneae and Carabidae) on 40 green roofs and 40 green sites at ground level in the city of Zurich, Switzerland. We assessed how the site's environmental variables (such as area, height, vegetation, substrate and connectivity among sites) affect species richness and functional diversity using generalized linear models. We used an extension of co-inertia analysis (RLQ) and fourth-corner analysis to highlight the mechanism underlying community assemblages across taxonomic groups on green roof and ground communities. Species richness was higher at ground-level sites, while no difference in functional diversity was found between green roofs and ground sites. Green roof arthropod diversity increased with higher connectivity and plant species richness, irrespective of substrate depth, height and area of green roofs. The species trait analysis reviewed the mechanisms related to the environmental predictors that shape the species assemblages of the different taxa at ground and roof sites. Our study shows the important contribution of green roofs in maintaining high functional diversity of arthropod communities across different taxonomic groups, despite their lower species richness compared with ground sites. Species communities on green roofs revealed to be characterized

  1. Secular Religious Establishment

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2013-01-01

    Secularism as a political doctrine claims that religion and politics should be separated. The compatibility question is whether secularism can accept some forms of religious establishment in the form of institutional linkages between state and organised religion. I argue that the answer...... to the compatibility question is not obvious and requires a systematic analysis of secularism. Based on a distinction between a general concept and specific conceptions of secularism I offer a general structure for conceptions of secularism that incorporates both a) basic values, e.g. political equality and freedom...

  2. Establishment of a System for Monitoring and Control of Cross Contamination in the Laboratory of Microbiological Analysis of Food during 2009

    Directory of Open Access Journals (Sweden)

    Corpa- Iguarán Eduardo Javid

    2012-03-01

    Full Text Available Within the activities for quality control in the laboratory, the final results of a particular analyteare now recognized as intermediates, due to the relevance given to quality assurance, as the ultimategoal of programs for quality management. This concept makes it necessary to establishmentof integral tools, to detect events such as cross-contamination, and measures to avoid affectingthe analysis method. Objective: to established a system for monitoring and control of crosscontaminationin the laboratory of microbiological analysis of food. Materials and methods:Flowcharts were developed to control the proceedings on the populations of aerobe mesophilicsand molds originated from pollution in the environment, surfaces, sterile material and culturemedia, which included a decision tree designed to perform control actions based on tolerance intervals,which were established as objective tool to decision-making leading to normalize countsof microbial populations in question. Results: Warning limits stricter were obtained for aerobicmesophilic and mold populations in the different controls, except for environment of media preparationand the corresponding for sterile material. Conclusion: The process developed allowedto complement the system of internal quality control in the laboratory, to provide of an objectivetool for closing nonconformities because of cross-contamination.

  3. Taxonomic and numerical resolutions of nepomorpha (insecta: heteroptera in cerrado streams.

    Directory of Open Access Journals (Sweden)

    Nubia França da Silva Giehl

    Full Text Available Transformations of natural landscapes and their biodiversity have become increasingly dramatic and intense, creating a demand for rapid and inexpensive methods to assess and monitor ecosystems, especially the most vulnerable ones, such as aquatic systems. The speed with which surveys can collect, identify, and describe ecological patterns is much slower than that of the loss of biodiversity. Thus, there is a tendency for higher-level taxonomic identification to be used, a practice that is justified by factors such as the cost-benefit ratio, and the lack of taxonomists and reliable information on species distributions and diversity. However, most of these studies do not evaluate the degree of representativeness obtained by different taxonomic resolutions. Given this demand, the present study aims to investigate the congruence between species-level and genus-level data for the infraorder Nepomorpha, based on taxonomic and numerical resolutions. We collected specimens of aquatic Nepomorpha from five streams of first to fourth order of magnitude in the Pindaíba River Basin in the Cerrado of the state of Mato Grosso, Brazil, totaling 20 sites. A principal coordinates analysis (PCoA applied to the data indicated that species-level and genus-level abundances were relatively similar (>80% similarity, although this similarity was reduced when compared with the presence/absence of genera (R = 0.77. The presence/absence ordinations of species and genera were similar to those recorded for their abundances (R = 0.95 and R = 0.74, respectively. The results indicate that analyses at the genus level may be used instead of species, given a loss of information of 11 to 19%, although congruence is higher when using abundance data instead of presence/absence. This analysis confirms that the use of the genus level data is a safe shortcut for environmental monitoring studies, although this approach must be treated with caution when the objectives include

  4. Taxonomic status and paleoecology of Rusingoryx atopocranion (Mammalia, Artiodactyla), an extinct Pleistocene bovid from Rusinga Island, Kenya

    Science.gov (United States)

    Faith, J. Tyler; Choiniere, Jonah N.; Tryon, Christian A.; Peppe, Daniel J.; Fox, David L.

    2011-05-01

    Rusingoryx atopocranion is a poorly known extinct alcelaphine bovid, documented in Pleistocene deposits associated with Middle Stone Age artifacts on Rusinga Island, Kenya. Following its initial description, Rusingoryx was subsumed into Megalotragus, which includes the extinct giant wildebeests, on the basis of its cranial architecture. Renewed investigations of the Pleistocene deposits on Rusinga Island recovered a large sample of Rusingoryx specimens that provide new taxonomic and paleoecological insight. This study (1) reviews the morphological and phylogenetic evidence concerning the taxonomic status of Rusingoryx and (2) evaluates its paleoecology and dietary habits . The morphology and phylogenetic data indicate that Rusingoryx is distinct from Megalotragus; they likely shared a common ancestor in the late Pliocene. Ecomorphology and mesowear analysis point to a specialized grazing adaptation, and its association with arid-adapted ungulates suggests a preference for arid grasslands. The confirmation of Rusingoryx as a valid taxonomic entity, together with the presence of other extinct taxa (including Megalotragus) on Rusinga Island, suggests an increasingly complex pattern of ungulate biogeography and extinctions in the late Quaternary of East Africa. Rusingoryx appears to have been part of an arid-adapted faunal community that potentially persisted in East Africa until the onset of the Holocene.

  5. prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME.

    Science.gov (United States)

    Lakhujani, Vijay; Badapanda, Chandan

    2017-06-01

    QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary . py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary . py , it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts . py , to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary . py but is also very fast in terms of CPU time and user friendly.

  6. TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels

    Directory of Open Access Journals (Sweden)

    Eric W. Triplett

    2010-07-01

    Full Text Available The high level of conservation of 16S ribosomal RNA gene (16S rRNA in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II and the Greengenes Project offer access to sets of ribosomal RNA sequence databases useful in identification of microbes in a culture-independent analysis of microbial communities. However, these databases do not contain all of the taxonomic levels attached to the published names of the bacterial and archaeal sequences. TaxCollector is a set of scripts developed in Python language that attaches taxonomic information to all 16S rRNA sequences in the RDP-II and Greengenes databases. These modified databases are referred to as TaxCollector databases, which when used in conjunction with BLAST allow for rapid classification of sequences from any environmental or clinical source at six different taxonomic levels, from domain to species. The TaxCollector database prepared from the RDP-II database is an important component of a new 16S rRNA pipeline called PANGEA. The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil. The six TaxCollector scripts are freely available on http://taxcollector.sourceforge.net and on http://www.microgator.org.

  7. Effects of land use on taxonomic and functional diversity

    DEFF Research Database (Denmark)

    Hevia, Violeta; Carmona, Carlos P.; Azcárate, Francisco M.

    2016-01-01

    Land-use change is the major driver of biodiversity loss. However, taxonomic diversity (TD) and functional diversity (FD) might respond differently to land-use change, and this response might also vary depending on the biotic group being analysed. In this study, we compare the TD and FD of four......: the sampling unit scale and the site scale. Land-use intensity effects on TD and FD were quite different and highly varied among the four biotic groups, with no single clear pattern emerging that could be considered general for all organisms. Additive partitioning of species diversity revealed clear...... contrasting patterns between TD and FD in the percentage of variability observed at each spatial scale. While most variability in TD was found at the larger scales, irregardless of organism group and land-use type, most variability in FD was found at the smallest scale, indicating that species turnover among...

  8. Taxonomic status of two morphotypes of Coryphaena hippurus (Perciformes: Coryphaenidae

    Directory of Open Access Journals (Sweden)

    Alan Bonner

    2017-03-01

    Full Text Available ABSTRACT Two Coryphaena hippurus morphotypes (dourado and palombeta are found along the Brazilian coast and are considered by Rio de Janeiro’s fisherman and fishmongers as two different species. Furthermore, these morphotypes are commercialized under different values and suffer different fishing pressure. Therefore, a definition of their taxonomic status is an important economic and biological matter. In order to investigate this problem, allozyme electrophoresis method was undertaken for seventeen loci on 117 individuals of C. hippurus sampled at Cabo Frio/RJ (Brazil. The data indicate homogeneity between the morphotypes gene pools. Nevertheless, differences were found for genetic variation among dourado and palombeta, especially due to alcohol dehydrogenase locus. Natural selection hypothesis is discussed in explaining these findings.

  9. Camallanus tridentatus (Drasche) (Nematoda: Camallanidae): new taxonomically important morphological data.

    Science.gov (United States)

    Santos, Cláudia Portes; Moravec, Frantisek

    2009-02-01

    Camallanus tridentatus is redescribed on the basis of the examination of specimens obtained from the stomach, caeca and intestine of the naturally infected arapaima Arapaima gigas (Schinz) from the Mexiana Island, Amazon River Delta, Brazil. Data on the surface morphology of adults inferred from confocal laser scanning and scanning electron microscopical observations are also provided. The study revealed some taxonomically important, previously unreported morphological features in this species, such as the presence of the poorly sclerotized left spicule and deirids. C. tridentatus distinctly differs from other congeneric species parasitizing freshwater fishes in South America mainly in the structure of the buccal capsule and the female caudal end. C. maculatus Martins, Garcia, Piazza and Ghiraldelli is considered a junior synonymm of Camallanus cotti Fujita.

  10. Camallanus tridentatus (Drasche (Nematoda: Camallanidae: new taxonomically important morphological data

    Directory of Open Access Journals (Sweden)

    Cláudia Portes Santos

    2009-02-01

    Full Text Available Camallanus tridentatus is redescribed on the basis of the examination of specimens obtained from the stomach, caeca and intestine of the naturally infected arapaima Arapaima gigas (Schinz from the Mexiana Island, Amazon River Delta, Brazil. Data on the surface morphology of adults inferred from confocal laser scanning and scanning electron microscopical observations are also provided. The study revealed some taxonomically important, previously unreported morphological features in this species, such as the presence of the poorly sclerotized left spicule and deirids. C. tridentatus distinctly differs from other congeneric species parasitizing freshwater fishes in South America mainly in the structure of the buccal capsule and the female caudal end. C. maculatus Martins, Garcia, Piazza and Ghiraldelli is considered a junior synonymm of Camallanus cotti Fujita.

  11. Seed morphology and its taxonomic significance in the family malvaceae

    International Nuclear Information System (INIS)

    Abid, R.; Ather, A.

    2016-01-01

    The seed morphological studies of 75 taxa belonging to 6 sub-families of the family Malvaceae were carried out from Pakistan. In Pakistan the family Malvaceae is represented by 6 sub-families viz., Byttnerioideae, Dombeyoideae, Malvoideae, Bombacoideae, Helicteroideae and Sterculioideae. The seed macro and micro morphological characters are examined, using light (LM) and scanning electron microscopy (SEM). Detailed seed morphological descriptions, micrographs and keys based on seed characters are also provided. A variety in various quantitative and qualitative seed characters was observed. The micro-morphological characters of seeds are quite significant to strengthen the taxonomic decisions within the family Malvaceae at various levels. The data obtained from the seed morphological characters were analyzed numerically to trace out the phylogenetic affinities for the taxa within the family Malvaceae from Pakistan. (author)

  12. Extrafloral nectaries in Combretaceae: morphology, anatomy and taxonomic significance

    Directory of Open Access Journals (Sweden)

    P. M. Tilney

    2004-09-01

    Full Text Available Extrafloral nectaries (EFNs in members of the Combretaceae are nectaries not involved with pollination and occurring on vegetative structures; they are believed to attract ants to protect plants against herbivorv by other insects. In the Combretaceae EFNs are reported in species of Terminalia L. and Pteleopsis Engl., putative EFNs in Meiostemon Exell & Stace and Quisqualis L., and an absence of EFNs in Combretum Loefl. and Lumnitzera Willd. EFNs in the family are generally spherical in shape and may be raised, level with the surface or somewhat concave. They are similar in the Terminalia and  Pteleopsis species where they display varying degrees of internal zonation and are composed of small cells; those species observed in the field were all found to have functional EFNs. In Meiostemon tetrandrum (Exell Exell & Stace, Quisqualis indica L.. Q. littorea (Engl. Exell and Q. paviflora Gerrard ex Sond.. apparent EFNs lack internal zonation and are composed of enlarged cells; confirmation is required as to whether these are functional . The formation of EFNs appears to be highly flexible. They are usually essentially associated with new growth but their occurrence is sporadic and they do not appear on every leaf or every' branch of a plant. The distribution of EFNs on leaves, when present, is of taxonomic significance to separate species of Pteleopsis and Terminalia: otherwise the presence or absence and distribution of EFNs are too variable and sporadic in occurrence to be of taxonomic significance at the species level. Indiscriminate use of the terms gland and domatium instead of EFN. and possible confusion with damage caused by other organisms, has probably con­tributed to many of these structures not previously being recorded as EFNs. Floral and extrafloral nectar samples of T. phanerophlebia Engl. & Diels differed in sugar composition.

  13. Is Homo sapiens polytypic? Human taxonomic diversity and its implications.

    Science.gov (United States)

    Woodley, Michael A

    2010-01-01

    The term race is a traditional synonym for subspecies, however it is frequently asserted that Homo sapiens is monotypic and that what are termed races are nothing more than biological illusions. In this manuscript a case is made for the hypothesis that H. sapiens is polytypic, and in this way is no different from other species exhibiting similar levels of genetic and morphological diversity. First it is demonstrated that the four major definitions of race/subspecies can be shown to be synonymous within the context of the framework of race as a correlation structure of traits. Next the issue of taxonomic classification is considered where it is demonstrated that H. sapiens possesses high levels morphological diversity, genetic heterozygosity and differentiation (F(ST)) compared to many species that are acknowledged to be polytypic with respect to subspecies. Racial variation is then evaluated in light of the phylogenetic species concept, where it is suggested that the least inclusive monophyletic units exist below the level of species within H. sapiens indicating the existence of a number of potential human phylogenetic species; and the biological species concept, where it is determined that racial variation is too small to represent differentiation at the level of biological species. Finally the implications of this are discussed in the context of anthropology where an accurate picture of the sequence and timing of events during the evolution of human taxa are required for a complete picture of human evolution, and medicine, where a greater appreciation of the role played by human taxonomic differences in disease susceptibility and treatment responsiveness will save lives in the future.

  14. HANFORD DOUBLE SHELL TANK (DST) THERMAL & SEISMIC PROJECT ESTABLISHMENT OF METHODOLOGY FOR TIME DOMAIN SOIL STRUCTURE INTERACTION ANALYSIS OF HANFORD DST

    Energy Technology Data Exchange (ETDEWEB)

    MACKEY, T.C.

    2006-03-14

    the frequency domain, but frequency domain analysis is limited to systems with linear responses. The nonlinear character of the coupled SSI model and tank structural model requires that the seismic analysis be solved in the time domain. However, time domain SSI analysis is somewhat nontraditional and requires that the appropriate methodology be developed and demonstrated. Moreover, the analysis of seismically induced fluid-structure interaction between the explicitly modeled waste and the primary tank must be benchmarked against known solutions to simpler problems before being applied to the more complex analysis of the DSTs. The objective of this investigation is to establish the methodology necessary to perform the required SSI analysis of the DSTs in the time domain. Specifically, the analysis establishes the capabilities and limitations of the time domain codes ANSYS and Dytran for performing seismic SSI analysis of the DSTs. The benchmarking of the codes Dytran and ANSYS for performing seismically induced fluid-structure interaction (FSI) between the contained waste and the DST primary tank are documented in Abatt (2006) and Carpenter and Abatt (2006), respectively. The results of those two studies show that both codes have the capability to analyze the fluid-structure interaction behavior of the primary tank and contained waste. As expected, Dytran appears to have more robust capabilities for FSI analysis. The ANSYS model used in that study captures much of the FSI behavior, but does have some limitations for predicting the convective response of the waste and possibly the response of the waste in the knuckle region of the primary tank. While Dytran appears to have somewhat stronger capabilities for the analysis of the FSI behavior in the primary tank, it is more practical for the overall analysis to use ANSYS. Thus, Dytran served the purpose of helping to identify limitations in the ANSYS FSI analysis so that those limitations can be addressed in the structural

  15. Establishment of turbidity forecasting model and early-warning system for source water turbidity management using back-propagation artificial neural network algorithm and probability analysis.

    Science.gov (United States)

    Yang, Tsung-Ming; Fan, Shu-Kai; Fan, Chihhao; Hsu, Nien-Sheng

    2014-08-01

    The purpose of this study is to establish a turbidity forecasting model as well as an early-warning system for turbidity management using rainfall records as the input variables. The Taipei Water Source Domain was employed as the study area, and ANOVA analysis showed that the accumulative rainfall records of 1-day Ping-lin, 2-day Ping-lin, 2-day Fei-tsui, 2-day Shi-san-gu, 2-day Tai-pin and 2-day Tong-hou were the six most significant parameters for downstream turbidity development. The artificial neural network model was developed and proven capable of predicting the turbidity concentration in the investigated catchment downstream area. The observed and model-calculated turbidity data were applied to developing the turbidity early-warning system. Using a previously determined turbidity as the threshold, the rainfall criterion, above which the downstream turbidity would possibly exceed this respective threshold turbidity, for the investigated rain gauge stations was determined. An exemplary illustration demonstrated the effectiveness of the proposed turbidity early-warning system as a precautionary alarm of possible significant increase of downstream turbidity. This study is the first report of the establishment of the turbidity early-warning system. Hopefully, this system can be applied to source water turbidity forecasting during storm events and provide a useful reference for subsequent adjustment of drinking water treatment operation.

  16. Taxonomic history and invasion biology of two Phyllonorycter leaf miners (Lepidoptera: Gracillariidae) with links to taxonomic and molecular datasets.

    Science.gov (United States)

    De Prins, Jurate; De Prins, Willy; De Coninck, Eliane; Kawahara, Akito Y; Milton, Megan A; Hebert, Paul D N

    2013-01-01

    This paper deals with two European species, Phyllonorycter mespilella (Hübner, 1805) and P. trifasciella (Haworth, 1828), that have colonized the subtropical Canary Islands. The Rosaceae leaf miner, P. mespilella, is recorded for the first time from Lanzarote and La Palma, while the Caprifoliaceae leaf miner, P. trifasciella, is recorded from Tenerife. We present the diagnoses of these species based on morphology, a preliminary DNA barcode (COI) library of congeneric and con-familial species, and discuss the taxonomic position of the colonizers within the blancardella and trifasciella species groups. The recent intensification of anthropogenic disturbance likely accounts for their range expansion, an event that may impact the relict flora present on the Canary Islands.

  17. [Cloning and sequence analysis of the DHBV genome of the brown ducks in Guilin region and establishment of the quantitative method for detecting DHBV].

    Science.gov (United States)

    Su, He-Ling; Huang, Ri-Dong; He, Song-Qing; Xu, Qing; Zhu, Hua; Mo, Zhi-Jing; Liu, Qing-Bo; Liu, Yong-Ming

    2013-03-01

    Brown ducks carrying DHBV were widely used as hepatitis B animal model in the research of the activity and toxicity of anti-HBV dugs. Studies showed that the ratio of DHBV carriers in the brown ducks in Guilin region was relatively high. Nevertheless, the characters of the DHBV genome of Guilin brown duck remain unknown. Here we report the cloning of the genome of Guilin brown duck DHBV and the sequence analysis of the genome. The full length of the DHBV genome of Guilin brown duck was 3 027bp. Analysis using ORF finder found that there was an ORF for an unknown peptide other than S-ORF, PORF and C-ORF in the genome of the DHBV. Vector NTI 8. 0 analysis revealed that the unknown peptide contained a motif which binded to HLA * 0201. Aligning with the DHBV sequences from different countries and regions indicated that there were no obvious differences of regional distribution among the sequences. A fluorescence quantitative PCR for detecting DHBV was establishment based on the recombinant plasmid pGEM-DHBV-S constructed. This study laid the groundwork for using Guilin brown duck as a hepatitis B animal model.

  18. Lago Maggiore oligotrophication as seen from the long-term evolution of its phytoplankton taxonomic size structure

    Directory of Open Access Journals (Sweden)

    Giuseppe MORABITO

    2009-02-01

    Full Text Available Due to the rapid and common deterioration of aquatic ecosystems, scientists and environmental protection organizations acutely need means capable of producing quantitative estimates for structural deformations of natural communities. Recently, very common biomass size spectra ignore community taxonomic composition, i.e., one of the most important kinds of biological information. Therefore, another very old, but rare in planktonology, method – the traditional taxonomic size spectrum (TTSS – can be helpful. TTSS, a specific form of size-frequency distribution of taxonomic units, reveals repeating patterns of deep subalpine Lago Maggiore (Italy phytoplankton taxonomic structure. The general TTSS pattern was safeguarded during 22 annual cycles (1984-2005, when many principal environmental characteristics were changed considerably during the lake oligotrophication. At the same time, the fine structure deformations of this pattern helped us divide the total oligotrophication process into several stages characterized by notable changes of TTSS peaks' proportions. These peak-height alterations were caused by pronounced changes in the species list and overall taxonomic diversity of the lake phytoplankton. The average cell volume decline was found. It was significantly correlated with the total phosphorus descending trend. This cell volume decline was produced by the addition of numerous species into the medium-and-small size fractions. Typical patterns of the stable and transitory stages were differentiated, which could be valuable for environmental protection and diagnostic applications. The central peak height difference between the stable and the transitory periods was statistically significant. Oligotrophication process decomposition into several more homogenous groups of years was supported by quantitative estimators produced by hierarchical cluster analysis. The highest level of the similarity measure (Pearson r in pairs of annual TTSS was

  19. Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications

    DEFF Research Database (Denmark)

    Harrington, C.S.; On, Stephen L.W.

    1999-01-01

    Phylogenetic relationships of Campylobacter hyointestinalis subspecies were examined by means of 16S rRNA gene sequencing. Sequence similarities among C. hyointestinalis subsp. lawsonii strains exceeded 99.0 %, but values among C. hyointestinalis subsp. hyointestinalis strains ranged from 96...... of the genus Campylobacter, emphasizing the need for multiple strain analysis when using 16S rRNA gene sequence comparisons for taxonomic investigations........4 to 100 %. Sequence similarites between strains representing the two different subspecies ranged from 95.7 to 99.0 %. An intervening sequence was identified in certain of the C. hyointestinalis subsp. lawsonii strains. C. hyointestinalis strains occupied two distinct branches in a phylogenetic analysis...

  20. Analysis of Transcription Factors Key for Mouse Pancreatic Development Establishes NKX2-2 and MNX1 Mutations as Causes of Neonatal Diabetes in Man

    Science.gov (United States)

    Flanagan, Sarah E.; De Franco, Elisa; Lango Allen, Hana; Zerah, Michele; Abdul-Rasoul, Majedah M.; Edge, Julie A.; Stewart, Helen; Alamiri, Elham; Hussain, Khalid; Wallis, Sam; de Vries, Liat; Rubio-Cabezas, Oscar; Houghton, Jayne A.L.; Edghill, Emma L.; Patch, Ann-Marie; Ellard, Sian; Hattersley, Andrew T.

    2014-01-01

    Summary Understanding transcriptional regulation of pancreatic development is required to advance current efforts in developing beta cell replacement therapies for patients with diabetes. Current knowledge of key transcriptional regulators has predominantly come from mouse studies, with rare, naturally occurring mutations establishing their relevance in man. This study used a combination of homozygosity analysis and Sanger sequencing in 37 consanguineous patients with permanent neonatal diabetes to search for homozygous mutations in 29 transcription factor genes important for murine pancreatic development. We identified homozygous mutations in 7 different genes in 11 unrelated patients and show that NKX2-2 and MNX1 are etiological genes for neonatal diabetes, thus confirming their key role in development of the human pancreas. The similar phenotype of the patients with recessive mutations and mice with inactivation of a transcription factor gene support there being common steps critical for pancreatic development and validate the use of rodent models for beta cell development. PMID:24411943

  1. Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity

    Directory of Open Access Journals (Sweden)

    Hannah L. Buckley

    2014-09-01

    Full Text Available The role of species’ interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran’s eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners’ genetic variation. Different lichen taxa showed some variation in

  2. Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

    Science.gov (United States)

    Buckley, Hannah L; Rafat, Arash; Ridden, Johnathon D; Cruickshank, Robert H; Ridgway, Hayley J; Paterson, Adrian M

    2014-01-01

    The role of species' interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran's eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners' genetic variation. Different lichen taxa showed some variation in their phylogenetic congruence

  3. NODC Standard Product: NODC Taxonomic Code on CD-ROM (NODC Accession 0050418)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The content of the NODC Taxonomic Code, Version 8 CD-ROM (CD-ROM NODC-68) distributed by NODC is archived in this accession. Version 7 of the NODC Taxonomic Code...

  4. Taxonomic status of the roses (Rosa) described by S.G. Dimitrov from Bulgaria

    DEFF Research Database (Denmark)

    Zielinski, J.; Petrova, A; Tan, Kit

    2004-01-01

    The original herbarium vouchers for six species of Rosa (Rosaceae) described by S. G. Dimitrov from Bulgaria are taxonomically evaluated. Two species (R. balcanica, R. orphei) are considered hybrids, four other names (R. bulgarica, R. parilica, R. pontica and R. rhodopaea) are taxonomic synonyms...

  5. Taxonomic significance of cypsela morphology for the tribe mutisieae (s.l.) (asteraceae) from Pakistan

    International Nuclear Information System (INIS)

    Abid, R.; Alam, J.

    2011-01-01

    Cypselas of 5 species distributed in 3 genera of the tribe Mutisieae (s.l.) were examined from Pakistan to assess their taxonomic significance. Micro morphological characters of cypsela including shape, pappus and carpopodium have been proved very rewarding to evaluate the taxonomic decisions both at the generic and specific levels. (author)

  6. Estudos taxonômicos em Philacra Dwyer (Ochnaceae = Taxonomic studies on Philacra Dwyer (Ochnaceae

    Directory of Open Access Journals (Sweden)

    Fabíola Feres

    2006-07-01

    Full Text Available As espécies de Philacra são encontradas principalmente na fronteira Brasil-Venezuela, e dentre outros gêneros de Ochnaceae, é o mais próximo a Luxemburgia, cujas espécies ocorrem somente no Brasil, especialmente na Cadeia do Espinhaço. A análise taxonômica das espécies de Philacra foi realizada com base no material tipo e em espécimes depositados em herbários. O trabalho objetivou a redescrição do gênero, a elaboração da chave taxonômica e a redescrição das espécies. É apresentada a redescrição do gênero, suadistribuição geográfica, a chave de identificação e a redescrição das espécies. Atualmente, são reconhecidas quatro espécies de Philacra: P. auriculata Dwyer, P. duidae (Gleason Dwyer, P. longifolia (Gleason Dwyer e, P. steyermarkii Maguire.The species of Philacra are found mainly at the Brazil-Venezuela border. Among other Ochnaceae genera, this is the most closely related to Luxemburgia, which occurs only in Brazil, especially at theEspinhaço Range. The taxonomic analysis of Philacra species was based on the type material and herbarium specimens. This work aimed to redescribe the genus, to prepare a taxonomic key and to redescribe the species. The genus redescription and the geographical distribution, a key to the species and species redescription, are presented. Currently, four Philacra species are recognized: P. auriculata Dwyer, P. duidae (Gleason Dwyer, P. longifolia (Gleason Dwyer, and P. steyermarkii Maguire.

  7. The apicoplast genomes of two taxonomic units of Babesia from sheep.

    Science.gov (United States)

    Wang, Tao; Guan, Guiquan; Korhonen, Pasi K; Koehler, Anson V; Hall, Ross S; Young, Neil D; Yin, Hong; Gasser, Robin B

    2017-01-15

    The apicoplast (ap) is a unique, non-photosynthetic organelle found in most apicomplexan parasites. Due to the essential roles that this organelle has, it has been widely considered as target for drugs against diseases caused by apicomplexans. Exploring the ap genomes of such parasites would provide a better understanding of their systematics and their basic molecular biology for therapeutics. However, there is limited information available on the ap genomes of apicomplexan parasites. In the present study, the ap genomes of two operational taxonomic units of Babesia (known as Babesia sp. Lintan [Bl] and Babesia sp. Xinjiang [Bx]) from sheep were sequenced, assembled and annotated using a massive parallel sequencing-based approach. Then, the gene content and gene order in these ap genomes (∼30.7kb in size) were defined and compared, and the genetic differences were assessed. In addition, a phylogenetic analysis of ap genomic data sets was carried out to assess the relationships of these taxonomic units with other apicomplexan parasites for which complete ap genomic data sets were publicly available. The results showed that the ap genomes of Bl and Bx encode 59 and 57 genes, respectively, including 2 ribosomal RNA genes, 25 transfer RNA genes and 30-32 protein-encoding genes, being similar in content to those of Babesia bovis and B. orientalis. Ap gene regions that might serve as markers for future epidemiological and population genetic studies of Babesia species were identified. Using sequence data for a subset of six protein-encoding genes, a close relationship of Bl and Bx with Babesia bovis from cattle and B. orientalis from water buffalo was inferred. Although the focus of the present study was on Babesia, we propose that the present sequencing-bioinformatic approach should be applicable to organellar genomes of a wide range of apicomplexans of veterinary importance. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Epidermal characters of Tamarix L. (Tamaricaceae from Northwest China and their taxonomic and palaeogeographic implications

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zhang

    2018-04-01

    Full Text Available The taxonomical position of species of the genus Tamarix (Tamaricaceae has been criticized because of their gross morphological similarities (such as slender, smooth and reddish–brown branches, grey–green foliage and scale leaves, and their systematic relationships remain unclear. In this paper, the leaf epidermal features of 17 species from China are studied based on the micro-morphological characters of the epidermal cells, stomata, salt glands, papillae and epidermal hairs. According to the studies, the leaf epidermal features, together with the character of the flower, are taxonomically clearly distinct. The establishment of Tamarix albiflonum is consolidated. Tamarix korolkowi and Tamarix ramosissima have minimal differences in epidermal characters, and the former is suggested to be a junior synonym. Tamarix ramosissima, Tamarix tarimensis, Tamarix arceuthoides and Tamarix hohenackeri are most similar with respect to their leaf epidermis; considering the common morphological features, habit, distribution and especially the hybridization, it is suggested that these four species are closely genetically related and that the variations among them are probably intraspecific. The new taxonomical evidence indicates the occurrence of 13 species and four variants in China. Presently, Tamarix is a typical plant of arid and semi-arid regions, but its Eocene ancestors lived in warm and humid climates in the coastal areas of the ancient Mediterranean Sea. Thus, the papillae or epidermal hairs, which are outgrowths of the outer epidermal cells facilitating the leaf to respond to water stress and commonly seen in the plants growing in arid or semi-arid areas rather than the plants in warm and humid climates, are of relatively recent origin in Tamarix. The primitive species lack papillae or epidermal hairs, while in evolved species these structures are abundant. Based on the ecological adaptations of the epidermal features, the palaeogeographic

  9. Character Selection During Interactive Taxonomic Identification: “Best Characters”

    Directory of Open Access Journals (Sweden)

    Nadia Talent

    2014-03-01

    Full Text Available Software interfaces for interactive multiple-entry taxonomic identification (polyclaves sometimes provide a “best character” or “separation” coefficient, to guide the user to choose a character that could most effectively reduce the number of identification steps required. The coefficient could be particularly helpful when difficult or expensive tasks are needed for forensic identification, and in very large databases, uses that appear likely to increase in importance. Several current systems also provide tools to develop taxonomies or single-entry identification keys, with a variety of coefficients that are appropriate to that purpose. For the identification task, however, information theory neatly applies, and provides the most appropriate coefficient. To our knowledge, Delta-Intkey is the only currently available system that uses a coefficient related to information theory, and it is currently being reimplemented, which may allow for improvement. We describe two improvements to the algorithm used by Delta-Intkey. The first improves transparency as the number of remaining taxa decreases, by normalizing the range of the coefficient to [0,1]. The second concerns numeric ranges, which require consistent treatment of sub-intervals and their end-points. A stand-alone Bestchar program for categorical data is provided, in the Python and R languages. The source code is freely available and dedicated to the Public Domain.

  10. The epidermis in Passerina/ (Thymelaeaceae: structure, function and taxonomic significance

    Directory of Open Access Journals (Sweden)

    C. L. Bredenkamp

    2000-02-01

    Full Text Available Epidermal features were studied in all 17 species of Passerina, a genus endemic to southern Africa. Leaves in Passerina are inversely ericoid, the adaxial surface concave and the abaxial surface convex. Leaves are inversely dorsiventral and epistomatic. The adaxial epidermis is villous, with unicellular, uniseriate trichomes and relatively small thin-walled cells, promoting flexibility of leaf margins owing to turgor changes. In common with many other Thymelaeaceae, abaxial epidermal cells are large and tanniniferous with mucilaginous cell walls. The cuticle is adaxially thin, but abaxially well devel­oped, probably enabling the leaf to restrict water loss and to tolerate high light intensity and UV-B radiation. Epicuticular waxes, present in all species, comprise both soft and plate waxes. Epidermal structure proves to be taxonomically impor­tant at family, genus and species levels. Interspecific differences include arrangement of stomata and presence or absence of abaxial epidermal hair. Other diagnostic characters of the abaxial epidermal cells are arrangement,size and shape, cutic- ular ornamentation and presence or absence of wax platelets. Two groups of species on the basis of abaxial epidermal cell orientation are recognised. Many leaf epidermal features in Passerina are interpreted as structural adaptations to the Mediterranean climate of the Cape.

  11. Recent progress in floristic and taxonomic studies in Bulgaria

    Directory of Open Access Journals (Sweden)

    Ana Petrova

    2018-02-01

    Full Text Available An overview of floristic and taxonomic research on vascular plants in Bulgaria during the period of 2005-2016 has been made. The Bulgarian flora currently comprises 4064 species, belonging to 921 genera and 159 families. About 490 published papers were checked, in which 127 species were reported for the first time for the country by Bulgarian or foreign botanists, 11 of these taxa being ones new to science, while 51 are aliens. In the papers checked, 17 subspecies (two of them new to science and 18 hybrids (four of them new to science were also reported for the first time for the country, nine species were confirmed, and another 78 were unconfirmed, synonymised, or erroneously reported. In numerous papers, new localities for various species in different floristic regions in Bulgaria were reported. The books Flora of the Republic of Bulgaria Vol. 11, Red Data Book of the Republic of Bulgaria Vol. 1. Plants and Fungi, Atlas of Endemic Plants in Bulgaria, Invasive Alien Species of Vascular Plants in Bulgaria, Proceedings of Balkan Botanical Congress IV, etc., were published during the given period.

  12. Taxonomic and phytogeographic implications from ITS phylogeny in Berberis (Berberidaceae).

    Science.gov (United States)

    Kim, Young-Dong; Kim, Sung-Hee; Landrum, Leslie R

    2004-06-01

    A phylogeny based on the internal transcribed spacer (ITS) sequences from 79 taxa representing much of the diversity of Berberis L. (four major groups and 22 sections) was constructed for the first time. The phylogeny was basically congruent with the previous classification schemes at higher taxonomic levels, such as groups and subgroups. A notable exception is the non-monophyly of the group Occidentales of compound-leaved Berberis (previously separated as Mahonia). At lower levels, however, most of previous sections and subsections were not evident especially in simple-leaved Berberis. Possible relationship between section Horridae (group Occidentales) and the simple-leaved Berberis clade implies paraphyly of the compound-leaved Berberis. A well-known South America-Old World (mainly Asia) disjunctive distribution pattern of the simple-leaved Berberis is explained by a vicariance event occurring in the Cretaceous period. The ITS phylogeny also suggests that a possible connection between the Asian and South American groups through the North American species ( Berberis canadensis or B. fendleri) is highly unlikely.

  13. A taxonomic revision of the genus Ceiba Mill. (Bombacaceae

    Directory of Open Access Journals (Sweden)

    Gibbs, Peter

    2003-12-01

    Full Text Available In this taxonomic revision of Ceiba Mill, (in which we include Chorisia Kunth we recognize 17 species, seven of which we group in the C. insignis. species aggregate. One new species is described, C. lupuna P.E. Gibbs & Semir from Peru, which is referred to the C. insignis agg., and one new subspecies, C. aesculifolia subsp. parvifolia (Rose P.E. Gibbs & Semir is recognized. Distribution maps are provided for 16 species (that for C. pentandra is restricted to the New World, and six species are illustrated.En esta revisión taxonómica de Ceiba, que incluye el género Chorisia, se reconocen 17 especies, siete de las cuales se agrupan en el complejo C. insignis. Se describe una nueva especie, C. lupuna P.E. Gibbs & Semir, del Perú, que pertenece al complejo de C. insignis, asf como una nueva subespecie, C. aesculifolia subsp. parvifolia (Rose P.E. Gibbs & Semir. Se incluyen mapas de distribuci6n de 16 especies (aunque en el caso de C. pentandra solo se representa su distribución americana y se dibujan detalles diagnósticos de seis especies.

  14. Taxonomic relationships among Phenacomys voles as inferred by cytochrome b

    Science.gov (United States)

    Bellinger, M.R.; Haig, S.M.; Forsman, E.D.; Mullins, T.D.

    2005-01-01

    Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. l. silvicola), the Sonoma tree vole (P. pomo), the white-footed vole (P. albipes), and the heather vole (P. intermedius) were examined using 664 base pairs of the mitochondrial cytochrome b gene. Results indicate specific differences among red tree voles, Sonoma tree voles, white-footed voles, and heather voles, but no clear difference between the 2 Oregon subspecies of red tree voles (P. l. longicaudus and P. l. silvicola). Our data further indicated a close relationship between tree voles and albipes, validating inclusion of albipes in the subgenus Arborimus. These 3 congeners shared a closer relationship to P. intermedius than to other arvicolids. A moderate association between porno and albipes was indicated by maximum parsimony and neighbor-joining phylogenetic analyses. Molecular clock estimates suggest a Pleistocene radiation of the Arborimus clade, which is concordant with pulses of diversification observed in other murid rodents. The generic rank of Arborimus is subject to interpretation of data.

  15. U.S. Food safety and Inspection Service testing for Salmonella in selected raw meat and poultry products in the United States, 1998 through 2003: an establishment-level analysis.

    Science.gov (United States)

    Eblen, Denise R; Barlow, Kristina E; Naugle, Alecia Larew

    2006-11-01

    The U.S. Food Safety and Inspection Service (FSIS) pathogen reduction-hazard analysis critical control point systems final rule, published in 1996, established Salmonella performance standards for broiler chicken, cow and bull, market hog, and steer and heifer carcasses and for ground beef, chicken, and turkey meat. In 1998, the FSIS began testing to verify that establishments are meeting performance standards. Samples are collected in sets in which the number of samples is defined but varies according to product class. A sample set fails when the number of positive Salmonella samples exceeds the maximum number of positive samples allowed under the performance standard. Salmonella sample sets collected at 1,584 establishments from 1998 through 2003 were examined to identify factors associated with failure of one or more sets. Overall, 1,282 (80.9%) of establishments never had failed sets. In establishments that did experience set failure(s), generally the failed sets were collected early in the establishment testing history, with the exception of broiler establishments where failure(s) occurred both early and late in the course of testing. Small establishments were more likely to have experienced a set failure than were large or very small establishments, and broiler establishments were more likely to have failed than were ground beef, market hog, or steer-heifer establishments. Agency response to failed Salmonella sample sets in the form of in-depth verification reviews and related establishment-initiated corrective actions have likely contributed to declines in the number of establishments that failed sets. A focus on food safety measures in small establishments and broiler processing establishments should further reduce the number of sample sets that fail to meet the Salmonella performance standard.

  16. Skilled delivery service utilization and its association with the establishment of Women's Health Development Army in Yeky district, South West Ethiopia: a multilevel analysis.

    Science.gov (United States)

    Negero, Melese Girmaye; Mitike, Yifru Berhan; Worku, Abebaw Gebeyehu; Abota, Tafesse Lamaro

    2018-01-30

    Because of the unacceptably high maternal and perinatal morbidity and mortality, the government of Ethiopia has established health extension program with a community-based network involving health extension workers (HEWs) and a community level women organization which is known as "Women's Health Development Army" (WHDA). Currently, the HEWs and WHDA network is the approach preferred by the government to register pregnant women and encourage them to link in the healthcare system. However, its association with skilled delivery service utilization is not well known. A community-based cross-sectional study was conducted from January to February 2015. Within 380 clusters of WHDA, a total of 748 reproductive-age women who gave birth in 1 year preceding the study, were included using multistage sampling technique. The data were entered into EPI info version 7 statistical software and exported to STATA version 11 for analysis. Multilevel analysis technique was applied to check for an association of selected variables with a utilization of skilled delivery service. About 45% of women have received skilled delivery care. A significant heterogeneity was observed between "Women's Health Development Teams (clusters)" for skilled delivery care service utilization which explains about 62% of the total variation. Individual-level predictors including urban residence [AOR (95% CI) 35.10 (4.62, 266.52)], previous exposure of complications [AOR (95% CI) 3.81 (1.60, 9.08)], at least four ANC visits [AOR (95% CI) 7.44 (1.48, 37.42)] and preference of skilled personnel [AOR (95% CI) 8.11 (2.61, 25.15)] were significantly associated with skilled delivery service use. Among cluster level variables, the distance of clusters within 2 km radius from the nearest health facility was significantly associated [AOR (95% CI) 6.03 (1.92, 18.93)] with skilled delivery service utilization. In this study, significant variation among clusters of WHDA was observed. Both individual and cluster level

  17. A taxonomic review of the Neoserica (sensu lato abnormis group (Coleoptera, Scarabaeidae, Sericini

    Directory of Open Access Journals (Sweden)

    Dirk Ahrens

    2014-09-01

    Full Text Available The present paper revises the species belonging to the Neoserica (sensu lato abnormis group, so far known only with two nominal species. Twenty new species are herein described from Indochina and southern China: N. abnormoides sp. n. (Vietnam, China, N. allolaotica sp. n., N. namthaensis sp. n., N. simplicissima sp. n. (Laos, N. thailandensis sp. n. (Thailand, N. alloputaoana sp. n., N. kanphantensis sp. n., N. natmatoungensis sp. n., N. putaoana sp. n., N. taunggyiana sp. n. (Myanmar, N. lamellosa sp. n., N. tonkinea sp. n. (Vietnam, N. bairailingshanica sp. n., N. euyunnanica sp. n., N. huangi sp. n., N. jiangxiensis sp. n., N. trifida sp. n., N. yaoi sp. n., N. yingjiangensis sp. n. (China, N. cardamomensis sp. n. (Indochina and southern China. One new combination is established: Neoserica ponderosa Arrow, 1946, comb. n. The lectotypes of Neoserica abnormis Moser, 1908 and the taxonomically uncertain N. inclinata Brenske, 1898, which very likely also belongs to this species group, are designated herein. A key to the species and to species groups is given, the genitalia of all species including their habitus are illustrated. Maps of species distribution are included.

  18. Establishment study of the in vivo imaging analysis with small animal imaging modalities (micro-PET and micro-SPECT/CT) for bio-drug development

    International Nuclear Information System (INIS)

    Jang, Beomsu; Park, Sanghyeon; Park, Jeonghoon; Jo, Sungkee; Jung, Uhee; Kim, Seolwha; Lee, Yunjong; Choi, Daeseong

    2011-01-01

    In this study, we established the image acquisition and analysis procedures of micro-PET, SPECT/CT using the experimental animal (mouse) for the development of imaging assessment method for the bio-drug. We examined the micro-SPECT/CT, PET imaging study using the Siemens Inveon micro-multimodality system (SPECT/CT) and micro-PET with 99m Tc-MDP, DMSA, and 18 F-FDG. SPECT imaging studies using 3 types of pinhole collimators. 5-MWB collimator was used for SPECT image study. To study whole-body distribution, 99m Tc-MDP SPECT image study was performed. We obtained the fine distribution image. And the CT images was obtained to provide the anatomical information. And then these two types images are fused. To study specific organ uptake, we examined 99 mTc-DMSA SPECT/CT imaging study. We also performed the PET image study using U87MG tumor bearing mice and 18 F-FDG. The overnight fasting, warming and anesthesia with 2% isoflurane pretreatment enhance the tumor image through reducing the background uptake including brown fat, harderian gland and skeletal muscles. Also we got the governmental approval for use of x-ray generator for CT and radioisotopes as sealed and open source. We prepared the draft of process procedure for the experimental animal imaging facility. These research results can be utilized as a basic image study protocols and data for the image assessment of drugs including biological drug

  19. Integrative analysis reveals CD38 as a therapeutic target for plasma cell-rich pre-disease and established rheumatoid arthritis and systemic lupus erythematosus.

    Science.gov (United States)

    Cole, Suzanne; Walsh, Alice; Yin, Xuefeng; Wechalekar, Mihir D; Smith, Malcolm D; Proudman, Susanna M; Veale, Douglas J; Fearon, Ursula; Pitzalis, Costantino; Humby, Frances; Bombardieri, Michele; Axel, Amy; Adams, Homer; Chiu, Christopher; Sharp, Michael; Alvarez, John; Anderson, Ian; Madakamutil, Loui; Nagpal, Sunil; Guo, Yanxia

    2018-05-02

    Plasmablasts and plasma cells play a key role in many autoimmune diseases, such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). This study was undertaken to evaluate the potential of targeting CD38 as a plasma cell/plasmablast depletion mechanism by daratumumab in the treatment of patients with RA and SLE. RNA-sequencing analysis of synovial biopsies from various stages of RA disease progression, flow cytometry analysis of peripheral blood mononuclear cells (PBMC) from patients with RA or SLE and healthy donors, immunohistochemistry assessment (IHC) of synovial biopsies from patients with early RA, and ex vivo immune cell depletion assays using daratumumab (an anti-CD38 monoclonal antibody) were used to assess CD38 as a therapeutic target. We demonstrated that the plasma cell/plasmablast-related genes CD38, XBP1, IRF4, PRDM1, IGJ and TNFSF13B are significantly up-regulated in synovial biopsies from patients with arthralgia, undifferentiated arthritis (UA), early RA and established RA as compared to healthy controls and control patients with osteoarthritis. In addition, the highest CD38 expression was observed on plasma cells and plasmablasts compared to natural killer (NK) cells, classical dendritic cells (DCs), plasmacytoid DCs (pDCs) and T cells, in blood from healthy controls and patients with SLE and RA. Furthermore, IHC showed CD38 staining in the same region as CD3 and CD138 staining in synovial tissue biopsies from patients with early RA. Most importantly, our data show for the first time that daratumumab effectively depletes plasma cells/plasmablasts in PBMC from patients with SLE and RA in a dose-dependent manner ex vivo. These results indicate that CD38 may be a potential target for RA disease interception and daratumumab should be evaluated clinically for the treatment of both RA and SLE.

  20. Combining groundwater quality analysis and a numerical flow simulation for spatially establishing utilization strategies for groundwater and surface water in the Pingtung Plain

    Science.gov (United States)

    Jang, Cheng-Shin; Chen, Ching-Fang; Liang, Ching-Ping; Chen, Jui-Sheng

    2016-02-01

    Overexploitation of groundwater is a common problem in the Pingtung Plain area of Taiwan, resulting in substantial drawdown of groundwater levels as well as the occurrence of severe seawater intrusion and land subsidence. Measures need to be taken to preserve these valuable groundwater resources. This study seeks to spatially determine the most suitable locations for the use of surface water on this plain instead of extracting groundwater for drinking, irrigation, and aquaculture purposes based on information obtained by combining groundwater quality analysis and a numerical flow simulation assuming the planning of manmade lakes and reservoirs to the increase of water supply. The multivariate indicator kriging method is first used to estimate occurrence probabilities, and to rank townships as suitable or unsuitable for groundwater utilization according to water quality standards for drinking, irrigation, and aquaculture. A numerical model of groundwater flow (MODFLOW) is adopted to quantify the recovery of groundwater levels in townships after model calibration when groundwater for drinking and agricultural demands has been replaced by surface water. Finally, townships with poor groundwater quality and significant increases in groundwater levels in the Pingtung Plain are prioritized for the groundwater conservation planning based on the combined assessment of groundwater quality and quantity. The results of this study indicate that the integration of groundwater quality analysis and the numerical flow simulation is capable of establishing sound strategies for joint groundwater and surface water use. Six southeastern townships are found to be suitable locations for replacing groundwater with surface water from manmade lakes or reservoirs to meet drinking, irrigation, and aquaculture demands.

  1. MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.

    Science.gov (United States)

    Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

    2010-02-15

    We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.

  2. Taxonomic formula of geoecological hazard for the cadastral districts of Moscow city

    Directory of Open Access Journals (Sweden)

    Karfidova E.A.

    2018-01-01

    Full Text Available the article proposes a method for calculating the taxonomic formula for the geoecological hazard of the cadastral district. The engineering-geological zoning map uses for calculating the balance of the territory by the hazard index – the basis of the taxonomic formula. The taxonomic formula as an open data set makes it possible to characterize the geoecological hazards of the territory of a district. The geoenvironmental hazard map of cadastral districts is necessary for regional model of spatial planning at the municipal level.

  3. A Taxonomic Reduced-Space Pollen Model for Paleoclimate Reconstruction

    Science.gov (United States)

    Wahl, E. R.; Schoelzel, C.

    2010-12-01

    Paleoenvironmental reconstruction from fossil pollen often attempts to take advantage of the rich taxonomic diversity in such data. Here, a taxonomically "reduced-space" reconstruction model is explored that would be parsimonious in introducing parameters needing to be estimated within a Bayesian Hierarchical Modeling context. This work involves a refinement of the traditional pollen ratio method. This method is useful when one (or a few) dominant pollen type(s) in a region have a strong positive correlation with a climate variable of interest and another (or a few) dominant pollen type(s) have a strong negative correlation. When, e.g., counts of pollen taxa a and b (r >0) are combined with pollen types c and d (r logistic generalized linear model (GLM). The GLM can readily model this relationship in the forward form, pollen = g(climate), which is more physically realistic than inverse models often used in paleoclimate reconstruction [climate = f(pollen)]. The specification of the model is: rnum Bin(n,p), where E(r|T) = p = exp(η)/[1+exp(η)], and η = α + β(T); r is the pollen ratio formed as above, rnum is the ratio numerator, n is the ratio denominator (i.e., the sum of pollen counts), the denominator-specific count is (n - rnum), and T is the temperature at each site corresponding to a specific value of r. Ecological and empirical screening identified the model (Spruce+Birch) / (Spruce+Birch+Oak+Hickory) for use in temperate eastern N. America. α and β were estimated using both "traditional" and Bayesian GLM algorithms (in R). Although it includes only four pollen types, the ratio model yields more explained variation ( 80%) in the pollen-temperature relationship of the study region than a 64-taxon modern analog technique (MAT). Thus, the new pollen ratio method represents an information-rich, reduced space data model that can be efficiently employed in a BHM framework. The ratio model can directly reconstruct past temperature by solving the GLM equations

  4. EAU standardised medical terminology for urologic imaging: a taxonomic approach.

    Science.gov (United States)

    Loch, Tillmann; Carey, Brendan; Walz, Jochen; Fulgham, Pat Fox

    2015-05-01

    The terminology and abbreviations used in urologic imaging have generally been adopted on an ad hoc basis by different speciality groups; however, there is a need for shared nomenclature to facilitate clinical communication and collaborative research. This work reviews the current nomenclature for urologic imaging used in clinical practice and proposes a taxonomy and terminology for urologic imaging studies. A list of terms used in urologic imaging were compiled from guidelines published by the European Association of Urology and the American Urological Association and from the American College of Radiology Appropriateness Criteria. Terms searched were grouped into broad categories based on technology, and imaging terms were further stratified based on the anatomic extent, contrast or phases, technique or modifiers, and combinations or fusions. Terms that had a high degree of utilisation were classified as accepted. We propose a new taxonomy to define a more useful and acceptable nomenclature model acceptable to all health professionals involved in urology. The major advantage of a taxonomic approach to the classification of urologic imaging studies is that it provides a flexible framework for classifying the modifications of current imaging modalities and allows the incorporation of new imaging modalities. The adoption of this hierarchical classification model ranging from the most general to the most detailed descriptions should facilitate hierarchical searches of the medical literature using both general and specific terms. This work is limited in its scope, as it is not currently all-inclusive. This will hopefully be addressed by future modification as others embrace the concept and work towards uniformity in nomenclature. This paper provides a noncomprehensive list of the most widely used terms across different specialties. This list can be used as the basis for further discussion, development, and enhancement. In this paper we describe a classification system

  5. [Risk factor analysis of the patients with solitary pulmonary nodules and establishment of a prediction model for the probability of malignancy].

    Science.gov (United States)

    Wang, X; Xu, Y H; Du, Z Y; Qian, Y J; Xu, Z H; Chen, R; Shi, M H

    2018-02-23

    Objective: This study aims to analyze the relationship among the clinical features, radiologic characteristics and pathological diagnosis in patients with solitary pulmonary nodules, and establish a prediction model for the probability of malignancy. Methods: Clinical data of 372 patients with solitary pulmonary nodules who underwent surgical resection with definite postoperative pathological diagnosis were retrospectively analyzed. In these cases, we collected clinical and radiologic features including gender, age, smoking history, history of tumor, family history of cancer, the location of lesion, ground-glass opacity, maximum diameter, calcification, vessel convergence sign, vacuole sign, pleural indentation, speculation and lobulation. The cases were divided to modeling group (268 cases) and validation group (104 cases). A new prediction model was established by logistic regression analying the data from modeling group. Then the data of validation group was planned to validate the efficiency of the new model, and was compared with three classical models(Mayo model, VA model and LiYun model). With the calculated probability values for each model from validation group, SPSS 22.0 was used to draw the receiver operating characteristic curve, to assess the predictive value of this new model. Results: 112 benign SPNs and 156 malignant SPNs were included in modeling group. Multivariable logistic regression analysis showed that gender, age, history of tumor, ground -glass opacity, maximum diameter, and speculation were independent predictors of malignancy in patients with SPN( P prediction model for the probability of malignancy as follow: p =e(x)/(1+ e(x)), x=-4.8029-0.743×gender+ 0.057×age+ 1.306×history of tumor+ 1.305×ground-glass opacity+ 0.051×maximum diameter+ 1.043×speculation. When the data of validation group was added to the four-mathematical prediction model, The area under the curve of our mathematical prediction model was 0.742, which is greater

  6. Taxonomía de riesgos de outsourcing de software Software outsourcing risk taxonomy

    Directory of Open Access Journals (Sweden)

    Gloria Piedad Gasca-Hurtado

    2013-04-01

    Full Text Available Para las organizaciones la estrategia de outsourcing de software (OS se ha constituido en una alternativa estratégica de reducción de costos y mejora de la calidad de software. Sin embargo, la complejidad de la gestión de este tipo de proyectos aumenta, debido a la relación de actores diferentes (cliente y proveedor, de la cual depende en gran medida el éxito de estos proyectos. Identificar, analizar y gestionar los riesgos que afectan este tipo de proyectos, son buenas prácticas que se pueden llevar a cabo para establecer indicadores de gestión claves para el éxito de los proyectos. Es por esta razón que el objetivo de este trabajo es diseñar una taxonomía de riesgos de OS, es decir, una estructura de clasificación jerárquica de riesgos basada en los proyectos de OS que facilite la identificación de riesgos, que contribuya a la realización de un análisis de riesgos ágil y preciso, para su posterior gestión a lo largo de todo el proceso de OS. La taxonomía que se propone ha sido validada en un caso de estudio correspondiente a un proyecto de compra de software preelaborado. Los resultados se muestran en la última parte de este trabajo y se analiza la forma como dichos resultados impacta el proyecto en el cual fue implementada la taxonomía y su utilidad en el refinamiento de los procesos organizacionales de la empresa, a partir de las lecciones aprendidas.In recent years, the software outsourcing (SO strategy for organizations has become a useful and important alternative, as well as SO projects. SO projects have many complexities due to several factors affecting management. These complexities and importance of SO require that successfull projects meet a parameter set: budget, cost, schedule, among others. This requirement can be met through the implementation of methods and techniques of risk management (RM. RM is a process to prevent problems, establish actions to follow, and monitor the project to ensure success. Likewise

  7. Advances in establishment and analysis of three-dimensional tumor spheroid-based functional assays for target validation and drug evaluation

    Directory of Open Access Journals (Sweden)

    Vinci Maria

    2012-03-01

    Full Text Available Abstract Background There is overwhelming evidence that in vitro three-dimensional tumor cell cultures more accurately reflect the complex in vivo microenvironment than simple two-dimensional cell monolayers, not least with respect to gene expression profiles, signaling pathway activity and drug sensitivity. However, most currently available three-dimensional techniques are time consuming and/or lack reproducibility; thus standardized and rapid protocols are urgently needed. Results To address this requirement, we have developed a versatile toolkit of reproducible three-dimensional tumor spheroid models for dynamic, automated, quantitative imaging and analysis that are compatible with routine high-throughput preclinical studies. Not only do these microplate methods measure three-dimensional tumor growth, but they have also been significantly enhanced to facilitate a range of functional assays exemplifying additional key hallmarks of cancer, namely cell motility and matrix invasion. Moreover, mutual tissue invasion and angiogenesis is accommodated by coculturing tumor spheroids with murine embryoid bodies within which angiogenic differentiation occurs. Highly malignant human tumor cells were selected to exemplify therapeutic effects of three specific molecularly-targeted agents: PI-103 (phosphatidylinositol-3-kinase (PI3K-mammalian target of rapamycin (mTOR inhibitor, 17-N-allylamino-17-demethoxygeldanamycin (17-AAG (heat shock protein 90 (HSP90 inhibitor and CCT130234 (in-house phospholipase C (PLCγ inhibitor. Fully automated analysis using a Celigo cytometer was validated for tumor spheroid growth and invasion against standard image analysis techniques, with excellent reproducibility and significantly increased throughput. In addition, we discovered key differential sensitivities to targeted agents between two-dimensional and three-dimensional cultures, and also demonstrated enhanced potency of some agents against cell migration

  8. A study on the establishment of national nuclear foreign policy -with reference to the strategy on the NPT extension and analysis of nuclear liability-

    International Nuclear Information System (INIS)

    Oh, Keun Bae; Choi, Yeong Myeong; Ham, Chol Hoon; Lee, Kwang Seok; Lee, Byeong Uk; Lee, Jae Seong; Choi, Yeong Rok; Ko, Han Seok

    1994-01-01

    The overall objectives of this study are to analyze the international nuclear export control system and the international non-proliferation circumstance, to establish national strategies for the NPT extension, to suggest revisions of the IAEA Statute Article VI giving Korea permanent membership on the IAEA board of Governors, and to analyze and establish counter measurements for nuclear liability in verious fields. (Author)

  9. Establishment Registration & Device Listing

    Data.gov (United States)

    U.S. Department of Health & Human Services — This searchable database contains establishments (engaged in the manufacture, preparation, propagation, compounding, assembly, or processing of medical devices...

  10. Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico.

    Science.gov (United States)

    Mason-Romo, Edgard David; Farías, Ariel A; Ceballos, Gerardo

    2017-01-01

    Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall) of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests-upland and lowland (arroyo or riparian) forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian) forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods) and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because of

  11. Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico.

    Directory of Open Access Journals (Sweden)

    Edgard David Mason-Romo

    Full Text Available Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests-upland and lowland (arroyo or riparian forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because

  12. Asian longhorned beetle complicates the relationship between taxonomic diversity and pest vulnerability in street tree assemblages

    Data.gov (United States)

    U.S. Environmental Protection Agency — Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to...

  13. Integrating DNA barcode data and taxonomic practice: determination, discovery, and description.

    Science.gov (United States)

    Goldstein, Paul Z; DeSalle, Rob

    2011-02-01

    DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.

  14. Partitioning taxonomic diversity of aquatic insect assemblages and functional feeding groups in Neotropical Savanna headwater streams

    Science.gov (United States)

    Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feedin...

  15. A review of the taxonomic status and biology of the Cape Parrot ...

    African Journals Online (AJOL)

    A review of the taxonomic status and biology of the Cape Parrot Poicephalus robustus , with reference to the Brown-necked Parrot P. fuscicollis fuscicollis and the Grey-headed Parrot P. f. suahelicus.

  16. Taxonomic value of stem anatomical characters in classification of some Adonis (Ranunculaceae species in Iran

    Directory of Open Access Journals (Sweden)

    Majid Ghorbani Nohooji

    2011-06-01

    (A. aestivalis, A. flammea and A. dentata were evaluated using numerical taxonomic methods. Obtained results demonstrated that simultaneous application of both qualitative and relative characters offers a better chance in species delimitation in future researches.

  17. Treatment of uncertainties in the existence of free berths with risk analysis techniques. Establishment of policies in port of Cadiz (SPAIN)

    Energy Technology Data Exchange (ETDEWEB)

    Awad Nuñez, S.; Camarero Orive, A.; Romero Sanchez-Brunete, M.; Camarero Orive, A.; Gonzalez Cancelas, N.

    2016-07-01

    This research discusses the challenges involved in the treatment of uncertainties in the existence of free berths during the arrival of cruise ships at seaports. Pursuing this goal, a three-step methodology is adopted: 1) Identifying risk sources and critical risk variables and how they are related; 2) Fitting the Probability Distribution Functions that best represent the behaviour of each critical risk variable; and 3) Simulating the probability of a ship having to wait because there are no free berths using a technique that combines statistical concepts (random sampling) with the ability of computers to generate pseudo-random numbers and automate estimations of the values of the set of critical risk variables. The innovative use of risk analysis techniques in this field allows the establishment of policies to improve the planning and management of port infrastructure, for example, deciding when it is necessary to work to increase the number of berths. As a case of study, we applied this methodology to study whether the enlargement of the wharf in the port of Cadiz (Spain) is necessary right now considering the number of cruise ships that have arrived at the port in the past three years, their date and hour of arrival, their length and draught, the duration of their stay in port and their waiting time before being able to enter the port. This action would require moving logistics activities to a new terminal, but would bring to the city the opportunity to rethink the seafront, introducing new cruiser links with the city centre and developing a better seaport-city integration. (Author)

  18. Cerebrospinal fluid neopterin analysis in neuropediatric patients: establishment of a new cut off-value for the identification of inflammatory-immune mediated processes.

    Directory of Open Access Journals (Sweden)

    Marta Molero-Luis

    Full Text Available OBJECTIVE: A high level of cerebrospinal fluid (CSF neopterin is a marker of central nervous system inflammatory-immune mediated processes. We aimed to assess data from 606 neuropediatric patients, describing the clinical and biochemical features of those neurological disorders presenting CSF neopterin values above a new cut-off value that was defined in our laboratory. METHODS: To establish the new CSF neopterin cut-off value, we studied two groups of patients: Group 1 comprised 68 patients with meningoencephalitis, and Group 2 comprised 52 children with a confirmed peripheral infection and no central nervous system involvement. We studied 606 CSF samples from neuropediatric patients who were classified into 3 groups: genetic diagnosis (A, acquired/unknown etiologic neurologic diseases (B and inflammatory-immune mediated processes (C. RESULTS: The CSF neopterin cut-off value was 61 nmol/L. Out of 606 cases, 56 presented a CSF neopterin level above this value. Group C had significantly higher CSF neopterin, protein and leukocyte values than the other groups. Sixteen of twenty-three patients in this group had a CSF neopterin level above the cut-off, whereas three and seven patients presented increased leukocyte and protein values, respectively. A significant association was found among CSF neopterin, proteins and leukocytes in the 606 patients. White matter disturbances were associated with high CSF neopterin concentrations. CONCLUSIONS: Although children with inflammatory-immune mediated processes presented higher CSF neopterin values, patients with other neurological disorders also showed increased CSF neopterin concentrations. These results stress the importance of CSF neopterin analysis for the identification of inflammatory-immune mediated processes.

  19. Establishment study of the in vivo imaging analysis with small animal imaging modalities (micro-PET and micro-SPECT/CT) for bio-drug development

    Energy Technology Data Exchange (ETDEWEB)

    Jang, Beomsu; Park, Sanghyeon; Park, Jeonghoon; Jo, Sungkee; Jung, Uhee; Kim, Seolwha; Lee, Yunjong; Choi, Daeseong

    2011-01-15

    In this study, we established the image acquisition and analysis procedures of micro-PET, SPECT/CT using the experimental animal (mouse) for the development of imaging assessment method for the bio-drug. We examined the micro-SPECT/CT, PET imaging study using the Siemens Inveon micro-multimodality system (SPECT/CT) and micro-PET with {sup 99m}Tc-MDP, DMSA, and {sup 18}F-FDG. SPECT imaging studies using 3 types of pinhole collimators. 5-MWB collimator was used for SPECT image study. To study whole-body distribution, {sup 99m}Tc-MDP SPECT image study was performed. We obtained the fine distribution image. And the CT images was obtained to provide the anatomical information. And then these two types images are fused. To study specific organ uptake, we examined {sup 99}mTc-DMSA SPECT/CT imaging study. We also performed the PET image study using U87MG tumor bearing mice and {sup 18}F-FDG. The overnight fasting, warming and anesthesia with 2% isoflurane pretreatment enhance the tumor image through reducing the background uptake including brown fat, harderian gland and skeletal muscles. Also we got the governmental approval for use of x-ray generator for CT and radioisotopes as sealed and open source. We prepared the draft of process procedure for the experimental animal imaging facility. These research results can be utilized as a basic image study protocols and data for the image assessment of drugs including biological drug.

  20. Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular.

    Science.gov (United States)

    Izuogu, Osagie G; Alhasan, Abd A; Mellough, Carla; Collin, Joseph; Gallon, Richard; Hyslop, Jonathon; Mastrorosa, Francesco K; Ehrmann, Ingrid; Lako, Majlinda; Elliott, David J; Santibanez-Koref, Mauro; Jackson, Michael S

    2018-04-20

    Circular RNAs (circRNAs) are predominantly derived from protein coding genes, and some can act as microRNA sponges or transcriptional regulators. Changes in circRNA levels have been identified during human development which may be functionally important, but lineage-specific analyses are currently lacking. To address this, we performed RNAseq analysis of human embryonic stem (ES) cells differentiated for 90 days towards 3D laminated retina. A transcriptome-wide increase in circRNA expression, size, and exon count was observed, with circRNA levels reaching a plateau by day 45. Parallel statistical analyses, controlling for sample and locus specific effects, identified 239 circRNAs with expression changes distinct from the transcriptome-wide pattern, but these all also increased in abundance over time. Surprisingly, circRNAs derived from long non-coding RNAs (lncRNAs) were found to account for a significantly larger proportion of transcripts from their loci of origin than circRNAs from coding genes. The most abundant, circRMST:E12-E6, showed a > 100X increase during differentiation accompanied by an isoform switch, and accounts for > 99% of RMST transcripts in many adult tissues. The second most abundant, circFIRRE:E10-E5, accounts for > 98% of FIRRE transcripts in differentiating human ES cells, and is one of 39 FIRRE circRNAs, many of which include multiple unannotated exons. Our results suggest that during human ES cell differentiation, changes in circRNA levels are primarily globally controlled. They also suggest that RMST and FIRRE, genes with established roles in neurogenesis and topological organisation of chromosomal domains respectively, are processed as circular lncRNAs with only minor linear species.

  1. Effect of dietary pulse intake on established therapeutic lipid targets for cardiovascular risk reduction: a systematic review and meta-analysis of randomized controlled trials.

    Science.gov (United States)

    Ha, Vanessa; Sievenpiper, John L; de Souza, Russell J; Jayalath, Viranda H; Mirrahimi, Arash; Agarwal, Arnav; Chiavaroli, Laura; Mejia, Sonia Blanco; Sacks, Frank M; Di Buono, Marco; Bernstein, Adam M; Leiter, Lawrence A; Kris-Etherton, Penny M; Vuksan, Vladimir; Bazinet, Richard P; Josse, Robert G; Beyene, Joseph; Kendall, Cyril W C; Jenkins, David J A

    2014-05-13

    Evidence from controlled trials encourages the intake of dietary pulses (beans, chickpeas, lentils and peas) as a method of improving dyslipidemia, but heart health guidelines have stopped short of ascribing specific benefits to this type of intervention or have graded the beneficial evidence as low. We conducted a systematic review and meta-analysis of randomized controlled trials (RCTs) to assess the effect of dietary pulse intake on established therapeutic lipid targets for cardiovascular risk reduction. We searched electronic databases and bibliographies of selected trials for relevant articles published through Feb. 5, 2014. We included RCTs of at least 3 weeks' duration that compared a diet emphasizing dietary pulse intake with an isocaloric diet that did not include dietary pulses. The lipid targets investigated were low-density lipoprotein (LDL) cholesterol, apolipoprotein B and non-high-density lipoprotein (non-HDL) cholesterol. We pooled data using a random-effects model. We identified 26 RCTs (n = 1037) that satisfied the inclusion criteria. Diets emphasizing dietary pulse intake at a median dose of 130 g/d (about 1 serving daily) significantly lowered LDL cholesterol levels compared with the control diets (mean difference -0.17 mmol/L, 95% confidence interval -0.25 to -0.09 mmol/L). Treatment effects on apolipoprotein B and non-HDL cholesterol were not observed. Our findings suggest that dietary pulse intake significantly reduces LDL cholesterol levels. Trials of longer duration and higher quality are needed to verify these results. ClinicalTrials.gov, no. NCT01594567.

  2. Discrimination between stages of Alzheimer's disease with subsets of Mini-Mental State Examination items. An analysis of Consortium to Establish a Registry for Alzheimer's Disease data.

    Science.gov (United States)

    Fillenbaum, G G; Wilkinson, W E; Welsh, K A; Mohs, R C

    1994-09-01

    To identify minimal sets of Mini-Mental State Examination (MMSE) items that can distinguish normal control subjects from patients with mild Alzheimer's disease (AD), patients with mild from those with moderate AD, and those with moderate from those with severe AD. Two randomly selected equivalent half samples. Results of logistic regression analysis from data from the first half of the sample were confirmed by receiver operating characteristic curves on the second half. Memory disorders clinics at major medical centers in the United States affiliated with the Consortium to establish a Registry for Alzheimer's Disease (CERAD). White, normal control subjects (n = 412) and patients with AD (n = 621) who met CERAD criteria; nonwhite subjects (n = 165) and persons with missing data (n = 27) were excluded. Three four-item sets of MMSE items that discriminate, respectively, (1) normal controls from patients with mild AD, (2) patients with mild from those with moderate AD, and (3) patients with moderate from those with severe AD. The MMSE items discriminating normal controls from patients with mild AD were day, date, recall of apple, and recall of penny; those discriminating patients with mild from those with moderate AD were month, city, spelling world backward, and county, and those discriminating patients with moderate from those with severe AD were floor of building, repeating the word table, naming watch, and folding paper in half. Performance on the first two four-item sets was comparable with that of the full MMSE; the third set distinguished patients with moderate from those with severe AD better than chance. A minimum set of MMSE items can effectively discriminate normal controls from patients with mild AD and between successive levels of severity of AD. Data apply only to white patients with AD. Performance in minorities, more heterogeneous groups, or normal subjects with questionable cognitive status has not been assessed.

  3. Prognostic significance of smoking in addition to established risk factors in patients with Dukes B and C colorectal cancer: a retrospective analysis.

    Science.gov (United States)

    Diamantis, N; Xynos, I D; Amptulah, S; Karadima, M; Skopelitis, H; Tsavaris, N

    2013-01-01

    To investigate the prognostic significance of smoking in addition to established risk factors in patients with Dukes stage B and C colorectal cancer (CRC). 291 consecutive non-selected CRC patients were studied retrospectively. Twenty-three variables were examined using a regression statistical model to identify relevant prognostic factors related to disease free survival (DFS) and overall survival (OS). On multivariate analysis DFS was found to be negatively affected in patients with a smoking history of ≤10 pack-years vs. non-smokers (p<0.016). Additionally, performance status (PS)<90 (p<0.001), Dukes stage C (p<0.001) and elevated tumor markers (p<0.001) at the time of diagnosis were found to adversely affect DFS. Smoking also had a significant association with relapse. Patients with a smoking history of ≤10 pack-years had 2.45 (p<0.018) higher risk of recurrence compared to patients with no smoking history. OS was influenced by Karnofsky performance status (PS), Dukes stage, and elevated tumor markers. In particular patients with PS< 90 had a 4.69-fold higher risk of death (p<0.001) than patients with better PS. Stage C disease was associated with 2.27-fold higher risk of death (p<0.001) than stage B disease, and patients with elevated tumor markers at the time of diagnosis had 2.74-fold higher risk of death (p<0.014) when compared to those whose tumor markers were normal at presentation. Our study associates smoking and relapse incidence in non-clinical- trial CRC patients and reiterates the prognostic significance of PS, stage and tumor markers at the time of diagnosis.

  4. Taxonomic research priorities for the conservation of the South African flora

    Directory of Open Access Journals (Sweden)

    Lize von Staden

    2013-04-01

    Full Text Available Taxonomic revisions, monographs and floras are the most important, and often the only source of data for assessing the extinction risk of plants, with recent revisions contributing to more accurate assessments. The recently completed Red List of South African plants involved an overview of the taxonomic literature pertaining to the South African flora, providing an opportunity to identify critical gaps in taxonomic coverage. In this study we identified taxonomic research priorities for effective conservation of South African plants. Priorities were identified at genus level, according to time since last revision, level of endemism, collecting effort, proportion of taxa included in revisions, and specimen identification confidence. Although the results indicate that 62% of the flora has been recently revised, revisionary taxonomic output has declined drastically, particularly in the past 10 years. This decline is a result of a decrease in revisionary productivity per taxonomist and not a result of a decline in the number of working taxonomists. The family Aizoaceae is the top priority for taxonomic research with 55% of taxa in need of revision, followed by Hyacinthaceae with 34% of taxa not yet revised. Ericaceae, Euphorbiaceae, Rutaceae, Malvaceae, Asteraceae and Acanthaceae are also priorities with over 30% of taxa last revised before 1970. We recommend the reinstatement of the Flora of Southern Africa project in an online format in order to centralise South Africa's existing taxonomic information and reinvigorate revisionary taxonomic study. This project will allow South Africa to fulfil its commitments to the Convention on Biodiversity by achieving Target 1 of the Global Strategy for Plant Conservation.

  5. The nutty world of hazel names - a crtitical taxonomic checklist of the genus Corylus (Betulaceae)

    OpenAIRE

    Holstein, Norbert; Tamer, Sarah el; Weigend, Maximilian

    2018-01-01

    Hazelnuts (Corylus L.) are the source of one of the globally most important nut crops. Despite their economic and cultural importance, taxonomic knowledge is poor, even the number of species is equivocal. Weak morphological differentiation, the inconsistent taxonomic treatment of horticultural selections and cultivars, and uncritical regional treatments generated a multitude of names. The situation is further complicated by an ancient history of use (at least 10 400 years), trade (at least 40...

  6. Human impacts on functional and taxonomic homogenization of plateau fish assemblages in Yunnan, China

    Directory of Open Access Journals (Sweden)

    Guohuan Su

    2015-07-01

    Full Text Available Human activities and the consequent extinctions of native species and invasions of non-native species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. However, much of the research effort to date has focused on changes in taxonomic dissimilarity (i.e. accounting for species composition whether assessments of functional dissimilarity (i.e. accounting for the diversity of biological traits are much more scarce, despite revealing important complimentary information by accounting for changes in the diversity of biological traits. Here, we assess the temporal (1950s against 2000s changes in both taxonomic and functional dissimilarities of freshwater fish assemblages across lakes from the Yunnan Plateau in China. The Jaccard index to quantify the changes in both taxonomic and functional dissimilarity. We then partitioned dissimilarity to extract its turnover component and measured the changes in the contribution of turnover to dissimilarity. We found that functional and taxonomic homogenization occurred simultaneously. However, patterns between these two processes differed for some lakes. Taxonomic and functional homogenizations were stronger when the historical level of taxonomic dissimilarity among assemblages was high. The impact of extinctions of native species and invasions of non-native species on homogenization was otherwise complex to disentangle with no significant effect of any of the studied environmental factors. In agreement with other studies, our study proved that change in taxonomic dissimilarity cannot be used to predict changes in functional dissimilarity and, as an indicator of ecosystem functioning, functional dissimilarity should be used together with taxonomic dissimilarity to attain a more holistic understanding of human impacts on natural ecosystems.

  7. MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

    Science.gov (United States)

    Konwar, Kishori M; Hanson, Niels W; Bhatia, Maya P; Kim, Dongjae; Wu, Shang-Ju; Hahn, Aria S; Morgan-Lang, Connor; Cheung, Hiu Kan; Hallam, Steven J

    2015-10-15

    Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. shallam@mail.ubc.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  8. Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov.

    Science.gov (United States)

    Landwehr, Wiebke; Kämpfer, Peter; Glaeser, Stefanie P; Rückert, Christian; Kalinowski, Jörn; Blom, Jochen; Goesmann, Alexander; Mack, Matthias; Schumann, Peter; Atasayar, Ewelina; Hahnke, Richard L; Rohde, Manfred; Martin, Karin; Stadler, Marc; Wink, Joachim

    2018-01-01

    Roseoflavin is the only known riboflavin (vitamin B2) analog with antibiotic properties. It is actively taken up by many micro-organisms and targets flavinmononucleotide riboswitches and flavoproteins. It is described as the product of the tentatively named 'Streptomyces davawensis' JCM 4913. Taxonomic analysis of this strain with a polyphasic approach showed that it is very closely related to Streptomyces cinnabarinus (DSM 40467). The two Streptomyces isolates were obtained from different geographical locations (the Philippines and the Kamchatka Peninsula, respectively), their genomes have been sequenced and the question was whether or not the two isolates were representatives of the same species. As we also worked with another isolate of Streptomyces cinnabarinus JS 360, the producer of the cinnabaramides, we wanted to clarify the taxonomic position of the three isolates by using a polyphasic approach. After analysis of the 16S rRNA gene sequence, we found in total 23 species of the genus Streptomyces that showed a similarity higher than 98.5 % to the three strains. We showed that 'S. davawensis' JCM 4913 and S. cinnabarinus DSM 40467 were very closely related but belong to two different species. Hence, we validate 'S. davawensis' as Streptomyces davaonensis sp. nov. with the type strain JCM 4913 T (=DSM 101723 T ). In addition, the cinnabaramide producer can be clearly differentiated from S. davaonensis and this isolate is described as Streptomyces cinnabarigriseus sp. nov. with strain JS360 T (=NCCB 100590 T =DSM 101724 T ) as the type strain.

  9. Avibase – a database system for managing and organizing taxonomic concepts

    Directory of Open Access Journals (Sweden)

    Denis Lepage

    2014-06-01

    Full Text Available Scientific names of biological entities offer an imperfect resolution of the concepts that they are intended to represent. Often they are labels applied to entities ranging from entire populations to individual specimens representing those populations, even though such names only unambiguously identify the type specimen to which they were originally attached. Thus the real-life referents of names are constantly changing as biological circumscriptions are redefined and thereby alter the sets of individuals bearing those names. This problem is compounded by other characteristics of names that make them ambiguous identifiers of biological concepts, including emendations, homonymy and synonymy. Taxonomic concepts have been proposed as a way to address issues related to scientific names, but they have yet to receive broad recognition or implementation. Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage. We present the on-line database Avibase as one possible approach to organizing taxonomic concepts. Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years. The use of taxonomic concepts in place of scientific names, coupled with efficient resolution services, is a major step toward addressing some of the main deficiencies in the current practices of scientific name dissemination and use.

  10. Establishing software quality assurance

    International Nuclear Information System (INIS)

    Malsbury, J.

    1983-01-01

    This paper is concerned with four questions about establishing software QA: What is software QA. Why have software QA. What is the role of software QA. What is necessary to ensure the success of software QA

  11. Blood Establishment Registration Database

    Data.gov (United States)

    U.S. Department of Health & Human Services — This application provides information for active, inactive, and pre-registered firms. Query options are by FEI, Applicant Name, Establishment Name, Other Names,...

  12. The concentration of 137Cs and stable Cs in zooplankton in the western North Pacific in relation to their taxonomic composition

    International Nuclear Information System (INIS)

    Kaeriyama, Hideki; Watabe, Teruhisa; Kusakabe, Masashi

    2008-01-01

    The objective of this study is to obtain information on the background level of 137 Cs in zooplankton in the waters close to Rokkasho-mura in Aomori Prefecture, Japan, where a large-scale project has been progressively promoted to establish the nuclear fuel cycle. Prior to the full-scale operation of the spent nuclear fuel reprocessing plant, zooplankton samples were collected in May and October 2005, June 2006, and June 2007 from the surface water (0-5 m depth). The samples were analyzed to determine the concentrations of 137 Cs and stable Cs in relation to taxonomic composition. The numerical abundance of the plankton varied from 253 to 1514 inds. m -3 . Taxonomic composition differed between the two sampling periods. Although copepods formed the most abundant taxonomic group during both seasons, gelatinous plankton (chaetognaths, siphonophores, appendicularians and doliolids) were more abundant in October 2005 than in June 2006 and June 2007. The concentration of 137 Cs in zooplankton varied from 11 to 24 mBq kg-WW -1 . At the same station, the 137 Cs concentration in zooplankton in October 2005 was almost twice as much as that in June 2006, although the concentration of 137 Cs in seawater did not show a difference. The concentration of stable Cs was measured for each taxonomic group: that in gelatinous zooplankton (chaetognaths) was higher than that in crustacean zooplankton (copepods, euphausiids and amphipods). These results suggest that the concentration of 137 Cs in zooplankton is affected by the occurrence of gelatinous zooplankton. (author)

  13. Establishment of prairies

    International Nuclear Information System (INIS)

    Lotero Cadavid, J.

    2001-01-01

    Are analyzed the establishment of prairies, such as the selection of the species, the factors of the environment, the impact in the establishment and forage production and its relation to the soil, the precipitation, the temperature, the light and the biotic factors. It is indicated that the selection of the species to settle down, is directly related with the climate and the soil and they group to be tolerant to drought, tolerant to flood soils, tolerant to humid soils, tolerant to soils very acids, moderately acids and saline. It is noticed that a bad establishment of the grasses can be due to the bad quality of the seed, a temperature and unfavorable humidity can cause low germination; equally seeds planted very deeply in heavy soils with excess of humidity. Considerations are made about the establishment and growth of the prairies in connection with the germination, cultures, sowing density and sowing on time, as well as for the soil preparation, the sowing in terrestrial mechanic and non mechanic and the use of cultivations forms of low cost and fertilization systems; equally the establishment of leguminous in mixture with gramineous, the renovation of prairies and the establishment of pastures

  14. Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

    Science.gov (United States)

    He, Yan; Caporaso, J Gregory; Jiang, Xiao-Tao; Sheng, Hua-Fang; Huse, Susan M; Rideout, Jai Ram; Edgar, Robert C; Kopylova, Evguenia; Walters, William A; Knight, Rob; Zhou, Hong-Wei

    2015-01-01

    The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.

  15. Taxonomic Identity, Geographic Distribution, and Commercial Exploitation of the Culinary-Medicinal Mushroom Pleurotus nebrodensis (Basidiomycetes).

    Science.gov (United States)

    Venturella, Giuseppe; Zervakis, Georgios I; Polemis, Elias; Gargano, Maria Letizia

    2016-01-01

    An updated overview of the outcome of studies conducted on the culinary-medicinal mushroom Pleurotus nebrodensis is presented by placing emphasis on the clarification of the taxonomic identity of P. nebrodensis and other related taxa possessing entirely white to cream basidiomes, which grow in association with different plants of the family Apiaceae. Cultivation techniques, quality of the product sold and sales price, as well as nutritional and medicinal aspects are discussed. Taking also into consideration the high economic importance of P. nebrodensis, it is essential to proceed with the verification of the commercial strains currently available in the international market under the name of "P. nebrodensis" since it is very probable that many (or most) of them do not represent the real P. nebrodensis. TO confirm this hypothesis, an in silico analysis was conducted on a large of number of ITS1-5.8S-ITS2 rRNA sequences deposited in the National Center for Biotechnology Information database under the name P. nebrodensis. Results demonstrated that all "P nebrodensis" material examined from China (plus several sequences of no reported origin) corresponded to P. eryngii subsp. tuoliensis, with only 2 exceptions, which were grouped within P. eryngii sensu stricto. The real P. nebrodensis biological material from Italy and Greece is certified and is available upon request by the authors at the University of Palermo and the Agricultural University of Athens.

  16. Taxonomic studies of centric diatoms (Diatomeae: unusual nanoplanktonic forms and new records for Brazil

    Directory of Open Access Journals (Sweden)

    Kaoli Pereira Cavalcante

    2013-06-01

    Full Text Available There have been few taxonomic studies of centric diatoms in lotic freshwater environments in Brazil, especially in terms of those including nanoplanktonic forms, which are often neglected in studies of local floras, because of their small size or confusing taxonomy. This is the first study focusing on centric diatoms in the flora of the state of Bahia, in northeastern Brazil. Plankton and periphyton attached to Eichornia crassipes were collected in the winter of 2009 in the Cachoeira River. The diatoms were analyzed and described under light and electron microscopies. Seventeen infrageneric taxa were identified. Cyclotella was represented by five taxa, and concerning of similarities between diacritical features of species in this genus, their descriptions were thoroughly detailed. This was the first time that Cyclotella atomus var. marina, previously recorded only in coastal areas of Japan and Korea, has been documented in a river in South America. We also identified two diatom taxa previously unrecorded in the flora of Brazil: C. cryptica and C. meduanae. Finally, we present a detailed light, transmission and scanning electron microscopy analysis of Skeletonema potamos, a diatom rarely found in the Brazilian literature.

  17. Taxamatch, an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases

    Science.gov (United States)

    Rees, Tony

    2014-01-01

    Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical. PMID:25247892

  18. Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil.

    Science.gov (United States)

    Pacchioni, Ralfo G; Carvalho, Fabíola M; Thompson, Claudia E; Faustino, André L F; Nicolini, Fernanda; Pereira, Tatiana S; Silva, Rita C B; Cantão, Mauricio E; Gerber, Alexandra; Vasconcelos, Ana T R; Agnez-Lima, Lucymara F

    2014-06-01

    Although microorganisms play crucial roles in ecosystems, metagenomic analyses of soil samples are quite scarce, especially in the Southern Hemisphere. In this work, the microbial diversity of soil samples from an Atlantic Forest and Caatinga was analyzed using a metagenomic approach. Proteobacteria and Actinobacteria were the dominant phyla in both samples. Among which, a significant proportion of stress-resistant bacteria associated to organic matter degradation was found. Sequences related to metabolism of amino acids, nitrogen, and DNA and stress resistance were more frequent in Caatinga soil, while the forest sample showed the highest occurrence of hits annotated in phosphorous metabolism, defense mechanisms, and aromatic compound degradation subsystems. The principal component analysis (PCA) showed that our samples are close to the desert metagenomes in relation to taxonomy, but are more similar to rhizosphere microbiota in relation to the functional profiles. The data indicate that soil characteristics affect the taxonomic and functional distribution; these characteristics include low nutrient content, high drainage (both are sandy soils), vegetation, and exposure to stress. In both samples, a rapid turnover of organic matter with low greenhouse gas emission was suggested by the functional profiles obtained, reinforcing the importance of preserving natural areas. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  19. An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods.

    Science.gov (United States)

    Aznar-Cormano, L; Brisset, J; Chan, T-Y; Corbari, L; Puillandre, N; Utge, J; Zbinden, M; Zuccon, D; Samadi, S

    2015-04-01

    During the past decade, a large number of multi-gene analyses aimed at resolving the phylogenetic relationships within Decapoda. However relationships among families, and even among sub-families, remain poorly defined. Most analyses used an incomplete and opportunistic sampling of species, but also an incomplete and opportunistic gene selection among those available for Decapoda. Here we test in the Caridea if improving the taxonomic coverage following the hierarchical scheme of the classification, as it is currently accepted, provides a better phylogenetic resolution for the inter-families relationships. The rich collections of the Muséum National d'Histoire Naturelle de Paris are used for sampling as far as possible at least two species of two different genera for each family or subfamily. All potential markers are tested over this sampling. For some coding genes the amplification success varies greatly among taxa and the phylogenetic signal is highly saturated. This result probably explains the taxon-heterogeneity among previously published studies. The analysis is thus restricted to the genes homogeneously amplified over the whole sampling. Thanks to the taxonomic sampling scheme the monophyly of most families is confirmed. However the genes commonly used in Decapoda appear non-adapted for clarifying inter-families relationships, which remain poorly resolved. Genome-wide analyses, like transcriptome-based exon capture facilitated by the new generation sequencing methods might provide a sounder approach to resolve deep and rapid radiations like the Caridea.

  20. Palyno-morphological characteristics of gymnosperm flora of pakistan and its taxonomic implications with LM and SEM methods.

    Science.gov (United States)

    Khan, Raees; Ul Abidin, Sheikh Zain; Ahmad, Mushtaq; Zafar, Muhammad; Liu, Jie; Amina, Hafiza

    2018-01-01

    The present study is intended to assess gymnosperms pollen flora of Pakistan using Light Microscope (LM) and Scanning Electron Microscopy (SEM) for its taxonomic significance in identification of gymnosperms. Pollens of 35 gymnosperm species (12 genera and five families) were collected from its various distributional sites of gymnosperms in Pakistan. LM and SEM were used to investigate different palyno-morphological characteristics. Five pollen types (i.e., Inaperturate, Monolete, Monoporate, Vesiculate-bisaccate and Polyplicate) were observed. Six In equatorial view seven types of pollens were observed, in which ten species were sub-angular, nine species were Traingular, six species were Perprolate, three species were Rhomboidal, three species were semi-angular, two species were rectangular and two species were prolate. While five types of pollen were observed in polar view, in which ten species were Spheroidal, nine species were Angular, eight were Interlobate, six species were Circular, two species were Elliptic. Eighteen species has rugulate and 17 species has faveolate ornamentation. Eighteen species has verrucate and 17 have gemmate type sculpturing. The data was analysed through cluster analysis. The study showed that these palyno-morphological features have significance value in classification and identification of gymnosperms. Based on these different palyno-morphological features, a taxonomic key was proposed for the accurate and fast identifications of gymnosperms from Pakistan. © 2017 Wiley Periodicals, Inc.

  1. Taxonomic and functional patterns of macrobenthic communities on a high-Arctic shelf: A case study from the Laptev Sea

    Science.gov (United States)

    Kokarev, V. N.; Vedenin, A. A.; Basin, A. B.; Azovsky, A. I.

    2017-11-01

    The studies of functional structure of high-Arctic Ecosystems are scarce. We used data on benthic macrofauna from 500-km latitudinal transect in the eastern Laptev Sea, from the Lena delta to the continental shelf break, to describe spatial patterns in species composition, taxonomic and functional structure in relation to environmental factors. Both taxonomy-based approach and Biological Trait analysis yielded similar results and showed general depth-related gradient in benthic diversity and composition. This congruence between taxonomical and functional dimensions of community organization suggests that the same environmental factors (primarily riverine input and regime of sedimentation) have similar effect on both community structure and functioning. BTA also revealed a distinct functional structure of stations situated at the Eastern Lena valley, with dominance of motile, burrowing sub-surface deposit-feeders and absence of sedentary tube-dwelling forms. The overall spatial distribution of benthic assemblages corresponds well to that described there in preceding decades, evidencing the long-term stability of bottom ecosystem. Strong linear relationship between species and traits diversity, however, indicates low functional redundancy, which potentially makes the ecosystem susceptible to a species loss or structural shifts.

  2. The Taxonomic and Phylogenetic Affinities of Bunopithecus sericus, a Fossil Hylobatid from the Pleistocene of China

    Science.gov (United States)

    Ortiz, Alejandra; Pilbrow, Varsha; Villamil, Catalina I.; Korsgaard, Jessica G.; Bailey, Shara E.; Harrison, Terry

    2015-01-01

    Fossil hylobatids are rare, but are known from late Miocene and Pleistocene sites throughout East Asia. The best-known fossil hylobatid from the Pleistocene of China is a left mandibular fragment with M2-3 (AMNH 18534), recovered from a pit deposit near the village of Yanjinggou in Wanzhou District, Chongqing Province. Matthew and Granger described this specimen in 1923 as a new genus and species, Bunopithecus sericus. Establishing the age of Bunopithecus has proved difficult because the Yanjinggou collection represents a mixed fauna of different ages, but it likely comes from early or middle Pleistocene deposits. Although the Bunopithecus specimen has featured prominently in discussions of hylobatid evolution and nomenclature, its systematic status has never been satisfactorily resolved. The present study reexamines the taxonomic and phylogenetic relationships of Bunopithecus by carrying out a detailed comparative morphometric study of its lower molars in relation to a large sample of modern hylobatids. Our results show that differences in M2 and M3 discriminate extant hylobatids fairly well, at least at the generic level, and that AMNH 18534 is not attributable to Hylobates, Nomascus or Symphalangus. Support for a close relationship between Bunopithecus and Hoolock is more equivocal. In most multivariate analyses, Bunopithecus presents a unique morphological pattern that falls outside the range of variation of any hylobatid taxon, although its distance from the cluster represented by extant hoolocks is relatively small. Our results support the generic distinction of Bunopithecus, which most likely represents an extinct crown hylobatid, and one that may possibly represent the sister taxon to Hoolock. PMID:26154175

  3. A neurocomputational account of taxonomic responding and fast mapping in early word learning.

    Science.gov (United States)

    Mayor, Julien; Plunkett, Kim

    2010-01-01

    We present a neurocomputational model with self-organizing maps that accounts for the emergence of taxonomic responding and fast mapping in early word learning, as well as a rapid increase in the rate of acquisition of words observed in late infancy. The quality and efficiency of generalization of word-object associations is directly related to the quality of prelexical, categorical representations in the model. We show how synaptogenesis supports coherent generalization of word-object associations and show that later synaptic pruning minimizes metabolic costs without being detrimental to word learning. The role played by joint-attentional activities is identified in the model, both at the level of selecting efficient cross-modal synapses and at the behavioral level, by accelerating and refining overall vocabulary acquisition. The model can account for the qualitative shift in the way infants use words, from an associative to a referential-like use, for the pattern of overextension errors in production and comprehension observed during early childhood and typicality effects observed in lexical development. Interesting by-products of the model include a potential explanation of the shift from prototype to exemplar-based effects reported for adult category formation, an account of mispronunciation effects in early lexical development, and extendability to include accounts of individual differences in lexical development and specific disorders such as Williams syndrome. The model demonstrates how an established constraint on lexical learning, which has often been regarded as domain-specific, can emerge from domain-general learning principles that are simultaneously biologically, psychologically, and socially plausible.

  4. Self-organizing maps: A tool to ascertain taxonomic relatedness ...

    Indian Academy of Sciences (India)

    MADHU

    what is known as numerical taxonomy (Garrity et al. 2001). ... Curvilinear component analysis; self-organizing maps; principal component analysis. Abbreviations used: ... This tool undergoes unsupervised learning and is particularly useful in ...

  5. The Analysis of the Relationship between Organizational Structure and Information Technology (IT): And the Barriers to Its Establishment at the University of Isfahan from the Faculty Member's Viewpoints

    Science.gov (United States)

    Peyman, Yarmohammadzadeh; Mohsen, Allammeh Sayyed; Hassan, Ghalavandi; Aboulghassim, Farhang; Zaman, Ajdari

    2011-01-01

    The purpose of the present study is to investigate the relationship between organizational structure between IT and the barriers to its establishment in University of Isfahan from faculty member's viewpoints in 2007-2008. The questionnaires were prepared and examined based on the organization dimensions of organizational structures (formality,…

  6. Sub-Saharan Botanical Collections:Taxonomic research and impediments

    OpenAIRE

    Demissew, Sebsebe; Beentje, Henk; Cheek, Martin; Friis, Ib

    2017-01-01

    Many historical specimens from sub-Saharan Africa are only found in European herbaria, but a higher number of newer specimens than widely assumed are kept in African herbaria, with a concentration in eastern and southern parts of the continent. Many of these herbaria were initiated in connection with independence of former European colonies in Africa, fewer were built on well-established herbaria from the colonial period. There are many gaps in collecting coverage, not least with regard to ar...

  7. Taxonomically restricted genes are associated with the evolution of sociality in the honey bee

    Directory of Open Access Journals (Sweden)

    Tsutsui Neil D

    2011-03-01

    Full Text Available Abstract Background Studies have shown that taxonomically restricted genes are significant in number and important for the evolution of lineage specific traits. Social insects have gained many novel morphological and behavioral traits relative to their solitary ancestors. The task repertoire of an advanced social insect, for example, can be 40-50 tasks, about twice that of a solitary wasp or bee. The genetic basis of this expansion in behavioral repertoire is still poorly understood, and a role for taxonomically restricted genes has not been explored at the whole genome level. Results Here we present comparative genomics results suggesting that taxonomically restricted genes may have played an important role in generating the expansion of behavioral repertoire associated with the evolution of eusociality. First, we show that the current honey bee official gene set contains about 700 taxonomically restricted genes. These are split between orphans, genes found only in the Hymenoptera, and genes found only in insects. Few of the orphans or genes restricted to the Hymenoptera have been the focus of experimental work, but several of those that have are associated with novel eusocial traits or traits thought to have changed radically as a consequence of eusociality. Second, we predicted that if taxonomically restricted genes are important for generating novel eusocial traits, then they should be expressed with greater frequency in workers relative to the queen, as the workers exhibit most of the novel behavior of the honey bee relative to their solitary ancestors. We found support for this prediction. Twice as many taxonomically restricted genes were found amongst the genes with higher expression in workers compared to those with higher expression in queens. Finally, we compiled an extensive list of candidate taxonomically restricted genes involved in eusocial evolution by analyzing several caste specific gene expression data sets. Conclusions This

  8. Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act.

    Science.gov (United States)

    Haig, Susan M; Beever, Erik A; Chambers, Steven M; Draheim, Hope M; Dugger, Bruce D; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B; Kesler, Dylan C; Knaus, Brian J; Lopes, Iara F; Loschl, Pete; Mullins, Thomas D; Sheffield, Lisa M

    2006-12-01

    The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

  9. Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias.

    Science.gov (United States)

    Clarke, Laurence J; Soubrier, Julien; Weyrich, Laura S; Cooper, Alan

    2014-11-01

    Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico 90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR-amplified the blend using five primer sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers. © 2014 John Wiley & Sons Ltd.

  10. Korean deaf adolescents' recognition of written words for taxonomic categories of different levels.

    Science.gov (United States)

    Li, Degao; Yi, Kwangoh; Kim, Jung Yeon

    2011-04-01

    Deaf college students seem to have relatively stronger associations from words for taxonomic categories of basic (e.g., snake) to those of super-ordinate (e.g., reptiles) level than vice versa compared with hearing students in word association (Marschark, Convertino, McEvoy & Masteller, 2004). In deciding whether two sequentially presented words for taxonomic categories of different levels are conceptually related, deaf adolescents might therefore have a poorer performance when they see a category name before than when they see it after one of the corresponding exemplar words. Deaf Korean adolescents were found to recognize words for taxonomic categories of super-ordinate level with lower efficiencies than those of basic level. Their accuracy seemed to reflect a reversed typicality effect when they decided that first-presented words for taxonomic categories of basic level were conceptually related to second-presented words for those of super-ordinate level. It was argued that deaf Korean adolescents went through a temporary stage of having iconic representations of several exemplars of the category aroused in working memory before the abstract semantic representation was fully activated when they saw the word for a taxonomic category of super-ordinate level. © 2010 The Authors. Scandinavian Journal of Psychology © 2010 The Scandinavian Psychological Associations.

  11. Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae

    Directory of Open Access Journals (Sweden)

    Priyanka Mishra

    2016-12-01

    outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Conclusion The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.

  12. Establishing a University Foundation.

    Science.gov (United States)

    Lemish, Donald L.

    A handbook on how to establish a university foundation is presented. It presupposes that a foundation will be used as the umbrella organization for receiving all private gifts, restricted and unrestricted, for the benefit of a public college or university; and hence it chiefly addresses readers from public colleges and universities. Information is…

  13. Skilled delivery service utilization and its association with the establishment of Women’s Health Development Army in Yeky district, South West Ethiopia: a multilevel analysis

    OpenAIRE

    Negero, Melese Girmaye; Mitike, Yifru Berhan; Worku, Abebaw Gebeyehu; Abota, Tafesse Lamaro

    2018-01-01

    Background Because of the unacceptably high maternal and perinatal morbidity and mortality, the government of Ethiopia has established health extension program with a community-based network involving health extension workers (HEWs) and a community level women organization which is known as “Women’s Health Development Army” (WHDA). Currently, the HEWs and WHDA network is the approach preferred by the government to register pregnant women and encourage them to link in the healthcare system. Ho...

  14. Trichome morphology in Teucrium L. (Labiatae. A taxonomic review

    Directory of Open Access Journals (Sweden)

    Navarro, Teresa

    1999-12-01

    Full Text Available The micromorphology of trichomes of 56 Teucrium L. species belonging to the 9 sections of the genus in the Mediterranean área was surveyed by scanning electrón microscopy (SEM of leaves, calyx, corolla and nutlets. 25 trichome types are described, 12 of them are new. Thin walled hairs are the exclusive type found in the corolla and are the most widespread type on the abaxial side of the leaves. Subsessile glandular hairs, 2-4-celled, are found on the nutlet and leaves of the semi-shrubby and paleoendemic species. The presence of short or elongated, generally adpressed simple thick-walled slighüy conical hairs provides an additional character to clarify the boundaries between sect. Chamedrys (Mill. Schreb, and sect. Polium (Mill. Schreb. Branched non-glandular hairs are confined to sect. Polium subsect Polium, except for the rare branched hair conical and thick-walled type found in Teucrium barbarum Jahand. & Maire (sect. Chamaedrys and T. heterophyllum L`Hér. from sect. Teucrium. This last section is well defined by the absence of simple slighüy conical thick-walled hairs and the glandular hairs in the corolla. Sect. Teucriopsis Benth, is of particular interest for the exclusive presence of branched and peltate glandular hairs on the nutlets surface. Sect. Chamedrys is a homogeneous group, distinguished from the other sections by an indumentum formed only by trichomes types evolved from the simple slighüy conical thick-walled hairs. This section overlaps, in the presence of glandular sub-sessile hair on the nutlets surface, with sects. Isotriodon Boiss, and sect. Polium subsect. Rotundifolia Cohén ex Valdés Berm. & Sánchez Crespo. The trichomes type of the calyx teeth, abaxial side of the leaf and latero-posterior corolla lobes can be used as a distinctive taxonomic character at specific and infra-specific level. This study supports Bentham's delimitaüon of sections with the addiüons subequently made by Boissier.La micromorfología de

  15. More than just orphans: are taxonomically-restricted genes important in evolution?

    Science.gov (United States)

    Khalturin, Konstantin; Hemmrich, Georg; Fraune, Sebastian; Augustin, René; Bosch, Thomas C G

    2009-09-01

    Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.

  16. Does taxonomic diversity in indicator groups influence their effectiveness in identifying priority areas for species conservation?

    DEFF Research Database (Denmark)

    Bladt, Jesper Stentoft; Larsen, Frank Wugt; Rahbek, Carsten

    2008-01-01

    The identification of priority areas for biodiversity conservation is a cornerstone of systematic conservation planning. However, biodiversity, or even the distribution of all species, cannot be directly quantified, due to the inherent complexity of natural systems. Species indicator groups may...... serve as important tools for the identification of priority areas for conservation. Yet, it is unclear which factors make certain indicator groups perform better than others. In this study, using data on the Danish distribution of 847 species of plants, vertebrates and insects, we assessed whether...... the taxonomic diversity in species indicator groups influence their effectiveness in the identification of priority areas for species conservation. We tested whether indicator groups comprising a higher taxonomic diversity (i.e. indicator groups consisting of species from many different taxonomic groups...

  17. Identification and conservation application of signal, noise, and taxonomic effects in diversity patterns

    Directory of Open Access Journals (Sweden)

    Fleishman, E.

    2005-01-01

    Full Text Available Ongoing research on butterflies and birds in the Great Basin has identified biogeographic patterns while elucidating how dynamic measures of diversity (species richness and turnover affect inferences for conservation planning and adaptive management. Nested subsets analyses suggested that processes influencing predictability of assemblage composition differ among taxonomic groups, and the relative importance of those processes may vary spatially within a taxonomic group. There may be a time lag between deterministic environmental changes and a detectable faunal response, even for taxonomic groups that are known to be sensitive to changes in climate and land cover. Measures of beta diversity were sensitive to correlations between sampling resolution and local environmental heterogeneity. Temporal and spatial variation in species composition indicated that spatially extensive sampling is more effective for drawing inferences about biodiversity responses to environmental change than intensive sampling at relatively few, smaller sites.

  18. Examination of taxonomic uncertainties surrounding Brucella abortus bv. 7 by phenotypic and molecular approaches.

    Science.gov (United States)

    Garin-Bastuji, Bruno; Mick, Virginie; Le Carrou, Gilles; Allix, Sebastien; Perrett, Lorraine L; Dawson, Claire E; Groussaud, Pauline; Stubberfield, Emma J; Koylass, Mark; Whatmore, Adrian M

    2014-03-01

    Brucella taxonomy is perpetually being reshuffled, at both the species and intraspecies levels. Biovar 7 of Brucella abortus was suspended from the Approved Lists of Bacterial Names Brucella classification in 1988, because of unpublished evidence that the reference strain 63/75 was a mixture of B. abortus biovars 3 and 5. To formally clarify the situation, all isolates previously identified as B. abortus bv. 7 in the AHVLA and ANSES strain collections were characterized by classical microbiological and multiple molecular approaches. Among the 14 investigated strains, including strain 63/75, only four strains, isolated in Kenya, Turkey, and Mongolia, were pure and showed a phenotypic profile in agreement with the former biovar 7, particularly agglutination with both anti-A/anti-M monospecific sera. These results were strengthened by molecular strategies. Indeed, genus- and species-specific methods allowed confirmation that the four pure strains belonged to the B. abortus species. The combination of most approaches excluded their affiliation with the recognized biovars (biovars 1 to 6 and 9), while some suggested that they were close to biovar 3.These assays were complemented by phylogenetic and/or epidemiological methods, such as multilocus sequence analysis (MLSA) and variable-number tandem repeat (VNTR) analysis. The results of this polyphasic investigation allow us to propose the reintroduction of biovar 7 into the Brucella classification, with at least three representative strains. Interestingly, the Kenyan strain, sharing the same biovar 7 phenotype, was genetically divergent from other three isolates. These discrepancies illustrate the complexity of Brucella taxonomy. This study suggests that worldwide collections could include strains misidentified as B. abortus bv. 7, and it highlights the need to verify their real taxonomic position.

  19. Re-visiting phylogenetic and taxonomic relationships in the genus Saga (Insecta: Orthoptera.

    Directory of Open Access Journals (Sweden)

    Balázs Kolics

    Full Text Available Twelve of the 13 bushcricket species of the Saga genus are bisexuals and diploids, except the parthenogenetic and tetraploid bush cricket, Saga pedo. Despite a continuous research effort stretching through the 1900s, the taxonomic relationships of the Saga species are still disputed. In this study, our primary aim was to reveal natural relationships of the European Saga species and three of their Asian relatives, with special attention to the problematic taxonomy of two subspecies: S. campbelli campbelli and S. c. gracilis. Following a phylogenetic analysis of eight species, a comprehensive study was carried out on the above three taxa by using acoustic and morphometric approaches in parallel. Our phylogenetic data showed that European Saga species evolved from a monophyletic lineage. The geographical transitional species S. cappadocica was positioned between European and Asian lineages supporting the idea that the European Saga lineage originated phylogeographically from the Asian clade. The above results showed better agreement with the morphological data than with earlier ones based either on karyology or acoustic information only. After reviewing our data, we concluded that Saga pedo has most likely evolved from S. c. gracilis and not from S. rammei or S. ephippigera, as proposed by earlier studies. S. c. gracilis shares the same ITS2 haplotype with S. pedo, indicating that the latter could have evolved from populations of the former, probably through whole genome duplication. Based on acoustic and morphometric differences, we propose to elevate the two subspecies, S. campbelli campbelli and S. c. gracilis, to species level status, as Saga gracilis Kis 1962, and Saga campbelli Uvarov 1921. The present work sets the stage for future genetic and experimental investigations of Saginae and highlights the need for additional comprehensive analysis involving more Asian Saga species.

  20. Re-visiting phylogenetic and taxonomic relationships in the genus Saga (Insecta: Orthoptera).

    Science.gov (United States)

    Kolics, Balázs; Ács, Zoltán; Chobanov, Dragan Petrov; Orci, Kirill Márk; Qiang, Lo Shun; Kovács, Balázs; Kondorosy, Előd; Decsi, Kincső; Taller, János; Specziár, András; Orbán, László; Müller, Tamás

    2012-01-01

    Twelve of the 13 bushcricket species of the Saga genus are bisexuals and diploids, except the parthenogenetic and tetraploid bush cricket, Saga pedo. Despite a continuous research effort stretching through the 1900s, the taxonomic relationships of the Saga species are still disputed. In this study, our primary aim was to reveal natural relationships of the European Saga species and three of their Asian relatives, with special attention to the problematic taxonomy of two subspecies: S. campbelli campbelli and S. c. gracilis. Following a phylogenetic analysis of eight species, a comprehensive study was carried out on the above three taxa by using acoustic and morphometric approaches in parallel. Our phylogenetic data showed that European Saga species evolved from a monophyletic lineage. The geographical transitional species S. cappadocica was positioned between European and Asian lineages supporting the idea that the European Saga lineage originated phylogeographically from the Asian clade. The above results showed better agreement with the morphological data than with earlier ones based either on karyology or acoustic information only. After reviewing our data, we concluded that Saga pedo has most likely evolved from S. c. gracilis and not from S. rammei or S. ephippigera, as proposed by earlier studies. S. c. gracilis shares the same ITS2 haplotype with S. pedo, indicating that the latter could have evolved from populations of the former, probably through whole genome duplication. Based on acoustic and morphometric differences, we propose to elevate the two subspecies, S. campbelli campbelli and S. c. gracilis, to species level status, as Saga gracilis Kis 1962, and Saga campbelli Uvarov 1921. The present work sets the stage for future genetic and experimental investigations of Saginae and highlights the need for additional comprehensive analysis involving more Asian Saga species.

  1. By Law Established

    DEFF Research Database (Denmark)

    Christoffersen, Lisbet

    2017-01-01

    An analysis of the degree and content of statutory law regulation of Nordic Lutheran majority churches in 2017......An analysis of the degree and content of statutory law regulation of Nordic Lutheran majority churches in 2017...

  2. Concordance and discordance between taxonomic and functional homogenization: responses of soil mite assemblages to forest conversion.

    Science.gov (United States)

    Mori, Akira S; Ota, Aino T; Fujii, Saori; Seino, Tatsuyuki; Kabeya, Daisuke; Okamoto, Toru; Ito, Masamichi T; Kaneko, Nobuhiro; Hasegawa, Motohiro

    2015-10-01

    The compositional characteristics of ecological assemblages are often simplified; this process is termed "biotic homogenization." This process of biological reorganization occurs not only taxonomically but also functionally. Testing both aspects of homogenization is essential if ecosystem functioning supported by a diverse mosaic of functional traits in the landscape is concerned. Here, we aimed to infer the underlying processes of taxonomic/functional homogenization at the local scale, which is a scale that is meaningful for this research question. We recorded species of litter-dwelling oribatid mites along a gradient of forest conversion from a natural forest to a monoculture larch plantation in Japan (in total 11 stands), and collected data on the functional traits of the recorded species to quantify functional diversity. We calculated the taxonomic and functional β-diversity, an index of biotic homogenization. We found that both the taxonomic and functional β-diversity decreased with larch dominance (stand homogenization). After further deconstructing β-diversity into the components of turnover and nestedness, which reflect different processes of community organization, a significant decrease in the response to larch dominance was observed only for the functional turnover. As a result, there was a steeper decline in the functional β-diversity than the taxonomic β-diversity. This discordance between the taxonomic and functional response suggests that species replacement occurs between species that are functionally redundant under environmental homogenization, ultimately leading to the stronger homogenization of functional diversity. The insights gained from community organization of oribatid mites suggest that the functional characteristics of local assemblages, which support the functionality of ecosystems, are of more concern in human-dominated forest landscapes.

  3. Functional and Taxonomic Differentiation of Macrophyte Assemblages Across the Yangtze River Floodplain Under Human Impacts.

    Science.gov (United States)

    Zhang, Min; García Molinos, Jorge; Zhang, Xiaolin; Xu, Jun

    2018-01-01

    Human activities and the consequent extirpations of species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. One of the main gaps in the assessment of biodiversity change in freshwater ecosystems is our limited understanding regarding how taxonomic and functional facets of macrophyte assemblages respond to human impacts on regional scales. Here, we assess the temporal (before 1970s against after 2000s) changes in taxonomic and functional richness and compositional dissimilarities, partitioned into its turnover and nestedness components, of freshwater macrophyte assemblages across the floodplain lakes of the Yangtze River in China. We found that functional and taxonomic assemblage differentiation occurred simultaneously under increasing human impact, concomitant to a general decrease in functional and taxonomic richness. However, this effect weakened when the historical level of taxonomic dissimilarity among assemblages was high. Macrophyte species with large dispersal range and submersed life form were significantly more susceptible to extirpation. The impact of human activities on differentiation was complex but habitat loss and fishery intensity were consistently the main drivers of assemblage change in these lakes, whereas water quality (i.e., light pollution and nutrient enrichment) had weaker effects. Further, macrophyte taxonomic and functional differentiation was mainly driven by the nestedness component of dissimilarity, accounting for changes in assemblage composition related to changes in species richness independent of species replacement. This result, markedly different from previous studies on freshwater fish assemblages conducted in these lakes, represents a novel contribution toward achieving a more holistic understanding of how human impacts contribute to shape community assemblages in natural ecosystems.

  4. Land use change has stronger effects on functional diversity than taxonomic diversity in tropical Andean hummingbirds.

    Science.gov (United States)

    Tinoco, Boris A; Santillán, Vinicio E; Graham, Catherine H

    2018-03-01

    Land use change modifies the environment at multiple spatial scales, and is a main driver of species declines and deterioration of ecosystem services. However, most of the research on the effects of land use change has focused on taxonomic diversity, while functional diversity, an important predictor of ecosystem services, is often neglected. We explored how local and landscape scale characteristics influence functional and taxonomic diversity of hummingbirds in the Andes Mountains in southern Ecuador. Data was collected in six landscapes along a land use gradient, from an almost intact landscape to one dominated by cattle pastures. We used point counts to sample hummingbirds from 2011 to 2012 to assessed how local factors (i.e., vegetation structure, flowering plants richness, nectar availability) and landscape factors (i.e., landscape heterogeneity, native vegetation cover) influenced taxonomic and functional diversity. Then, we analyzed environment - trait relationships (RLQ test) to explore how different hummingbird functional traits influenced species responses to these factors. Taxonomic and functional diversity of hummingbirds were positively associated with landscape heterogeneity but only functional diversity was positively related to native vegetation coverage. We found a weak response of taxonomic and functional diversity to land use change at the local scale. Environment-trait associations showed that body mass of hummingbirds likely influenced species sensitivity to land use change. In conclusion, landscape heterogeneity created by land use change can positively influence hummingbird taxonomic and functional diversity; however, a reduction of native vegetation cover could decrease functional diversity. Given that functional diversity can mediate ecosystem services, the conservation of native vegetation cover could play a key role in the maintenance of hummingbird pollination services in the tropical Andes. Moreover, there are particular functional

  5. Atomic Weapons Establishment Bill

    International Nuclear Information System (INIS)

    Clark, Alan; Dalyell, Tam; Haynes, Frank

    1990-01-01

    The Bill debated concerns the government's proposal for the future organisations of the atomic weapons establishment in the United Kingdom. The proposals arise from a full review carried out in 1989 and include points raised by the Select Committee on the Trident programme. Studies of productivity, pay and conditions, information systems and long term manufacturing strategy have been started to enable recommendations of the reorganisation of the establishments to be made. The details of the Bill were debated for just over two hours. The debate is reported verbatim. The main issues were over the principle of contractorisation, possible staff redundancies, conditions of employment, safety and security. The proposal that the Bill be read a second time was carried. (UK)

  6. Chrysomya albiceps and C. rufifacies (Diptera: Calliphoridae): contribution to an ongoing taxonomic problem.

    Science.gov (United States)

    Tantawi, T I; Greenberg, B

    1993-05-01

    Until recently, the two biologically equivalent blow flies Chrysomya albiceps (Wiedemann) and Chrysomya rufifacies (Macquart) had disjunct distributions outside the Americas; the former was Palaearctic, the latter Australasian and Oriental. The two species are now spreading throughout the Americas and coexist in Argentina. The predatory "hairy" larvae of both species are difficult to separate, which could result in taxonomic errors. New diagnostic characters are presented to differentiate the third instars of the two species. The usefulness of the prostigmatic bristle as a diagnostic taxonomic character in distinguishing adults of these species is questioned.

  7. A STUDY ESTABLISHING THE IMPORTANCE OF BODY COMPOSITION ANALYSIS, REGULAR PHYSIOTHERAPY AND DIETARY MODIFICATIONS FOR INDEPENDENT AND HEALTHY LIVING AMONG GERIATRIC POPULATION: A DETAILED SYSTEMATIC REVIEW ARTICLE

    OpenAIRE

    Rohit Subhedar; R. K. Sinha; Saumi Sinha

    2015-01-01

    Background: This systematic review article aims towards comprehensive and elaborative collection of research articles related to the importance of body composition analysis, Physiotherapy and nutrition for independent geriatric lifestyle. The review article includes articles which suggest the importance of Body composition analysis, Physiotherapy interventions, specific exercises and a combination of fat free, fiber, fruit and fluid diet. Methods: A comprehensive electronic search was cond...

  8. A re-consideration of the taxonomic status of Nebria lacustris Casey (Coleoptera, Carabidae, Nebriini based on multiple datasets – a single species or a species complex?

    Directory of Open Access Journals (Sweden)

    David Kavanaugh

    2011-11-01

    Full Text Available This study gathered evidence from principal component analysis (PCA of morphometric data and molecular analyses of nucleotide sequence data for four nuclear genes (28S, TpI, CAD1, and Wg and two mitochondrial genes (COI and 16S, using parsimony, maximum likelihood, and Bayesian methods. This evidence was combined with morphological and chorological data to re-evaluate the taxonomic status of Nebria lacustris Casey sensu lato. PCA demonstrated that both body size and one conspicuous aspect of pronotal shape vary simultaneously with elevation, latitude, and longitude and served to distinguish populations from the southern Appalachian highlands, south of the French Broad, from all other populations. Molecular analyses revealed surprisingly low overall genetic diversity within N. lacustris sensu lato, with only 0.39% of 4605 bp varied in the concatenated dataset. Evaluation of patterns observed in morphological and genetic variation and distribution led to the following taxonomic conclusions: (1 Nebria lacustris Casey and Nebria bellorum Kavanaugh should be considered distinct species, which is a NEW STATUS for N. bellorum. (2 No other distinct taxonomic subunits could be distinguished with the evidence at hand, but samples from northeastern Iowa, in part of the region known as the “Driftless Zone”, have unique genetic markers for two genes that hint at descent from a local population surviving at least the last glacial advance. (3 No morphometric or molecular evidence supports taxonomic distinction between lowland populations on the shores of Lake Champlain and upland populations in the adjacent Green Mountains of Vermont, despite evident size and pronotal shape differences between many of their members.

  9. From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories.

    Science.gov (United States)

    Smith, B Eugene; Johnston, Mark K; Lücking, Robert

    2016-01-01

    Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of

  10. Molecular Taxonomical Re-classification of the Genus Suillus Micheli ex S. F. Gray in South Korea.

    Science.gov (United States)

    Min, Young Ju; Park, Myung Soo; Fong, Jonathan J; Seok, Soon Ja; Han, Sang-Kuk; Lim, Young Woon

    2014-09-01

    The fungal genus Suillus Micheli ex S. F. Gray plays important roles in the survival and growth of plant seedlings. Humans have utilized these ectomycorrhizal fungi to enhance the nutrient uptake and defense systems of plants, particularly in the reforestation of coniferous forests. The genus Suillus is easily distinguishable by its distinctive morphological features, although the morphology of the fruiting body does not facilitate reliable interspecies discrimination. On the basis of micro-morphological features and internal transcribed spacer sequence analysis, we found that 51 of 117 Korean Suillus specimens had initially been misidentified. The list of the 12 Suillus species previously recorded in Korea was re-evaluated and revised to only eight distinct species: S. americanus, S. bovinus, S. granulatus, S. grevillei, S. luteus, S. pictus, S. placidus, and S. viscidus. We provide taxonomical descriptions for six of these species from the sample specimens.

  11. Establishing benchmarks for the management of elevated liver enzymes and/or dilated biliary trees in an urban safety net hospital: analysis of 915 subjects.

    Science.gov (United States)

    Liu, Laindy; Cripps, Michael W; Riggle, Andrew J; Wolf, Steven E; Nakonezny, Paul A; Phelan, Herb A

    2015-12-01

    The push for public reporting of outcomes necessitates relevant benchmarks for disease states across different settings. This study establishes benchmarks for choledocholithiasis management in a safety net hospital setting. We reviewed all patients admitted to our acute care surgery service with biochemical evidence of choledocholithiasis who underwent same-admission cholecystectomy (CCY) between July 2012 and December 2013. During this 18-month period, 915 patients were admitted with biochemical evidence of choledocholithiasis. Descriptive statistics for the cohort are provided, which include a 51% rate of obesity and 95% rate of pathologic cholecystitis. Conversion rates of 4% and complication rates of 6% were found. The majority had a CCY without biliary imaging (n = 630, 68.9%). Relevant benchmarks are characterized, and results of a practice pattern of omitting pre- or intraoperative biliary tree imaging are described. These findings serve as a first benchmark of choledocholithiasis management for urban safety net hospitals. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Taxonomic differences in deciduous upper second molar crown outlines of Homo sapiens, Homo neanderthalensis and Homo erectus.

    Science.gov (United States)

    Bailey, Shara E; Benazzi, Stefano; Souday, Caroline; Astorino, Claudia; Paul, Kathleen; Hublin, Jean-Jacques

    2014-07-01

    A significant number of Middle to Late Pleistocene sites contain primarily (and sometimes only) deciduous teeth (e.g., Grotta del Cavallo, Mezmaiskaya, Blombos). Not surprisingly, there has been a recent renewed interest in deciduous dental variation, especially in the context of distinguishing Homo neanderthalensis and Homo sapiens. Most studies of the deciduous dentition of fossil hominins have focused on standard metrical variation but morphological (non-metric and morphometric) variation also promises to shed light on long standing taxonomic questions. This study examines the taxonomic significance of the crown outline of the deciduous upper second molar through principal components analysis and linear discriminant analysis. We examine whether or not the crown shape of the upper deciduous second molar separates H. neanderthalensis from H. sapiens and explore whether it can be used to correctly assign individuals to taxa. It builds on previous studies by focusing on crown rather than cervical outline and by including a large sample of geographically diverse recent human populations. Our samples include 17 H. neanderthalensis, five early H. sapiens, and 12 Upper Paleolithic H. sapiens. In addition, we include two Homo erectus specimens in order to evaluate the polarity of crown shape differences observed between H. neanderthalensis and H. sapiens. Our results show that crown outline shape discriminates H. sapiens and H. neanderthalensis quite well, but does not do well at distinguishing H. erectus from H. sapiens. We conclude that the crown outline shape observed in H. sapiens is a primitive retention and that the skewed shape observed in H. neanderthalensis is a derived condition. Finally, we explore the phylogenetic implications of the results for the H. erectus molars. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. The taxonomic status of common dolphins Delphinus spp. in South ...

    African Journals Online (AJOL)

    Aside from gender differences, a principal components analysis of skull measurements of 72 adult common dolphins from South Africa failed to distinguish more than one form of Delphinus. Plots of rostral length against zygomatic width indicated most could be referred to the long-beaked form D. capensis, but three ...

  14. Taxonomic Composition of the Diet of Hawksbill Turtles ...

    African Journals Online (AJOL)

    Preliminary analysis reveals at least16 animal and four plant species. Sponges predominated with 10 genera identified. Although our list of food items is similar to those compiled for hawksbills at other study sites in the Pacific and Atlantic Oceans, we record six genera of diet items not previously recorded. This study is the ...

  15. Numerical taxonomic studies of some tribes of Brassicaceae from Egypt

    NARCIS (Netherlands)

    Abdel Khalik, K.; Maesen, van der L.J.G.; Koopman, W.J.M.; Berg, van den R.G.

    2002-01-01

    A systematic study of 45 taxa belonging to 23 genera of tribes Arabideae, Euclidieae, Hesperideae, Lunarieae, Matthioleae and Sisymbrieae of Brassicaceae from Egypt was conducted by means of numerical analysis based on sixty two morphological characters, including vegetative parts, pollen grains and

  16. Taxonomic position and identity of Stenocephalum monticola (Vernonieae, Asteraceae)

    NARCIS (Netherlands)

    Dematteis, M.; Angulo, M.B.

    2008-01-01

    The genus Stenocephalum (Vernonieae, Asteraceae) includes six South American species that have cylindrical heads, 4–11 florets by capitula, cymose inflorescences and type ‘C’ pollen. Until now, Stenocephalum monticola has been considered as a synonym of S. apiculatum. However, the analysis of the

  17. Cremastosperma (and other evolutionary digressions) : Molecular phylogenetic, biogeographic, and taxonomic studies in Neotropical Annonaceae

    NARCIS (Netherlands)

    Pirie, Michael David

    2005-01-01

    Results are presented of research on a family of flowering plants, the Annonaceae, species of which are found in tropical rainforest across the world. The project focussed on one group of species, the genus Cremastosperma, which is found in the South and Central American tropics. A taxonomic

  18. The effect of taxonomic resolution on the assessment of ecological water quality classes

    NARCIS (Netherlands)

    Schmidt-Kloiber, A.; Nijboer, R.C.

    2004-01-01

    Within the ecological assessment of running waters based on benthic macroinvertebrates different levels of taxonomic resolution (species, genus, family and higher) are in use. Although assessment systems are often developed with detailed data on species level, water managers and other end-users

  19. Low Functional β-Diversity Despite High Taxonomic β-Diversity among Tropical Estuarine Fish Communities

    Science.gov (United States)

    Villéger, Sébastien; Miranda, Julia Ramos; Hernandez, Domingo Flores; Mouillot, David

    2012-01-01

    The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395

  20. A Taxonomic Note on the Misidentification of Anemone tschernjaewii Regel. in Kashmir Himalaya

    Directory of Open Access Journals (Sweden)

    Aijaz Hassan Ganie

    2015-03-01

    Full Text Available The correct identification of Anemone tschernjaewii Regel. previously misidentified as A. biflora DC. in the Kashmir Himalaya, India is reported. In this brief report, a detailed taxonomic description and photo-plates of its diagnostic morphological and anatomical characters are provided to validate this plant record for the region and to facilitate its easier field identification.

  1. A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema

    DEFF Research Database (Denmark)

    Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper Tataru

    2016-01-01

    Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exa...

  2. Using geographical and taxonomic metadata to set priorities in specimen digitization

    Directory of Open Access Journals (Sweden)

    Walter G. Berendsohn

    2010-10-01

    Full Text Available Digitizing the information carried by specimens in natural history collections is a key endeavor providing falsifiable information about past and present biodiversity on a global scale, for application in a variety of research fields far beyond the current application in biosystematics. Existing digitization efforts are driven by individual institutional necessities and are not coordinated on a global scale. This led to an over-all information resource that is patchy in taxonomic and geographic coverage as well as in quality. Digitizing all specimens is not an achievable aim at present, so that priorities need to be set. Most biodiversity studies are both taxonomically and geographically restricted, but access to non-digitized collection information is almost exclusively by taxon name. Creating a “Geotaxonomic Index” providing metadata on the number of specimens from a specific geographic region belonging to a specific higher taxonomic category may provide a means to attract the attention of researchers and governments towards relevant non-digitized holdings of the collections and set priorities for their digitization according to the needs of information users outside the taxonomic community.

  3. Frost tolerance in wild potatoes : Assessing the predictivity of taxonomic, geographic and ecological factors

    NARCIS (Netherlands)

    Hijmans, R.J.; Jacobs, M.; Bamberg, J.B.; Spooner, D.M.

    2003-01-01

    The use of genetic resources could be more effective and efficient if we were able to predict the presence or absence of useful traits in different populations or accessions. We analyzed the extent to which taxonomic, geographic and ecological factors can predict the presence of frost tolerance in

  4. Differences in Processing of Taxonomic and Sequential Relations in Semantic Memory: An fMRI Investigation

    Science.gov (United States)

    Kuchinke, Lars; van der Meer, Elke; Krueger, Frank

    2009-01-01

    Conceptual knowledge of our world is represented in semantic memory in terms of concepts and semantic relations between concepts. We used functional magnetic resonance imaging (fMRI) to examine the cortical regions underlying the processing of sequential and taxonomic relations. Participants were presented verbal cues and performed three tasks:…

  5. Environmental quality of a stream can be better predicted by phylogenetic than by taxonomic diversity

    Directory of Open Access Journals (Sweden)

    Koperski Paweł

    2017-01-01

    Full Text Available Different indices of taxonomic diversity (TD and phylogenetic diversity (PD of the macrobenthos were compared to determine the efficient predictors of environmental quality (EQ in different types of watercourses in Poland. Archived data of 864 samples of benthic invertebrates identified to the family level were analysed on the basis of linear and non-linear multiply regression. The strengths of the correlations between two measures of EQ:BMWPpl (British Monitoring Working Party score system, Polish modification and MMI (Multimetric Macroinvertebrate Index and the values of taxonomic richness and three well-known TD indices: Shannon, Margalef and J' Evenness were compared to those for values of three PD indices, based on taxonomic distinctness. Taxonomic richness and all PD indices correlated more strongly with both measures of EQ than all TD indices. Correlations with both types of diversity indices were visibly stronger for BMWPpl when compared with MMI. We suggest that analysed indices of PD, especially MDis (mean phylogenetic distance between families in a sample, are related with EQ strongly enough to be taken into account as potential metrics in selection procedures of biological assessment.

  6. Developmental Antecedents of Taxonomic and Thematic Strategies at 3 Years of Age.

    Science.gov (United States)

    Dunham, Philip; Dunham, Frances

    1995-01-01

    Individual differences in children's conceptual strategies at 3 years of age were predicted by aspects of children's behavior and language at 13 and 24 months. Production of pointing gestures at 13 months and nouns and attributive adjectives at 24 months were positively associated with the use of a taxonomic matching strategy at 3 years of age.…

  7. Caloplaca subpallida (Teloschistaceae, a lichen species new to Poland: distribution, ecology and taxonomic affinities

    Directory of Open Access Journals (Sweden)

    Katarzyna Szczepańska

    2013-03-01

    Full Text Available Caloplaca subpallida is reported from basic and altered ultrabasic rocks (i.e. basalt, greenstone, and serpentinite at nine sites in SW Poland. A detailed description of the species and a discussion on its taxonomic affinities are provided.

  8. Urbanization alters the functional composition, but not taxonomic diversity, of the soil nematode community

    Science.gov (United States)

    Mitchell A. Pavao-Zuckerman; David C. Coleman

    2007-01-01

    We evaluated the response of riparian forest soil nematode community structure to the physico-chemical environment associated with urban land use. Soils were sampled seasonally between December 2000 and October 2002 along an urban-rural transect in Asheville, North Carolina. We characterized the taxonomic (to genus) and functional composition (trophic groups) of the...

  9. Asian longhorned beetle complicates the relationship between taxonomic diversity and pest vulnerability in street tree assemblages

    Science.gov (United States)

    Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven c...

  10. Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina

    NARCIS (Netherlands)

    Wang, Q. -M.; Begerow, D.; Groenewald, M.; Liu, X. -Z.; Theelen, B.; Bai, F. -Y.; Boekhout, T.

    The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and

  11. Taxonomic and nomenclatural rearrangements in Artemisia subgen. Tridentatae, including a redefinition of Sphaeromeria (Asteraceae, Anthemideae)

    Science.gov (United States)

    Sonia Garcia; Teresa Garnatje; E. Durant McArthur; Jaume Pellicer; Stewart C. Sanderson; Joan Valles

    2011-01-01

    A recent molecular phylogenetic study of all members of Artemisia subgenus Tridentatae, as well as most of the other New World endemic Artemisia and the allied genera Sphaeromeria and Picrothamnus, raised the necessity of revising the taxonomic framework of the North American endemic Artemisia. Composition of the subgenus Tridentatae is enlarged to accommodate other...

  12. Environmental Scanning Electron Microscopy as a Useful Tool for Taxonomical Documentation of Parasitical Helminths

    Czech Academy of Sciences Publication Activity Database

    Tihlaříková, Eva; Neděla, Vilém; Mašová, Š.

    2016-01-01

    Roč. 22, S3 (2016), s. 1178-1179 ISSN 1431-9276 R&D Projects: GA ČR(CZ) GA14-22777S Institutional support: RVO:68081731 Keywords : parasitical Helminths * ESEM * taxonomical documentation Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.891, year: 2016

  13. Classification of Pinus patula, P. tecunumanii, P. oocarpa, P. caribaea var. hondurensis, and Related Taxonomic Entities

    Science.gov (United States)

    A.E. Squillace; Jesse P. Perry

    1992-01-01

    Stem xylem terpenes of 75 pine populations were studied to determine relationships among taxonomic entities. Typical Pinus patula populations occurring in areas north and west of Oaxaca, Mexico, had very high proportions of 3-phellandrene and low proportions of other constituents. Terpene compositions of populations of variety longipeduncalatain...

  14. Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16 M.

    Directory of Open Access Journals (Sweden)

    Aniel Jessica Leticia Brambila-Tapia

    Full Text Available Many virulence genes have been detected in attenuated mutants of Brucella melitensis 16 M; nevertheless, a complete report of these genes, including the main Cluster of Orthologous Groups (COG represented as well as the taxonomical distribution among all complete bacterial and archaeal genomes, has not been analyzed. In this work a total of 160 virulence genes that have been reported in attenuated mutants in B. melitensis were included and analyzed. Additionally, we obtained 250 B. melitensis randomly selected genes as a reference group for the taxonomical comparisons. The COGs and the taxonomical distribution profile for 789 nonredundant bacterial and archaeal genomes were obtained and compared with the whole-genome COG distribution and with the 250 randomly selected genes, respectively. The main COGs associated with virulence genes corresponded to the following: intracellular trafficking, secretion and vesicular transport (U; cell motility (N; nucleotide transport and metabolism (F; transcription (K; and cell wall/membrane/envelope biogenesis (M. In addition, we found that virulence genes presented a higher proportion of orthologs in the Euryarchaeota and Proteobacteria phyla, with a significant decrease in Chlamydiae, Bacteroidetes, Tenericutes, Firmicutes and Thermotogae. In conclusion, we found that genes related to specific functions are more relevant to B. melitensis virulence, with the COG U the most significant. Additionally, the taxonomical distribution of virulence genes highlights the importance of these genes in the related Proteobacteria, being less relevant in distant groups of organisms with the exception of Euryarchaeota.

  15. Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

    NARCIS (Netherlands)

    Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; Vos, de Willem M.

    2015-01-01

    Background: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to

  16. Establishing Substantial Equivalence: Transcriptomics

    Science.gov (United States)

    Baudo, María Marcela; Powers, Stephen J.; Mitchell, Rowan A. C.; Shewry, Peter R.

    Regulatory authorities in Western Europe require transgenic crops to be substantially equivalent to conventionally bred forms if they are to be approved for commercial production. One way to establish substantial equivalence is to compare the transcript profiles of developing grain and other tissues of transgenic and conventionally bred lines, in order to identify any unintended effects of the transformation process. We present detailed protocols for transcriptomic comparisons of developing wheat grain and leaf material, and illustrate their use by reference to our own studies of lines transformed to express additional gluten protein genes controlled by their own endosperm-specific promoters. The results show that the transgenes present in these lines (which included those encoding marker genes) did not have any significant unpredicted effects on the expression of endogenous genes and that the transgenic plants were therefore substantially equivalent to the corresponding parental lines.

  17. Establishing Political Deliberation Systems

    DEFF Research Database (Denmark)

    Rose, Jeremy; Sæbø, Øystein

    2008-01-01

    The extension and transformation of political participation is dependent on widespread deliberation supported by information and communication technologies.  The most commonly found examples of these eParticipation systems are political discussion forums.  Though much of the discussion...... of these technologies is conducted in the eGovernment and (particularly) the eDemocracy literature, political discussion forums present a distinct set of design and management challenges which relate directly to IS concerns. In this article we analyze problems in establishing political deliberation systems under five...... headings: stakeholder engagement, web platform design, web platform management, political process re-shaping and evaluation and improvement. We review the existing literature and present a longitudinal case study of a political discussion forum: the Norwegian DemokratiTorget (Democracy Square).  We define...

  18. Round one of the Adelaide and Meath Hospital/Trinity College Colorectal Cancer Screening Programme: programme report and analysis based on established international key performance indices.

    LENUS (Irish Health Repository)

    McNamara, D

    2012-02-01

    BACKGROUND: In Ireland, colorectal cancer (CRC) is the second most frequently diagnosed cancer in men, after prostate cancer, and the second most frequently diagnosed cancer in women, after breast cancer. By 2020, the number of new cases diagnosed annually in Ireland is projected to have increased by 79% in men and 56% in women. Organised screening for CRC is already underway or is in the process of being rolled out in several European countries, either at a regional or national level. The Adelaide and Meath Hospital\\/ Trinity College Dublin Colorectal Cancer Screening Programme (TTC-CRC-SP) is Ireland\\'s first pilot population based bowel screening programme. METHOD: Based on a biennial test model the pilot aimed to assess the accuracy of FIT and to evaluate the whole programme based on established international key performance indices. RESULTS: To date 9,993 individuals aged 50-74 years have been invited to participate in the TTC-CRC-SP with over 5,000 FIT\\'s analysed. Overall uptake was 51% and FIT positivity was 10%. The programme has undertaken over 400 screening colonoscopies and detected 154 precancerous adenomas and 38 cancerous lesions. CONCLUSIONS: The first round of The Adelaide and Meath Hospital Tallaght\\/Trinity College Dublin Colorectal Cancer Screening Programme has been highly successful and confirmed that there is an advantage for FIT based two stage bowel cancer screening programmes.

  19. A study on an establishment for collaboration system with the OECD/NEA by means of the analysis of its main activities related to nuclear safety

    International Nuclear Information System (INIS)

    Song, J. H.; Kim, M. C.; Park, J. S.; Jeong, J. W.; Oh, C. W.

    2005-12-01

    The OECD Nuclear Energy Agency (NEA) was established on 1st February 1958 under the name of the OEEC European Nuclear Energy Agency. It received its present designation on 20th April 1972, when Japan became its first non-European full member. NEA membership today consists of 28 OECD member countries: Australia, Austria, Belgium, Canada, the Czech Republic, Denmark, Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Japan, Luxembourg, Mexico, the Netherlands, Norway, Portugal, the Republic of Korea, the Slovak Republic, Spain, Sweden, Switzerland, Turkey, the United Kingdom and the United States. The Commission of the European Communities also takes part in the work of the Agency. The mission of the NEA is: o to assist its member countries in maintaining and further developing, through international cooperation, the scientific, technological and legal bases required for a safe, environmentally friendly and economical use of nuclear energy for peaceful purposes, as well as o to provide authoritative assessments and to forge common understandings on key issues, as input to government decisions on nuclear energy policy and to broader OECD policy analyses in areas such as energy and sustainable development. OECD Nuclear Energy Agency performs the work putting emphasis on safety enhancement and regulatory safety. Having Analyzed activities areas of Nuclear Development Committee (NDC), Committee on the Safety of Nuclear Installations (CSNI), Committee on Nuclear Regulatory Activities (CNRA) and drew out cooperation methods relating to nuclear safety regulation with them, it will be helpful economically and technically in meeting with improvement of nuclear safety efficiently

  20. Causality re-established.

    Science.gov (United States)

    D'Ariano, Giacomo Mauro

    2018-07-13

    Causality has never gained the status of a 'law' or 'principle' in physics. Some recent literature has even popularized the false idea that causality is a notion that should be banned from theory. Such misconception relies on an alleged universality of the reversibility of the laws of physics, based either on the determinism of classical theory, or on the multiverse interpretation of quantum theory, in both cases motivated by mere interpretational requirements for realism of the theory. Here, I will show that a properly defined unambiguous notion of causality is a theorem of quantum theory, which is also a falsifiable proposition of the theory. Such a notion of causality appeared in the literature within the framework of operational probabilistic theories. It is a genuinely theoretical notion, corresponding to establishing a definite partial order among events, in the same way as we do by using the future causal cone on Minkowski space. The notion of causality is logically completely independent of the misidentified concept of 'determinism', and, being a consequence of quantum theory, is ubiquitous in physics. In addition, as classical theory can be regarded as a restriction of quantum theory, causality holds also in the classical case, although the determinism of the theory trivializes it. I then conclude by arguing that causality naturally establishes an arrow of time. This implies that the scenario of the 'block Universe' and the connected 'past hypothesis' are incompatible with causality, and thus with quantum theory: they are both doomed to remain mere interpretations and, as such, are not falsifiable, similar to the hypothesis of 'super-determinism'.This article is part of a discussion meeting issue 'Foundations of quantum mechanics and their impact on contemporary society'. © 2018 The Author(s).

  1. Coastal habitats as surrogates for taxonomic, functional and trophic structures of benthic faunal communities.

    Science.gov (United States)

    Törnroos, Anna; Nordström, Marie C; Bonsdorff, Erik

    2013-01-01

    Due to human impact, there is extensive degradation and loss of marine habitats, which calls for measures that incorporate taxonomic as well as functional and trophic aspects of biodiversity. Since such data is less easily quantifiable in nature, the use of habitats as surrogates or proxies for biodiversity is on the rise in marine conservation and management. However, there is a critical gap in knowledge of whether pre-defined habitat units adequately represent the functional and trophic structure of communities. We also lack comparisons of different measures of community structure in terms of both between- (β) and within-habitat (α) variability when accounting for species densities. Thus, we evaluated a priori defined coastal habitats as surrogates for traditional taxonomic, functional and trophic zoobenthic community structure. We focused on four habitats (bare sand, canopy-forming algae, seagrass above- and belowground), all easily delineated in nature and defined through classification systems. We analyzed uni- and multivariate data on species and trait diversity as well as stable isotope ratios of benthic macrofauna. A good fit between habitat types and taxonomic and functional structure was found, although habitats were more similar functionally. This was attributed to within-habitat heterogeneity so when habitat divisions matched the taxonomic structure, only bare sand was functionally distinct. The pre-defined habitats did not meet the variability of trophic structure, which also proved to differentiate on a smaller spatial scale. The quantification of trophic structure using species density only identified an epi- and an infaunal unit. To summarize the results we present a conceptual model illustrating the match between pre-defined habitat types and the taxonomic, functional and trophic community structure. Our results show the importance of including functional and trophic aspects more comprehensively in marine management and spatial planning.

  2. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

    Science.gov (United States)

    Franz, Nico M; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

    2015-01-01

    Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.

  3. ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications.

    Science.gov (United States)

    Lespinats, Sylvain; Fertil, Bernard

    2011-01-01

    Color may be very useful to visualise complex data. As far as taxonomy is concerned, color may help observing various species' characteristics in correlation with classification. However, choosing the number of subclasses to display is often a complex task: on the one hand, assigning a limited number of colors to taxa of interest hides the structure imbedded in the subtrees of the taxonomy; on the other hand, differentiating a high number of taxa by giving them specific colors, without considering the underlying taxonomy, may lead to unreadable results since relationships between displayed taxa would not be supported by the color code. In the present paper, an automatic color coding scheme is proposed to visualise the levels of taxonomic relationships displayed as overlay on any kind of data plot. To achieve this goal, a dimensionality reduction method allows displaying taxonomic "distances" onto a Euclidean two-dimensional space. The resulting map is projected onto a 2D color space (the Hue, Saturation, Brightness colorimetric space with brightness set to 1). Proximity in the taxonomic classification corresponds to proximity on the map and is therefore materialised by color proximity. As a result, each species is related to a color code showing its position in the taxonomic tree. The so called ColorPhylo displays taxonomic relationships intuitively and can be combined with any biological result. A Matlab version of ColorPhylo is available at http://sy.lespi.free.fr/ColorPhylo-homepage.html. Meanwhile, an ad-hoc distance in case of taxonomy with unknown edge lengths is proposed.

  4. Combining Taxonomic and Functional Approaches to Unravel the Spatial Distribution of an Amazonian Butterfly Community.

    Science.gov (United States)

    Graça, Márlon B; Morais, José W; Franklin, Elizabeth; Pequeno, Pedro A C L; Souza, Jorge L P; Bueno, Anderson Saldanha

    2016-04-01

    This study investigated the spatial distribution of an Amazonian fruit-feeding butterfly assemblage by linking species taxonomic and functional approaches. We hypothesized that: 1) vegetation richness (i.e., resources) and abundance of insectivorous birds (i.e., predators) should drive changes in butterfly taxonomic composition, 2) larval diet breadth should decrease with increase of plant species richness, 3) small-sized adults should be favored by higher abundance of birds, and 4) communities with eyespot markings should be able to exploit areas with higher predation pressure. Fruit-feeding butterflies were sampled with bait traps and insect nets across 25 km(2) of an Amazonian ombrophilous forest in Brazil. We measured larval diet breadth, adult body size, and wing marking of all butterflies. Our results showed that plant species richness explained most of the variation in butterfly taxonomic turnover. Also, community average diet breadth decreased with increase of plant species richness, which supports our expectations. In contrast, community average body size increased with the abundance of birds, refuting our hypothesis. We detected no influence of environmental gradients on the occurrence of species with eyespot markings. The association between butterfly taxonomic and functional composition points to a mediator role of the functional traits in the environmental filtering of butterflies. The incorporation of the functional approach into the analyses allowed for the detection of relationships that were not observed using a strictly taxonomic perspective and provided an extra insight into comprehending the potential adaptive strategies of butterflies. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  5. Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

    Science.gov (United States)

    Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

    2016-06-01

    Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

  6. Fast and sensitive taxonomic classification for metagenomics with Kaiju

    DEFF Research Database (Denmark)

    Menzel, Peter; Ng, Kim Lee; Krogh, Anders

    2016-01-01

    heuristic. We show in a genome exclusion study that Kaiju can classify more reads with higher sensitivity and similar precision compared to fast k-mer based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies more than twice as many...... reads in ten real metagenomes compared to programs based on genomic k-mers. Kaiju can process up to millions of reads per minute, and its memory footprint is below 5 GB of RAM, allowing the analysis on a standard PC. The program is available under the GPL3 license at: github.com/bioinformatics-centre/kaiju...

  7. Functional grouping and establishment of distribution patterns of invasive plants in China using self-organizing maps and indicator species analysis

    Directory of Open Access Journals (Sweden)

    Wang Zi-Bo

    2009-01-01

    Full Text Available In the present study, we introduce two techniques - self-organizing maps (SOM and indicator species analysis (INDVAL - for understanding the richness patterns of invasive species. We first employed SOM to identify functional groups and then used INDVAL to identify the representative areas characterizing these functional groups. Quantitative traits and distributional information on 127 invasive plants in 28 provinces of China were collected to form the matrices for our study. The results indicate Jiangsu to be the top province with the highest number of invasive species, while Ningxia was the lowest. Six functional groups were identified by the SOM method, and five of them were found to have significantly representative provinces by the INDVAL method. Our study represents the first attempt to combine self-organizing maps and indicator species analysis to assess the macro-scale distribution of exotic species.

  8. Establishment of a sensitive system for analysis of human vaginal microbiota on the basis of rRNA-targeted reverse transcription-quantitative PCR.

    Science.gov (United States)

    Kurakawa, Takashi; Ogata, Kiyohito; Tsuji, Hirokazu; Kado, Yukiko; Takahashi, Takuya; Kida, Yumi; Ito, Masahiro; Okada, Nobuhiko; Nomoto, Koji

    2015-04-01

    Ten specific primer sets, for Lactobacillus gasseri, Lactobacillus crispatus, Atopobium vaginae, Gardnerella vaginalis, Mobiluncus curtisii, Chlamydia trachomatis/muridarum, Bifidobacterium longum subsp. longum, Bifidobacterium longum subsp. infantis, Bifidobacterium adolescentis, and Bifidobacterium angulatum, were developed for quantitative analysis of vaginal microbiota. rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) analysis of the vaginal samples from 12 healthy Japanese volunteers using the new primer sets together with 25 existing primer sets revealed the diversity of their vaginal microbiota: Lactobacilli such as L. crispatus, L. gasseri, Lactobacillus jensenii, Lactobacillus iners, and Lactobacillus vaginalis, as the major populations at 10(7) cells/ml vaginal fluid, were followed by facultative anaerobes such as Streptococcus and strict anaerobes at lower population levels of 10(4) cells/ml or less. Certain bacterial vaginosis (BV)-related bacteria, such as G. vaginalis, A. vaginae, M. curtisii, and Prevotella, were also detected in some subjects. Especially in one subject, both G. vaginalis and A. vaginae were detected at high population levels of 10(8.8) and 10(8.9) cells/ml vaginal fluid, suggesting that she is an asymptomatic BV patient. These results suggest that the RT-qPCR system is effective for accurate analysis of major vaginal commensals and diagnosis of several vaginal infections. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Taxonomic evaluation of selected Ganoderma species and database sequence validation

    Directory of Open Access Journals (Sweden)

    Suldbold Jargalmaa

    2017-07-01

    Full Text Available Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily on DNA sequencing using BLAST searches, which are only reliable if the GenBank submissions are accurately labeled. In this study, we examined 113 specimens collected from 1969 to 2016 from various regions in Korea using morphological features and multigene analysis (internal transcribed spacer, translation elongation factor 1-α, and the second largest subunit of RNA polymerase II. These specimens were identified as four Ganoderma species: G. sichuanense, G. cf. adspersum, G. cf. applanatum, and G. cf. gibbosum. With the exception of G. sichuanense, these species were difficult to distinguish based solely on morphological features. However, phylogenetic analysis at three different loci yielded concordant phylogenetic information, and supported the four species distinctions with high bootstrap support. A survey of over 600 Ganoderma sequences available on GenBank revealed that 65% of sequences were either misidentified or ambiguously labeled. Here, we suggest corrected annotations for GenBank sequences based on our phylogenetic validation and provide updated global distribution patterns for these Ganoderma species.

  10. Taxonomic evaluation of selected Ganoderma species and database sequence validation

    Science.gov (United States)

    Jargalmaa, Suldbold; Eimes, John A.; Park, Myung Soo; Park, Jae Young; Oh, Seung-Yoon

    2017-01-01

    Species in the genus Ganoderma include several ecologically important and pathogenic fungal species whose medicinal and economic value is substantial. Due to the highly similar morphological features within the Ganoderma, identification of species has relied heavily on DNA sequencing using BLAST searches, which are only reliable if the GenBank submissions are accurately labeled. In this study, we examined 113 specimens collected from 1969 to 2016 from various regions in Korea using morphological features and multigene analysis (internal transcribed spacer, translation elongation factor 1-α, and the second largest subunit of RNA polymerase II). These specimens were identified as four Ganoderma species: G. sichuanense, G. cf. adspersum, G. cf. applanatum, and G. cf. gibbosum. With the exception of G. sichuanense, these species were difficult to distinguish based solely on morphological features. However, phylogenetic analysis at three different loci yielded concordant phylogenetic information, and supported the four species distinctions with high bootstrap support. A survey of over 600 Ganoderma sequences available on GenBank revealed that 65% of sequences were either misidentified or ambiguously labeled. Here, we suggest corrected annotations for GenBank sequences based on our phylogenetic validation and provide updated global distribution patterns for these Ganoderma species. PMID:28761785

  11. Establishing Substantial Equivalence: Proteomics

    Science.gov (United States)

    Lovegrove, Alison; Salt, Louise; Shewry, Peter R.

    Wheat is a major crop in world agriculture and is consumed after processing into a range of food products. It is therefore of great importance to determine the consequences (intended and unintended) of transgenesis in wheat and whether genetically modified lines are substantially equivalent to those produced by conventional plant breeding. Proteomic analysis is one of several approaches which can be used to address these questions. Two-dimensional PAGE (2D PAGE) remains the most widely available method for proteomic analysis, but is notoriously difficult to reproduce between laboratories. We therefore describe methods which have been developed as standard operating procedures in our laboratory to ensure the reproducibility of proteomic analyses of wheat using 2D PAGE analysis of grain proteins.

  12. Population genetic analysis of a medicinally significant Australian rainforest tree, Fontainea picrosperma C.T. White (Euphorbiaceae): biogeographic patterns and implications for species domestication and plantation establishment.

    Science.gov (United States)

    Lamont, R W; Conroy, G C; Reddell, P; Ogbourne, S M

    2016-02-29

    Fontainea picrosperma, a subcanopy tree endemic to the rainforests of northeastern Australia, is of medicinal significance following the discovery of the novel anti-cancer natural product, EBC-46. Laboratory synthesis of EBC-46 is unlikely to be commercially feasible and consequently production of the molecule is via isolation from F. picrosperma grown in plantations. Successful domestication and plantation production requires an intimate knowledge of a taxon's life-history attributes and genetic architecture, not only to ensure the maximum capture of genetic diversity from wild source populations, but also to minimise the risk of a detrimental loss in genetic diversity via founder effects during subsequent breeding programs designed to enhance commercially significant agronomic traits. Here we report the use of eleven microsatellite loci (PIC = 0.429; P ID  = 1.72 × 10(-6)) to investigate the partitioning of genetic diversity within and among seven natural populations of F. picrosperma. Genetic variation among individuals and within populations was found to be relatively low (A = 2.831; H E  = 0.407), although there was marked differentiation among populations (PhiPT = 0.248). Bayesian, UPGMA and principal coordinates analyses detected three main genotypic clusters (K = 3), which were present at all seven populations. Despite low levels of historical gene flow (N m  = 1.382), inbreeding was negligible (F = -0.003); presumably due to the taxon's dioecious breeding system. The data suggests that F. picrosperma was previously more continuously distributed, but that rainforest contraction and expansion in response to glacial-interglacial cycles, together with significant anthropogenic effects have resulted in significant fragmentation. This research provides important tools to support plantation establishment, selection and genetic improvement of this medicinally significant Australian rainforest species.

  13. Multi-scale functional and taxonomic β-diversity of the macroinvertebrate communities in a Mediterranean coastal lagoon

    Directory of Open Access Journals (Sweden)

    D. CABANA

    2017-03-01

    Full Text Available Benthic macroinvertebrate communities form the basis of the intricate lagoonal food web. Understanding their functional and taxonomic response, from a β-diversity perspective, is essential to disclose underlying patterns with potential applicability in conservation and management actions. Within the central lagoon of Messolonghi we studied the main environmental components structuring the macroinvertebrate community. We analyzed the β-taxonomic and β-functional diversity across the main habitats and seasons, over a year time frame. Our results outline habitat type and vegetation biomass as the major factors structuring the communities. We found environmental variability to have a positive correlation with functional β-diversity, however no correlation was found with taxonomic β-diversity. Across the seasons an asynchronous response of the functional and taxonomic β-diversity was identified. The taxonomic composition displayed significant heterogeneity during the driest period and the functional during the rainy season. Across the habitats the unvegetated presented higher taxonomic homogeneity and functionally heterogeneity, contrary the vegetated habitats present higher taxonomic variability and functional homogeneity. Across the seasons and habitats a pattern of functional redundancy and taxonomic replacement was identified. Besides high functional turnover versus low taxonomic turnover was documented in an anthropogenic organically enriched habitat We conclude that habitats display independent functional and taxonomic seasonal patterns, thus different processes may contribute to their variability. The framework presented here highlights the importance of studying both β-diversity components framed in a multiscale approach to better understand ecological processes and variability patterns. These results are important to understand macroinvertebrate community assembly processes and are valuable for conservation purposes.

  14. Towards stressor-specific macroinvertebrate indices: Which traits and taxonomic groups are associated with vulnerable and tolerant taxa?

    Science.gov (United States)

    Berger, Elisabeth; Haase, Peter; Schäfer, Ralf B; Sundermann, Andrea

    2018-04-01

    Monitoring of macroinvertebrate communities is frequently used to define the ecological health status of rivers. Ideally, biomonitoring should also give an indication on the major stressors acting on the macroinvertebrate communities supporting the selection of appropriate management measures. However, most indices are affected by more than one stressor. Biological traits (e.g. size, generation time, reproduction) could potentially lead to more stressor-specific indices. However, such an approach has rarely been tested. In this study we classify 324 macroinvertebrate taxa as vulnerable (decreasing abundances) or tolerant (increasing abundances) along 21 environmental gradients (i.e. nutrients, major ions, oxygen and micropollutants) from 422 monitoring sites in Germany using Threshold Indicator Taxa Analysis (TITAN). Subsequently, we investigate which biological traits and taxonomic groups are associated with taxa classified as vulnerable or tolerant with regard to specific gradients. The response of most taxa towards different gradients was similar and especially high for correlated gradients. Traits associated with vulnerable taxa across most gradients included: larval aquatic life stages, isolated cemented eggs, reproductive cycle per year macrophytes, microphytes, silt or mud and a body size >2-4cm. Our results question whether stressor-specific indices based on macroinvertebrate assemblages can be achieved using single traits, because we observed that similar taxa responded to different gradients and also similar traits were associated with vulnerable and tolerant taxa across a variety of water quality gradients. Future studies should examine whether combinations of traits focusing on specific taxonomic groups achieve higher stressor specificity. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Global taxonomic diversity of anomodonts (tetrapoda, therapsida and the terrestrial rock record across the Permian-Triassic boundary.

    Directory of Open Access Journals (Sweden)

    Jörg Fröbisch

    Full Text Available The end-Permian biotic crisis (~252.5 Ma represents the most severe extinction event in Earth's history. This paper investigates diversity patterns in Anomodontia, an extinct group of therapsid synapsids ('mammal-like reptiles', through time and in particular across this event. As herbivores and the dominant terrestrial tetrapods of their time, anomodonts play a central role in assessing the impact of the end-Permian extinction on terrestrial ecosystems. Taxonomic diversity analysis reveals that anomodonts experienced three distinct phases of diversification interrupted by the same number of extinctions, i.e. an end-Guadalupian, an end-Permian, and a mid-Triassic extinction. A positive correlation between the number of taxa and the number of formations per time interval shows that anomodont diversity is biased by the Permian-Triassic terrestrial rock record. Normalized diversity curves indicate that anomodont richness continuously declines from the Middle Permian to the Late Triassic, but also reveals all three extinction events. Taxonomic rates (origination and extinction indicate that the end-Guadalupian and end-Permian extinctions were driven by increased rates of extinction as well as low origination rates. However, this pattern is not evident at the final decline of anomodont diversity during the Middle Triassic. Therefore, it remains unclear whether the Middle Triassic extinction represents a gradual or abrupt event that is unique to anomodonts or more common among terrestrial tetrapods. The end-Permian extinction represents the most distinct event in terms of decline in anomodont richness and turnover rates.

  16. Re-establishing dignity

    DEFF Research Database (Denmark)

    Høy, Bente; Hall, E.O.C

    2012-01-01

    appearance’. The study documents that caring for older people is about creating small everyday circumstances in which patient dignity can flourish. Shortcomings of a secondary analysis are discussed and suggestions for future research, such as how older hospital patients experience caring and dignity...

  17. A STUDY ESTABLISHING THE IMPORTANCE OF BODY COMPOSITION ANALYSIS, REGULAR PHYSIOTHERAPY AND DIETARY MODIFICATIONS FOR INDEPENDENT AND HEALTHY LIVING AMONG GERIATRIC POPULATION: A DETAILED SYSTEMATIC REVIEW ARTICLE

    Directory of Open Access Journals (Sweden)

    Rohit Subhedar

    2015-10-01

    Full Text Available Background: This systematic review article aims towards comprehensive and elaborative collection of research articles related to the importance of body composition analysis, Physiotherapy and nutrition for independent geriatric lifestyle. The review article includes articles which suggest the importance of Body composition analysis, Physiotherapy interventions, specific exercises and a combination of fat free, fiber, fruit and fluid diet. Methods: A comprehensive electronic search was conducted using electronic databases Pub Med, MEDLINE, Google Scholar, Science Direct, Research gate, ICMJE, DOAJ, DRJI, IOSR, WAME and many others. In Total 3714, Research papers were reviewed which reported, Age ≥50 years, changes in Body composition in elderly , effects of Diet &Exercises on Body composition and effects of regular Physiotherapy in Geriatric health and obesity. Literature search was restricted to the studies conducted during 1980-2015. Results: Finally 55 papers along with references in research proposal were included. Review shows that ageing, body composition, Physiotherapeutic intervention and nutrition play an interdependent role in providing independent and healthy living among geriatric population. Conclusion: Combined and comprehensive interventions in form of periodic Body Composition Analysis, Physiotherapy interventions with Exercise therapy sessions and Nutritional Supplementation, will be more effective in combating ageing and independent healthy living among Geriatric population. Finally with this review we shall conclude that achieving perfect geriatric health depends upon awareness among the geriatric community to periodically analyze their body composition and regularly comply with exercise therapy sessions, subjective Physiotherapy modality sessions and nutritional supplementation. These principles help in achieving physically fit, healthy, happy and independent geriatric Community.

  18. Risoe Research Establishment, Denmark

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1973-07-01

    On the poetic Roskilde Fjord, 40 kilometers from Copenhagen, and near Roskilde, capital of Denmark in the 12th century, stands the Risoe Research Establishment of the Danish Atomic Energy Commission. ere 700 men and women are engaged in searching for ways in which atomic energy can be used to make the world a better and healthier place. The work at Risoe comprises fundamental research, reactor technology and other technological studies, agricultural research and health and safety studies. Nuclear power stations are scheduled to be operative in Denmark some time between 1975 and 1980, and the planning of these stations and development of the many processes this will involve has become a major task at Risoe. Special conditions have to be fulfilled in selecting the site of an atomic research station, and the barren Risoe peninsula had them all: safety, because the site was free from buildings to permit continuous control; closeness to the scientific institutions of the capital, Copenhagen; social amenities in Roskilde; finally, access to an a adequate water supply. his special series of photos covering some aspects of the work and safety conditions at Risoe was commissioned by WHO. (author)

  19. Risoe Research Establishment, Denmark

    International Nuclear Information System (INIS)

    1973-01-01

    On the poetic Roskilde Fjord, 40 kilometers from Copenhagen, and near Roskilde, capital of Denmark in the 12th century, stands the Risoe Research Establishment of the Danish Atomic Energy Commission. ere 700 men and women are engaged in searching for ways in which atomic energy can be used to make the world a better and healthier place. The work at Risoe comprises fundamental research, reactor technology and other technological studies, agricultural research and health and safety studies. Nuclear power stations are scheduled to be operative in Denmark some time between 1975 and 1980, and the planning of these stations and development of the many processes this will involve has become a major task at Risoe. Special conditions have to be fulfilled in selecting the site of an atomic research station, and the barren Risoe peninsula had them all: safety, because the site was free from buildings to permit continuous control; closeness to the scientific institutions of the capital, Copenhagen; social amenities in Roskilde; finally, access to an a adequate water supply. his special series of photos covering some aspects of the work and safety conditions at Risoe was commissioned by WHO. (author)

  20. Anatomically preserved "strobili" and leaves from the Permian of China (Dorsalistachyaceae, fam. nov.) broaden knowledge of Noeggerathiales and constrain their possible taxonomic affinities.

    Science.gov (United States)

    Wang, Shi-Jun; Bateman, Richard M; Spencer, Alan R T; Wang, Jun; Shao, Longyi; Hilton, Jason

    2017-01-01

    Noeggerathiales are an extinct group of heterosporous shrubs and trees that were widespread and diverse during the Pennsylvanian-Permian Epochs (323-252 Ma) but are of controversial taxonomic affinity. Groups proposed as close relatives include leptosporangiate ferns, sphenopsids, progymnosperms, or the extant eusporangiate fern Tmesipteris. Previously identified noeggerathialeans lacked anatomical preservation, limiting taxonomic comparisons to their external morphology and spore structure. We here document from the upper Permian of China the first anatomically preserved noeggerathialeans, which enhance the perceived distinctiveness of the group and better indicate its systematic affinity. We describe in detail the newly discovered, anatomically preserved heterosporous strobilus Dorsalistachya quadrisegmentorum, gen. et sp. nov., and redescribe its suspected foliar correlate, the pinnate leaf Plagiozamites oblongifolius. Plagiozamites possesses an omega (Ω)-shaped vascular trace and prominent cortical secretory cavities-a distinctive anatomical organization that is echoed in the newly discovered strobili. Dorsalistachya strobili bear highly dissected sporophylls alternately in two vertical rows, suggesting that they are homologs of leaf pinnae. If so, the "strobilus" is strictly a pseudostrobilus and consists of sporangium-bearing units that are one hierarchical level below true sporophylls. The "sporophylls" bear four microsporangia on the lower (abaxial) surface, occasionally interspersed with short longitudinal rows of megasporangia. A single functional megaspore develops within each winged megasporangium, suggesting adaptation for dispersal as a single unit. Dorsalistachya presents a unique combination of reproductive features that amply justifies establishment of a new family, Dorsalistachyaceae. Noeggerathiales represent a distinct taxonomic Order of free-sporing plants that most resembles early-divergent eusporangiate ferns and the more derived among the

  1. Interpreting "Personality" Taxonomies: Why Previous Models Cannot Capture Individual-Specific Experiencing, Behaviour, Functioning and Development. Major Taxonomic Tasks Still Lay Ahead.

    Science.gov (United States)

    Uher, Jana

    2015-12-01

    As science seeks to make generalisations, a science of individual peculiarities encounters intricate challenges. This article explores these challenges by applying the Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals (TPS-Paradigm) and by exploring taxonomic "personality" research as an example. Analyses of researchers' interpretations of the taxonomic "personality" models, constructs and data that have been generated in the field reveal widespread erroneous assumptions about the abilities of previous methodologies to appropriately represent individual-specificity in the targeted phenomena. These assumptions, rooted in everyday thinking, fail to consider that individual-specificity and others' minds cannot be directly perceived, that abstract descriptions cannot serve as causal explanations, that between-individual structures cannot be isomorphic to within-individual structures, and that knowledge of compositional structures cannot explain the process structures of their functioning and development. These erroneous assumptions and serious methodological deficiencies in widely used standardised questionnaires have effectively prevented psychologists from establishing taxonomies that can comprehensively model individual-specificity in most of the kinds of phenomena explored as "personality", especially in experiencing and behaviour and in individuals' functioning and development. Contrary to previous assumptions, it is not universal models but rather different kinds of taxonomic models that are required for each of the different kinds of phenomena, variations and structures that are commonly conceived of as "personality". Consequently, to comprehensively explore individual-specificity, researchers have to apply a portfolio of complementary methodologies and develop different kinds of taxonomies, most of which have yet to be developed. Closing, the article derives some meta-desiderata for future research on individuals' "personality".

  2. Detailed oil spill contingency analysis in establishment of preparedness plans for exploration drilling in environmentally sensitive areas: an integrated management process

    Energy Technology Data Exchange (ETDEWEB)

    Spikkerud, Cathrine S.; Skeie, Geir Morten; Brude, Odd Willy; Gravir, Gjermund [DNV Managing Risk, Oslo (Norway)

    2008-07-01

    This paper describes the integrated management process leading up to a dynamic oil spill preparedness plan based on detailed analysis of oil spill contingency requirements and environmental risk in environmentally sensitive areas. Starting with a detailed environmental risk and oil spill contingency analysis, oil spill preparedness plans are developed. These plans are generic for the area possibly affected by an oil spill, and are developed in detail for environmental 'hot spots' that are highly challenging in terms of oil spill response. The detailed plans make use of detailed data sets on shoreline substrate sensitivities and cleanup methodology, photographic inventory, logistical issues and access to real-time incident data for important areas. This detailed approach ensures sufficient knowledge about the sensitive area in advance to provide fast and correct strategic and tactical operational recovery decisions. A final element of the integrated process is a web based GIS, providing all parties involved with one common situation overview, ensuring that the facts remain in focus throughout the operation and that those responsible for informing stake-holders have access to correct and timely updated information. (author)

  3. Establishment and Analysis of Cancer Stem-Like and Non-Cancer Stem-Like Clone Cells from the Human Colon Cancer Cell Line SW480.

    Directory of Open Access Journals (Sweden)

    Akari Takaya

    Full Text Available Human cancer stem-like cells (CSCs/cancer-initiating cells (CICs can be isolated as side population (SP cells, aldehyde dehydrogenase high (ALDHhigh cells or cell surface marker-positive cells including CD44+ cells and CD133+ cells. CSCs/CICs and non-CSCs/CICs are unstable in in vitro culture, and CSCs/CICs can differentiate into non-CSCs/CICs and some non-CSCs/CICs can dedifferentiate into CSCs/CICs. Therefore, experiments using a large amount of CSCs/CICs are technically very difficult. In this study, we isolated single cell clones from SP cells and main population (MP cells derived from the human colon cancer cell line SW480. SP analysis revealed that SP clone cells had relatively high percentages of SP cells, whereas MP clone cells showed very few SP cells, and the phenotypes were sustainable for more than 2 months of in vitro culture. Xenograft transplantation revealed that SP clone cells have higher tumor-initiating ability than that of MP clone cells and SP clone cell showed higher chemo-resistance compared with MP clone cells. These results indicate that SP clone cells derived from SW480 cells are enriched with CSCs/CICs, whereas MP clone cells are pure non-CSCs/CICs. SP clone cells and MP clone cells are a very stable in vitro CSC/CIC-enriched and non-CSC/CIC model for further analysis.

  4. Establishment and Analysis of Cancer Stem-Like and Non-Cancer Stem-Like Clone Cells from the Human Colon Cancer Cell Line SW480.

    Science.gov (United States)

    Takaya, Akari; Hirohashi, Yoshihiko; Murai, Aiko; Morita, Rena; Saijo, Hiroshi; Yamamoto, Eri; Kubo, Terufumi; Nakatsugawa, Munehide; Kanaseki, Takayuki; Tsukahara, Tomohide; Tamura, Yasuaki; Takemasa, Ichiro; Kondo, Toru; Sato, Noriyuki; Torigoe, Toshihiko

    2016-01-01

    Human cancer stem-like cells (CSCs)/cancer-initiating cells (CICs) can be isolated as side population (SP) cells, aldehyde dehydrogenase high (ALDHhigh) cells or cell surface marker-positive cells including CD44+ cells and CD133+ cells. CSCs/CICs and non-CSCs/CICs are unstable in in vitro culture, and CSCs/CICs can differentiate into non-CSCs/CICs and some non-CSCs/CICs can dedifferentiate into CSCs/CICs. Therefore, experiments using a large amount of CSCs/CICs are technically very difficult. In this study, we isolated single cell clones from SP cells and main population (MP) cells derived from the human colon cancer cell line SW480. SP analysis revealed that SP clone cells had relatively high percentages of SP cells, whereas MP clone cells showed very few SP cells, and the phenotypes were sustainable for more than 2 months of in vitro culture. Xenograft transplantation revealed that SP clone cells have higher tumor-initiating ability than that of MP clone cells and SP clone cell showed higher chemo-resistance compared with MP clone cells. These results indicate that SP clone cells derived from SW480 cells are enriched with CSCs/CICs, whereas MP clone cells are pure non-CSCs/CICs. SP clone cells and MP clone cells are a very stable in vitro CSC/CIC-enriched and non-CSC/CIC model for further analysis.

  5. A taxonomic monograph of Nearctic Scolytus Geoffroy (Coleoptera, Curculionidae, Scolytinae).

    Science.gov (United States)

    Smith, Sarah M; Cognato, Anthony I

    2014-01-01

    The Nearctic bark beetle genus Scolytus Geoffroy was revised based in part on a molecular and morphological phylogeny. Monophyly of the native species was tested using mitochondrial (COI) and nuclear (28S, CAD, ArgK) genes and 43 morphological characters in parsimony and Bayesian phylogenetic analyses. Parsimony analyses of molecular and combined datasets provided mixed results while Bayesian analysis recovered most nodes with posterior probabilities >90%. Native hardwood- and conifer-feeding Scolytus species were recovered as paraphyletic. Native Nearctic species were recovered as paraphyletic with hardwood-feeding species sister to Palearctic hardwood-feeding species rather than to native conifer-feeding species. The Nearctic conifer-feeding species were monophyletic. Twenty-five species were recognized. Four new synonyms were discovered: Scolytuspraeceps LeConte, 1868 (= Scolytusabietis Blackman, 1934; = Scolytusopacus Blackman, 1934), Scolytusreflexus Blackman, 1934 (= Scolytusvirgatus Bright, 1972; = Scolytuswickhami Blackman, 1934). Two species were reinstated: Scolytusfiskei Blackman, 1934 and Scolytussilvaticus Bright, 1972. A diagnosis, description, distribution, host records and images were provided for each species and a key is presented to all species.

  6. Corporate and philanthropic models of hospital governance: a taxonomic evaluation.

    Science.gov (United States)

    Weiner, B J; Alexander, J A

    1993-08-01

    We assess the theoretical integrity and practical utility of the corporate-philanthropic governance typology frequently invoked in debates about the appropriate form of governance for nonprofit hospitals operating in increasingly competitive health care environments. Data were obtained from a 1985 national mailed survey of nonprofit hospitals conducted by the American Hospital Association (AHA) and the Hospital Research and Educational Trust (HRET). A sample 1,577 nonprofit community hospitals were selected for study. Representativeness was assessed by comparing the sample with the population of non-profit community hospitals on the dimensions of bed size, ownership type, urban-rural location, multihospital system membership, and census region. Measurement of governance types was based on hospital governance attributes conforming to those cited in the literature as distinguishing corporate from philanthropic models and classified into six central dimensions of governance: (1) size, (2) committee structure and activity, (3) board member selection, (4) board composition, (5) CEO power and influence, and (6) bylaws and activities. Cluster analysis and ANCOVA indicated that hospital board forms adhered only partially to corporate and philanthropic governance models. Further, board forms varied systematically by specific organizational and environmental conditions. Boards exhibiting more corporate governance forms were more likely to be large, privately owned, urban, and operating in competitive markets than were hospitals showing more philanthropic governance forms. Findings suggest that the corporate-philanthropic governance distinction must be seen as an ideal rather than an actual depiction of hospital governance forms. Implications for health care governance are discussed.

  7. Analysis on learning curves of end-use appliances for the establishment of price-sensitivity load model in competitive electricity market

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Sung Wook; Kim, Jung Hoon [Hongik University (Korea); Song, Kyung Bin [Keimyung University (Korea); Choi, Joon Young [Jeonju University (Korea)

    2001-07-01

    The change of the electricity charge from cost base to price base due to the introduction to the electricity market competition causes consumer to choose a variety of charge schemes and a portion of loads to be affected by this change. Besides, it is required the index that consolidate the price volatility experienced on the power exchange with gaming and strategic bidding by suppliers to increase profits. Therefore, in order to find a mathematical model of the sensitively-responding to-price loads, the price-sensitive load model is needed. And the development of state-of- the-art technologies affects the electricity price, so the diffusion of high-efficient end-uses and these price affect load patterns. This paper shows the analysis on learning curves algorithms which is used to investigate the correlation of the end-uses' price and load patterns. (author). 6 refs., 4 figs., 4 tabs.

  8. A cephalometric analysis of Class II dentate subjects to establish a formula to determine the occlusal plane in Class II edentate subjects: A neo adjunct.

    Science.gov (United States)

    Sinha, Nikita; Reddy, K Mahendranadh; Gupta, Nidhi; Shastry, Y M

    2017-01-01

    Occlusal plane (OP) differs considerably in participants with skeletal Class I and Class II participants. In this study, cephalometrics has been used to help in the determination of orientation of the OP utilizing the nonresorbable bony anatomic landmarks in skeletal Class II participants and an attempt has been made to predict and examine the OP in individuals with skeletal class II jaw relationship. One hundred dentulous participants with skeletal Class II malocclusion who came to the hospital for correcting their jaw relationship participated in the study. Their right lateral cephalogram was taken using standardized procedures, and all the tracings were manually done by a single trained examiner. The cephalograms which were taken for the diagnostic purpose were utilized for the study, and the patient was not exposed to any unnecessary radiation. The numerical values obtained from the cephalograms were subjected to statistical analysis. Pearson's correlation of orientation of the OP in Class II edentulous participants. Pearson's correlation coefficient and linear regression analysis were performed, and a high correlation was found between A2 and (A2 + B2)/(B2 + C2) with " r " value of 0.5. A medium correlation was found between D2 and (D2 + E2)/(E2 + F2) with " r " value of 0.42. The formula obtained for posterior reference frame through linear regression equation was y = 0.018* × +0.459 and the formula obtained for anterior reference frame was y1 = 0.011* × 1 + 0.497. It was hypothesized that by substituting these formulae in the cephalogram obtained from the Class II edentate individual, the OP can be obtained and verified. It was concluded that cephalometrics can be useful in examining the orientation of OP in skeletal Class II participants.

  9. Establishment of a simple and rapid identification method for Listeria spp. by using high-resolution melting analysis, and its application in food industry.

    Science.gov (United States)

    Ohshima, Chihiro; Takahashi, Hajime; Phraephaisarn, Chirapiphat; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

    2014-01-01

    Listeria monocytogenes is the causative bacteria of listeriosis, which has a higher mortality rate than that of other causes of food poisoning. Listeria spp., of which L. monocytogenes is a member, have been isolated from food and manufacturing environments. Several methods have been published for identifying Listeria spp.; however, many of the methods cannot identify newly categorized Listeria spp. Additionally, they are often not suitable for the food industry, owing to their complexity, cost, or time consumption. Recently, high-resolution melting analysis (HRMA), which exploits DNA-sequence differences, has received attention as a simple and quick genomic typing method. In the present study, a new method for the simple, rapid, and low-cost identification of Listeria spp. has been presented using the genes rarA and ldh as targets for HRMA. DNA sequences of 9 Listeria species were first compared, and polymorphisms were identified for each species for primer design. Species specificity of each HRM curve pattern was estimated using type strains of all the species. Among the 9 species, 7 were identified by HRMA using rarA gene, including 3 new species. The remaining 2 species were identified by HRMA of ldh gene. The newly developed HRMA method was then used to assess Listeria isolates from the food industry, and the method efficiency was compared to that of identification by 16S rDNA sequence analysis. The 2 methods were in coherence for 92.6% of the samples, demonstrating the high accuracy of HRMA. The time required for identifying Listeria spp. was substantially low, and the process was considerably simplified, providing a useful and precise method for processing multiple samples per day. Our newly developed method for identifying Listeria spp. is highly valuable; its use is not limited to the food industry, and it can be used for the isolates from the natural environment.

  10. Variable-Number Tandem-Repeat Analysis of Respiratory and Household Water Biofilm Isolates of “Mycobacterium avium subsp. hominissuis” with Establishment of a PCR Database

    Science.gov (United States)

    Iakhiaeva, Elena; Howard, Susan T.; Brown Elliott, Barbara A.; McNulty, Steven; Newman, Kristopher L.; Falkinham, Joseph O.; Williams, Myra; Kwait, Rebecca; Lande, Leah; Vasireddy, Ravikiran; Turenne, Christine

    2016-01-01

    “Mycobacterium avium subsp. hominissuis” is an important cause of pulmonary disease. It is acquired from environmental sources, but there is no methodology for large population studies. We evaluated the potential of variable-number tandem-repeat (VNTR) analysis. Clinical and household biofilm M. avium isolates underwent molecular identification. Testing for IS901 was done to separate M. avium subsp. avium from M. avium subsp. hominissuis. VNTR types were defined using VNTR loci, and subtyping was performed using 3′ hsp65 and internal transcribed spacer (ITS) sequencing. Forty-nine VNTR types and eight subtypes of M. avium subsp. hominissuis (IS901 negative) were identified among 416 isolates of M. avium from 121 patients and 80 biofilm sites. Of those types, 67% were found only among patient isolates, 11% only among household water isolates, and 23% among both. Of 13 VNTR types that included ≥4 patients, the majority (61.5%) represented geographic clustering (same city). Most VNTR types with multiple patients belonged to the same 3′ hsp65 sequence code (sequevar). A total of 44 isolates belonging to four M. avium subsp. hominissuis VNTR types (8%), including three with the rare Mav-F ITS sequence and 0/8 subspecies, produced amplicons with IS901 PCR primers. By sequencing, all 44 amplicons were not IS901 but ISMav6, which was recently observed in Japan but had not been previously described among U.S. isolates. VNTR analysis of M. avium subsp. hominissuis isolates is easier and faster than pulsed-field gel electrophoresis. Seven VNTR loci separated 417 isolates into 49 types. No isolates of M. avium subsp. avium were identified. The distributions of the VNTR copy numbers, the allelic diversity, and the low prevalence of ISMav6 differed from the findings for respiratory isolates reported from Japan. PMID:26739155

  11. Instrumental neutron activation analysis as an analytical tool on supporting the establishment of guidelines and data basis for worker's health awareness program

    International Nuclear Information System (INIS)

    Menezes, Maria Angela de B.C.; Maia, Elene C.P.; Albinati, Claudia

    2002-01-01

    This investigation project was the first action in order to assess the elemental concentration level in a galvanising industry. Besides the Cr, one of the most important elements not considered essential for human beings in terms of health hazards and one of the most studied elements in this kind of industry, other elements such as Ag, Au and Sb were determined. Other elements considered essential as Fe, Cr, Cu, or essential in very small concentration like As, were determined but in high concentrations, playing, maybe, a role as toxic. This first study alerts for the need of assessing the influence of a long-term exposure to pollutants in the workplace. Scalp hair was used as bioindicator and the industry environment was evaluated through airborne particulate matter. The elemental concentration results have pointed out a high exposure to pollutants at workplaces and a high elemental concentration in biomonitors suggested endogenous contamination. The majority of elements determined in airborne particulate matter, 85%, were also determined in hair samples. This result evidences the efficiency of hair as biomonitor and the importance to carry out a simultaneous airborne particulate matter sampling mainly in occupational epidemiological studies. The k 0 Instrumental Neutron Activation Analysis was applied to all matrixes. (author)

  12. Automatic processing of semantic relations in fMRI: neural activation during semantic priming of taxonomic and thematic categories.

    Science.gov (United States)

    Sachs, Olga; Weis, Susanne; Zellagui, Nadia; Huber, Walter; Zvyagintsev, Mikhail; Mathiak, Klaus; Kircher, Tilo

    2008-07-07

    Most current models of knowledge organization are based on hierarchical or taxonomic categories (animals, tools). Another important organizational pattern is thematic categorization, i.e. categories held together by external relations, a unifying scene or event (car and garage). The goal of this study was to compare the neural correlates of these categories under automatic processing conditions that minimize strategic influences. We used fMRI to examine neural correlates of semantic priming for category members with a short stimulus onset asynchrony (SOA) of 200 ms as subjects performed a lexical decision task. Four experimental conditions were compared: thematically related words (car-garage); taxonomically related (car-bus); unrelated (car-spoon); non-word trials (car-derf). We found faster reaction times for related than for unrelated prime-target pairs for both thematic and taxonomic categories. However, the size of the thematic priming effect was greater than that of the taxonomic. The imaging data showed signal changes for the taxonomic priming effects in the right precuneus, postcentral gyrus, middle frontal and superior frontal gyri and thematic priming effects in the right middle frontal gyrus and anterior cingulate. The contrast of neural priming effects showed larger signal changes in the right precuneus associated with the taxonomic but not with thematic priming response. We suggest that the greater involvement of precuneus in the processing of taxonomic relations indicates their reduced salience in the knowledge structure compared to more prominent thematic relations.

  13. Biomechanical comparison of a new stand-alone anterior lumbar interbody fusion cage with established fixation techniques – a three-dimensional finite element analysis

    Directory of Open Access Journals (Sweden)

    Hsieh Pang-Hsing

    2008-06-01

    Full Text Available Abstract Background Initial promise of a stand-alone interbody fusion cage to treat chronic back pain and restore disc height has not been realized. In some instances, a posterior spinal fixation has been used to enhance stability and increase fusion rate. In this manuscript, a new stand-alone cage is compared with conventional fixation methods based on the finite element analysis, with a focus on investigating cage-bone interface mechanics and stress distribution on the adjacent tissues. Methods Three trapezoid 8° interbody fusion cage models (dual paralleled cages, a single large cage, or a two-part cage consisting of a trapezoid box and threaded cylinder were created with or without pedicle screws fixation to investigate the relative importance of the screws on the spinal segmental response. The contact stress on the facet joint, slip displacement of the cage on the endplate, and rotational angle of the upper vertebra were measured under different loading conditions. Results Simulation results demonstrated less facet stress and slip displacement with the maximal contact on the cage-bone interface. A stand-alone two-part cage had good slip behavior under compression, flexion, extension, lateral bending and torsion, as compared with the other two interbody cages, even with the additional posterior fixation. However, the two-part cage had the lowest rotational angles under flexion and torsion, but had no differences under extension and lateral bending. Conclusion The biomechanical benefit of a stand-alone two-part fusion cage can be justified. This device provided the stability required for interbody fusion, which supports clinical trials of the cage as an alternative to circumferential fixations.

  14. Studies of labelling conditions for gentamicin with sup(99m)Tc. Complexation with ruthexium. Establishment of pharmacokinetics parameters through compartmental analysis

    International Nuclear Information System (INIS)

    Carvalho, O.G. de.

    1988-01-01

    Gentamicin sulphate is an aminoglycoside antibiotic type specifically used for treatment of infections produced by Gram-negative bacterias but at the other hand it presents ototoxic reactions as a serious side effect. The main purpose of labelling gentamicin with sup(99m)Tc was to obtain a radioactive tracer to carry out biological studies and compartmental analysis of this antibiotic. The optimal labelling conditions of gentamicin sulphate with sup(99m)Tc, using sodium pertechnetate solution eluted from a sup(99)Mo- sup(99m)Tc generator, were stablished by testing different masses of antibiotic, and reduction agent (SnCl sub(2).2H sub(2)O), and also different reaction time and final labelling PH. The same labelling procedure was used with Re (amonium perrenate) in order to obtain some semi-quantitative approximations of the chemical structure of the complex formed, since Re and Tc present similar chemical characteristics. In this way it is possible to suggest the role that the groups NH2 and C-O bonding of the gentamicin play in the complexation process. From the studies of the biological uptake of sup(99m)Tc-gentamicin sulphate in rats, the kidneys showed the highest affinity for the antibiotic. The maximum uptake was observed in 180 to 240 minutes followed by a decrease of it afterwards. For the dose and time used, no significative uptake by the auricular region was detected. Curve of plasma decay of sup(99m)Tc-gentamicin was obtained, and from the exponentials of each beanch of this curve respective half-lives were calculated. Furthermore the apparent volume of distribution was determined, and with the residual radioactivity in the body, the biological half-life and total clearance were obtained. The distribution of sup(99m)Tc-gentamicin in rats was set in a bi-compartments in addition to a retention one for the 24 hours time interval studied. (author)

  15. Morphological, Physiological, and Taxonomic Characterization of Actinobacterial Isolates Living as Endophytes of Cacao Pods and Cacao Seeds.

    Science.gov (United States)

    Tchinda, Romaric Armel Mouafo; Boudjeko, Thaddée; Simao-Beaunoir, Anne-Marie; Lerat, Sylvain; Tsala, Éric; Monga, Ernest; Beaulieu, Carole

    2016-01-01

    Vascular plants are commonly colonized by endophytic actinobacteria. However, very little is known about the relationship between these microorganisms and cacao fruits. In order to determine the physiological and taxonomic relationships between the members of this community, actinobacteria were isolated from cacao fruits and seeds. Among the 49 isolates recovered, 11 morphologically distinct isolates were selected for further characterization. Sequencing of the 16S rRNA gene allowed the partition of the selected isolates into three phylogenetic clades. Most of the selected endophytic isolates belonged to the Streptomyces violaceusniger clade. Physiological characterization was carried out and a similarity index was used to cluster the isolates. However, clustering based on physiological properties did not match phylogenetic lineages. Isolates were also characterized for traits commonly associated with plant growth-promoting bacteria, including antibiosis and auxin biosynthesis. All isolates exhibited resistance to geldanamycin, whereas only two isolates were shown to produce this antibiotic. Endophytes were inoculated on radish seedlings and most isolates were found to possess plant growth-promoting abilities. These endophytic actinobacteria inhibited the growth of various plant pathogenic fungi and/or bacteria. The present study showed that S. violaceusniger clade members represent a significant part of the actinobacterial community living as endophytes in cacao fruits and seeds. While several members of this clade are known to be geldanamycin producers and efficient biocontrol agents of plant diseases, we herein established the endophytic lifestyle of some of these microorganisms, demonstrating their potential as plant health agents.

  16. Different Influences on Lexical Priming for Integrative, Thematic, and Taxonomic Relations

    Directory of Open Access Journals (Sweden)

    Lara L. Jones

    2012-07-01

    Full Text Available Word pairs may be integrative (i.e., combination of two concepts into one meaningful entity; e.g., fruit - cake, thematically related (i.e., connected in time and place; e.g., party - cake, and/or taxonomically related (i.e., shared features and category co-members; e.g., muffin - cake. Using participant ratings and computational measures, we demonstrated distinct patterns across measures of similarity and co-occurrence, and familiarity for each relational construct in two different item sets. Overall, target RTs and priming magnitudes were consistent across the SOAs for both item sets. However, results of a standard lexical decision task with various delays between prime and target presentation further demonstrated distinct patterns among these three relations on some of the underlying measures influencing target word recognition (LSA, Google, and BEAGLE. These distinct patterns suggest different mechanisms of lexical priming and further demonstrate that integrative relations are distinct from thematic and taxonomic relations.

  17. How to deal with cryptic species in Enchytraeidae, with recommendations on taxonomical descriptions

    Directory of Open Access Journals (Sweden)

    Schmelz, R. M.

    2017-11-01

    Full Text Available During the 12th International Symposium on Enchytraeidae, held in Tihany, Hungary (27–29 June 2016, the participants discussed cryptic species, i.e., species that are morphologically so similar that they are classified as the same species (Bickford et al. 2007, and how to deal with them taxonomically. Here we summarise the discussion together with a few additional comments, and we give recommendations for species descriptions in Enchytraeidae.

  18. The Identification, Types, Taxonomic Orders, Biodiversity and Importance of Aquatic Insects

    OpenAIRE

    J.F.N. Abowei; B.R. Ukoroije

    2012-01-01

    The identification, types, taxonomic orders, biodiversity and importance of aquatic insects was reviewed to facilitate sustainable culture fisheries management and practice. Aquatic insects contribute significantly to fresh water ecosystems, one of many groups of organisms that, together, must be considered in the study of aquatic ecology. As such their study may be a significant part of understanding the ecological state of a given ecosystem and in gauging how that ecosystem will respond to ...

  19. Non-native vascular plants from Canary Islands (Spain): nomenclatural and taxonomical adjustments

    OpenAIRE

    Verloove, F.

    2013-01-01

    Se propone correcciones taxonómicas y nomenclaturales respecto a 88 taxones no nativos de la lista de plantas vasculares de las Islas Canarias (España). Non-native vascular plants from Canary Islands (Spain): nomenclatural and taxonomical adjustments. Corrections and other adjustments are proposed for 88 non-native taxa from the checklist of vascular plants from the Canary Islands (Spain).

  20. Colombian coca plants. A critical discussion on taxonomic aspects of cultivated Erythroxylum species (Erythroxylaceae)

    International Nuclear Information System (INIS)

    Galindo Bonilla, Aida; Fernandez Alonzo, Jose Luis

    2010-01-01

    Forensic botany is in high demand in Colombia in connection with plant material, mainly coca from illicit crops. The taxonomic study of the two species and four varieties of Erythroxylum P. Browne (Erythroxylaceae) cultivated in Colombia was carried out. Hybridization between E. coca and E. novogranatense and between the two varieties of E. coca is suggested, and important changes in the geographic distribution of all taxa are described. Both, hybridization and changes in distribution patterns are due to anthropic intervention.

  1. Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

    Directory of Open Access Journals (Sweden)

    Luis F Aguirre

    Full Text Available Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups. Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for

  2. Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

    Science.gov (United States)

    Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

    2016-01-01

    Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

  3. The taxonomic identity of Heliconius melpomene f. pyritosa var. fumigata Zikán (Lepidoptera: Nymphalidae

    Directory of Open Access Journals (Sweden)

    André Victor Lucci Freitas

    2015-06-01

    Full Text Available The taxonomic identity of the butterfly Heliconius melpomene f. pyritosa var. fumigata Zikán, 1937 (Nymphalidae: Heliconiinae is discussed based on the discovery of the specimen based on which this name was assigned. The specimen is not a variation of Eueides tales surdus Stichel, 1903, as previously stated, but is in fact a variation of H. melpomene f. pyritosa, which is a synonym of Heliconius erato amalfreda Riffarth, 1901.

  4. Critical Taxonomic Appraisal of Some Taxa of Pedicularis from Indian Himalayas Belonging to Section Siphonanthae

    Directory of Open Access Journals (Sweden)

    Arti Garg

    2009-06-01

    Full Text Available The existing confusion on the taxonomic status of five taxa of Pedicularis viz. P. punctata Decne, P. siphonantha D. Don, P. hookeriana Wall. ex Benth., P. megalantha D. Don and P. hoffmeisteri Kl. ex Kl. & Garcke is resolved on the basis of critical morphological study. These taxa belong to section Siphonanthae, subgenus Longirostres. Pennell’s view of segregating these taxa into distinct species is defended and upheld.

  5. A taxonomic revision of Maurocenia (Celastraceae, a Western Cape monotypic endemic

    Directory of Open Access Journals (Sweden)

    R. H. Archer

    1998-10-01

    Full Text Available A taxonomic account is given of the monotypic genus Maurocenia Mill. Maurocenia frangula Mill, has a restricted range and is endemic to the Cape Peninsula and the West Coast National Park. Western Cape. Maurocenia frangularia (L.Mill., the species name and author citation widely used in the past, is incorrect. It is characterized by. among others, pendulous ovules and gynodioecy, rare states in the Celastraceae. Maurocenia is apparently most closely related to the southern African genus Lauridia Eckl. & Zeyh.

  6. Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae)

    OpenAIRE

    Wagner,Warren; Krakos,Kyra; Hoch,Peter C.

    2013-01-01

    Abstract The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had in...

  7. Morphological variation and taxonomic interpretation in the moss genus Bryum in Antarctica

    OpenAIRE

    Seppelt,Rodney D.; Kanda,Hiroshi

    1986-01-01

    The potential for morphological variation in Antarctic species of Bryum is evaluated and related to problems associated with taxonomic interpretation based on specimens from the Soya Coast, Mac. Robertson Coast, Vestfold Hills and Knox Coast. B. argenteum HEDW. Has been positively determined for Continental Antarctica from six localities on the Soya Coast and from Ross Island, southern Victoria Land. Specimens from the Vestfold Hills and Knox Coast considered with some reservation as this spe...

  8. Contrasting taxonomic and functional responses of a tropical tree community to selective logging

    OpenAIRE

    Baraloto, C.; Hérault, B.; Paine, C. E. T.; Massot, H.; Blanc, L.; Bonal, D.; Molino, Jean-François; Nicolini, E. A.; Sabatier, Daniel

    2012-01-01

    1. Considerable debate surrounds the extent to which tropical forests can be managed for resource extraction while conserving biodiversity and ecosystem properties, which depend on functional composition. Here we evaluate the compatibility of these aims by examining the effects of logging on taxonomic and functional diversity and composition in a tropical forest. 2. Twenty years after selective logging, we inventoried 4140 stems regenerating in logging gaps and adjacent undisturbed areas, and...

  9. Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles.

    Science.gov (United States)

    Tanner, Kristie; Martí, Jose Manuel; Belliure, Josabel; Fernández-Méndez, Mar; Molina-Menor, Esther; Peretó, Juli; Porcar, Manuel

    2018-02-01

    Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp. and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  10. The kinome of Phytophthora infestans reveals oomycete-specific innovations and links to other taxonomic groups

    Directory of Open Access Journals (Sweden)

    Ah-Fong Audrey MV

    2010-12-01

    Full Text Available Abstract Background Oomycetes are a large group of economically and ecologically important species. Its most notorious member is Phytophthora infestans, the cause of the devastating potato late blight disease. The life cycle of P. infestans involves hyphae which differentiate into spores used for dispersal and host infection. Protein phosphorylation likely plays crucial roles in these stages, and to help understand this we present here a genome-wide analysis of the protein kinases of P. infestans and several relatives. The study also provides new insight into kinase evolution since oomycetes are taxonomically distant from organisms with well-characterized kinomes. Results Bioinformatic searches of the genomes of P. infestans, P. ramorum, and P. sojae reveal they have similar kinomes, which for P. infestans contains 354 eukaryotic protein kinases (ePKs and 18 atypical kinases (aPKs, equaling 2% of total genes. After refining gene models, most were classifiable into families seen in other eukaryotes. Some ePK families are nevertheless unusual, especially the tyrosine kinase-like (TKL group which includes large oomycete-specific subfamilies. Also identified were two tyrosine kinases, which are rare in non-metazoans. Several ePKs bear accessory domains not identified previously on kinases, such as cyclin-dependent kinases with integral cyclin domains. Most ePKs lack accessory domains, implying that many are regulated transcriptionally. This was confirmed by mRNA expression-profiling studies that showed that two-thirds vary significantly between hyphae, sporangia, and zoospores. Comparisons to neighboring taxa (apicomplexans, ciliates, diatoms revealed both clade-specific and conserved features, and multiple connections to plant kinases were observed. The kinome of Hyaloperonospora arabidopsidis, an oomycete with a simpler life cycle than P. infestans, was found to be one-third smaller. Some differences may be attributable to gene clustering, which

  11. Distribution of taxonomic classes and the compositional structure of the astreroid belt

    International Nuclear Information System (INIS)

    Gradie, J.C.; Tedesco, E.F.

    1989-01-01

    The distribution of asteroid taxonomic classes and, presumably, actual composition varies systematically with heliocentric distance and is seen qualitatively in the results of a variety of taxonomy methods. In general, the distribution of taxonomic classes is characterized by moderate-albedo asteroids dominant in the inner belt with low-albedo asteroids prevalent in the outer belt and beyond. If the differences in taxonomic classes are assumed to be due to differences in composition, then the asteroid belt can be divided into many compositionally distinct regions defined by peaks and troughs in the distributions of the various classes. Unfortunately, differences in the class definitions used by different classification methods are manifested in the bias-corrected distribution of the classes, which makes detailed interpretation of these trends difficult. UBV color differences among members of the moderate-albedo S class show a distribution in semimajor axis which indicates subgroups in the S class. Explanations of the causes of the overall trends range from primarily dynamical to primarily in situ arrangements of igneous, metamorphic and unaltered primitive material, but a combination of several of these factors may be more likely

  12. Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals

    Science.gov (United States)

    Raia, P.; Carotenuto, F.; Passaro, F.; Piras, P.; Fulgione, D.; Werdelin, L.; Saarinen, J.; Fortelius, M.

    2013-01-01

    A classic question in evolutionary biology concerns the tempo and mode of lineage evolution. Considered variously in relation to resource utilization, intrinsic constraints or hierarchic level, the question of how evolutionary change occurs in general has continued to draw the attention of the field for over a century and a half. Here we use the largest species-level phylogeny of Coenozoic fossil mammals (1031 species) ever assembled and their body size estimates, to show that body size and taxonomic diversification rates declined from the origin of placentals towards the present, and very probably correlate to each other. These findings suggest that morphological and taxic diversifications of mammals occurred hierarchically, with major shifts in body size coinciding with the birth of large clades, followed by taxonomic diversification within these newly formed clades. As the clades expanded, rates of taxonomic diversification proceeded independently of phenotypic evolution. Such a dynamic is consistent with the idea, central to the Modern Synthesis, that mammals radiated adaptively, with the filling of adaptive zones following the radiation. PMID:23173207

  13. Notes on the taxonomic position