Taxonomic triage and the poverty of phylogeny.

PubMed Central

Wheeler, Quentin D

2004-01-01

Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis-driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high-throughput species hypothesis-testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age. PMID:15253345

Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation

PubMed Central

Sangster, George

2009-01-01

The impact and significance of modern taxonomy on other fields in biology have been subjects of much debate. It has been proposed that increasing numbers of vertebrate species are largely owing to ‘taxonomic inflation’. According to this hypothesis, newly recognized species result from reinterpretations of species limits based on phylogenetic species concepts (PSCs) rather than from new discoveries. Here, I examine 747 proposals to change the taxonomic rank of birds in the period 1950–2007. The trend to recognize more species of birds started at least two decades before the introduction of PSCs. Most (84.6%) newly recognized species were supported by new taxonomic data. Proposals to recognize more species resulted from application of all six major taxonomic criteria. Many newly recognized species (63.4%) were not based exclusively on PSC-based criteria (diagnosability, monophyly and exclusive coalescence of gene trees). Therefore, this study finds no empirical support for the idea that the increase in species is primarily epistemological rather than data-driven. This study shows that previous claims about the causes and effects of taxonomic inflation lack empirical support. I argue that a more appropriate term for the increase in species is ‘taxonomic progress’. PMID:19520805

Taxonomic bias in biodiversity data and societal preferences.

PubMed

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.

Chinese deaf adolescents' free recall of taxonomic, slot-filler, and thematic categories.

PubMed

Li, Degao; Zhang, Jijia

2009-08-01

Four experiments were conducted to show that deaf adolescents tended to process information in different ways from hearing adolescents. Memorizing items sequentially shown on computer screens under the control of their articulators' movements, deaf adolescents tended to treat items that cohered as taxonomic, thematic, or slot-filler categories as isolated pieces of information. Having to perceive information by means of sign language, however, their achievements were not worse than those of hearing adolescents anymore, no matter whether the stimuli were presented as words or pictures. They could not only utilize categories relations to help memorize categories exemplars but were relatively better aware of slot-filler or thematic than taxonomic relations as well, suggesting that they had a relatively delayed development of taxonomic category representations in comparison with hearing adolescents.

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

PubMed

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.

Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

PubMed

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.

Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

PubMed Central

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. PMID:25700173

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae)

PubMed Central

Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G.

2018-01-01

Abstract 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. PMID:29416412

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae).

PubMed

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.

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods

PubMed Central

Dröge, J.; Gregor, I.; McHardy, A. C.

2015-01-01

Motivation: Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows identifying the sequenced community members and reconstructing taxonomic bins with sequence data for the individual taxa. For the massive datasets generated by next-generation sequencing technologies, this cannot be performed with de-novo phylogenetic inference methods. We describe an algorithm and the accompanying software, taxator-tk, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities. Results: Taxator-tk was precise in its taxonomic assignment across all ranks and taxa for a range of evolutionary distances and for short as well as for long sequences. In addition to the taxonomic binning of metagenomes, it is well suited for profiling microbial communities from metagenome samples because it identifies bacterial, archaeal and eukaryotic community members without being affected by varying primer binding strengths, as in marker gene amplification, or copy number variations of marker genes across different taxa. Taxator-tk has an efficient, parallelized implementation that allows the assignment of 6 Gb of sequence data per day on a standard multiprocessor system with 10 CPU cores and microbial RefSeq as the genomic reference data. Availability and implementation: Taxator-tk source and binary program files are publicly available at http://algbio.cs.uni-duesseldorf.de/software/. Contact: Alice.McHardy@uni-duesseldorf.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388150

The LifeWatch approach to the exploration of distributed species information

PubMed Central

Fuentes, Daniel; Fiore, Nicola

2014-01-01

Abstract This paper introduces a new method of automatically extracting, integrating and presenting information regarding species from the most relevant online taxonomic resources. First, the information is extracted and joined using data wrappers and integration solutions. Then, an analytical tool is used to provide a visual representation of the data. The information is then integrated into a user friendly content management system. The proposal has been implemented using data from the Global Biodiversity Information Facility (GBIF), the Catalogue of Life (CoL), the World Register of Marine Species (WoRMS), the Integrated Taxonomic Information System (ITIS) and the Global Names Index (GNI). The approach improves data quality, avoiding taxonomic and nomenclature errors whilst increasing the availability and accessibility of the information. PMID:25589865

The Neural Bases of Taxonomic and Thematic Conceptual Relations: An MEG Study

PubMed Central

Lewis, Gwyneth A.; Poeppel, David; Murphy, Gregory L.

2015-01-01

Converging evidence from behavioral and neuroimaging studies of human concepts indicate distinct neural systems for taxonomic and thematic knowledge. A recent study of naming in aphasia found involvement of the anterior temporal lobe (ATL) during taxonomic (feature-based) processing, and involvement of the temporoparietal junction (TPJ) during thematic (function-based) processing. We conducted an online magnetoencephalography (MEG) study to examine the spatio-temporal nature of taxonomic and thematic relations. We measured participants’ brain responses to words preceded by either a taxonomically or thematically related item (e.g., cottage→castle, king→castle). In a separate experiment we collected relatedness ratings of the word pairs from participants. We examined effects of relatedness and relation type on activation in ATL and TPJ regions of interest (ROIs) using permutation t-tests to identify differences in ROI activation between conditions as well as single-trial correlational analyses to examine the millisecond-by-millisecond influence of the stimulus variables on the ROIs. Taxonomic relations strongly predicted ATL activation, and both kinds of relations influenced the TPJ. Our results further strengthen the view of the ATL's importance to taxonomic knowledge. Moreover, they provide a nuanced view of thematic relations as involving taxonomic knowledge. PMID:25582406

Spatio-temporal variation of fish taxonomic composition in a South-East Asian flood-pulse system.

PubMed

Kong, Heng; Chevalier, Mathieu; Laffaille, Pascal; Lek, Sovan

2017-01-01

The Tonle Sap Lake (TSL) is a flood-pulse system. It is the largest natural lake in South-East Asia and constitutes one of the largest fisheries over the world, supporting the livelihood of million peoples. Nonetheless, the Mekong River Basin is changing rapidly due to accelerating water infrastructure development (hydropower, irrigation, flood control, and water supply) and climate change, bringing considerable modifications to the annual flood-pulse of the TSL. Such modifications are expected to have strong impacts on fish biodiversity and abundance. This paper aims to characterize the spatio-temporal variations of fish taxonomic composition and to highlights the underlying determinants of these variations. For this purpose, we used data collected from a community catch monitoring program conducted at six sites during 141 weeks, covering two full hydrological cycles. For each week, we estimated beta diversity as the total variance of the site-by-species community matrix and partitioned it into Local Contribution to Beta Diversity (LCBD) and Species Contribution to Beta Diversity (SCBD). We then performed multiple linear regressions to determine whether species richness, species abundances and water level explained the temporal variation in the contribution of site and species to beta diversity. Our results indicate strong temporal variation of beta diversity due to differential contributions of sites and species to the spatial variation of fish taxonomic composition. We further found that the direction, the shape and the relative effect of species richness, abundances and water level on temporal variation in LCBD and SCBD values greatly varied among sites, thus suggesting spatial variation in the processes leading to temporal variation in community composition. Overall, our results suggest that fish taxonomic composition is not homogeneously distributed over space and time and is likely to be impacted in the future if the flood-pulse dynamic of the system is

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

PubMed

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

Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

PubMed

Montaña, José Salvador; Jiménez, Diego Javier; Hernández, Mónica; Angel, Tatiana; Baena, Sandra

2012-02-01

Total metagenomic DNA was isolated from high Andean forest soil and subjected to taxonomical and functional composition analyses by means of clone library generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used to construct a metagenomic library of approximately 20,000 clones (in the plasmid p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs (0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX, resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer v3.8 software, respectively. Most clone sequences were classified as Bacteria belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the most represented orders were Actinomycetales (34% average), Rhizobiales, Burkholderiales and Myxococcales and with a greater number of sequences in the genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The vast majority of sequences were associated with the metabolism of carbohydrates, proteins, lipids and catalytic functions, such as phosphatases, glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and epoxide hydrolases. In this study we compared different methods of taxonomic and functional assignment of metagenomic clone sequences to evaluate microbial diversity in an unexplored soil ecosystem, searching for putative enzymes of biotechnological interest and generating important information for further functional screening of clone libraries.

An Information System for European culture collections: the way forward.

PubMed

Casaregola, Serge; Vasilenko, Alexander; Romano, Paolo; Robert, Vincent; Ozerskaya, Svetlana; Kopf, Anna; Glöckner, Frank O; Smith, David

2016-01-01

Culture collections contain indispensable information about the microorganisms preserved in their repositories, such as taxonomical descriptions, origins, physiological and biochemical characteristics, bibliographic references, etc. However, information currently accessible in databases rarely adheres to common standard protocols. The resultant heterogeneity between culture collections, in terms of both content and format, notably hampers microorganism-based research and development (R&D). The optimized exploitation of these resources thus requires standardized, and simplified, access to the associated information. To this end, and in the interest of supporting R&D in the fields of agriculture, health and biotechnology, a pan-European distributed research infrastructure, MIRRI, including over 40 public culture collections and research institutes from 19 European countries, was established. A prime objective of MIRRI is to unite and provide universal access to the fragmented, and untapped, resources, information and expertise available in European public collections of microorganisms; a key component of which is to develop a dynamic Information System. For the first time, both culture collection curators as well as their users have been consulted and their feedback, concerning the needs and requirements for collection databases and data accessibility, utilised. Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible. Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently. Moreover, complex searches are rarely possible in online databases thus limiting the extent of search queries. Curators also consider that overall harmonization-including Standard Operating Procedures, data structure, and software tools-is necessary to facilitate their work and to make high-quality data easily accessible

A Falsification of the Citation Impediment in the Taxonomic Literature

PubMed Central

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

2015-01-01

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

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.

PubMed

Mende, Daniel R; Letunic, Ivica; Huerta-Cepas, Jaime; Li, Simone S; Forslund, Kristoffer; Sunagawa, Shinichi; Bork, Peer

2017-01-04

The availability of microbial genomes has opened many new avenues of research within microbiology. This has been driven primarily by comparative genomics approaches, which rely on accurate and consistent characterization of genomic sequences. It is nevertheless difficult to obtain consistent taxonomic and integrated functional annotations for defined prokaryotic clades. Thus, we developed proGenomes, a resource that provides user-friendly access to currently 25 038 high-quality genomes whose sequences and consistent annotations can be retrieved individually or by taxonomic clade. These genomes are assigned to 5306 consistent and accurate taxonomic species clusters based on previously established methodology. proGenomes also contains functional information for almost 80 million protein-coding genes, including a comprehensive set of general annotations and more focused annotations for carbohydrate-active enzymes and antibiotic resistance genes. Additionally, broad habitat information is provided for many genomes. All genomes and associated information can be downloaded by user-selected clade or multiple habitat-specific sets of representative genomes. We expect that the availability of high-quality genomes with comprehensive functional annotations will promote advances in clinical microbial genomics, functional evolution and other subfields of microbiology. proGenomes is available at http://progenomes.embl.de. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Contrasting responses of functional diversity to major losses in taxonomic diversity.

PubMed

Edie, Stewart M; Jablonski, David; Valentine, James W

2018-01-23

Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian-Triassic and Cretaceous-Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.

Taxonomic chauvinism revisited: insight from parental care research.

PubMed

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

A Falsification of the Citation Impediment in the Taxonomic Literature.

PubMed

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

Taxonomic and Numerical Resolutions of Nepomorpha (Insecta: Heteroptera) in Cerrado Streams

PubMed Central

Giehl, Nubia França da Silva; Dias-Silva, Karina; Juen, Leandro; Batista, Joana Darc; Cabette, Helena Soares Ramos

2014-01-01

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 conservation

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

PubMed

Giehl, Nubia França da Silva; Dias-Silva, Karina; Juen, Leandro; Batista, Joana Darc; Cabette, Helena Soares Ramos

2014-01-01

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 conservation

More than just orphans: are taxonomically-restricted genes important in evolution?

PubMed

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.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

PubMed

Fan, Chunyu; Tan, Lingzhao; Zhang, Chunyu; Zhao, Xiuhai; von Gadow, Klaus

2017-10-30

One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach. As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which

A laboratory information management system for DNA barcoding workflows.

PubMed

Vu, Thuy Duong; Eberhardt, Ursula; Szöke, Szániszló; Groenewald, Marizeth; Robert, Vincent

2012-07-01

This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA sequence markers. We aim at generating barcode data for all strains (or specimens) included in the collection (currently ca. 80 k). The LIMS has been developed to better manage large amounts of sequence data and to keep track of the whole experimental procedure. The system has allowed us to classify strains more efficiently as the quality of sequence data has improved, and as a result, up-to-date taxonomic names have been given to strains and more accurate correlation analyses have been carried out.

Macroinvertebrate Taxonomic and Functional Trait Compositions within Lotic Habitats Affected By River Restoration Practices

NASA Astrophysics Data System (ADS)

White, J. C.; Hill, M. J.; Bickerton, M. A.; Wood, P. J.

2017-09-01

The widespread degradation of lotic ecosystems has prompted extensive river restoration efforts globally, but many studies have reported modest ecological responses to rehabilitation practices. The functional properties of biotic communities are rarely examined within post-project appraisals, which would provide more ecological information underpinning ecosystem responses to restoration practices and potentially pinpoint project limitations. This study examines macroinvertebrate community responses to three projects which aimed to physically restore channel morphologies. Taxonomic and functional trait compositions supported by widely occurring lotic habitats (biotopes) were examined across paired restored and non-restored (control) reaches. The multivariate location (average community composition) of taxonomic and functional trait compositions differed marginally between control and restored reaches. However, changes in the amount of multivariate dispersion were more robust and indicated greater ecological heterogeneity within restored reaches, particularly when considering functional trait compositions. Organic biotopes (macrophyte stands and macroalgae) occurred widely across all study sites and supported a high alpha (within-habitat) taxonomic diversity compared to mineralogical biotopes (sand and gravel patches), which were characteristic of restored reaches. However, mineralogical biotopes possessed a higher beta (between-habitat) functional diversity, although this was less pronounced for taxonomic compositions. This study demonstrates that examining the functional and structural properties of taxa across distinct biotopes can provide a greater understanding of biotic responses to river restoration works. Such information could be used to better understand the ecological implications of rehabilitation practices and guide more effective management strategies.

Updates on information about free-living marine nematodes in Brazil: new records and comments on problems in taxonomic studies.

PubMed

Venekey, Virág

2017-10-17

New records of nematode species in Brazil, which appeared after or were not mentioned in the last review, are shown in this paper. All environments were considered, including the continental margin. In addition, all studies on marine nematodes in Brazil, including grey literature, ecological papers and book chapters, are listed. Furthermore, information on genera/species richness, dominant genera, and densities is also presented. A total of 11 orders, 72 families, 372 genera, and 450 species of nematodes were recorded in Brazilian marine environments by April 2017. Following problems are discussed: taxonomic lists available only in grey literature, use of outdated identification keys (leading to incorrect identifications), and identifications mostly to putative species or to the genus level.

Insights from Zootaxa on potential trends in zoological taxonomic activity

PubMed Central

2011-01-01

Background An opinion currently shared by taxonomists and non taxonomists alike is that the work of inventorying biodiversity is unbalanced: firstly, in favour of countries in which taxonomy has been studied for a long time, and, secondly, in favour of vertebrates. In the current context of threats of species extinction, access for taxonomists to biological material and information becomes crucial if the scientific community really aims at a better knowledge of biological diversity before it is severely and irreversibly impoverished. We performed an analysis of 748 papers published in Zootaxa in 2006 and 2007, as well as 434 questionnaires sent to their authors to test these opinions. A generalization of these results to zoological taxonomy as a whole is discussed. Discussion We found that the disequilibrium is not exactly what it usually considered to be. The USA, China and Brazil are currently the three leading countries in zoological taxonomy. Each of them presents, however, a different pattern. Taxonomists from Asia and South America are younger and mainly work in universities, not museums. A bias in favour of vertebrates still exists if we refer to the effort invested in each group to produce taxonomic data, but not to the number of papers. Finally, we insist on the idea that "describing a species" is very different from "knowing a species". Summary The taxonomic involvement of a country, in terms of manpower and funding, appears to be a key factor in the development of fruitful taxonomic research. This message seems to have been understood by the countries that recently decided to increase considerably their taxonomic involvement. It still has to be received by those who did not. PMID:21418568

Variance Component Selection With Applications to Microbiome Taxonomic Data.

PubMed

Zhai, Jing; Kim, Juhyun; Knox, Kenneth S; Twigg, Homer L; Zhou, Hua; Zhou, Jin J

2018-01-01

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.

Unbiased Taxonomic Annotation of Metagenomic Samples

PubMed Central

Fosso, Bruno; Pesole, Graziano; Rosselló, Francesc

2018-01-01

Abstract The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ancestor of the candidate sequences in the reference taxonomy with the least classification error. However, this taxonomic annotation can be biased by an imbalanced taxonomy and also by the presence of multiple nodes in the taxonomy with the least classification error for a given read. In this article, we show that the Rand index is a better indicator of classification error than the often used area under the receiver operating characteristic (ROC) curve and F-measure for both balanced and imbalanced reference taxonomies, and we also address the second source of bias by reducing the taxonomic annotation problem for a whole metagenomic sample to a set cover problem, for which a logarithmic approximation can be obtained in linear time and an exact solution can be obtained by integer linear programming. Experimental results with a proof-of-concept implementation of the set cover approach to taxonomic annotation in a next release of the TANGO software show that the set cover approach further reduces ambiguity in the taxonomic annotation obtained with TANGO without distorting the relative abundance profile of the metagenomic sample. PMID:29028181

Identifying taxonomic and functional surrogates for spring biodiversity conservation.

PubMed

Jyväsjärvi, Jussi; Virtanen, Risto; Ilmonen, Jari; Paasivirta, Lauri; Muotka, Timo

2018-02-27

Surrogate approaches are widely used to estimate overall taxonomic diversity for conservation planning. Surrogate taxa are frequently selected based on rarity or charisma, whereas selection through statistical modeling has been applied rarely. We used boosted-regression-tree models (BRT) fitted to biological data from 165 springs to identify bryophyte and invertebrate surrogates for taxonomic and functional diversity of boreal springs. We focused on these 2 groups because they are well known and abundant in most boreal springs. The best indicators of taxonomic versus functional diversity differed. The bryophyte Bryum weigelii and the chironomid larva Paratrichocladius skirwithensis best indicated taxonomic diversity, whereas the isopod Asellus aquaticus and the chironomid Macropelopia spp. were the best surrogates of functional diversity. In a scoring algorithm for priority-site selection, taxonomic surrogates performed only slightly better than random selection for all spring-dwelling taxa, but they were very effective in representing spring specialists, providing a distinct improvement over random solutions. However, the surrogates for taxonomic diversity represented functional diversity poorly and vice versa. When combined with cross-taxon complementarity analyses, surrogate selection based on statistical modeling provides a promising approach for identifying groundwater-dependent ecosystems of special conservation value, a key requirement of the EU Water Framework Directive. © 2018 Society for Conservation Biology.

Current Taxonomical Situation of Streptococcus suis

PubMed Central

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

2016-01-01

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. PMID:27348006

Current Taxonomical Situation of Streptococcus suis.

PubMed

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.

Evolutionary history of Leishmania killicki (synonymous Leishmania tropica) and taxonomic implications.

PubMed

Chaara, Dhekra; Ravel, Christophe; Bañuls, Anne- Laure; Haouas, Najoua; Lami, Patrick; Talignani, Loïc; El Baidouri, Fouad; Jaouadi, Kaouther; Harrat, Zoubir; Dedet, Jean-Pierre; Babba, Hamouda; Pratlong, Francine

2015-04-01

The taxonomic status of Leishmania (L.) killicki, a parasite that causes chronic cutaneous leishmaniasis, is not well defined yet. Indeed, some researchers suggested that this taxon could be included in the L. tropica complex, whereas others considered it as a distinct phylogenetic complex. To try to solve this taxonomic issue we carried out a detailed study on the evolutionary history of L. killicki relative to L. tropica. Thirty-five L. killicki and 25 L. tropica strains isolated from humans and originating from several countries were characterized using the MultiLocus Enzyme Electrophoresis (MLEE) and the MultiLocus Sequence Typing (MLST) approaches. The results of the genetic and phylogenetic analyses strongly support the hypothesis that L. killicki belongs to the L. tropica complex. Our data suggest that L. killicki emerged from a single founder event and that it evolved independently from L. tropica. However, they do not validate the hypothesis that L. killicki is a distinct complex. Therefore, we suggest naming this taxon L. killicki (synonymous L. tropica) until further epidemiological and phylogenetic studies justify the L. killicki denomination. This study provides taxonomic and phylogenetic information on L. killicki and improves our knowledge on the evolutionary history of this taxon.

Marine benthic ecological functioning over decreasing taxonomic richness

NASA Astrophysics Data System (ADS)

Törnroos, Anna; Bonsdorff, Erik; Bremner, Julie; Blomqvist, Mats; Josefson, Alf B.; Garcia, Clement; Warzocha, Jan

2015-04-01

Alterations to ecosystem function due to reductions in species richness are predicted to increase as humans continue to affect the marine environment, especially in coastal areas, which serve as the interface between land and sea. The potential functional consequences due to reductions in species diversity have attracted considerable attention recently but little is known about the consequence of such loss in natural communities. We examined how the potential for function is affected by natural reductions in taxon richness using empirical (non-simulated) coastal marine benthic macrofaunal data from the Skagerrak-Baltic Sea region (N. Europe), where taxon richness decreases 25-fold, from 151 to 6 taxa. To estimate functional changes we defined multiple traits (10 traits and 51 categories) on which trait category richness, functional diversity (FD) and number of taxa per trait category were calculated. Our results show that decrease in taxon richness leads to an overall reduction in function but functional richness remains comparatively high even at the lowest level of taxon richness. Although the taxonomic reduction was sharp, up to 96% of total taxon richness, we identified both potential thresholds in functioning and subtler changes where function was maintained along the gradient. The functional changes were not only caused by reductions in taxa per trait category, some categories were maintained or even increased. Primarily, the reduction in species richness altered trait categories related to feeding, living and movement and thus potentially could have an effect on various ecosystem processes. This highlights the importance of recognising ecosystem multifunctionality, especially at low taxonomic richness. We also found that in this system rare species (singletons) did not stand for the functional complexities and changes. Our findings were consistent with theoretical and experimental predictions and suggest that a large proportion of the information about

Rapid evolution in lekking grouse: Implications for taxonomic definitions

USGS Publications Warehouse

Oyler-McCance, Sara J.; St. John, Judy; Quinn, Thomas W.

2010-01-01

Species and subspecies delineations were traditionally defined by morphological and behavioral traits, as well as by plumage characteristics. Molecular genetic data have more recently been used to assess these classifications and, in many cases, to redefine them. The recent practice of utilizing molecular genetic data to examine taxonomic questions has led some to suggest that molecular genetic methods are more appropriate than traditional methods for addressing taxonomic uncertainty and management units. We compared the North American Tetraoninae—which have been defined using plumage, morphology, and behavior—and considered the effects of redefinition using only neutral molecular genetic data (mitochondrial control region and cytochrome oxidase subunit 1). Using the criterion of reciprocal monophyly, we failed to recognize the five species whose mating system is highly polygynous, with males displaying on leks. In lek-breeding species, sexual selection can act to influence morphological and behavioral traits at a rate much faster than can be tracked genetically. Thus, we suggest that at least for lek-breeding species, it is important to recognize the possibility that morphological and behavioral changes may occur at an accelerated rate compared with the processes that led to reciprocal monophyly of putatively neutral genetic markers. Therefore, it is particularly important to consider the possible disconnect between such lines of evidence when making taxonomic revisions and definitions of management units.

Hitting the right target: taxonomic challenges for, and of, plant invasions

PubMed Central

Pyšek, Petr; Hulme, Philip E.; Meyerson, Laura A.; Smith, Gideon F.; Boatwright, James S.; Crouch, Neil R.; Figueiredo, Estrela; Foxcroft, Llewellyn C.; Jarošík, Vojtěch; Richardson, David M.; Suda, Jan; Wilson, John R. U.

2013-01-01

This paper explores how a lack of taxonomic expertise, and by implication a dearth of taxonomic products such as identification tools, has hindered progress in understanding and managing biological invasions. It also explores how the taxonomic endeavour could benefit from studies of invasive species. We review the literature on the current situation in taxonomy with a focus on the challenges of identifying alien plant species and explore how this has affected the study of biological invasions. Biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa. However, such identification can be challenging because the taxonomic skill base in most countries is diffuse and lacks critical mass. Taxonomic resources are essential for the effective management of invasive plants and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Better integration of classical alpha taxonomy and modern genetic taxonomic approaches will improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches. In particular, differing points of view between the proponents of morphological and molecular approaches should be negotiated because a narrow taxonomic perspective is harmful; the rigour of taxonomic decision-making clearly increases if insights from a variety of different complementary disciplines are combined and confronted. Taxonomy plays a critical role in the study of plant invasions and in turn benefits from the insights gained from these studies.

Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome.

PubMed

Manor, Ohad; Borenstein, Elhanan

2017-02-08

Comparative analyses of the human microbiome have identified both taxonomic and functional shifts that are associated with numerous diseases. To date, however, microbiome taxonomy and function have mostly been studied independently and the taxonomic drivers of functional imbalances have not been systematically identified. Here, we present FishTaco, an analytical and computational framework that integrates taxonomic and functional comparative analyses to accurately quantify taxon-level contributions to disease-associated functional shifts. Applying FishTaco to several large-scale metagenomic cohorts, we show that shifts in the microbiome's functional capacity can be traced back to specific taxa. Furthermore, the set of taxa driving functional shifts and their contribution levels vary markedly between functions. We additionally find that similar functional imbalances in different diseases are driven by both disease-specific and shared taxa. Such integrated analysis of microbiome ecological and functional dynamics can inform future microbiome-based therapy, pinpointing putative intervention targets for manipulating the microbiome's functional capacity. Copyright © 2017 Elsevier Inc. All rights reserved.

Predicting taxonomic and functional structure of microbial communities in acid mine drainage

PubMed Central

Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-01-01

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

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

PubMed

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

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

PubMed

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.

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

PubMed Central

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. PMID:29236767

Integrating and visualizing primary data from prospective and legacy taxonomic literature

PubMed Central

Agosti, Donat; Penev, Lyubomir; Sautter, Guido; Georgiev, Teodor; Catapano, Terry; Patterson, David; King, David; Pereira, Serrano; Vos, Rutger Aldo; Sierra, Soraya

2015-01-01

Abstract Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions

Designing Multimedia Games for Young Children's Taxonomic Concept Development

ERIC Educational Resources Information Center

Sung, Yao-Ting; Chang, Kuo-En; Lee, Meng-Da

2008-01-01

This study aimed to design and evaluate multimedia games which were based on the theories of children's development of taxonomic concepts. Factors that might affect children's classification skills, such as use of single physical characteristics of objects, competition between thematic and taxonomic relationships, difficulty in forming…

Preschool Children's Taxonomic Knowledge of Animal Species

ERIC Educational Resources Information Center

Allen, Michael

2015-01-01

Although taxonomic proficiency is a prerequisite for understanding ideas central to biology, previous research has established that learners frequently misclassify animals by not following the tenets of accepted taxonomic rubrics. This has immediate relevance with the recently revised English National Curriculum now requiring concepts of animal…

Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

PubMed Central

Liu, Kuan-Liang; Porras-Alfaro, Andrea; Eichorst, Stephanie A.

2012-01-01

Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (http://rdp.cme.msu.edu/classifier/classifier.jsp). PMID:22194300

[The taxonomic rank and place of Colpodellida in the system of the Protista].

PubMed

Myl'nikov, A P; Krylov, M V; Frolov, A O

2000-01-01

The analysis of ultrastructure organisation and divergent processes in Colpodellida, Perkinsida, Gregarinea and Coccidea has confirmed the presence of unique basic structures in all of these organisms and the necessity to combine them into the single phylum Sporozoa. A taxonomic rank and place of Colpodellida in the system of living organisms is represented as follows: phylum Sporozoa Leuckart, 1879; em. Krylov, Mylnikov, 1986. (Syn.: Apicomplexa Levine, 1970). Predators or parasites. Common basic structure: pellicular membranes, subpellicular microtubules, micropores, conoid, rhoptries and micronemes, tubular mitochondrial cristae. Class Perkinsea Levine, 1978. Predators or parasites, vegetative stages with two heterodynamic flagella. Subclass 1. Colpodellia nom. nov. (Syn.: Spiromonadia Krylov, Mylnikov, 1986). Predators, two heterodynamic flagella with string-like mastigonemes (if present), division is exclusively within a cyst, with 2-4 daughter cells being produced, extrusomes are trichocyst-like. Subclass 2. Perkinsia Levine, 1978. Parasites, zoospores with two heterodynamic flagella, mastigonemes (if present) bristle-like or string-like.

Genus age, provincial area and the taxonomic structure of marine faunas.

PubMed

Harnik, Paul G; Jablonski, David; Krug, Andrew Z; Valentine, James W

2010-11-22

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf-Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area.

Genus age, provincial area and the taxonomic structure of marine faunas

PubMed Central

Harnik, Paul G.; Jablonski, David; Krug, Andrew Z.; Valentine, James W.

2010-01-01

Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area. PMID:20534619

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

PubMed Central

Chen, Tsute; Yu, Wen-Han; Izard, Jacques; Baranova, Oxana V.; Lakshmanan, Abirami; Dewhirst, Floyd E.

2010-01-01

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD—taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites. Database URL: http://www.homd.org PMID:20624719

A singular value decomposition approach for improved taxonomic classification of biological sequences

PubMed Central

2011-01-01

Background Singular value decomposition (SVD) is a powerful technique for information retrieval; it helps uncover relationships between elements that are not prima facie related. SVD was initially developed to reduce the time needed for information retrieval and analysis of very large data sets in the complex internet environment. Since information retrieval from large-scale genome and proteome data sets has a similar level of complexity, SVD-based methods could also facilitate data analysis in this research area. Results We found that SVD applied to amino acid sequences demonstrates relationships and provides a basis for producing clusters and cladograms, demonstrating evolutionary relatedness of species that correlates well with Linnaean taxonomy. The choice of a reasonable number of singular values is crucial for SVD-based studies. We found that fewer singular values are needed to produce biologically significant clusters when SVD is employed. Subsequently, we developed a method to determine the lowest number of singular values and fewest clusters needed to guarantee biological significance; this system was developed and validated by comparison with Linnaean taxonomic classification. Conclusions By using SVD, we can reduce uncertainty concerning the appropriate rank value necessary to perform accurate information retrieval analyses. In tests, clusters that we developed with SVD perfectly matched what was expected based on Linnaean taxonomy. PMID:22369633

Selective extinction drives taxonomic and functional alpha and beta diversities in island bird assemblages.

PubMed

Si, Xingfeng; Baselga, Andrés; Leprieur, Fabien; Song, Xiao; Ding, Ping

2016-03-01

Taxonomic diversity considers all species being equally different from each other and thus disregards species' different ecological functions. Exploring taxonomic and functional aspects of biodiversity simultaneously can better understand the processes of community assembly. We analysed taxonomic and functional alpha and beta diversities of breeding bird assemblages on land-bridge islands in the Thousand Island Lake, China. Given the high dispersal ability of most birds at this spatial scale (several kilometres), we predicted (i) selective extinction driving alpha and beta diversities after the creation of land-bridge islands of varying area and (ii) low taxonomic and functional beta diversities that were not correlated to spatial distance. Breeding birds were surveyed on 37 islands annually from 2007 to 2014. We decomposed beta diversity of breeding birds into spatial turnover and nestedness-resultant components, and related taxonomic and functional diversities to island area and isolation using power regression models (for alpha diversity) and multiple regression models on distance matrices (for beta diversity). We then ran simulations to assess the strength of the correlations between taxonomic and functional diversities. Results revealed that both taxonomic and functional alpha diversities increased with island area. The taxonomic nestedness-resultant and turnover components increased and decreased with difference in area, respectively, but functional counterparts did not. Isolation played a minor role in explaining alpha- and beta-diversity patterns. By partitioning beta diversity, we found low levels of overall taxonomic and functional beta diversities. The functional nestedness-resultant component dominated overall functional beta diversity, whereas taxonomic turnover was the dominant component for taxonomic beta diversity. The simulation showed that functional alpha and beta diversities were significantly correlated with taxonomic diversities, and the

Taxonomic and systematic revisions to the North American Nimravidae (Mammalia, Carnivora)

PubMed Central

2016-01-01

The Nimravidae is a family of extinct carnivores commonly referred to as “false saber-tooth cats.” Since their initial discovery, they have prompted difficulty in taxonomic assignments and number of valid species. Past revisions have only examined a handful of genera, while recent advances in cladistic and morphometric analyses have granted us additional avenues to answering questions regarding our understanding of valid nimravid taxa and their phylogenetic relationships. To resolve issues of specific validity, the phylogenetic species concept (PSC) was utilized to maintain consistency in diagnosing valid species, while simultaneously employing character and linear morphometric analyses for confirming the validity of taxa. Determined valid species and taxonomically informative characters were then employed in two differential cladistic analyses to create competing hypotheses of interspecific relationships. The results suggest the validity of twelve species and six monophyletic genera. The first in depth reviews of Pogonodon and Dinictis returned two valid species (P. platycopis, P. davisi) for the former, while only one for the latter (D. felina). The taxonomic validity of Nanosmilus is upheld. Two main clades with substantial support were returned for all cladistic analyses, the Hoplophoneini and Nimravini, with ambiguous positions relative to these main clades for the European taxa: Eofelis, Dinailurictis bonali, and Quercylurus major; and the North American taxa Dinictis and Pogonodon. Eusmilus is determined to represent a non-valid genus for North American taxa, suggesting non-validity for Old World nimravid species as well. Finally, Hoplophoneus mentalis is found to be a junior synonym of Hoplophoneus primaevus, while the validity of Hoplophoneus oharrai is reinstated. PMID:26893959

Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.

PubMed

McIntyre, K M; Setzkorn, C; Wardeh, M; Hepworth, P J; Radford, A D; Baylis, M

2014-10-01

What are all the species of pathogen that affect our livestock? As 6 out of every 10 human pathogens came from animals, with a good number from livestock and pets, it seems likely that the majority that emerge in the future, and which could threaten or devastate human health, will come from animals. Only 10 years ago, the first comprehensive pathogen list was compiled for humans; we still have no equivalent for animals. Here we describe the creation of a novel pathogen database, and present outputs from the database that demonstrate its value. The ENHanCEd Infectious Diseases database (EID2) is open-access and evidence-based, and it describes the pathogens of humans and animals, their host and vector species, and also their global occurrence. The EID2 systematically collates information on pathogens into a single resource using evidence from the NCBI Taxonomy database, the NCBI Nucleotide database, the NCBI MeSH (Medical Subject Headings) library and PubMed. Information about pathogens is assigned using data-mining of meta-data and semi-automated literature searches. Here we focus on 47 mammalian and avian hosts, including humans and animals commonly used in Europe as food or kept as pets. Currently, the EID2 evidence suggests that: • Within these host species, 793 (30.5%) pathogens were bacteria species, 395 (15.2%) fungi, 705 (27.1%) helminths, 372 (14.3%) protozoa and 332 (12.8%) viruses. • The odds of pathogens being emerging compared to not emerging differed by taxonomic division, and increased when pathogens had greater numbers of host species associated with them, and were zoonotic rather than non-zoonotic. • The odds of pathogens being zoonotic compared to non-zoonotic differed by taxonomic division and also increased when associated with greater host numbers. • The pathogens affecting the greatest number of hosts included: Escherichia coli, Giardia intestinalis, Toxoplasma gondii, Anaplasma phagocytophilum, Cryptosporidium parvum, Rabies virus

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean

USGS Publications Warehouse

Yasuhara, Moriaki; Stepanova, Anna; Okahashi, Hisayo; Cronin, Thomas M.; Brouwers, Elisabeth M.

2015-01-01

Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean was conducted to reduce taxonomic uncertainty that will improve our understanding of species ecology, biogeography and relationship to faunas from other deep-sea regions. Fifteen genera and 40 species were examined and (re-)illustrated with high-resolution scanning electron microscopy images, covering most of known deep-sea species in the central Arctic Ocean. Seven new species are described: Bythoceratina lomonosovensis n. sp., Cytheropteron parahamatum n. sp., Cytheropteron lanceae n. sp.,Cytheropteron irizukii n. sp., Pedicythere arctica n. sp., Cluthiawhatleyi n. sp., Krithe hunti n. sp. This study provides a robust taxonomic baseline for application to paleoceanographical reconstruction and biodiversity analyses in this climatically sensitive region.

Taxonomic and functional distinctness of the fish assemblages in three coastal environments (bays, coastal lagoons and oceanic beaches) in Southeastern Brazil.

PubMed

Azevedo, Márcia Cristina Costa; Gomes-Gonçalves, Rafaela de Sousa; Mattos, Tailan Moretti; Uehara, Wagner; Guedes, Gustavo Henrique Soares; Araújo, Francisco Gerson

2017-08-01

Several species of marine fish use different coastal systems especially during their early development. However, these habitats are jeopardized by anthropogenic influences threatening the success of fish populations, and urgent measures are needed to priorize areas to protect their sustainability. We applied taxonomic (Δ+) and functional (X+) distinctiveness indices that represent taxonomic composition and functional roles to assess biodiversity of three different costal systems: bays, coastal lagoons and oceanic beaches. We hypothesized that difference in habitat characteristics, especially in the more dynamism and habitat homogeneity of oceanic beaches compared with more habitat diversity and sheltered conditions of bays and coastal lagoons results in differences in fish richness and taxonomic and functional diversity. The main premise is that communities phylogenetically and functionally more distinct have more interest in conservation policies. Significant differences (P < 0.004) were found in the species richness, Δ+ and X+ among the three systems according to PERMANOVA. Fish richness was higher in bays compared with the coastal lagoons and oceanic beaches. Higher Δ+ was found for the coastal lagoons compared with the bays and oceanic beaches, with the bays having some values below the confidence limit. Similar patterns were found for X+, although all values were within the confidence limits for the bays, suggesting that the absence of some taxa does not interfere in functional diversity. The hypothesis that taxonomic and functional structure of fish assemblages differ among the three systems was accepted and we suggest that coastal lagoons should be priorized in conservation programs because they support more taxonomic and functional distinctiveness. Copyright © 2017 Elsevier Ltd. All rights reserved.

Coastal habitats as surrogates for taxonomic, functional and trophic structures of benthic faunal communities.

PubMed

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.

Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

PubMed Central

Anwar, Nadia; Hunt, Ela

2009-01-01

Background TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection. PMID:19426482

DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

PubMed Central

Kekkonen, Mari; Hebert, Paul D N

2014-01-01

The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies. PMID:24479435

Global hotspots and correlates of alien species richness across taxonomic groups

USGS Publications Warehouse

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.

Taxonomic changes in Solanum section Petota

USDA-ARS?s Scientific Manuscript database

In 1990, the latest comprehensive taxonomic monograph of Solanum section Petota Dumort. recognized 236 species partitioned into 21 series. Of these, 227 were tuber-bearing and nine non-tuber-bearing. NSF-sponsored research has drastically altered knowledge of their species boundaries and interrelati...

The best data design for applying the taxonomic distinctness index in lotic systems: A case study of the Southern Morava River basin.

PubMed

Stojković Piperac, Milica; Milošević, Djuradj; Petrović, Ana; Simić, Vladica

2018-01-01

The taxonomic distinctness (Δ+) index has been recognized as a robust measure to assess human impacts on marine biodiversity. However, its applicability in freshwater ecosystems has still not been confirmed. We aimed to propose the most suitable data design for calculating the Δ+ index for application in assessing anthropogenically caused degradation in lotic environments. We calculated the values of Δ+ based on different taxa groups and taxa resolutions, in order to examine its utility as a potential metric in bioassessment programs. We found that the exclusion of non-insect taxa and selected insect orders significantly increased the index sensitivity. Thus, we believe that an appropriate data design for Δ+ calculation based on macroinvertebrate assemblages is the main prerequisite for the effective estimation of degradation in lotic environments. In addition, we argue that a decrease in taxonomic resolution up to genus level is completely acceptable, as it results in only minor information loss. Bearing this in mind would significantly facilitate its application in rapid bioassessment programs. Despite the observed correlation, the utility of Δ+ as a potential bioassessment metric is rather limited, since its fails to detect fine differences in environmental stress, and instead only roughly distinguishes between two basic classes of degradation level, unimpacted and impacted. Copyright © 2017 Elsevier B.V. All rights reserved.

Taxonomic uncertainty and the loss of biodiversity on Christmas Island, Indian Ocean.

PubMed

Eldridge, Mark D B; Meek, Paul D; Johnson, Rebecca N

2014-04-01

The taxonomic uniqueness of island populations is often uncertain which hinders effective prioritization for conservation. The Christmas Island shrew (Crocidura attenuata trichura) is the only member of the highly speciose eutherian family Soricidae recorded from Australia. It is currently classified as a subspecies of the Asian gray or long-tailed shrew (C. attenuata), although it was originally described as a subspecies of the southeast Asian white-toothed shrew (C. fuliginosa). The Christmas Island shrew is currently listed as endangered and has not been recorded in the wild since 1984-1985, when 2 specimens were collected after an 80-year absence. We aimed to obtain DNA sequence data for cytochrome b (cytb) from Christmas Island shrew museum specimens to determine their taxonomic affinities and to confirm the identity of the 1980s specimens. The Cytb sequences from 5, 1898 specimens and a 1985 specimen were identical. In addition, the Christmas Island shrew cytb sequence was divergent at the species level from all available Crocidura cytb sequences. Rather than a population of a widespread species, current evidence suggests the Christmas Island shrew is a critically endangered endemic species, C. trichura, and a high priority for conservation. As the decisions typically required to save declining species can be delayed or deferred if the taxonomic status of the population in question is uncertain, it is hoped that the history of the Christmas Island shrew will encourage the clarification of taxonomy to be seen as an important first step in initiating informed and effective conservation action. © 2013 Society for Conservation Biology.

The National Biological Information Infrastructure: Coming of age

USGS Publications Warehouse

Cotter, G.; Frame, M.; Sepic, R.; Zolly, L.

2000-01-01

Coordinated by the US Geological Survey, the National Biological Information Infrastructure (NBII) is a Web-based system that provides increased access to data and information on the nation's biological resources. The NBII can be viewed from a variety of perspectives. This article - an individual case study and not a broad survey with extensive references to the literature - addresses the structure of the NBII related to thematic sections, infrastructure sections and place-based sections, and other topics such as the Integrated Taxonomic Information System (one of our more innovative tools) and the development of our controlled vocabulary.

Analyses of the Stability and Core Taxonomic Memberships of the Human Microbiome

PubMed Central

Li, Kelvin; Bihan, Monika; Methé, Barbara A.

2013-01-01

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. PMID

The rDNA Internal Transcribed Spacer Region as a Taxonomic Marker for Nematodes

PubMed Central

Powers, T. O.; Todd, T. C.; Burnell, A. M.; Murray, P. C. B.; Fleming, C. C.; Szalanski, A. L.; Adams, B. A.; Harris, T. S.

1997-01-01

The ITS region from a wide taxonomic range of nematodes, including secernentean and adenophorean taxa, and free-living, entomopathogenic, and plant-parasitic species, was evaluated as a taxonomic marker. Size of the amplified product aided in the initial determination of group membership, and also suggested groups that may require taxonomic reevaluation. Congeneric species often displayed identically sized ITS regions, but genera such as Pratylenchus and Tylenchorhynchus had species with large differences in size. ITS heterogeneity in individuals and populations was identified in several nematode taxa. PCR-RFLP of ITS1 is advocated as a method of taxonomic analysis in genera such as Helicotylenchus that contain numerous species with few diagnostic morphological characteristics. PMID:19274180

Partitioning taxonomic diversity of aquatic insect assemblages ...

EPA Pesticide Factsheets

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

Seed traits and taxonomic relationships determine the occurrence of mutualisms versus seed predation in a tropical forest rodent and seed dispersal system.

PubMed

Wang, Zhenyu; Cao, Lin; Zhang, Zhibin

2014-06-01

Although many studies have been carried out on plant-animal mutualistic assemblages, the roles of functional traits and taxonomy in determining both whether interactions involve mutualisms or predation and the structure of such assemblages are unclear. We used semi-natural enclosures to quantitatively assess the interaction strengths between seeds of 8 sympatric tree species and 4 rodent species in a tropical forest in Xishuangbanna, Yunnan, Southwest China. We found 2 clusters of species in the seed-rodent network represented by 2 genera in the Fagaceae (Castanopsis, Lithocarpus). Compared to seeds of 3 Castanopsis species, seeds with heavy weight, hard coat or caloric content (including 3 Lithocarpus species) were eaten less and more frequently hoarded by rodents. In turn, hoarded seeds showed less predation and more mutualism with rodents. Our results suggest that seed traits significantly affected the hoarding behavior of rodents, and, consequently, the occurrence of mutualisms and predation as well as assemblage structure in the plant-animal seed dispersal system. Taxonomically-related species with similar seed traits as functional groups belong to the same substructures in the assemblage. Our results indicate that both seed traits and taxonomic relationships may simplify thinking about seed dispersal systems by helping to elucidate whether interactions are likely to be dominated by predation or mutualism. © 2013 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri

PubMed Central

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

Seasonality, Dietary Overlap and the Role of Taxonomic Resolution in the Study of the Diet of Three Congeneric Fishes from a Tropical Bay

PubMed Central

Pombo, Maíra; Denadai, Márcia Regina; Turra, Alexander

2013-01-01

Not only seasonality but also taxonomic resolution of prey categories has been shown to affect diet studies. We analyzed the stomach contents of three sympatric species, Stellifer rastrifer, S. brasiliensis and S. stellifer, sampled monthly from August 2003 to October 2004 in Caraguatatuba Bay, southeastern Brazil. General characteristics and similarities among their diets were evaluated by considering high taxonomic ranks of all prey groups, and also the lower taxonomic ranks of the main prey groups. Dietary similarity was relatively high among species and low between seasons, and both evaluation criteria gave the equivalent results. The rare items, however, provided information about resource partition, and the species compositions of the most important groups were apparently good indicators of food availability. PMID:23405256

Taxonomic and Functional Metagenomic Signature of Turfs in the Abrolhos Reef System (Brazil)

PubMed Central

Walter, Juline M.; Tschoeke, Diogo A.; Meirelles, Pedro M.; de Oliveira, Louisi; Leomil, Luciana; Tenório, Márcio; Valle, Rogério; Salomon, Paulo S.; Thompson, Cristiane C.; Thompson, Fabiano L.

2016-01-01

Turfs are widespread assemblages (consisting of microbes and algae) that inhabit reef systems. They are the most abundant benthic component in the Abrolhos reef system (Brazil), representing greater than half the coverage of the entire benthic community. Their presence is associated with a reduction in three-dimensional coral reef complexity and decreases the habitats available for reef biodiversity. Despite their importance, the taxonomic and functional diversity of turfs remain unclear. We performed a metagenomics and pigments profile characterization of turfs from the Abrolhos reefs. Turf microbiome primarily encompassed Proteobacteria (mean 40.57% ± s.d. 10.36, N = 1.548,192), Cyanobacteria (mean 35.04% ± s.d. 15.5, N = 1.337,196), and Bacteroidetes (mean 11.12% ± s.d. 4.25, N = 424,185). Oxygenic and anoxygenic phototrophs, chemolithotrophs, and aerobic anoxygenic phototrophic (AANP) bacteria showed a conserved functional trait of the turf microbiomes. Genes associated with oxygenic photosynthesis, AANP, sulfur cycle (S oxidation, and DMSP consumption), and nitrogen metabolism (N2 fixation, ammonia assimilation, dissimilatory nitrate and nitrite ammonification) were found in the turf microbiomes. Principal component analyses of the most abundant taxa and functions showed that turf microbiomes differ from the other major Abrolhos benthic microbiomes (i.e., corals and rhodoliths) and seawater. Taken together, these features suggest that turfs have a homogeneous functional core across the Abrolhos Bank, which holds diverse microbial guilds when comparing with other benthic organisms. PMID:27548380

Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates

PubMed Central

Calderón-Patrón, Jaime M.; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E.; Sánchez-Rojas, Gerardo; Zuria, Iriana

2016-01-01

Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project “Biodiversity in the state of Hidalgo”. Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area. PMID:27500934

Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates.

PubMed

Calderón-Patrón, Jaime M; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E; Sánchez-Rojas, Gerardo; Zuria, Iriana; Moreno, Claudia E

2016-01-01

Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project "Biodiversity in the state of Hidalgo". Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area.

Geographical and taxonomic biases in invasion ecology.

PubMed

Pysek, Petr; Richardson, David M; Pergl, Jan; Jarosík, Vojtech; Sixtová, Zuzana; Weber, Ewald

2008-05-01

Invasive alien species come from most taxonomic groups, and invasion biology is searching for robust cross-taxon generalizations and principles. An analysis of 2,670 papers dealing with 892 invasive species showed that all major groups of invaders are well studied, but that most information on the mechanisms of invasion has emerged from work on a limited number of the most harmful invaders. A strong geographical bias, with Africa and Asia understudied, inhibits a balanced understanding of invasion, because we might be lacking knowledge of specific invasion mechanisms from poorly studied, regionally specific habitats. International cooperation is required to achieve a more geographically balanced picture of biological invasions. Invasive species with the greatest impact are best studied, but more studies of species that are naturalized but not (yet) invasive are needed to improve understanding of the mechanisms acting during the naturalization phase of invasions and leading to successful invasion.

Flexible taxonomic assignment of ambiguous sequencing reads

PubMed Central

2011-01-01

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. PMID:21211059

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act.

PubMed

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.

Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act

USGS Publications Warehouse

Beever, E.A.; Haig, S.M.; 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, Peter J.; Mullins, Thomas D.; Sheffield, Lisa M.

2006-01-01

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.

Application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment.

PubMed

Xu, Henglong; Jiang, Yong; Al-Rasheid, Khaled A S; Al-Farraj, Saleh A; Song, Weibo

2011-08-01

Ciliated protozoa play important roles in aquatic ecosystems especially regarding their functions in micro-food web and have many advantages in environmental assessment compared with most other eukaryotic organisms. The aims of this study were focused on analyzing the application of an indicator based on taxonomic relatedness of ciliated protozoan assemblages for marine environmental assessment. The spatial taxonomic patterns and diversity measures in response to physical-chemical variables were studied based on data from samples collected during 1-year cycle in the semi-enclosed Jiaozhou Bay, northern China. The spatial patterns of ciliate communities were significantly correlated with the changes of environmental status. The taxonomic distinctness (Δ*) and the average taxonomic distinctness (Δ+) were significantly negatively correlated with the changes of nutrients (e.g., nitrate nitrogen and soluble active phosphate; P<0.05). Pairwise indices of Δ+ and the variation in taxonomic distinctness (Λ+) showed a decreasing trend of departure from the expected taxonomic breadth in response to the eutrophication stress and anthropogenic impact. The taxonomic relatedness (especially the pairwise Δ+ and Λ+) indices of ciliate communities are robust as an indicator with scientifically operational value in marine environmental assessment.

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets.

PubMed

Scheuch, Matthias; Höper, Dirk; Beer, Martin

2015-03-03

Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck. To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS - Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets. RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.

Trends in Taxonomic and Functional Composition of Soil Microbiome Along a Precipitation Gradient in Israel.

PubMed

Tripathi, Binu M; Moroenyane, Itumeleng; Sherman, Chen; Lee, Yoo Kyung; Adams, Jonathan M; Steinberger, Yosef

2017-07-01

The soil microbiome is important for the functioning of terrestrial ecosystems. However, the impacts of climate on taxonomic and functional diversity of soil microbiome are not well understood. A precipitation gradient along regional scale transects may offer a model setting for understanding the effect of climate on the composition and function of the soil microbiome. Here, we compared taxonomic and functional attributes of soil microorganisms in arid, semiarid, Mediterranean, and humid Mediterranean climatic conditions of Israel using shotgun metagenomic sequencing. We hypothesized that there would be a distinct taxonomic and functional soil community for each precipitation zone, with arid environments having lower taxonomic and functional diversity, greater relative abundance of stress response and sporulation-related genes, and lower relative abundance of genes related to nutrient cycling and degradation of complex organic compounds. As hypothesized, our results showed a distinct taxonomic and functional community in each precipitation zone, revealing differences in soil taxonomic and functional selection in the different climates. Although the taxonomic diversity remained similar across all sites, the functional diversity was-as hypothesized-lower in the arid environments, suggesting that functionality is more constrained in "extreme" environments. Also, with increasing aridity, we found a significant increase in genes related to dormancy/sporulation and a decrease in those related to nutrient cycling (genes related to nitrogen, potassium, and sulfur metabolism), respectively. However, relative abundance of genes related to stress response were lower in arid soils. Overall, these results indicate that climatic conditions play an important role in shaping taxonomic and functional attributes of soil microbiome. These findings have important implications for understanding the impacts of climate change (e.g., precipitation change) on structure and function of the

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

PubMed

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.

Approaching the taxonomic affiliation of unidentified sequences in public databases--an example from the mycorrhizal fungi.

PubMed

Nilsson, R Henrik; Kristiansson, Erik; Ryberg, Martin; Larsson, Karl-Henrik

2005-07-18

contain a thorough sampling of taxonomically well-annotated sequences. Taxonomy, held by some to be an old-fashioned trade, has accordingly never been more important. emerencia does not automate the taxonomic process, but it does allow researchers to focus their efforts elsewhere than countless manual BLAST runs and arduous sieving of BLAST hit lists. The emerencia system is available on an open source basis for local installation with any organism and gene group as targets.

Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community.

PubMed

Bretschger, Orianna; Carpenter, Kayla; Phan, Tony; Suzuki, Shino; Ishii, Shun'ichi; Grossi-Soyster, Elysse; Flynn, Michael; Hogan, John

2015-11-01

The functional and taxonomic microbial dynamics of duplicate electricity-consuming methanogenic communities were observed over a 6 months period to characterize the reproducibility, stability and recovery of electromethanogenic consortia. The highest rate of methanogenesis was 0.72 mg-CH4/L/day, which occurred during the third month of enrichment when multiple methanogenic phylotypes and associated Desulfovibrionaceae phylotypes were present in the electrode-associated microbial community. Results also suggest that electromethanogenic microbial communities are very sensitive to electron donor-limiting open-circuit conditions. A 45 min exposure to open-circuit conditions induced an 87% drop in volumetric methane production rates. Methanogenic performance recovered after 4 months to a maximum value of 0.30 mg-CH4/L/day under set potential operation (-700 mV vs Ag/AgCl); however, current consumption and biomass production was variable over time. Long-term functional and taxonomic analyses from experimental replicates provide new knowledge toward understanding how to enrich electromethanogenic communities and operate bioelectrochemical systems for stable and reproducible performance. Copyright © 2015 Elsevier Ltd. All rights reserved.

Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

PubMed

Huang, Qiuyuan; Briggs, Brandon R; Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

PubMed Central

Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change. PMID:25365331

Low Functional β-Diversity Despite High Taxonomic β-Diversity among Tropical Estuarine Fish Communities

PubMed Central

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 (<1.5%) despite high dissimilarity in species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic 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

Polysemy and the Taxonomic Constraint: Children's Representation of Words That Label Multiple Kinds

ERIC Educational Resources Information Center

Srinivasan, Mahesh; Snedeker, Jesse

2014-01-01

How do children resolve the problem of indeterminacy when learning a new word? By one account, children adopt a "taxonomic assumption" and expect the word to denote only members of a particular taxonomic category. According to one version of this constraint, young children should represent polysemous words that label multiple kinds--for…

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

PubMed Central

Diaz, Naryttza N; Krause, Lutz; Goesmann, Alexander; Niehaus, Karsten; Nattkemper, Tim W

2009-01-01

Background Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offers the potential to lay solid basis on our understanding of the entire living world. However, the taxonomic classification is an essential task in the analysis of metagenomics data sets that it is still far from being solved. We present a novel strategy to predict the taxonomic origin of environmental genomic fragments. The proposed classifier combines the idea of the k-nearest neighbor with strategies from kernel-based learning. Results Our novel strategy was extensively evaluated using the leave-one-out cross validation strategy on fragments of variable length (800 bp – 50 Kbp) from 373 completely sequenced genomes. TACOA is able to classify genomic fragments of length 800 bp and 1 Kbp with high accuracy until rank class. For longer fragments ≥ 3 Kbp accurate predictions are made at even deeper taxonomic ranks (order and genus). Remarkably, TACOA also produces reliable results when the taxonomic origin of a fragment is not represented in the reference set, thus classifying such fragments to its known broader taxonomic class or simply as "unknown". We compared the classification accuracy of TACOA with the latest intrinsic classifier PhyloPythia using 63 recently published complete genomes. For fragments of length 800 bp and 1 Kbp the overall accuracy of TACOA is higher than that obtained by PhyloPythia at all taxonomic ranks. For all fragment lengths, both methods achieved comparable high specificity results up to rank class and low false negative rates are also obtained. Conclusion An accurate multi-class taxonomic classifier was developed for environmental genomic fragments. TACOA can predict with high reliability the taxonomic origin of genomic fragments as short as 800 bp. The proposed method is transparent, fast, accurate and the reference

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

PubMed

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.

Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias.

PubMed

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 <75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided >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.

Evaluative and Taxonomic Encoding in Children's Memory.

ERIC Educational Resources Information Center

Kail, Robert V., Jr.; Schroll, John T.

Two experiments were conducted to investigate the development of evaluative and taxonomic encoding in children's memory. The task used was a modification of the Wickens short-term memory task in which subjects' recall of words is tested following a distraction task. The first experiment found that 11-year-old children, but not 8-year-old children,…

taxonomic diversity and pest vulnerability in street tree assemblages

EPA Pesticide Factsheets

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 communities in metropolitan Cincinnati, Ohio, USA, we tested the hypothesis that communities with higher diversity would exhibit lower vulnerability to the polyphagous Asian longhorned beetle, which currently threatens the region. Based on street tree compositions and the beetle??s host preferences, Asian longhorned beetle threatened up to 35.6% of individual street trees and 47.5% of the total basal area across the study area, but we did not see clear connections between taxonomic diversity and beetle vulnerability among study communities. For example, the city of Fairfield was among the least diverse communities but had the lowest proportion of trees vulnerable to Asian longhorned beetle, whereas the city of Wyoming exhibited high diversity and high vulnerability. On the other hand, Forest Park aligned with our original hypothesis, as it was characterised by low diversity and high vulnerability. Our results demonstrate that relatively high taxonomic diversity in street tree assemblages does not necessarily lead to reduced vulnerability to a polyphagous pest. Considering the threats posed by polyphagous pests, selecting a set of relatively pest resistant trees known to perform well in ur

Taxonomical and functional microbial community selection in soybean rhizosphere

PubMed Central

Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

2014-01-01

This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities

DTIC Science & Technology

2001-09-30

1 Pigment Fluorescence Signatures as an Index to the Taxonomic Structure of Phytoplankton Communities Dr. Gary Hitchcock Marine Biology and... Fisheries Rosenstiel School of Marine and Atmospheric Science 4600 Rickenbacker Cswy. Miami, FL 3149 phone: (305) 361-4926 fax: (305) 361-4765...ghitchcock.html LONG-TERM GOALS The spatial distribution and taxonomic composition of phytoplankton communities are important determinants of the

Information Systems Administration. Course Seven. Information Systems Curriculum.

ERIC Educational Resources Information Center

O'Neil, Sharon Lund; Everett, Donna R.

This course is the seventh of seven in the Information Systems curriculum. The purpose of this capstone course is to build on skills acquired in the earlier courses. Emphasis is placed on realistic situations and challenges that exist in the automated office and for which information systems technology and skills are pertinent. These components…

Evaluation of health information systems research in information systems research: A meta-analysis.

PubMed

Haried, Peter; Claybaugh, Craig; Dai, Hua

2017-04-01

Given the importance of the health-care industry and the promise of health information systems, researchers are encouraged to build on the shoulders of giants as the saying goes. The health information systems field has a unique opportunity to learn from and extend the work that has already been done by the highly correlated information systems field. As a result, this research article presents a past, present and future meta-analysis of health information systems research in information systems journals over the 2000-2015 time period. Our analysis reviewed 126 articles on a variety of topics related to health information systems research published in the "Senior Scholars" list of the top eight ranked information systems academic journals. Across the selected information systems academic journals, our findings compare research methodologies applied, health information systems topic areas investigated and research trends. Interesting results emerge in the range and evolution of health information systems research and opportunities for health information systems researchers and practitioners to consider moving forward.

Increasing fish taxonomic and functional richness affects ecosystem properties of small headwater prairie streams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, Erika C.; Gido, Keith B.; Bello, Nora

across habitat types and locations within a reach can therefore be influenced by the taxonomic and functional composition of fishes in small prairie streams. Thus, disturbances that alter diversity of these systems might have unexpected ecosystem-level consequences.« less

Increasing fish taxonomic and functional richness affects ecosystem properties of small headwater prairie streams

DOE PAGES

Martin, Erika C.; Gido, Keith B.; Bello, Nora; ...

2016-04-06

across habitat types and locations within a reach can therefore be influenced by the taxonomic and functional composition of fishes in small prairie streams. Thus, disturbances that alter diversity of these systems might have unexpected ecosystem-level consequences.« less

Data Entities and Information System Matrix for Integrated Agriculture Information System (IAIS)

NASA Astrophysics Data System (ADS)

Budi Santoso, Halim; Delima, Rosa

2018-03-01

Integrated Agriculture Information System is a system that is developed to process data, information, and knowledge in Agriculture sector. Integrated Agriculture Information System brings valuable information for farmers: (1) Fertilizer price; (2) Agriculture technique and practise; (3) Pest management; (4) Cultivation; (5) Irrigation; (6) Post harvest processing; (7) Innovation in agriculture processing. Integrated Agriculture Information System contains 9 subsystems. To bring an integrated information to the user and stakeholder, it needs an integrated database approach. Thus, researchers describes data entity and its matrix relate to subsystem in Integrated Agriculture Information System (IAIS). As a result, there are 47 data entities as entities in single and integrated database.

Information Requirements for a Procurement Management Information System.

DTIC Science & Technology

1975-08-01

Management Information System is...described and some justification for this type of procurement management information system is presented. A literature search was made to determine...information systems. If information requirements are correctly identified and satisfied by a procurement management information system , contract administration and procurement management can be

High taxonomic variability despite stable functional structure across microbial communities.

PubMed

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.

Lactobacillus species: taxonomic complexity and controversial susceptibilities.

PubMed

Goldstein, Ellie J C; Tyrrell, Kerin L; Citron, Diane M

2015-05-15

The genus Lactobacillus is a taxonomically complex and is composed of over 170 species that cannot be easily differentiated phenotypically and often require molecular identification. Although they are part of the normal human gastrointestinal and vaginal flora, they can also be occasional human pathogens. They are extensively used in a variety of commercial products including probiotics. Their antimicrobial susceptibilities are poorly defined in part because of their taxonomic complexity and are compounded by the different methods recommended by Clinical Laboratory Standards Institute and International Dairy Foundation. Their use as probiotics for prevention of Clostridium difficile infection is prevalent among consumers worldwide but raises the question of will the use of any concurrent antibiotic effect their ability to survive. Lactobacillus species are generally acid resistant and are able to survive ingestion. They are generally resistant to metronidazole, aminoglycosides and ciprofloxacin with L. acidophilus being susceptible to penicillin and vancomycin, whereas L. rhamnosus and L. casei are resistant to metronidazole and vancomycin. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina.

PubMed

Wang, Q-M; Begerow, D; Groenewald, M; Liu, X-Z; Theelen, B; Bai, F-Y; Boekhout, T

2015-06-01

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 largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the 'One Fungus = One Name' principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained.

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.

PubMed

O'Leary, Nuala A; Wright, Mathew W; Brister, J Rodney; Ciufo, Stacy; Haddad, Diana; McVeigh, Rich; Rajput, Bhanu; Robbertse, Barbara; Smith-White, Brian; Ako-Adjei, Danso; Astashyn, Alexander; Badretdin, Azat; Bao, Yiming; Blinkova, Olga; Brover, Vyacheslav; Chetvernin, Vyacheslav; Choi, Jinna; Cox, Eric; Ermolaeva, Olga; Farrell, Catherine M; Goldfarb, Tamara; Gupta, Tripti; Haft, Daniel; Hatcher, Eneida; Hlavina, Wratko; Joardar, Vinita S; Kodali, Vamsi K; Li, Wenjun; Maglott, Donna; Masterson, Patrick; McGarvey, Kelly M; Murphy, Michael R; O'Neill, Kathleen; Pujar, Shashikant; Rangwala, Sanjida H; Rausch, Daniel; Riddick, Lillian D; Schoch, Conrad; Shkeda, Andrei; Storz, Susan S; Sun, Hanzhen; Thibaud-Nissen, Francoise; Tolstoy, Igor; Tully, Raymond E; Vatsan, Anjana R; Wallin, Craig; Webb, David; Wu, Wendy; Landrum, Melissa J; Kimchi, Avi; Tatusova, Tatiana; DiCuccio, Michael; Kitts, Paul; Murphy, Terence D; Pruitt, Kim D

2016-01-04

The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Weather Information System

NASA Technical Reports Server (NTRS)

1995-01-01

WxLink is an aviation weather system based on advanced airborne sensors, precise positioning available from the satellite-based Global Positioning System, cockpit graphics and a low-cost datalink. It is a two-way system that uplinks weather information to the aircraft and downlinks automatic pilot reports of weather conditions aloft. Manufactured by ARNAV Systems, Inc., the original technology came from Langley Research Center's cockpit weather information system, CWIN (Cockpit Weather INformation). The system creates radar maps of storms, lightning and reports of surface observations, offering improved safety, better weather monitoring and substantial fuel savings.

What Belongs in Your 15-Bean Soup? Using the Learning Cycle to Address Misconceptions about Construction of Taxonomic Keys

ERIC Educational Resources Information Center

Ross, Ann; Vanderspool, Staria

2004-01-01

Students can use seed characteristics to discriminate between the different kinds of legumes using taxonomic classification processes of sorting and ranking, followed by construction of taxonomic keys. The application of the Learning Cycle process to taxonomic principles, hierarchical classification, and construction of keys presents the…

Health information systems.

PubMed

Hovenga, Evelyn J S; Grain, Heather

2013-01-01

Health information provides the foundation for all decision making in healthcare whether clinical at the bed side, or at a national government level. This information is generally collected as part of systems which support administrative or clinical workflow and practice. This chapter describes the many and varied features of systems such as electronic health records (EHRs), how they fit with health information systems and how they collectively manage information flow. Systems engineering methods and tools are described together with their use to suit the health industry. This focuses on the need for suitable system architectures and semantic interoperability. These concepts and their relevance to the health industry are explained. The relationship and requirements for appropriate data governance in these systems is also considered.

Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation

PubMed Central

Laplante, Karine; Sébastien, Boutin; Derome, Nicolas

2013-01-01

Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities. PMID:23789031

Functional and Taxonomic Differentiation of Macrophyte Assemblages Across the Yangtze River Floodplain Under Human Impacts

PubMed Central

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. PMID

Comparing efficacy of different taxonomic resolutions and surrogates in detecting changes in soft bottom assemblages due to coastal defence structures.

PubMed

Bertasi, Fabio; Colangelo, Marina Antonia; Colosio, Francesco; Gregorio, Gianni; Abbiati, Marco; Ceccherelli, Victor Ugo

2009-05-01

Sandy shores on the West coast of the North Adriatic Sea are extensively protected by different types of defence structures to prevent coastal erosion. Coastal defence schemes modify the hydrodynamic regime, the sediment structure and composition thus affecting the benthic assemblages. This study examines the effectiveness in detecting changes in soft bottom assemblages caused by coastal defence structures by using different levels of taxonomic resolution, polychaetes and/or bivalves as surrogates and different data transformations. A synoptic analyses of three datasets of subtidal benthic macrofauna used in studies aimed at assessing the impact of breakwaters along the North Adriatic coast has been done. Analyses of similarities and correlations between distance matrices were done using matrices with different levels of taxonomic resolution, and with polychaetes or bivalves data alone. Lentidium mediterraneum was the most abundant species in all datasets. Its abundance was not consistently related to the presence of defence structures. Moreover, distribution patterns of L. mediterraneum were masking the structure of the whole macrofaunal assemblages. Removal of L. mediterraneum from the datasets allowed the detection of changes in benthic assemblages due to coastal defences. Analyses on different levels of taxonomic resolution showed that the level of family maintained sufficient information to detect the impacts of coastal defence structures on benthic assemblages. Moreover, the outcomes depended on the transformation used. Patterns of distribution of bivalves, used as surrogates, showed low correlations with the patterns of the total macrofaunal species assemblages. Patterns of polychaetes, if identified to the species or genus level showed higher correlations with the whole dataset. However, the identification of polychaetes to species and genus level is as costly as the identification of all macrobenthic taxa at family level. This study provided additional

Distinct progression of the deterioration of thematic and taxonomic links in natural and manufactured objects in Alzheimer's disease.

PubMed

Simoes Loureiro, Isabelle; Lefebvre, Laurent

2016-10-01

Taxonomic and thematic relationships are core elements of lexico-semantic networks. However, the weight of both links differs in semantic memory, with distinct support for natural and manufactured objects: natural objects tend to be more taxonomically identified while manufactured objects benefit more from the underlying thematic relationships. Alzheimer's disease (AD) causes early semantic memory impairment characterized by a category-specific deterioration, where natural objects are more sensitive to the disease than manufactured objects. However, relatively few studies have examined the progressive deterioration of specific thematic versus taxonomic relations in both categories of objects in AD. To better understand semantic memory disorganization in AD and analyze the potential interaction effect between the category (natural/manufactured), the condition (thematic/taxonomic) and AD, we will investigate the lexico-semantic network in 82 AD patients (divided into three groups depending on their global cognitive deterioration and their performance in a preliminary semantic knowledge questionnaire (mild (AD1), moderate (AD2) and advanced (AD3) stages of semantic knowledge alteration). The experimental protocol contains two tasks: an implicit semantic priming paradigm and an explicit card-sorting test that uses the same items, equally divided between natural and manufactured objects. Results show a distinct taxonomic and thematic evolution pattern with early taxonomic deterioration. Natural objects are also more vulnerable to the disease. Lastly, there is an interaction effect between the category and the condition in the priming task indicating that natural objects are more taxonomically organized and manufactured objects benefit more from both thematic and taxonomic organizations, reinforcing the idea of the robustness of this category. The theoretical accounts of these observations will be discussed in detail. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Taxonomic Approach to the Gestalt Theory of Perls

ERIC Educational Resources Information Center

Raming, Henry E.; Frey, David H.

1974-01-01

This study applied content analysis and cluster analysis to the ideas of Fritz Perls to develop a taxonomy of Gestalt processes and goals. Summaries of the typal groups or clusters were written and the implications of taxonomic research in counseling discussed. (Author)

A taxonomic synopsis of Altingiaceae with nine new combinations

PubMed Central

Ickert-Bond, Stefanie M.; Wen, Jun

2013-01-01

Abstract 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, Liquidambar caudata (H. T. Chang) Ickert-Bond & J. Wen, Liquidambar chingii (Metcalf) Ickert-Bond & J. Wen, Liquidambar gracilipes (Hemsl.) Ickert-Bond & J. Wen, Liquidambar multinervis(Cheng) Ickert-Bond & J. Wen, Liquidambar obovata (Merrill & Chun) Ickert-Bond & J. Wen, Liquidambar poilanei (Tardieu) Ickert-Bond & J. Wen, Liquidambar siamensis (Craib) Ickert-Bond & J. Wen, and Liquidambar yunnanensis (Rehder & Wilson) Ickert-Bond & J. Wen. PMID:24399902

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

PubMed

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.

Automatic processing of semantic relations in fMRI: neural activation during semantic priming of taxonomic and thematic categories.

PubMed

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.

Information extraction system

DOEpatents

Lemmond, Tracy D; Hanley, William G; Guensche, Joseph Wendell; Perry, Nathan C; Nitao, John J; Kidwell, Paul Brandon; Boakye, Kofi Agyeman; Glaser, Ron E; Prenger, Ryan James

2014-05-13

An information extraction system and methods of operating the system are provided. In particular, an information extraction system for performing meta-extraction of named entities of people, organizations, and locations as well as relationships and events from text documents are described herein.

Community Information Systems.

ERIC Educational Resources Information Center

Freeman, Andrew

Information is provided on technological and social trends as background for a workshop designed to heighten the consciousness of workers in community information systems. Initially, the basic terminology is considered in its implications for an integrated perspective of community information systems, with particular attention given to the meaning…

Rotational Study of Ambiguous Taxonomic Classified Asteroids

NASA Astrophysics Data System (ADS)

Linder, Tyler R.; Sanchez, Rick; Wuerker, Wolfgang; Clayson, Timothy; Giles, Tucker

2017-01-01

The Sloan Digital Sky Survey (SDSS) moving object catalog (MOC4) provided the largest ever catalog of asteroid spectrophotometry observations. Carvano et al. (2010), while analyzing MOC4, discovered that individual observations of asteroids which were observed multiple times did not classify into the same photometric-based taxonomic class. A small subset of those asteroids were classified as having both the presence and absence of a 1um silicate absorption feature. If these variations are linked to differences in surface mineralogy, the prevailing assumption that an asteroid’s surface composition is predominantly homogenous would need to be reexamined. Furthermore, our understanding of the evolution of the asteroid belt, as well as the linkage between certain asteroids and meteorite types may need to be modified.This research is an investigation to determine the rotational rates of these taxonomically ambiguous asteroids. Initial questions to be answered:Do these asteroids have unique or nonstandard rotational rates?Is there any evidence in their light curve to suggest an abnormality?Observations were taken using PROMPT6 a 0.41-m telescope apart of the SKYNET network at Cerro Tololo Inter-American Observatory (CTIO). Observations were calibrated and analyzed using Canopus software. Initial results will be presented at AAS.

Industrial activated sludge exhibit unique bacterial community composition at high taxonomic ranks.

PubMed

Ibarbalz, Federico M; Figuerola, Eva L M; Erijman, Leonardo

2013-07-01

Biological degradation of domestic and industrial wastewater by activated sludge depends on a common process of separation of the diverse self-assembled and self-sustained microbial flocs from the treated wastewater. Previous surveys of bacterial communities indicated the presence of a common core of bacterial phyla in municipal activated sludge, an observation consistent with the concept of ecological coherence of high taxonomic ranks. The aim of this work was to test whether this critical feature brings about a common pattern of abundance distribution of high bacterial taxa in industrial and domestic activated sludge, and to relate the bacterial community structure of industrial activated sludge with relevant operational parameters. We have applied 454 pyrosequencing of 16S rRNA genes to evaluate bacterial communities in full-scale biological wastewater treatment plants sampled at different times, including seven systems treating wastewater from different industries and one plant that treats domestic wastewater, and compared our datasets with the data from municipal wastewater treatment plants obtained by three different laboratories. We observed that each industrial activated sludge system exhibited a unique bacterial community composition, which is clearly distinct from the common profile of bacterial phyla or classes observed in municipal plants. The influence of process parameters on the bacterial community structure was evaluated using constrained analysis of principal coordinates (CAP). Part of the differences in the bacterial community structure between industrial wastewater treatment systems were explained by dissolved oxygen and pH. Despite the ecological relevance of floc formation for the assembly of bacterial communities in activated sludge, the wastewater characteristics are likely to be the major determinant that drives bacterial composition at high taxonomic ranks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages

PubMed Central

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

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

PubMed

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

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

PubMed Central

Lu, Hsiao-Pei; Yeh, Yi-Chun; Sastri, Akash R; Shiah, Fuh-Kwo; Gong, Gwo-Ching; Hsieh, Chih-hao

2016-01-01

We propose a method for detecting evolutionary forces underlying community assembly by quantifying the strength of community–environment relationships hierarchically along taxonomic ranks. This approach explores the potential role of phylogenetic conservatism on habitat preferences: wherein, phylogenetically related taxa are expected to exhibit similar environmental responses. Thus, when niches are conserved, broader taxonomic classification should not diminish the strength of community–environment relationships and may even yield stronger associations by summarizing occurrences and abundances of ecologically equivalent finely resolved taxa. In contrast, broader taxonomic classification should weaken community–environment relationships when niches are under great divergence (that is, by combining finer taxa with distinct environmental responses). Here, we quantified the strength of community–environment relationships using distance-based redundancy analysis, focusing on soil and seawater prokaryotic communities. We considered eight case studies (covering a variety of sampling scales and sequencing strategies) and found that the variation in community composition explained by environmental factors either increased or remained constant with broadening taxonomic resolution from species to order or even phylum level. These results support the niche conservatism hypothesis and indicate that broadening taxonomic resolution may strengthen niche-related signals by removing uncertainty in quantifying spatiotemporal distributions of finely resolved taxa, reinforcing the current notion of ecological coherence in deep prokaryotic branches. PMID:27177191

Detecting taxonomic signal in an under-utilised character system: geometric morphometrics of the forcipular coxae of Scutigeromorpha (Chilopoda)

PubMed Central

Gutierrez, Beatriz Lopez; MacLeod, Norman; Edgecombe, Gregory D.

2011-01-01

Abstract To date, the forcipules have played almost no role in determining the systematics of scutigeromorph centipedes though in his 1974 review of taxonomic characters Markus Würmli suggested some potentially informative variation might be found in these structures. Geometric morphometric analyses were used to evaluate Würmli’s suggestion, specifically to determine whether the shape of the forcipular coxa contains information useful for diagnosing species. The geometry of the coxae of eight species from the genera Sphendononema, Scutigera, Dendrothereua, Thereuonema, Thereuopoda, Thereuopodina, Allothereua and Parascutigera was characterised using a combination of landmark- and semi-landmark-based sampling methods to summarize group-specific morphological variation. Canonical variates analysis of shape data characterizing the forcipular coxae indicates that these structures differ significantly between taxa at various systematic levels. Models calculated for the canonical variates space facilitate identification of the main shape differences between genera, including overall length/width, curvature of the external coxal margin, and the extent to which the coxofemoral condyle projects laterally. Jackknifed discriminant function analysis demonstrates that forcipular coxal training-set specimens were assigned to correct species in 61% of cases on average, the most accurate assignments being those of Parascutigera (Parascutigera guttata) and Thereuonema (Thereuonema microstoma). The geographically widespread species Thereuopoda longicornis, Sphendononema guildingii, Scutigera coleoptrata, and Dendrothereua linceci exhibit the least diagnostic coxae in our dataset. Thereuopoda longicornis populations sampled from different parts of East and Southeast Asia were significantly discriminated from each other, suggesting that, in this case, extensive synonymy may be obscuring diagnosable inter-species coxal shape differences. PMID:22303095

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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.

Concordance and discordance between taxonomic and functional homogenization: responses of soil mite assemblages to forest conversion.

PubMed

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.

A "taxonomic affidavit": Why it is needed?

PubMed

Por, Francis Dov

2007-06-01

Imprecise and faulty taxonomic identification of the biological objects of many ecological and experimental studies renders these studies irreproducible. Incomplete identification to the species level and excessive use of vernacular species names are additional problems. Good science must be able to be falsified. I recommend that publications and granting agencies use and mention the names of the zoologists or botanists who identified the species. Voucher specimens should be marked and deposited in scientific museums for future checking.

Taxonomic relationships among Phenacomys voles as inferred by cytochrome b.

Treesearch

M. Renee Bellinger; Susan M. Haig; Eric D. Forsmann; Thomas D. Mullins

2005-01-01

Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. I. 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...

Information Systems in Universities.

ERIC Educational Resources Information Center

Siegmann, Robert M.

This report considers universities as information systems because their effective operation is based on the storage, processing, and communication of various types of information. Three basic types of information systems (administrator-, teacher-, and researcher-oriented) are discussed in an attempt to understand each system's operation from the…

Earthquake Information System

NASA Technical Reports Server (NTRS)

1991-01-01

IAEMIS (Integrated Automated Emergency Management Information System) is the principal tool of an earthquake preparedness program developed by Martin Marietta and the Mid-America Remote Sensing Center (MARC). It is a two-component set of software, data and procedures to provide information enabling management personnel to make informed decisions in disaster situations. The NASA-developed program ELAS, originally used to analyze Landsat data, provides MARC with a spatially-oriented information management system. Additional MARC projects include land resources management, and development of socioeconomic data.

Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

PubMed Central

Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

2014-01-01

Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

Taxonomic Knowledge of Children with and without Cochlear Implants

ERIC Educational Resources Information Center

Lund, Emily; Dinsmoor, Jessica

2016-01-01

Purpose: The purpose of this study was to compare the taxonomic vocabulary knowledge and organization of children with cochlear implants to (a) children with normal hearing matched for age, and (b) children matched for vocabulary development. Method: Ten children with cochlear implants, 10 age-matched children with normal hearing, and 10…

Symposium on Geographic Information Systems.

ERIC Educational Resources Information Center

Felleman, John, Ed.

1990-01-01

Six papers on geographic information systems cover the future of geographic information systems, land information systems modernization in Wisconsin, the Topologically Integrated Geographic Encoding and Referencing (TIGER) System of the U.S. Bureau of the Census, satellite remote sensing, geographic information systems and sustainable development,…

Revitalizing executive information systems.

PubMed

Crockett, F

1992-01-01

As the saying goes, "garbage in, garbage out"--and this is as true for executive information systems as for any other computer system. Crockett presents a methodology he has used with clients to help them develop more useful systems that produce higher quality information. The key is to develop performance measures based on critical success factors and stakeholder expectations and then to link them cross functionally to show how progress is being made on strategic goals. Feedback from the executive information system then informs strategy formulation, business plan development, and operational activities.

Taxonomic and thematic organisation of proper name conceptual knowledge.

PubMed

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.

Taxonomic and Thematic Organisation of Proper Name Conceptual Knowledge

PubMed Central

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. PMID:22063815

Space Station Information Systems

NASA Technical Reports Server (NTRS)

Pittman, Clarence W.

1988-01-01

The utility of the Space Station is improved, the ability to manage and integrate its development and operation enhanced, and the cost and risk of developing the software for it is minimized by three major information systems. The Space Station Information System (SSIS) provides for the transparent collection and dissemination of operational information to all users and operators. The Technical and Management Information System (TMIS) provides all the developers with timely and consistent program information and a project management 'window' to assess the project status. The Software Support Environment (SSE) provides automated tools and standards to be used by all software developers. Together, these three systems are vital to the successful execution of the program.

A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy.

PubMed

Gao, Xiang; Lin, Huaiying; Revanna, Kashi; Dong, Qunfeng

2017-05-10

Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provide species-level classification, or their classification results are unreliable. The unreliable results are due to the limitations in the existing methods which either lack solid probabilistic-based criteria to evaluate the confidence of their taxonomic assignments, or use nucleotide k-mer frequency as the proxy for sequence similarity measurement. We have developed a method that shows significantly improved species-level classification results over existing methods. Our method calculates true sequence similarity between query sequences and database hits using pairwise sequence alignment. Taxonomic classifications are assigned from the species to the phylum levels based on the lowest common ancestors of multiple database hits for each query sequence, and further classification reliabilities are evaluated by bootstrap confidence scores. The novelty of our method is that the contribution of each database hit to the taxonomic assignment of the query sequence is weighted by a Bayesian posterior probability based upon the degree of sequence similarity of the database hit to the query sequence. Our method does not need any training datasets specific for different taxonomic groups. Instead only a reference database is required for aligning to the query sequences, making our method easily applicable for different regions of the 16S rRNA gene or other phylogenetic marker genes. Reliable species-level classification for 16S rRNA or other phylogenetic marker genes is critical for microbiome research. Our software shows significantly higher classification accuracy than the existing tools and we provide probabilistic-based confidence scores to evaluate the reliability of our taxonomic classification assignments based on multiple database matches to query sequences. Despite

Biodiversity Analysis of Forest Litter Ant Assemblages in the Wayanad Region of Western Ghats Using Taxonomic and Conventional Diversity Measures

PubMed Central

Anu, Anto; Sabu, Thomas K.

2007-01-01

The diversity of litter ant assemblages in evergreen, deciduous and Shola evergreen (Shola) forest vegetation types of the Wayanad region of the Western Ghats was assessed employing conventional and taxonomic diversity indices. Non-dependence on quantitative data and the ability to relate the phylogenetic structure of assemblages with ecological conditions of the habitat, and to ascertain priorities for conservation of habitats, makes non-parametric taxonomic diversity measures, such as variation in taxonomic distinctness Λ+ and average taxonomic distinctness Δ+, highly useful tools for assessment of litter ant biodiversity. Although Δ+ values saturated leading to closer values for the 3 litter ant assemblages, Λ+ proved to be a more dependable index. Evenness in taxonomic spread was high in ant assemblages in deciduous forests and low in evergreen forests compared to the regional master list. Low Λ+ of ant assemblage in deciduous forests indicates that among the 3 forest vegetation types, deciduous forests provided the most favorable habitat conditions for litter ants. Low evenness, as is indicated by Λ+ in evergreen forests, was attributed to the presence of a group of taxonomically closely related ant assemblage more adapted to prevail in moist and wet ecological conditions. PMID:20334594

Information Systems Plan.

ERIC Educational Resources Information Center

Tulsa Public Schools, OK.

A task force sought to determine the information needs of the Tulsa Public Schools (Oklahoma) by studying goals of the school district, identifying all processes necessary for operation of the school system, and conducting interviews with 48 key members. A detailed information systems matrix was constructed to show the interrelationships between…

Combining Taxonomic and Functional Approaches to Unravel the Spatial Distribution of an Amazonian Butterfly Community.

PubMed

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.

Distribution of taxonomic classes and the compositional structure of the asteroid belt

NASA Technical Reports Server (NTRS)

Gradie, Jonathan C.; Chapman, Clark R.; Tedesco, Edward F.

1989-01-01

This paper reviews previous studies on the distribution of the asteroid taxonomic classes and analyzes the techniques, results, and interpretations of these studies, with special attention given to the strong and weak points of these studies and the important caveat for their interpretation. It is concluded that, in spite of the differences in class definition, the rather ordered heliocentric distribution of the composition is real and must be due to either primordial, evolutionary, or dynamical processes, or to a combination of all three. In general, the distribution of asteroid taxonomic classes is characterized by moderate-albedo asteroids dominant in the inner asteroid belt, and low-albedo asteroids prevalent in the outer belt and beyond.

Evaluation of Online Information Sources on Alien Species in Europe: The Need of Harmonization and Integration

NASA Astrophysics Data System (ADS)

Gatto, Francesca; Katsanevakis, Stelios; Vandekerkhove, Jochen; Zenetos, Argyro; Cardoso, Ana Cristina

2013-06-01

Europe is severely affected by alien invasions, which impact biodiversity, ecosystem services, economy, and human health. A large number of national, regional, and global online databases provide information on the distribution, pathways of introduction, and impacts of alien species. The sufficiency and efficiency of the current online information systems to assist the European policy on alien species was investigated by a comparative analysis of occurrence data across 43 online databases. Large differences among databases were found which are partially explained by variations in their taxonomical, environmental, and geographical scopes but also by the variable efforts for continuous updates and by inconsistencies on the definition of "alien" or "invasive" species. No single database covered all European environments, countries, and taxonomic groups. In many European countries national databases do not exist, which greatly affects the quality of reported information. To be operational and useful to scientists, managers, and policy makers, online information systems need to be regularly updated through continuous monitoring on a country or regional level. We propose the creation of a network of online interoperable web services through which information in distributed resources can be accessed, aggregated and then used for reporting and further analysis at different geographical and political scales, as an efficient approach to increase the accessibility of information. Harmonization, standardization, conformity on international standards for nomenclature, and agreement on common definitions of alien and invasive species are among the necessary prerequisites.

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

PubMed

Vaníčková, Lucie; Nagy, Radka; Pompeiano, Antonio; Kalinová, Blanka

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.

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

PubMed Central

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

Photometric survey and taxonomic identifications of 92 near-Earth asteroids

NASA Astrophysics Data System (ADS)

Lin, Chien-Hsien; Ip, Wing-Huen; Lin, Zhong-Yi; Cheng, Yu-Chi; Lin, Hsing-Wen; Chang, Chan-Kao

2018-03-01

A photometric survey of near-Earth asteroids (NEAs) was conducted from 2012 through 2014 at Lulin Observatory, Taiwan. The measurements of the color indices, B-V, V-R, and V-I allow the classification of 92 NEAs into seven taxonomic types. Of these samples, 39 of them are new classifications. The fractional abundances of these taxonomic complexes are: A ∼3%, C∼6.5%, D∼8%, Q∼26%, S∼37%, V∼6.5%, and X∼13%. This result is similar to that of Thomas et al. (2011) even though the populations of the D- and X-complex with low albedos are under-represented. The ratio of the C-cluster to the total population of S + C clusters are 0.22 ± 0.06 for H ≤ 17.0 and 0.31 ± 0.06 for H > 17.0, indicating a slightly higher fraction of dark-object population with sizes smaller than 1 km.

Hypothesis-confirming information search strategies and computerized information-retrieval systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacobs, S.M.

A recent trend in information-retrieval systems technology is the development of on-line information retrieval systems. One objective of these systems has been to attempt to enhance decision effectiveness by allowing users to preferentially seek information, thereby facilitating the reduction or elimination of information overload. These systems do not necessarily lead to more-effective decision making, however. Recent research in information-search strategy suggests that when users are seeking information subsequent to forming initial beliefs, they may preferentially seek information to confirm these beliefs. It seems that effective computer-based decision support requires an information retrieval system capable of: (a) retrieving a subset ofmore » all available information, in order to reduce information overload, and (b) supporting an information search strategy that considers all relevant information, rather than merely hypothesis-confirming information. An information retrieval system with an expert component (i.e., a knowledge-based DSS) should be able to provide these capabilities. Results of this study are non conclusive; there was neither strong confirmatory evidence nor strong disconfirmatory evidence regarding the effectiveness of the KBDSS.« less

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

Mission Medical Information System

NASA Technical Reports Server (NTRS)

Johnson-Throop, Kathy A.; Joe, John C.; Follansbee, Nicole M.

2008-01-01

This viewgraph presentation gives an overview of the Mission Medical Information System (MMIS). The topics include: 1) What is MMIS?; 2) MMIS Goals; 3) Terrestrial Health Information Technology Vision; 4) NASA Health Information Technology Needs; 5) Mission Medical Information System Components; 6) Electronic Medical Record; 7) Longitudinal Study of Astronaut Health (LSAH); 8) Methods; and 9) Data Submission Agreement (example).

Strategic Information Systems Planning.

ERIC Educational Resources Information Center

Rowley, Jennifer

1995-01-01

Strategic Information Systems Planning (SISP) is the process of establishing a program for implementation and use of information systems in ways that will optimize effectiveness of information resources and use them to support the objectives of the organization. Basic steps in SISP methodology are outlined. (JKP)

Benthic impacts of intertidal oyster culture, with consideration of taxonomic sufficiency.

PubMed

Forrest, Barrie M; Creese, Robert G

2006-01-01

An investigation of the impacts from elevated intertidal Pacific oyster culture in a New Zealand estuary showed enhanced sedimentation beneath culture racks compared with other sites. Seabed elevation beneath racks was generally lower than between them, suggesting that topographic patterns more likely result from a local effect of rack structures on hydrodynamic processes than from enhanced deposition. Compared with control sites, seabed sediments within the farm had a greater silt/clay and organic content, and a lower redox potential and shear strength. While a marked trend in macrofaunal species richness was not evident, species composition and dominance patterns were consistent with a disturbance gradient, with farm effects not evident 35 m from the perimeter of the racks. Of the environmental variables measured, sediment shear strength was most closely associated with the distribution and density of macrofauna, suggesting that human-induced disturbance from farming operations may have contributed to the biological patterns. To evaluate the taxonomic sufficiency needed to document impacts, aggregation to the family level based on Linnean classification was compared with an aggregation scheme based on ;general groups' identifiable with limited taxonomic expertise. Compared with species-level analyses, spatial patterns of impact were equally discernible at both aggregation levels used, provided density rather than presence/absence data were used. Once baseline conditions are established and the efficacy of taxonomic aggregation demonstrated, a ;general group' scheme provides an appropriate and increasingly relevant tool for routine monitoring.

Management Information Systems Research.

DTIC Science & Technology

Research on management information systems is illusive in many respects. Part of the basic research problem in MIS stems from the absence of standard...decision making. But the transition from these results to the realization of ’satisfactory’ management information systems remains difficult indeed. The...paper discusses several aspects of research on management information systems and reviews a selection of efforts that appear significant for future progress. (Author)

Network Information System

DOE Office of Scientific and Technical Information (OSTI.GOV)

1996-05-01

The Network Information System (NWIS) was initially implemented in May 1996 as a system in which computing devices could be recorded so that unique names could be generated for each device. Since then the system has grown to be an enterprise wide information system which is integrated with other systems to provide the seamless flow of data through the enterprise. The system Iracks data for two main entities: people and computing devices. The following are the type of functions performed by NWIS for these two entities: People Provides source information to the enterprise person data repository for select contractors andmore » visitors Generates and tracks unique usernames and Unix user IDs for every individual granted cyber access Tracks accounts for centrally managed computing resources, and monitors and controls the reauthorization of the accounts in accordance with the DOE mandated interval Computing Devices Generates unique names for all computing devices registered in the system Tracks the following information for each computing device: manufacturer, make, model, Sandia property number, vendor serial number, operating system and operating system version, owner, device location, amount of memory, amount of disk space, and level of support provided for the machine Tracks the hardware address for network cards Tracks the P address registered to computing devices along with the canonical and alias names for each address Updates the Dynamic Domain Name Service (DDNS) for canonical and alias names Creates the configuration files for DHCP to control the DHCP ranges and allow access to only properly registered computers Tracks and monitors classified security plans for stand-alone computers Tracks the configuration requirements used to setup the machine Tracks the roles people have on machines (system administrator, administrative access, user, etc...) Allows systems administrators to track changes made on the machine (both hardware and software) Generates an

Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)

PubMed Central

Nilsson, R. Henrik; Taylor, Andy F. S.; Adams, Rachel I.; Baschien, Christiane; Johan Bengtsson-Palme; Cangren, Patrik; Coleine, Claudia; Heide-Marie Daniel; Glassman, Sydney I.; Hirooka, Yuuri; Irinyi, Laszlo; Reda Iršėnaitė; Pedro M. Martin-Sanchez; Meyer, Wieland; Seung-Yoon Oh; Jose Paulo Sampaio; Seifert, Keith A.; Sklenář, Frantisek; Dirk Stubbe; Suh, Sung-Oui; Summerbell, Richard; Svantesson, Sten; Martin Unterseher; Cobus M. Visagie; Weiss, Michael; Woudenberg, Joyce HC; Christian Wurzbacher; den Wyngaert, Silke Van; Yilmaz, Neriman; Andrey Yurkov; Kõljalg, Urmas; Abarenkov, Kessy

2018-01-01

Abstract Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi – whether transient visitors or more persistent residents – may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions – such as country and host/substrate of collection – are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10–11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes – including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences – were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment. PMID:29559822

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

PubMed

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.

A Clinical Information Display System

PubMed Central

Blum, Bruce J.; Lenhard, Raymond E.; Braine, Hayden; Kammer, Anne

1977-01-01

A clinical information display system has been implemented as part of a prototype Oncology Clinical Information System for the Johns Hopkins Oncology Center. The information system has been developed to support the management of patient therapy. Capabilities in the prototype include a patient data system, a patient abstract, a tumor registry, an appointment system, a census system, and a clinical information display system. This paper describes the clinical information display component of the prototype. It has the capability of supporting up to 10,000 patient records with online data entry and editing. At the present time, the system is being used only in the Oncology Center. There are plans, however, for trial use by other departments, and the system represents a tool with a potential for more general application.

Health Information Systems.

PubMed

Sirintrapun, S Joseph; Artz, David R

2015-06-01

This article provides surgical pathologists an overview of health information systems (HISs): what they are, what they do, and how such systems relate to the practice of surgical pathology. Much of this article is dedicated to the electronic medical record. Information, in how it is captured, transmitted, and conveyed, drives the effectiveness of such electronic medical record functionalities. So critical is information from pathology in integrated clinical care that surgical pathologists are becoming gatekeepers of not only tissue but also information. Better understanding of HISs can empower surgical pathologists to become stakeholders who have an impact on the future direction of quality integrated clinical care. Copyright © 2015 Elsevier Inc. All rights reserved.

Medical-Information-Management System

NASA Technical Reports Server (NTRS)

Alterescu, Sidney; Friedman, Carl A.; Frankowski, James W.

1989-01-01

Medical Information Management System (MIMS) computer program interactive, general-purpose software system for storage and retrieval of information. Offers immediate assistance where manipulation of large data bases required. User quickly and efficiently extracts, displays, and analyzes data. Used in management of medical data and handling all aspects of data related to care of patients. Other applications include management of data on occupational safety in public and private sectors, handling judicial information, systemizing purchasing and procurement systems, and analyses of cost structures of organizations. Written in Microsoft FORTRAN 77.

Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing.

PubMed

Endara, Lorena; Cui, Hong; Burleigh, J Gordon

2018-03-01

Phenotypic data sets are necessary to elucidate the genealogy of life, but assembling phenotypic data for taxa across the tree of life can be technically challenging and prohibitively time consuming. We describe a semi-automated protocol to facilitate and expedite the assembly of phenotypic character matrices of plants from formal taxonomic descriptions. This pipeline uses new natural language processing (NLP) techniques and a glossary of over 9000 botanical terms. Our protocol includes the Explorer of Taxon Concepts (ETC), an online application that assembles taxon-by-character matrices from taxonomic descriptions, and MatrixConverter, a Java application that enables users to evaluate and discretize the characters extracted by ETC. We demonstrate this protocol using descriptions from Araucariaceae. The NLP pipeline unlocks the phenotypic data found in taxonomic descriptions and makes them usable for evolutionary analyses.

Mobile Student Information System

ERIC Educational Resources Information Center

Asif, Muhammad; Krogstie, John

2011-01-01

Purpose: A mobile student information system (MSIS) based on mobile computing and context-aware application concepts can provide more user-centric information services to students. The purpose of this paper is to describe a system for providing relevant information to students on a mobile platform. Design/methodology/approach: The research…

Global Taxonomic Diversity of Living Reptiles

PubMed Central

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

Global taxonomic diversity of living reptiles.

PubMed

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

Air System Information Management

NASA Technical Reports Server (NTRS)

Filman, Robert E.

2004-01-01

I flew to Washington last week, a trip rich in distributed information management. Buying tickets, at the gate, in flight, landing and at the baggage claim, myriad messages about my reservation, the weather, our flight plans, gates, bags and so forth flew among a variety of travel agency, airline and Federal Aviation Administration (FAA) computers and personnel. By and large, each kind of information ran on a particular application, often specialized to own data formats and communications network. I went to Washington to attend an FAA meeting on System-Wide Information Management (SWIM) for the National Airspace System (NAS) (http://www.nasarchitecture.faa.gov/Tutorials/NAS101.cfm). NAS (and its information infrastructure, SWIM) is an attempt to bring greater regularity, efficiency and uniformity to the collection of stovepipe applications now used to manage air traffic. Current systems hold information about flight plans, flight trajectories, weather, air turbulence, current and forecast weather, radar summaries, hazardous condition warnings, airport and airspace capacity constraints, temporary flight restrictions, and so forth. Information moving among these stovepipe systems is usually mediated by people (for example, air traffic controllers) or single-purpose applications. People, whose intelligence is critical for difficult tasks and unusual circumstances, are not as efficient as computers for tasks that can be automated. Better information sharing can lead to higher system capacity, more efficient utilization and safer operations. Better information sharing through greater automation is possible though not necessarily easy.

Advanced radiology information system.

PubMed

Kolovou, L; Vatousi, M; Lymperopoulos, D; Koukias, M

2005-01-01

The innovative features of an advanced Radiology Information System (RIS) are presented in this paper. The interoperability of RIS with the other Intra-hospital Information Systems that interacts with, dealing with the compatibility and open architecture issues, are accomplished by two novel mechanisms [1]. The first one is the particular message handling system that is applied for the exchange of information, according to the Health Level Seven (HL7) protocol's specifications and serves the transfer of medical and administrative data among the RIS applications and data store unit. The same mechanism allows the secure and HL7-compatible interactions with the Hospital Information System (HIS) too. The second one implements the translation of information between the formats that HL7 and Digital Imaging and Communication in Medicine (DICOM) protocols specify, providing the communication between RIS and Picture and Archive Communication System (PACS). The whole structure ensures the automation of the every-day procedures that the ;medical protocol' specifies and provides its services through a friendly and easy to manage graphical user interface.

Majoring in Information Systems: Reasons Why Students Select (or Not) Information Systems as a Major

ERIC Educational Resources Information Center

Snyder, Johnny; Slauson, Gayla Jo

2014-01-01

Filling the pipeline for information systems workers is critical in the information era. Projected growth rates for jobs requiring information systems expertise are significantly higher than the projected growth rates for other jobs. Why then do relatively few students choose to major in information systems? This paper reviews survey results from…

Concordant Biogeographic Patterns among Multiple Taxonomic Groups in the Mexican Freshwater Biota

PubMed Central

Quiroz-Martínez, Benjamín; Álvarez, Fernando; Espinosa, Héctor; Salgado-Maldonado, Guillermo

2014-01-01

In this paper we analyse the degree of concordance in species richness and taxonomic distinctness (diversity) patterns among different freshwater taxonomic groups in order to test three long held patterns described in Mexican freshwater biogeography: 1. The aquatic biota of Mexico includes two distinct faunas, a rich Neotropical component in the south and a south-eastern region and a less rich Nearctic component towards central and northern latitudes of the country. 2. A hotspot of species richness and diversity has been recorded in the Usumacinta, including the Yucatan Peninsula. 3. The presence of two distinct biotas in Mexico, an eastern one distributed along the Gulf of Mexico slope, and a western one associated to the Pacific versant. We use species richness and taxonomic distinctness to explore patterns of diversity and how these patterns change between zoogeographical regions. This paper points out a clear separation between Neotropical and Nearctic drainage basins but also between eastern (Gulf of Mexico) and western (Pacific) drainage basins. Present data gives additional empirical support from freshwater biota for three long held beliefs regarding distributional patterns of the Mexican biota. The neotropical basins of Mexico are generally host to a richest and more diversified fauna, that includes more families, genera and species, compared to the less rich and less diverse fauna in the nearctic basins. PMID:25136979

Taxonomic status of Myotis occultus

USGS Publications Warehouse

Valdez, E.W.; Choate, Jerry R.; Bogan, M.A.; Yates, Terry L.

1999-01-01

The taxonomic status of the Arizona myotis (Myotis occultus) is uncertain. Although the taxon was described as a distinct species and currently is regarded as such by some authors, others have noted what they interpreted as intergradation with the little brown bat (M. lucifugus carissima) near the Colorado-New Mexico state line. In this study, we used protein electrophoresis to compare bats of these nominal taxa. We examined 20 loci from 142 specimens referable to M. occultus and M. lucifugus from New Mexico, Colorado, and Wyoming. Nine of the 20 loci were polymorphic. Results show that there were high similarities among samples, no fixed alleles, and minor divergence from Hardy-Weinberg equilibrium. Our results suggest that the two nominal taxa represent only one species and that M. occultus should be regarded as a subspecies of M. lucifugus.

Medical Information Management System (MIMS): A generalized interactive information system

NASA Technical Reports Server (NTRS)

Alterescu, S.; Friedman, C. A.; Hipkins, K. R.

1975-01-01

An interactive information system is described. It is a general purpose, free format system which offers immediate assistance where manipulation of large data bases is required. The medical area is a prime area of application. Examples of the system's operation, commentary on the examples, and a complete listing of the system program are included.

Medical Information Management System (MIMS): An automated hospital information system

NASA Technical Reports Server (NTRS)

Alterescu, S.; Simmons, P. B.; Schwartz, R. A.

1971-01-01

An automated hospital information system that handles all data related to patient-care activities is described. The description is designed to serve as a manual for potential users, nontechnical medical personnel who may use the system. Examples of the system's operation, commentary on the examples, and a complete listing of the system program are included.

From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories

PubMed Central

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

From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories.

PubMed

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

Comparative SEM and LM foliar epidermal and palyno-morphological studies of Amaranthaceae and its taxonomic implications.

PubMed

Hussain, Amara Noor; Zafar, Muhammad; Ahmad, Mushtaq; Khan, Raees; Yaseen, Ghulam; Khan, Muhammad Saleem; Nazir, Abdul; Khan, Amir Muhammad; Shaheen, Shabnum

2018-05-01

Palynological features as well as comparative foliar epidermal using light and scanning electron microscope (SEM) of 17 species (10genera) of Amaranthaceae have been studied for its taxonomic significance. Different foliar and palynological micro-morphological characters were examined to explain their value in resolving the difficulty in identification. All species were amphistomatic but stomata on abaxial surface were more abundant. Taxonomically significant epidermal character including stomata type, trichomes (unicellular, multicellular, and capitate) and epidermal cells shapes (polygonal and irregular) were also observed. Pollens of this family are Polypantoporate, pores large, spheroidal, mesoporous region is sparsely to scabrate, densely psilate, and spinulose. All these characters can be active at species level for identification purpose. This study indicates that at different taxonomic levels, LM and SEM pollen and epidermal morphology is explanatory and significant to identify species and genera. © 2018 Wiley Periodicals, Inc.

Research Review: Evaluating and reformulating the developmental taxonomic theory of antisocial behaviour

PubMed Central

Fairchild, Graeme; Goozen, Stephanie HM; Calder, Andrew J; Goodyer, Ian M

2013-01-01

BackgroundThe developmental taxonomic theory proposes that there are two subtypes of antisocial behaviour. The first is a neurodevelopmental disorder which emerges in early childhood and follows a life-course persistent course, whereas the second emerges in adolescence, remits in early adulthood and reflects peer processes such as mimicry of antisocial peers. The aim of this review was to evaluate the developmental taxonomic theory in the light of recent empirical research. MethodsWe conducted a comprehensive literature review comparing these subtypes of antisocial behaviour based on searches on PubMed and other scientific databases covering the period from 1993 to 2013. We focused on research encompassing psychiatric epidemiology, personality assessment, neuropsychology, neuroendocrinology, genetics, and structural and functional neuroimaging. Sixty one empirical studies were identified that investigated one of these forms of antisocial behaviour separately or explicitly compared childhood-onset and adolescence-onset forms of antisocial behaviour. ResultsEmpirical research provides support for the hypothesis that life-course persistent antisocial behaviour is a neurodevelopmental disorder which emerges in the transactions between individual vulnerabilities and environmental adversity. In contrast to the developmental taxonomic theory, however, empirical findings suggest that severe antisocial behaviour that emerges in adolescence frequently has a negative prognosis and is rarely limited to the adolescent period. In addition, both forms of antisocial behaviour are associated with emotion processing deficits, changes in brain structure and function, alterations in cortisol secretion, and atypical personality traits (such as increased callous-unemotional traits). ConclusionsWe conclude that the developmental taxonomic theory is in need of revision, as differences between life-course persistent and adolescence-onset forms of antisocial behaviour appear to be

HS3 Information System

NASA Astrophysics Data System (ADS)

Maskey, M.; Conover, H.; Ramachandran, R.; Kulkarni, A.; Mceniry, M.; Stone, B.

2015-12-01

The Global Hydrology Resource Center (GHRC) is developing an enterprise information system to manage and better serve data for Hurricane and Severe Storm Sentinel (HS3), a NASA airborne field campaign. HS3 is a multiyear campaign aimed at helping scientists understand the physical processes that contribute to hurricane intensification. For in-depth analysis, HS3 encompasses not only airborne data but also variety of in-situ, satellite, simulation, and flight report data. Thus, HS3 provides a unique challenge in information system design. The GHRC team is experienced with previous airborne campaigns to handle such challenge. Many supplementary information and reports collected during the mission include information rich contents that provide mission snapshots. In particular, flight information, instrument status, weather reports, and summary statistics offer vital knowledge about the corresponding science data. Furthermore, such information help narrow the science data of interest. Therefore, the GHRC team is building HS3 information system that augments the current GHRC data management framework to support search and discover of airborne science data with interactive visual exploration. Specifically, the HS3 information system is developing a tool to visually playback mission flights along with other traditional search and discover interfaces. This playback capability allows the users to follow the flight in time and visualize collected data. The flight summary and analyzed information are also presented during the playback. If the observed data is of interest, then they can order the data from GHRC using the interface. The users will be able to order just the data for the part of the flight that they are interested in. This presentation will demonstrate use of visual exploration to data download along with other components that comprise the HS3 information system.

Taxonomic revision of Neotropical Murdannia Royle (Commelinaceae)

PubMed Central

Pellegrini, Marco Octávio de Oliveira; Faden, Robert B.; de Almeida, Rafael Felipe

2016-01-01

Abstract This study provides a taxonomic revision for the Neotropical species of the genus Murdannia. Six species are recognized as native, including a new species and a new combination, while two Asian species are recognized as invasive. We present an identification key, a table summarizing the morphologic differences among the species, a new synonym, six lectotypifications, a distribution map, and descriptions, comments and photographic plates for each species. We also provide comments on the morphology of the Neotropical species of Murdannia, comparing them with the Paleotropical species, and a discussion of inflorescence architecture in the genus as a whole. PMID:28127236

Taxonomic updates in Dolichandra Cham. (Bignonieae, Bignoniaceae)

PubMed Central

Fonseca, Luiz Henrique M.; Cabral, Simone Miranda; Agra, Maria de Fátima; Lohmann, Lúcia G.

2015-01-01

Abstract Dolichandra is a genus of lianas found in dry and wet Neotropical forests. The genus currently includes eight species and is well characterized by molecular and morphological synapomorphies. Here, Macfadyena hispida (DC.) Seemann is removed from synonomy with Dolichandra uncata (Andrews) L.G. Lohmann based on the presence of the hispid indument, vinaceus ovary, long fruits, and winged seeds. The combination Dolichandra hispida (DC.) L.H. Fonseca & L.G. Lohmann, comb. nov. is proposed, increasing the number of accepted species of Dolichandra to nine. A taxonomic key for all species of Dolichandra is presented. PMID:25878548

On Management "Myth"-Information Systems.

ERIC Educational Resources Information Center

Mitroff, Ian I.; And Others

Management Myth-Information Systems (MMIS) are information systems which present information to a decision maker by means of stories. In MMIS a scientific datum by itself is not information, but is information if and only if it is tied to an appropriate story or myth that has meaning to the individual who needs the information, the organization in…

Materials management information systems.

PubMed

1996-01-01

The hospital materials management function--ensuring that goods and services get from a source to an end user--encompasses many areas of the hospital and can significantly affect hospital costs. Performing this function in a manner that will keep costs down and ensure adequate cash flow requires effective management of a large amount of information from a variety of sources. To effectively coordinate such information, most hospitals have implemented some form of materials management information system (MMIS). These systems can be used to automate or facilitate functions such as purchasing, accounting, inventory management, and patient supply charges. In this study, we evaluated seven MMISs from seven vendors, focusing on the functional capabilities of each system and the quality of the service and support provided by the vendor. This Evaluation is intended to (1) assist hospitals purchasing an MMIS by educating materials managers about the capabilities, benefits, and limitations of MMISs and (2) educate clinical engineers and information system managers about the scope of materials management within a healthcare facility. Because software products cannot be evaluated in the same manner as most devices typically included in Health Devices Evaluations, our standard Evaluation protocol was not applicable for this technology. Instead, we based our ratings on our observations (e.g., during site visits), interviews we conducted with current users of each system, and information provided by the vendor (e.g., in response to a request for information [RFI]). We divided the Evaluation into the following sections: Section 1. Responsibilities and Information Requirements of Materials Management: Provides an overview of typical materials management functions and describes the capabilities, benefits, and limitations of MMISs. Also includes the supplementary article, "Inventory Cost and Reimbursement Issues" and the glossary, "Materials Management Terminology." Section 2. The

Individual Differences in the Strength of Taxonomic versus Thematic Relations

ERIC Educational Resources Information Center

Mirman, Daniel; Graziano, Kristen M.

2012-01-01

Knowledge about word and object meanings can be organized taxonomically (fruits, mammals, etc.) on the basis of shared features or thematically (eating breakfast, taking a dog for a walk, etc.) on the basis of participation in events or scenarios. An eye-tracking study showed that both kinds of knowledge are activated during comprehension of a…

Integrating Child Health Information Systems

PubMed Central

Hinman, Alan R.; Eichwald, John; Linzer, Deborah; Saarlas, Kristin N.

2005-01-01

The Health Resources and Services Administration and All Kids Count (a national technical assistance center fostering development of integrated child health information systems) have been working together to foster development of integrated child health information systems. Activities have included: identification of key elements for successful integration of systems; development of principles and core functions for the systems; a survey of state and local integration efforts; and a conference to develop a common vision for child health information systems to meet medical care and public health needs. We provide 1 state (Utah) as an example that is well on the way to development of integrated child health information systems. PMID:16195524

Taxonomic and ad hoc categorization within the two cerebral hemispheres.

PubMed

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.

Amazon plant diversity revealed by a taxonomically verified species list.

PubMed

Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M; Bittrich, Volker; Celis, Marcela; Daly, Douglas C; Fiaschi, Pedro; Funk, Vicki A; Giacomin, Leandro L; Goldenberg, Renato; Heiden, Gustavo; Iganci, João; Kelloff, Carol L; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F P; Dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A; Nunes, Teonildes Sacramento; Pennington, Terry D; Pirani, José Rubens; Prance, Ghillean T; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Riina, Ricarda; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D; Taylor, Charlotte M; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E; Forzza, Rafaela Campostrini

2017-10-03

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests.

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria.

PubMed

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.

EFFECTS OF NONINDIGENOUS SPECIES ON THE TAXONOMIC DIVERSITY OF ESTUARINE ASSEMBLAGES

EPA Science Inventory

The effects of the few numerically dominant invasive species on benthic community abundance patterns has been documented in a number of estuaries. What is less appreciated is that the entire suite of nonindigenous species may alter the taxonomic composition of a community or biog...

Taxonomic re-evaluation of black koji molds.

PubMed

Hong, Seung-Beom; Yamada, Osamu; Samson, Robert A

2014-01-01

Black koji molds including its albino mutant, the white koji mold, have been widely used for making the distilled spirit shochu in Northeast Asia because they produce citric acid which prevents undesirable contamination from bacteria. Since Inui reported Aspergillus luchuensis from black koji in Okinawa in 1901, many fungal names associated with black koji molds were reported. However, some species are similar and differentiation between species is difficult. Fungal taxonomists tried to arrange a taxonomic system for black koji molds, but the results were not clear. Recently, multi-locus sequence typing has been successfully used to taxonomy of black Aspergillus. According to β-tubulin and calmodulin gene sequences, black koji molds can be subdivided in three species, A. luchuensis, Aspergillus niger, and Aspergillus tubingensis. Aspergillus awamori, Aspergillus kawachii, Aspergillus inuii, Aspergillus nakazawai, and Aspergillus coreanus are synonyms of A. luchuensis, Aspergillus batatae, Aspergillus aureus (or Aspergillus foetidus), Aspergillus miyakoensis, and Aspergillus usamii (including A. usamii mut. shirousamii) are synonyms of A. niger and Aspergillus saitoi and A. saitoi var. kagoshimaensis are synonyms of A. tubingensis. A. luchuensis mut. kawachii was suggested particular names for A. kawachii because of their industrial importance. The history and modern taxonomy of black koji molds is further discussed.

The taxonomic distribution of asteroids from multi-filter all-sky photometric surveys

NASA Astrophysics Data System (ADS)

DeMeo, F. E.; Carry, B.

2013-09-01

The distribution of asteroids across the main belt has been studied for decades to understand the current compositional distribution and what that tells us about the formation and evolution of our Solar System. All-sky surveys now provide orders of magnitude more data than targeted surveys. We present a method to bias-correct the asteroid population observed in the Sloan Digital Sky Survey (SDSS) according to size, distance, and albedo. We taxonomically classify this dataset consistent with the Bus and Binzel (Bus, S.J., Binzel, R.P. [2002]. Icarus 158, 146-177) and Bus-DeMeo et al. (DeMeo, F.E., Binzel, R.P., Slivan, S.M., Bus, S.J. [2009]. Icarus 202(July), 160-180) systems and present the resulting taxonomic distribution. The dataset includes asteroids as small as 5 km, a factor of three in diameter smaller than in previous work such as by Mothé-Diniz et al. (Mothé-Diniz, T., Carvano, J.M.Á., Lazzaro, D. [2003]. Icarus 162(March), 10-21). Because of the wide range of sizes in our sample, we present the distribution by number, surface area, volume, and mass whereas previous work was exclusively by number. While the distribution by number is a useful quantity and has been used for decades, these additional quantities provide new insights into the distribution of total material. We find evidence for D-types in the inner main belt where they are unexpected according to dynamical models of implantation of bodies from the outer Solar System into the inner Solar System during planetary migration (Levison, H.F., Bottke, W.F., Gounelle, M., Morbidelli, A., Nesvorný, D., Tsiganis, K. [2009]. Nature 460(July), 364-366). We find no evidence of S-types or other unexpected classes among Trojans and Hildas, albeit a bias favoring such a detection. Finally, we estimate for the first time the total amount of material of each class in the inner Solar System. The main belt’s most massive classes are C, B, P, V and S in decreasing order. Excluding the four most massive

Concept of JINR Corporate Information System

NASA Astrophysics Data System (ADS)

Filozova, I. A.; Bashashin, M. V.; Korenkov, V. V.; Kuniaev, S. V.; Musulmanbekov, G.; Semenov, R. N.; Shestakova, G. V.; Strizh, T. A.; Ustenko, P. V.; Zaikina, T. N.

2016-09-01

The article presents the concept of JINR Corporate Information System (JINR CIS). Special attention is given to the information support of scientific researches - Current Research Information System as a part of the corporate information system. The objectives of such a system are focused on ensuring an effective implementation and research by using the modern information technology, computer technology and automation, creation, development and integration of digital resources on a common conceptual framework. The project assumes continuous system development, introduction the new information technologies to ensure the technological system relevance.

Collaborative Processes in Species Identification Using an Internet-Based Taxonomic Resource

ERIC Educational Resources Information Center

Kontkanen, Jani; Kärkkäinen, Sirpa; Dillon, Patrick; Hartikainen-Ahia, Anu; Åhlberg, Mauri

2016-01-01

Visual databases are increasingly important resources through which individuals and groups can undertake species identification. This paper reports research on the collaborative processes undertaken by pre-service teacher students when working in small groups to identify birds using an Internet-based taxonomic resource. The student groups are…

Archival Information Management System.

DTIC Science & Technology

1995-02-01

management system named Archival Information Management System (AIMS), designed to meet the audit trail requirement for studies completed under the...are to be archived to the extent that future reproducibility and interrogation of results will exist. This report presents a prototype information

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

PubMed

Bryant, Harold N; Cantino, Philip D

2002-02-01

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.

Different influences on lexical priming for integrative, thematic, and taxonomic relations

PubMed Central

Jones, Lara L.; Golonka, Sabrina

2012-01-01

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. In a standard lexical decision task (LDT) with various delays between prime and target presentation (SOAs), target RTs and priming magnitudes were consistent across the three relations for both item sets. However, across the SOAs, there were distinct patterns among the 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. PMID:22798950

A global organism detection and monitoring system for non-native species

USGS Publications Warehouse

Graham, J.; Newman, G.; Jarnevich, C.; Shory, R.; Stohlgren, T.J.

2007-01-01

Harmful invasive non-native species are a significant threat to native species and ecosystems, and the costs associated with non-native species in the United States is estimated at over $120 Billion/year. While some local or regional databases exist for some taxonomic groups, there are no effective geographic databases designed to detect and monitor all species of non-native plants, animals, and pathogens. We developed a web-based solution called the Global Organism Detection and Monitoring (GODM) system to provide real-time data from a broad spectrum of users on the distribution and abundance of non-native species, including attributes of their habitats for predictive spatial modeling of current and potential distributions. The four major subsystems of GODM provide dynamic links between the organism data, web pages, spatial data, and modeling capabilities. The core survey database tables for recording invasive species survey data are organized into three categories: "Where, Who & When, and What." Organisms are identified with Taxonomic Serial Numbers from the Integrated Taxonomic Information System. To allow users to immediately see a map of their data combined with other user's data, a custom geographic information system (GIS) Internet solution was required. The GIS solution provides an unprecedented level of flexibility in database access, allowing users to display maps of invasive species distributions or abundances based on various criteria including taxonomic classification (i.e., phylum or division, order, class, family, genus, species, subspecies, and variety), a specific project, a range of dates, and a range of attributes (percent cover, age, height, sex, weight). This is a significant paradigm shift from "map servers" to true Internet-based GIS solutions. The remainder of the system was created with a mix of commercial products, open source software, and custom software. Custom GIS libraries were created where required for processing large datasets

GOBASE—a database of mitochondrial and chloroplast information

PubMed Central

O'Brien, Emmet A.; Badidi, Elarbi; Barbasiewicz, Ania; deSousa, Cristina; Lang, B. Franz; Burger, Gertraud

2003-01-01

GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over 130 000 mitochondrial sequences, an increase of 37% over the previous release, and more than 30 000 chloroplast sequences in a new auxiliary database. To handle this flood of new data, we have designed and implemented GOpop, a Java system for population and verification of the database. We have also implemented a more powerful and flexible user interface using the PHP programming language. http://megasun.bch.umontreal.ca/gobase/gobase.html. PMID:12519975

Predicted taxonomic patterns in pheromone production by longhorned beetles

NASA Astrophysics Data System (ADS)

Ray, Ann M.; Lacey, Emerson S.; Hanks, Lawrence M.

2006-11-01

Males of five species of three tribes in the longhorned beetle subfamily Cerambycinae produce volatile pheromones that share a structural motif (hydroxyl or carbonyl groups at carbons two and three in straight-chains of six, eight, or ten carbons). Pheromone gland pores are present on the prothoraces of males, but are absent in females, suggesting that male-specific gland pores could provide a convenient morphological indication that a species uses volatile pheromones. In this article, we assess the taxonomic distribution of gland pores within the Cerambycinae by examining males and females of 65 species in 24 tribes using scanning electron microscopy. Gland pores were present in males and absent in females of 49 species, but absent in both sexes of the remaining 16 species. Pores were confined to indentations in the cuticle. Among the species that had male-specific gland pores were four species already known to produce volatile compounds consistent with the structural motif. These findings support the initial assumption that gland pores are associated with the production of pheromones by males. There were apparently no taxonomic patterns in the presence of gland pores. These findings suggest that volatile pheromones play an important role in reproduction for many species of the Cerambycinae, and that the trait is evolutionarily labile.

Medical Information Management System

NASA Technical Reports Server (NTRS)

Alterescu, S.; Hipkins, K. R.; Friedman, C. A.

1979-01-01

On-line interactive information processing system easily and rapidly handles all aspects of data management related to patient care. General purpose system is flexible enough to be applied to other data management situations found in areas such as occupational safety data, judicial information, or personnel records.

Illustrated catalogue of Neotropical Ctenuchina, Euchromiina and Pericopina types (Lepidoptera, Erebidae, Arctiinae, Arctiini) described by Hans Zerny, with discussion on their taxonomic status.

PubMed

Pinheiro, L R; Gaal-Haszler, S

2015-03-03

The type material of 54 names of Ctenuchina, Euchromiina and Pericopina proposed by Hans Zerny are treated. Of these, the material belonging to 43 of the 54 names, represented by 118 specimens, are deposited at the Naturhistorisches Museum Wien (NHMW). The remaining are at the BMNH, NMNH, ZMHB or the ZSM, except for one of the species, which material was not traced. Comments on each name and its current taxonomic status, illustrations of holotypes and lectotypes, as well as information about their conservation status are provided. Lectotypes are designated for 23 of the taxa, and two new synonyms are proposed Eucyane variabilis flavofasciata and E. variabilis roseofasciata (=Hypocrita variabilis variabilis). Additionally, nine names have their taxonomic status changed: Correbia columbiana stat. nov., Autochloris jordani comb. nov., Chrostosoma exomelan comb. nov., C. flavothoracides comb. nov., C. pseudothia comb. nov., C. xanthomelan comb. nov., Ecdemus imbecillus comb. nov., Pseudomya clandestina comb. nov., and Uranophora felderi, comb. nov. Illustrations of the genitalia of some of the species are also provided.

The Co-Creation of Information Systems

ERIC Educational Resources Information Center

Gomillion, David

2013-01-01

In information systems development, end-users have shifted in their role: from consumers of information to informants for requirements to developers of systems. This shift in the role of users has also changed how information systems are developed. Instead of systems developers creating specifications for software or end-users creating small…

Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals

PubMed Central

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

Solar-phase-angle effects on the taxonomic classification of asteroids

NASA Astrophysics Data System (ADS)

Carvano, J.; Davallos, J.

2014-07-01

Asteroid taxonomy is the effort of grouping asteroids into classes based on similarities of a number of their observational properties. The most used properties include measurements of their spectral reflectance (by means of low-resolution spectra, spectro-photometry, or colors), and geometric albedo. The usefulness of asteroid taxonomic classes derived in this way relies on the assumption that the classes bear some correspondence to the mineralogy of the asteroids, and on the fact that such classification can be made using types of observations that presently are available to a large number of asteroids. Therefore, asteroid taxonomy can be used to infer trends in the distribution of compositions in the main belt and other populations, as an additional parameter in defining asteroid families, and as a selection tool to identify candidates for more detailed observations. However, the fact that the correspondence between taxonomic class and composition is far from perfect is still sometimes overlooked in the literature. Indeed, although a taxonomic classification narrows down the possible mineralogies of a given asteroid, it will seldom point univocally to one particular mineralogy. This happens for a number of reasons, some linked to the intrinsic difficulty involved in the remote characterization of the mineralogy of an asteroid, since it depends on the presence of absorption bands in its reflectance spectrum which may be absent or not completely sampled by the observations used to derive taxonomy. Other problem here is the exposure of the material on the surface of the asteroid to space-weathering effects, such as solar wind implantation and micro-meteorite bombardment, which can change the optical properties of the material. Finally, the overall shape of the reflectance spectrum of an asteroid is also affected by the geometry of the observation, as well as by its shape. In this work, we analyze how the classification of asteroids observed by the Sloan Digital Sky

Strategic Planning and Information Systems.

ERIC Educational Resources Information Center

Shuman, Jack N.

1982-01-01

Discusses the functions of business planning systems and analyzes the underlying assumptions of the information systems that support strategic planning efforts within organizations. Development of a system framework, obstacles to the successful creation of strategic planning information systems, and resource allocation in organizations are…

Screening and expression of selected taxonomically conserved and unique hypothetical proteins in Burkholderia pseudomallei K96243

NASA Astrophysics Data System (ADS)

Akhir, Nor Azurah Mat; Nadzirin, Nurul; Mohamed, Rahmah; Firdaus-Raih, Mohd

2015-09-01

Hypothetical proteins of bacterial pathogens represent a large numbers of novel biological mechanisms which could belong to essential pathways in the bacteria. They lack functional characterizations mainly due to the inability of sequence homology based methods to detect functional relationships in the absence of detectable sequence similarity. The dataset derived from this study showed 550 candidates conserved in genomes that has pathogenicity information and only present in the Burkholderiales order. The dataset has been narrowed down to taxonomic clusters. Ten proteins were selected for ORF amplification, seven of them were successfully amplified, and only four proteins were successfully expressed. These proteins will be great candidates in determining the true function via structural biology.

High-throughput amplicon sequencing and stream benthic bacteria: identifying the best taxonomic level for multiple-stressor research

PubMed Central

Salis, R. K.; Bruder, A.; Piggott, J. J.; Summerfield, T. C.; Matthaei, C. D.

2017-01-01

Disentangling the individual and interactive effects of multiple stressors on microbial communities is a key challenge to our understanding and management of ecosystems. Advances in molecular techniques allow studying microbial communities in situ and with high taxonomic resolution. However, the taxonomic level which provides the best trade-off between our ability to detect multiple-stressor effects versus the goal of studying entire communities remains unknown. We used outdoor mesocosms simulating small streams to investigate the effects of four agricultural stressors (nutrient enrichment, the nitrification inhibitor dicyandiamide (DCD), fine sediment and flow velocity reduction) on stream bacteria (phyla, orders, genera, and species represented by Operational Taxonomic Units with 97% sequence similarity). Community composition was assessed using amplicon sequencing (16S rRNA gene, V3-V4 region). DCD was the most pervasive stressor, affecting evenness and most abundant taxa, followed by sediment and flow velocity. Stressor pervasiveness was similar across taxonomic levels and lower levels did not perform better in detecting stressor effects. Community coverage decreased from 96% of all sequences for abundant phyla to 28% for species. Order-level responses were generally representative of responses of corresponding genera and species, suggesting that this level may represent the best compromise between stressor sensitivity and coverage of bacterial communities. PMID:28327636

Applied Information Systems Research Program Workshop

NASA Technical Reports Server (NTRS)

Bredekamp, Joe

1991-01-01

Viewgraphs on Applied Information Systems Research Program Workshop are presented. Topics covered include: the Earth Observing System Data and Information System; the planetary data system; Astrophysics Data System project review; OAET Computer Science and Data Systems Programs; the Center of Excellence in Space Data and Information Sciences; and CASIS background.

Informational analysis involving application of complex information system

NASA Astrophysics Data System (ADS)

Ciupak, Clébia; Vanti, Adolfo Alberto; Balloni, Antonio José; Espin, Rafael

The aim of the present research is performing an informal analysis for internal audit involving the application of complex information system based on fuzzy logic. The same has been applied in internal audit involving the integration of the accounting field into the information systems field. The technological advancements can provide improvements to the work performed by the internal audit. Thus we aim to find, in the complex information systems, priorities for the work of internal audit of a high importance Private Institution of Higher Education. The applied method is quali-quantitative, as from the definition of strategic linguistic variables it was possible to transform them into quantitative with the matrix intersection. By means of a case study, where data were collected via interview with the Administrative Pro-Rector, who takes part at the elaboration of the strategic planning of the institution, it was possible to infer analysis concerning points which must be prioritized at the internal audit work. We emphasize that the priorities were identified when processed in a system (of academic use). From the study we can conclude that, starting from these information systems, audit can identify priorities on its work program. Along with plans and strategic objectives of the enterprise, the internal auditor can define operational procedures to work in favor of the attainment of the objectives of the organization.

BIO-Plex Information System Concept

NASA Technical Reports Server (NTRS)

Jones, Harry; Boulanger, Richard; Arnold, James O. (Technical Monitor)

1999-01-01

This paper describes a suggested design for an integrated information system for the proposed BIO-Plex (Bioregenerative Planetary Life Support Systems Test Complex) at Johnson Space Center (JSC), including distributed control systems, central control, networks, database servers, personal computers and workstations, applications software, and external communications. The system will have an open commercial computing and networking, architecture. The network will provide automatic real-time transfer of information to database server computers which perform data collection and validation. This information system will support integrated, data sharing applications for everything, from system alarms to management summaries. Most existing complex process control systems have information gaps between the different real time subsystems, between these subsystems and central controller, between the central controller and system level planning and analysis application software, and between the system level applications and management overview reporting. An integrated information system is vitally necessary as the basis for the integration of planning, scheduling, modeling, monitoring, and control, which will allow improved monitoring and control based on timely, accurate and complete data. Data describing the system configuration and the real time processes can be collected, checked and reconciled, analyzed and stored in database servers that can be accessed by all applications. The required technology is available. The only opportunity to design a distributed, nonredundant, integrated system is before it is built. Retrofit is extremely difficult and costly.

Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities.

PubMed

Guo, Yanqing; Chen, Xiaotian; Wu, Yuanyuan; Zhang, Lu; Cheng, Jimin; Wei, Gehong; Lin, Yanbing

2018-04-18

Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems. Copyright © 2018. Published by Elsevier B.V.

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

PubMed

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.

Taxonomic Distinctness and Richness of Helminth Parasite Assemblages of Freshwater Fishes in Mexican Hydrological Basins

PubMed Central

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. PMID:24086342

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

PubMed

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

Harmonizing health information systems with information systems in other social and economic sectors.

PubMed Central

Macfarlane, Sarah B.

2005-01-01

Efforts to strengthen health information systems in low- and middle-income countries should include forging links with systems in other social and economic sectors. Governments are seeking comprehensive socioeconomic data on the basis of which to implement strategies for poverty reduction and to monitor achievement of the Millennium Development Goals. The health sector is looking to take action on the social factors that determine health outcomes. But there are duplications and inconsistencies between sectors in the collection, reporting, storage and analysis of socioeconomic data. National offices of statistics give higher priority to collection and analysis of economic than to social statistics. The Report of the Commission for Africa has estimated that an additional US$ 60 million a year is needed to improve systems to collect and analyse statistics in Africa. Some donors recognize that such systems have been weakened by numerous international demands for indicators, and have pledged support for national initiatives to strengthen statistical systems, as well as sectoral information systems such as those in health and education. Many governments are working to coordinate information systems to monitor and evaluate poverty reduction strategies. There is therefore an opportunity for the health sector to collaborate with other sectors to lever international resources to rationalize definition and measurement of indicators common to several sectors; streamline the content, frequency and timing of household surveys; and harmonize national and subnational databases that store socioeconomic data. Without long-term commitment to improve training and build career structures for statisticians and information technicians working in the health and other sectors, improvements in information and statistical systems cannot be sustained. PMID:16184278

Research review: evaluating and reformulating the developmental taxonomic theory of antisocial behaviour.

PubMed

Fairchild, Graeme; van Goozen, Stephanie H M; Calder, Andrew J; Goodyer, Ian M

2013-09-01

The developmental taxonomic theory proposes that there are two subtypes of antisocial behaviour. The first is a neurodevelopmental disorder which emerges in early childhood and follows a life-course persistent course, whereas the second emerges in adolescence, remits in early adulthood and reflects peer processes such as mimicry of antisocial peers. The aim of this review was to evaluate the developmental taxonomic theory in the light of recent empirical research. We conducted a comprehensive literature review comparing these subtypes of antisocial behaviour based on searches on PubMed and other scientific databases covering the period from 1993 to 2013. We focused on research encompassing psychiatric epidemiology, personality assessment, neuropsychology, neuroendocrinology, genetics, and structural and functional neuroimaging. Sixty one empirical studies were identified that investigated one of these forms of antisocial behaviour separately or explicitly compared childhood-onset and adolescence-onset forms of antisocial behaviour. Empirical research provides support for the hypothesis that life-course persistent antisocial behaviour is a neurodevelopmental disorder which emerges in the transactions between individual vulnerabilities and environmental adversity. In contrast to the developmental taxonomic theory, however, empirical findings suggest that severe antisocial behaviour that emerges in adolescence frequently has a negative prognosis and is rarely limited to the adolescent period. In addition, both forms of antisocial behaviour are associated with emotion processing deficits, changes in brain structure and function, alterations in cortisol secretion, and atypical personality traits (such as increased callous-unemotional traits). We conclude that the developmental taxonomic theory is in need of revision, as differences between life-course persistent and adolescence-onset forms of antisocial behaviour appear to be quantitative, rather than qualitative, in

Amazon plant diversity revealed by a taxonomically verified species list

PubMed Central

Cardoso, Domingos; Särkinen, Tiina; Alexander, Sara; Amorim, André M.; Bittrich, Volker; Celis, Marcela; Daly, Douglas C.; Fiaschi, Pedro; Funk, Vicki A.; Giacomin, Leandro L.; Heiden, Gustavo; Iganci, João; Kelloff, Carol L.; Knapp, Sandra; Cavalcante de Lima, Haroldo; Machado, Anderson F. P.; dos Santos, Rubens Manoel; Mello-Silva, Renato; Michelangeli, Fabián A.; Mitchell, John; Moonlight, Peter; de Moraes, Pedro Luís Rodrigues; Mori, Scott A.; Nunes, Teonildes Sacramento; Pennington, Terry D.; Pirani, José Rubens; Prance, Ghillean T.; de Queiroz, Luciano Paganucci; Rapini, Alessandro; Rincon, Carlos Alberto Vargas; Roque, Nádia; Shimizu, Gustavo; Sobral, Marcos; Stehmann, João Renato; Stevens, Warren D.; Taylor, Charlotte M.; Trovó, Marcelo; van den Berg, Cássio; van der Werff, Henk; Viana, Pedro Lage; Zartman, Charles E.; Forzza, Rafaela Campostrini

2017-01-01

Recent debates on the number of plant species in the vast lowland rain forests of the Amazon have been based largely on model estimates, neglecting published checklists based on verified voucher data. Here we collate taxonomically verified checklists to present a list of seed plant species from lowland Amazon rain forests. Our list comprises 14,003 species, of which 6,727 are trees. These figures are similar to estimates derived from nonparametric ecological models, but they contrast strongly with predictions of much higher tree diversity derived from parametric models. Based on the known proportion of tree species in neotropical lowland rain forest communities as measured in complete plot censuses, and on overall estimates of seed plant diversity in Brazil and in the neotropics in general, it is more likely that tree diversity in the Amazon is closer to the lower estimates derived from nonparametric models. Much remains unknown about Amazonian plant diversity, but this taxonomically verified dataset provides a valid starting point for macroecological and evolutionary studies aimed at understanding the origin, evolution, and ecology of the exceptional biodiversity of Amazonian forests. PMID:28923966

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

PubMed Central

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

High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence.

PubMed

Thomas, Pious; Sekhar, Aparna C; Shaik, Sadiq Pasha

2017-11-01

Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood ® -kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates

Power System Information Delivering System Based on Distributed Object

NASA Astrophysics Data System (ADS)

Tanaka, Tatsuji; Tsuchiya, Takehiko; Tamura, Setsuo; Seki, Tomomichi; Kubota, Kenji

In recent years, improvement in computer performance and development of computer network technology or the distributed information processing technology has a remarkable thing. Moreover, the deregulation is starting and will be spreading in the electric power industry in Japan. Consequently, power suppliers are required to supply low cost power with high quality services to customers. Corresponding to these movements the authors have been proposed SCOPE (System Configuration Of PowEr control system) architecture for distributed EMS/SCADA (Energy Management Systems / Supervisory Control and Data Acquisition) system based on distributed object technology, which offers the flexibility and expandability adapting those movements. In this paper, the authors introduce a prototype of the power system information delivering system, which was developed based on SCOPE architecture. This paper describes the architecture and the evaluation results of this prototype system. The power system information delivering system supplies useful power systems information such as electric power failures to the customers using Internet and distributed object technology. This system is new type of SCADA system which monitors failure of power transmission system and power distribution system with geographic information integrated way.

Information System Plan.

ERIC Educational Resources Information Center

McIntyre, Chuck

Prepared for review and discussion by the Board of Governors of the California Community Colleges (CCC), this report provides background and recommendations for the refinement, expansion, and increased use of the information system of the CCC Chancellor's Office. Following introductory material proposing an expanded scope of the information system…

Insights into discriminating environmental quality status using taxonomic distinctness based on a small species pool of ciliated protozoa in marine ecosystems.

PubMed

Jiang, Yong; Xu, Henglong; Warren, Alan

2014-01-15

The objective of this study was to determine the feasibility of developing a protocol for assessing marine water quality based on taxonomic relatedness within a small pool of planktonic ciliates. An annual dataset was compiled based on samples collected biweekly at five sites, with a gradient of environmental stress, during a 1-year cycle in Jiaozhou Bay, northern China. A total of 60 species, belonging to 17 genera 10 families, 5 orders and 2 classes of the phylum Ciliophora, were identified. Among five orders, Tintinnida showed a low variability mainly at species level whereas the other orders (especially Strombidiida and Choreotrichida, although with the exception of the genus Strombidium) represented a high variability at higher taxonomic ranks (e.g. family or order). Mantel analyses showed that spatial patterns of the ciliate assemblages, with tinitinnids and Strombidium spp. excluded, were significantly correlated with those of the total planktonic ciliate communities in terms of their response to environmental status. The average taxonomic distinctness (Δ(+)) based on the small species pool was significantly negatively correlated with the changes in concentrations of nutrients (P<0.05). Furthermore, the paired indices of Δ(+) and the variation in taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that it is possible to assess the status of marine water quality using the taxonomic relatedness within a small pool of planktonic ciliates. © 2013.

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

USGS Publications Warehouse

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.

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

PubMed

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.

Information retrieval system

NASA Technical Reports Server (NTRS)

Berg, R. F.; Holcomb, J. E.; Kelroy, E. A.; Levine, D. A.; Mee, C., III

1970-01-01

Generalized information storage and retrieval system capable of generating and maintaining a file, gathering statistics, sorting output, and generating final reports for output is reviewed. File generation and file maintenance programs written for the system are general purpose routines.

The use of information systems to transform utilities and regulatory commissions: The application of geographic information systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wirick, D.W.; Montgomery, G.E.; Wagman, D.C.

1995-09-01

One technology that can assist utilities remain financially viable in competitive markets and help utilities and regulators to better serve the public is information technology. Because geography is an important part of an electric, natural gas, telecommunications, or water utility, computer-based Geographic Information Systems (GIS) and related Automated Mapping/Facilities Management systems are emerging as core technologies for managing an ever-expanding variety of formerly manual or paper-based tasks. This report focuses on GIS as an example of the types of information systems that can be used by utilities and regulatory commissions. Chapter 2 provides general information about information systems and effectsmore » of information on organizations; Chapter 3 explores the conversion of an organization to an information-based one; Chapters 4 and 5 set out GIS as an example of the use of information technologies to transform the operations of utilities and commissions; Chapter 6 describes the use of GIS and other information systems for organizational reengineering efforts; and Chapter 7 examines the regulatory treatment of information systems.« less

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

PubMed

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.

Activity Theory in Information Systems Research and Practice: Theoretical Underpinnings for an Information Systems Development Model

ERIC Educational Resources Information Center

Mursu, Anja; Luukkonen, Irmeli; Toivanen, Marika; Korpela, Mikko

2007-01-01

Introduction: The purpose of information systems is to facilitate work activities: here we consider how Activity Theory can be applied in information systems development. Method. The requirements for an analytical model for emancipatory, work-oriented information systems research and practice are specified. Previous research work in Activity…

Glycosides from Marine Sponges (Porifera, Demospongiae): Structures, Taxonomical Distribution, Biological Activities and Biological Roles

PubMed Central

Kalinin, Vladimir I.; Ivanchina, Natalia V.; Krasokhin, Vladimir B.; Makarieva, Tatyana N.; Stonik, Valentin A.

2012-01-01

Literature data about glycosides from sponges (Porifera, Demospongiae) are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed. PMID:23015769

Notes on the taxonomic position of several species of the genus Diphascon (Tardigrada, Hypsibiidae).

PubMed

Tumanov, Denis V

2018-03-20

For this paper I analysed the descriptions of all species, attributed to the genus Diphascon Plate, 1889, to ascertain if they fit the diagnosis of this genus, provided by Bertolani et al. 2014. Thirty four species (the majority of the species diversity classified within the genus) fully match its emended diagnosis, while three: Diphascon opisthoglyptum Maucci, 1987, Diphascon procerum Pilato, Sabella Lisi, 2014 and Diphascon ziliense Lisi, Sabella Pilato, 2014, demonstrate a combination of characters, typical to the genus Pilatobius Bertolani et al., 2014. I propose the transfer these three species to the genus Pilatobius, thus their new taxonomic positions are as follows: Pilatobius opisthoglyptus (Maucci, 1987) comb. nov., Pilatobius procerus (Pilato, Sabella Lisi, 2014) comb. nov. and Pilatobius ziliense (Lisi, Sabella Pilato, 2014) comb. nov. Descriptions of three other Diphascon species (Diphascon mariae (Mihelčič, 1951), Diphascon rivulare (Mihelčič, 1967) and Diphascon punctatum (Iharos, 1962)) contain too little detail to conclude on their taxonomic position. The species Pilatobius halapiense (Iharos, 1964) was erroneously transferred from the genus Diphascon, and here I suggest it is transferred back to Diphascon. The new taxonomic position of this species is: Diphascon halapiense (Iharos, 1964) comb. nov. Emended list of species, attributed to the genus Diphascon is given.

Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases.

PubMed

De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E; Hendrix, Stephen D; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M E; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S; Morales, Carolina L; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Poveda, Katja; Power, Eileen F; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H; Roulston, T'ai; Rousseau, Laurent; Sadler, Jonathan P; Samnegård, Ulrika; Schellhorn, Nancy A; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H; Steffan-Dewenter, Ingolf; Stout, Jane C; Tonietto, Rebecca K; Tscharntke, Teja; Tylianakis, Jason M; Verboven, Hans A F; Vergara, Carlos H; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

2016-08-11

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases

PubMed Central

De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A.; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J.; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A.; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H.; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J.; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E.; Hendrix, Stephen D.; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M. E.; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A.; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S.; Morales, Carolina L.; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G.; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A.; Persson, Anna S.; Petanidou, Theodora; Poveda, Katja; Power, Eileen F.; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H.; Roulston, T’ai; Rousseau, Laurent; Sadler, Jonathan P.; Samnegård, Ulrika; Schellhorn, Nancy A.; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H.; Steffan-Dewenter, Ingolf; Stout, Jane C.; Tonietto, Rebecca K.; Tscharntke, Teja; Tylianakis, Jason M.; Verboven, Hans A. F.; Vergara, Carlos H.; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

2016-01-01

Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises. PMID:27509831

Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae).

PubMed

Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

2015-01-01

The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x-18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus.

Developing a clinical information system: the role of the chief information officer.

PubMed

Glaser, J

1994-11-01

Chief information officers (CIOs) must play a pivotal role in the formation and implementation of a clinical information system, the subset of an organizational information system that deals specifically with support of clinical care activities. Major elements include the applications software, technology and data architecture, databases, and analysis. The organizational structures and processes that manage the development of improvement activities, including the clinical information system itself, are just as vital to the design of an information system as the hardware and software. To develop, sustain, and advance an information infrastructure, the CIO must help establish certain organizational precursors, such as medical staff involvement, experience with quality improvement, and ability to meet data needs. The CIO must then work with the senior administrative and medical leadership in developing a vision for the information system. The CIO must also create new roles and knowledge for information system and medical staff members. Interaction between information services and medical staff is vitally important to the success of a clinical information system. Organizational committees and structures that Brigham and Women's Hospital in Boston put in place to formalize the relationship between information systems and medical staff include the Clinical Initiative Development Program and the Center for Applied Medical Information Systems Research. Improving the clinical management of care and the efficacy of care processes involves complex changes in organizational culture and processes, medical practice and information system applications, technologies, staff, and data.

Intelligent Information Systems.

ERIC Educational Resources Information Center

Zabezhailo, M. I.; Finn, V. K.

1996-01-01

An Intelligent Information System (IIS) uses data warehouse technology to facilitate the cycle of data and knowledge processing, including input, standardization, storage, representation, retrieval, calculation, and delivery. This article provides an overview of IIS products and artificial intelligence systems, illustrates examples of IIS…

28 CFR 25.3 - System information.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 28 Judicial Administration 1 2013-07-01 2013-07-01 false System information. 25.3 Section 25.3 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The National Instant Criminal Background Check System § 25.3 System information. (a) There is established at the FBI a...

28 CFR 25.3 - System information.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 28 Judicial Administration 1 2011-07-01 2011-07-01 false System information. 25.3 Section 25.3 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The National Instant Criminal Background Check System § 25.3 System information. (a) There is established at the FBI a...

28 CFR 25.3 - System information.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 28 Judicial Administration 1 2014-07-01 2014-07-01 false System information. 25.3 Section 25.3 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The National Instant Criminal Background Check System § 25.3 System information. (a) There is established at the FBI a...

28 CFR 25.3 - System information.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 28 Judicial Administration 1 2012-07-01 2012-07-01 false System information. 25.3 Section 25.3 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The National Instant Criminal Background Check System § 25.3 System information. (a) There is established at the FBI a...

28 CFR 25.3 - System information.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 1 2010-07-01 2010-07-01 false System information. 25.3 Section 25.3 Judicial Administration DEPARTMENT OF JUSTICE DEPARTMENT OF JUSTICE INFORMATION SYSTEMS The National Instant Criminal Background Check System § 25.3 System information. (a) There is established at the FBI a...

A taxonomic review of white grubs and leaf chafers (Coleoptera: Scarabaeidae: Melolonthinae) recorded from forestry and agricultural crops in Sub-Saharan Africa.

PubMed

Harrison, J du G; Wingfield, M J

2016-04-01

Integrated pest management (IPM) is difficult to implement when one knows little about the pest complex or species causing the damage in an agricultural system. To implement IPM on Sub-Saharan African melolonthine pests access to taxon specific knowledge (their identity) and what is known (their biology) of potential pest species is a crucial step. What is known about Sub-Saharan African melolonthine white grubs and chafers has not yet been amalgamated, and this review thus synthesizes all available literature for the Region. The comprehensive nature of the review highlights pest taxon trends within African melolonthines. To facilitate the retrieval of this information for IPM purposes, all relevant taxonomic and biological information is provided for the taxa covered including an on-line supplementary annotated-checklist of taxon, crop, locality and reference(s). Based on the literature reviewed, recommendations are made to promote effective and efficient management of African melolonthine scarab pests. An on-line supplementary appendix provides a list of specialists, useful internet resources, keys, catalogues and sampling methods for the larvae and adults of melolonthine scarab beetles for subsequent morphological or molecular work.

Financing a Career Information System.

ERIC Educational Resources Information Center

Franklin, Paul L.

This practical introduction and guide to the financing of a state-based system of career information is intended for policy makers and practitioners engaged in implementing career information services. Chapter 1 is an introduction to both career information systems and their financing with concentration on service fees as the base for attaining…

Natural history and information overload: The case of Linnaeus

PubMed Central

Müller-Wille, Staffan; Charmantier, Isabelle

2012-01-01

Natural History can be seen as a discipline paradigmatically engaged in ‘data-driven research.’ Historians of early modern science have begun to emphasize its crucial role in the Scientific Revolution, and some observers of present day genomics see it as engaged in a return to natural history practices. A key concept that was developed to understand the dynamics of early modern natural history is that of ‘information overload.’ Taxonomic systems, rules of nomenclature, and technical terminologies were developed in botany and zoology to catch up with the ever increasing amount of information on hitherto unknown plant and animal species. In our contribution, we want to expand on this concept. After all, the same people who complain about information overload are usually the ones who contribute to it most significantly. In order to understand this complex relationship, we will turn to the annotation practices of the Swedish naturalist Carl Linnaeus (1707–1778). The very tools that Linnaeus developed to contain and reduce information overload, as we aim to demonstrate, facilitated a veritable information explosion that led to the emergence of a new research object in botany: the so-called ‘natural’ system. PMID:22326068

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession.

PubMed

Ortiz-Álvarez, Rüdiger; Fierer, Noah; de Los Ríos, Asunción; Casamayor, Emilio O; Barberán, Albert

2018-02-20

Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.

Seasonal dynamics alter taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

PubMed Central

Barboza, Anthony Diego Muller; Pylro, Victor Satler; Jacques, Rodrigo Josemar Seminot; Gubiani, Paulo Ivonir; de Quadros, Fernando Luiz Ferreira; da Trindade, Júlio Kuhn; Triplett, Eric W.

2018-01-01

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. Our data suggest that grasslands maintained a stable microbial community membership along the year with oscillation in abundance. Apparently soil microbial taxa are more susceptible to natural climatic disturbances while functions are more stable and change with less intensity along the year. Finally, our data allow us to conclude that the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

PubMed

Blank, Carrine E; Cui, Hong; Moore, Lisa R; Walls, Ramona L

2016-01-01

MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. MicrO currently has ~14550 classes (~2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by ~24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we

Wide Area Information Servers: An Executive Information System for Unstructured Files.

ERIC Educational Resources Information Center

Kahle, Brewster; And Others

1992-01-01

Describes the Wide Area Information Servers (WAIS) system, an integrated information retrieval system for corporate end users. Discussion covers general characteristics of the system, search techniques, protocol development, user interfaces, servers, selective dissemination of information, nontextual data, access to other servers, and description…

Information Systems for University Planning.

ERIC Educational Resources Information Center

Robinson, Robert J.

This paper proposes construction of a separate data base environment for university planning information, distinct from data bases and systems supporting operational functioning and management. The data base would receive some of its input from the management information systems (MIS)/transactional data bases and systems through a process of…

Pharmaceutical information systems and possible implementations of informed consent -- developing an heuristic.

PubMed

Ploug, Thomas; Holm, Søren

2012-11-16

Denmark has implemented a comprehensive, nationwide pharmaceutical information system, and this system has been evaluated by the Danish Council of Ethics. The system can be seen as an exemplar of a comprehensive health information system for clinical use. The paper analyses 1) how informed consent can be implemented in the system and how different implementations create different impacts on autonomy and control of information, and 2) arguments directed towards justifying not seeking informed consent in this context. Based on the analysis a heuristic is provided which enables a ranking and estimation of the impact on autonomy and control of information of different options for consent to entry of data into the system and use of data from the system.The danger of routinisation of consent is identified.The Danish pharmaceutical information system raises issues in relation to autonomy and control of information, issues that will also occur in relation to other similar comprehensive health information systems. Some of these issues are well understood and their impact can be judged using the heuristic which is provided. More research is, however needed in relation to routinisation of consent.

Pharmaceutical information systems and possible implementations of informed consent - developing an heuristic

PubMed Central

2012-01-01

Background Denmark has implemented a comprehensive, nationwide pharmaceutical information system, and this system has been evaluated by the Danish Council of Ethics. The system can be seen as an exemplar of a comprehensive health information system for clinical use. Analysis The paper analyses 1) how informed consent can be implemented in the system and how different implementations create different impacts on autonomy and control of information, and 2) arguments directed towards justifying not seeking informed consent in this context. Results and Conclusion Based on the analysis a heuristic is provided which enables a ranking and estimation of the impact on autonomy and control of information of different options for consent to entry of data into the system and use of data from the system. The danger of routinisation of consent is identified. The Danish pharmaceutical information system raises issues in relation to autonomy and control of information, issues that will also occur in relation to other similar comprehensive health information systems. Some of these issues are well understood and their impact can be judged using the heuristic which is provided. More research is, however needed in relation to routinisation of consent. PMID:23157854

A taxonomic revision of Herminium L. (Orchidoideae, Orchidaceae)

PubMed Central

Raskoti, Bhakta Bahadur; Schuiteman, André; Jin, Wei-Tao; Jin, Xiao-Hua

2017-01-01

Abstract Herminium (Orchidaceae, Orchidoideae) is a medium-sized genus widespread in the northern hemisphere, with a clear centre of diversity in the Himalayas. We present a comprehensive taxonomic revision of Herminium based on field observations and morphological studies, for which we examined about 2500 specimens. We recognize 49 species grouped into six formal sections, including one new species, Herminium tibeticum, from Tibet. We provide an identification key to the species, descriptions of the species, notes on ecology and distribution, and complete nomenclature for each species, including typifications. We here designate lectotypes for five species and reduce four taxa to synonymy. PMID:28794677

Strengthening Rehabilitation in Health Systems Worldwide by Integrating Information on Functioning in National Health Information Systems.

PubMed

Stucki, Gerold; Bickenbach, Jerome; Melvin, John

2017-09-01

A complete understanding of the experience of health requires information relevant not merely to the health indicators of mortality and morbidity but also to functioning-that is, information about what it means to live in a health state, "the lived experience of health." Not only is functioning information relevant to healthcare and the overall objectives of person-centered healthcare but to the successful operation of all components of health systems.In light of population aging and major epidemiological trends, the health strategy of rehabilitation, whose aim has always been to optimize functioning and minimize disability, will become a key health strategy. The increasing prominence of the rehabilitative strategy within the health system drives the argument for the integration of functioning information as an essential component in national health information systems.Rehabilitation professionals and researchers have long recognized in WHO's International Classification of Functioning, Disability and Health the best prospect for an internationally recognized, sufficiently complete and powerful information reference for the documentation of functioning information. This paper opens the discussion of the promise of integrating the ICF as an essential component in national health systems to secure access to functioning information for rehabilitation, across health systems and countries.

Functional and Taxonomic Diversity of Stinging Wasps in Brazilian Atlantic Rainforest Areas.

PubMed

Dos Santos, E F; Noll, F B; Brandão, C R F

2014-04-01

Vespoidea are the most functionally diverse superfamily of Hymenoptera. Ecological studies involving this family are primarily based on eusocial groups, including ants and social paper wasps. In the present study, we examine stinging wasp (Vespoidea) faunal diversity in the Atlantic Rain Forest, which is one of the most diverse and threatened ecosystems in the World. Three conservation areas were sampled employing a standardized sample protocol. Families and functional groups of Vespoidea were collected in each area, with the exception ants (Formicidae), and analyzed using diversity analyses, to generate taxonomic diversity and distinctness indices. Results indicated Pompilidae was the most diverse family, and the idiobiont parasitoid type was the most diverse functional group in the three study areas. Núcleo Picinguaba of the Parque Estadual da Serra do Mar was taxonomically and functionally the most diverse and species rich area. Parque Estadual Intervales showed the highest number of dominant species and diversity of koinobiont parasitoids, while the Rebio Sooretama exhibited a decrease in several diversity parameters.

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

PubMed

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.

Global Land Information System (GLIS)

USGS Publications Warehouse

,

1992-01-01

The Global Land Information System (GLIS) is an interactive computer system developed by the U.S. Geological Survey (USGS) for scientists seeking sources of information about the Earth's land surfaces. GLIS contains "metadata," that is, descriptive information about data sets. Through GLIS, scientists can evaluate data sets, determine their availability, and place online requests for products. GLIS is more, however, than a mere list of products. It offers online samples of earth science data that may be ordered through the system.

Information technology equipment cooling system

DOEpatents

Schultz, Mark D.

2014-06-10

According to one embodiment, a system for removing heat from a rack of information technology equipment may include a sidecar indoor air to liquid heat exchanger that cools warm air generated by the rack of information technology equipment. The system may also include a liquid to liquid heat exchanger and an outdoor heat exchanger. The system may further include configurable pathways to connect and control fluid flow through the sidecar heat exchanger, the liquid to liquid heat exchanger, the rack of information technology equipment, and the outdoor heat exchanger based upon ambient temperature and/or ambient humidity to remove heat from the rack of information technology equipment.

Case Studies of Ecological Integrative Information Systems: The Luquillo and Sevilleta Information Management Systems

NASA Astrophysics Data System (ADS)

San Gil, Inigo; White, Marshall; Melendez, Eda; Vanderbilt, Kristin

The thirty-year-old United States Long Term Ecological Research Network has developed extensive metadata to document their scientific data. Standard and interoperable metadata is a core component of the data-driven analytical solutions developed by this research network Content management systems offer an affordable solution for rapid deployment of metadata centered information management systems. We developed a customized integrative metadata management system based on the Drupal content management system technology. Building on knowledge and experience with the Sevilleta and Luquillo Long Term Ecological Research sites, we successfully deployed the first two medium-scale customized prototypes. In this paper, we describe the vision behind our Drupal based information management instances, and list the features offered through these Drupal based systems. We also outline the plans to expand the information services offered through these metadata centered management systems. We will conclude with the growing list of participants deploying similar instances.

An intercomparison of the taxonomic and size composition of tropical macrozooplankton and micronekton collected using three sampling gears

NASA Astrophysics Data System (ADS)

Kwong, Lian E.; Pakhomov, Evgeny A.; Suntsov, Andrey V.; Seki, Michael P.; Brodeur, Richard D.; Pakhomova, Larisa G.; Domokos, Réka

2018-05-01

A micronekton intercalibration experiment was conducted off the southwest coast of Oahu Island, Hawaii in October 2004. Day and night samples were collected in the epipelagic and mesopelagic zones using three micronekton sampling gears: the Cobb Trawl, the Isaacs-Kidd Midwater Trawl (IKMT), and the Hokkaido University Frame Trawl (HUFT). Taxonomic composition and contribution by main size groups to total catch varied among gear types. However, the three gears exhibited similar taxonomic composition for macrozooplankton and micronekton ranging from 20 to 100 mm length (MM20-100). The HUFT and IKMT captured more mesozooplankton and small MM20-100, while the Cobb trawl selected towards larger MM20-100 and nekton. Taxonomic composition was described and inter-compared among gears. The relative efficacy of the three gears was assessed, and size dependent intercalibration coefficients were developed for MM20-100.

What are the taxonomic and evolutionary relationships of the Protozoa to the Protista?

PubMed

Corliss, J O

1981-01-01

In order to consider the problems of protist-protozoan interrelationships in proper perspective, a new "packaging" of phyla within the great kingdom Protista is proposed. Although it is based largely on historical groupings and is admittedly "unnatural" (nor are taxonomic names proposed for my five supraphyletic groupings), the arrangement may clarify some long-persisting problems, especially with regard to mixed algal-protozoan groups and/or phylogenies. Some three dozen phyla are recognized as comprising the kingdom, with the number that might be considered as "protozoan" ranging from 10 to 25, depending on one's viewpoint. No taxon should have the formal name "Protozoa", "Phytoflagellate" and "zooflagellate" are also misleading categories. Taxonomic and evolutionary relationships of phyla containing protozoa (with small "p") are inextricably intermeshed with those of other protist phyla, and thus no unified protozoan super-group exists.

Advanced Fire Information System - A real time fire information system for Africa

NASA Astrophysics Data System (ADS)

Frost, P. E.; Roy, D. P.

2012-12-01

The Council for Scientific and Industrial Research (CSIR) lead by the Meraka Institute and supported by the South African National Space Agency (SANSA) developed the Advanced Fire Information System (AFIS) to provide near real time fire information to a variety of operational and science fire users including disaster managers, fire fighters, farmers and forest managers located across Southern and Eastern Africa. The AFIS combines satellite data with ground based observations and statistics and distributes the information via mobile phone technology. The system was launched in 2004, and Eskom (South Africa' and Africa's largest power utility) quickly became the biggest user and today more than 300 Eskom line managers and support staff receive cell phone and email fire alert messages whenever a wildfire is within 2km of any of the 28 000km of Eskom electricity transmission lines. The AFIS uses Earth observation satellites from NASA and Europe to detect possible actively burning fires and their fire radiative power (FRP). The polar orbiting MODIS Terra and Aqua satellites provide data at around 10am, 15pm, 22am and 3am daily, while the European Geostationary MSG satellite provides 15 minute updates at lower spatial resolution. The AFIS processing system ingests the raw satellite data and within minutes of the satellite overpass generates fire location and FRP based fire intensity information. The AFIS and new functionality are presented including an incident report and permiting system that can be used to differentiate between prescribed burns and uncontrolled wild fires, and the provision of other information including 5-day fire danger forecasts, vegetation curing information and historical burned area maps. A new AFIS mobile application for IOS and Android devices as well as a fire reporting tool are showcased that enable both the dissemination and alerting of fire information and enable user upload of geo tagged photographs and on the fly creation of fire reports

Review: evaluating information systems in nursing.

PubMed

Oroviogoicoechea, Cristina; Elliott, Barbara; Watson, Roger

2008-03-01

To review existing nursing research on inpatient hospitals' information technology (IT) systems in order to explore new approaches for evaluation research on nursing informatics to guide further design and implementation of effective IT systems. There has been an increase in the use of IT and information systems in nursing in recent years. However, there has been little evaluation of these systems and little guidance on how they might be evaluated. A literature review was conducted between 1995 and 2005 inclusive using CINAHL and Medline and the search terms 'nursing information systems', 'clinical information systems', 'hospital information systems', 'documentation', 'nursing records', 'charting'. Research in nursing information systems was analysed and some deficiencies and contradictory results were identified which impede a comprehensive understanding of effective implementation. There is a need for IT systems to be understood from a wider perspective that includes aspects related to the context where they are implemented. Social and organizational aspects need to be considered in evaluation studies and realistic evaluation can provide a framework for the evaluation of information systems in nursing. The rapid introduction of IT systems for clinical practice urges evaluation of already implemented systems examining how and in what circumstances they work to guide effective further development and implementation of IT systems to enhance clinical practice. Evaluation involves more factors than just involving technologies such as changing attitudes, cultures and healthcare practices. Realistic evaluation could provide configurations of context-mechanism-outcomes that explain the underlying relationships to understand why and how a programme or intervention works.

NASA's Earth Observing System Data and Information System - EOSDIS

NASA Technical Reports Server (NTRS)

Ramapriyan, Hampapuram K.

2011-01-01

This slide presentation reviews the work of NASA's Earth Observing System Data and Information System (EOSDIS), a petabyte-scale archive of environmental data that supports global climate change research. The Earth Science Data Systems provide end-to-end capabilities to deliver data and information products to users in support of understanding the Earth system. The presentation contains photographs from space of recent events, (i.e., the effects of the tsunami in Japan, and the wildfires in Australia.) It also includes details of the Data Centers that provide the data to EOSDIS and Science Investigator-led Processing Systems. Information about the Land, Atmosphere Near-real-time Capability for EOS (LANCE) and some of the uses that the system has made possible are reviewed. Also included is information about how to access the data, and evolutionary plans for the future of the system.

NEEDS - Information Adaptive System

NASA Technical Reports Server (NTRS)

Kelly, W. L.; Benz, H. F.; Meredith, B. D.

1980-01-01

The Information Adaptive System (IAS) is an element of the NASA End-to-End Data System (NEEDS) Phase II and is focused toward onboard image processing. The IAS is a data preprocessing system which is closely coupled to the sensor system. Some of the functions planned for the IAS include sensor response nonuniformity correction, geometric correction, data set selection, data formatting, packetization, and adaptive system control. The inclusion of these sensor data preprocessing functions onboard the spacecraft will significantly improve the extraction of information from the sensor data in a timely and cost effective manner, and provide the opportunity to design sensor systems which can be reconfigured in near real-time for optimum performance. The purpose of this paper is to present the preliminary design of the IAS and the plans for its development.

Zooplankton taxonomic and size diversity in Mediterranean coastal lagoons (NE Iberian Peninsula): Influence of hydrology, nutrient composition, food resource availability and predation

NASA Astrophysics Data System (ADS)

Badosa, Anna; Boix, Dani; Brucet, Sandra; López-Flores, Rocío; Gascón, Stéphanie; Quintana, Xavier D.

2007-01-01

The influence of hydrology, nutrient composition, food resource availability and predation on zooplankton taxonomic and size diversity was analyzed in several shallow lagoons of a Mediterranean salt marsh (Baix Ter Wetlands, NE Iberian Peninsula). Taxonomic diversity correlated better with variables related to the trophic state, such as nutrient concentrations, whereas size diversity was more sensitive to fish predation. However, the fish predation influence on the size diversity was only significant when fishes reached high densities. Under low fish densities no predation effects were observed and the food resource availability (FR a) appeared to be more important in structuring the zooplankton community. Nevertheless, the two diversity indexes showed opposite responses to this factor. With increasing FR a the taxonomic diversity increased and the size diversity decreased. Neither taxonomic nor size diversity of the zooplankton community correlated with other physical or biotic factors such as hydrological variability or macroinvertebrate predation. The relationships found suggest that the size diversity is mainly related to biotic interactions, such as fish predation or inter/intraspecific competition, while the taxonomic diversity appears to be more sensitive to abiotic factors such as the nutrient composition.

Deaf and hard of hearing adolescents' processing of pictures and written words for taxonomic categories in a priming task of semantic categorization.

PubMed

Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

2013-01-01

Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written words for those of superordinate level (category names), in a priming task of semantic categorization. Stimulus onset asynchrony (SOA) was manipulated. The adolescents were less aware of taxonomic relations and were more likely to show the advantage of pictures over written words than their hearing counterparts. Their processing of exemplar primes steadily deepened as SOA increased, reaching its deepest level when SOA was 237 ms. Their processing of category names seemed immune to changes in SOA, probably because of their fuzzy representations of taxonomic categories of superordinate level.

Developing Information Systems for Competitive Intelligence Support.

ERIC Educational Resources Information Center

Hohhof, Bonnie

1994-01-01

Discusses issues connected with developing information systems for competitive intelligence support; defines the elements of an effective competitive information system; and summarizes issues affecting system design and implementation. Highlights include intelligence information; information needs; information sources; decision making; and…

COMPARISON OF TAXONOMIC, COLONY MORPHOTYPE AND PCR-RFLP METHODS TO CHARACTERIZE MICROFUNGAL DIVERSITY

EPA Science Inventory

We compared three methods for estimating fungal species diversity in soil samples. A rapid screening method based on gross colony morphological features and color reference standards was compared with traditional fungal taxonomic methods and PCR-RFLP for estimation of ecological ...

Usability evaluation of Laboratory and Radiology Information Systems integrated into a hospital information system.

PubMed

Nabovati, Ehsan; Vakili-Arki, Hasan; Eslami, Saeid; Khajouei, Reza

2014-04-01

This study was conducted to evaluate the usability of widely used laboratory and radiology information systems. Three usability experts independently evaluated the user interfaces of Laboratory and Radiology Information Systems using heuristic evaluation method. They applied Nielsen's heuristics to identify and classify usability problems and Nielsen's severity rating to judge their severity. Overall, 116 unique heuristic violations were identified as usability problems. In terms of severity, 67 % of problems were rated as major and catastrophic. Among 10 heuristics, "consistency and standards" was violated most frequently. Moreover, mean severity of problems concerning "error prevention" and "help and documentation" heuristics was higher than of the others. Despite widespread use of specific healthcare information systems, they suffer from usability problems. Improving the usability of systems by following existing design standards and principles from the early phased of system development life cycle is recommended. Especially, it is recommended that the designers design systems that inhibit the initiation of erroneous actions and provide sufficient guidance to users.

Science Information Systems Newsletter, issue 28

NASA Technical Reports Server (NTRS)

1993-01-01

The purpose of the Information Systems Newsletter is to inform the space science and applications research community about information systems development and to promote coordination and collaboration by providing a forum for communication. This quarterly publication focuses on programs sponsored by the Information Systems Branch in support of NASA's Office of Space Science. Articles of interest for other programs and agencies are presented as well. The April 1993 issue is presented.

An Expertise Based Energy Information System.

ERIC Educational Resources Information Center

Rosenberg, S.

This paper describes an intelligent decision support system for information on petroleum resources and use currently being designed by the Information Methodology Research Project as the first step in the development of a comprehensive intelligent information system for dealing with energy resources in the United States. The system draws on…

36 CFR 1192.61 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Public information system... Rapid Rail Vehicles and Systems § 1192.61 Public information system. (a)(1) Requirements. Each vehicle... line identification information. (2) Exception. Where station announcement systems provide information...

Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups

PubMed Central

Ord, Terry J.; Garcia-Porta, Joan

2012-01-01

Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet, informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis alongside alternative explanations for the evolution of communicative complexity. We compiled data documenting variations in signal complexity among closely related species for several case study groups—ants, frogs, lizards and birds—and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably leads to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups. PMID:22641820

Distinct Growth and Secretome Strategies for Two Taxonomically Divergent Brown Rot Fungi.

PubMed

Presley, Gerald N; Schilling, Jonathan S

2017-04-01

use a nonenzymatic oxidative pretreatment before enzymatic carbohydrate hydrolysis, enabling selective removal of carbohydrates from lignin. This capacity has independently evolved multiple times, but it is unclear if different mechanisms underpin similar outcomes. Here, we grew fungi directionally on wood wafers and we found similar two-step mechanisms in taxonomically divergent brown rot fungi. The results, however, revealed strikingly different growth strategies, with S. lacrymans investing more in biomass production than secretion of proteins and G. trabeum showing the opposite pattern, with a high diversity of uncharacterized proteins. The "simplified" S. lacrymans secretomic system could help narrow gene targets central to oxidative brown rot pretreatments, and a comparison of its distinctions with G. trabeum and other brown rot fungi (e.g., Postia placenta ) might offer similar traction in noncatabolic genes. Copyright © 2017 American Society for Microbiology.

Information management challenges of the EOS Data and Information System

NASA Technical Reports Server (NTRS)

Mcdonald, Kenneth R.; Blake, Deborah J.

1991-01-01

An overview of the current information management concepts that are embodied in the plans for the Earth Observing System Data and Information System (EOSDIS) is presented, and some of the technology development and application areas that are envisioned to be particularly challenging are introduced. The Information Management System (IMS) is the EOSDIS element that provides the primary interface between the science users and the data products and services of EOSDIS. The goals of IMS are to define a clear and complete set of functional requirements and to apply innovative methods and technologies to satisfy them. The information management functions are described in detail, and some applicable technolgies are discussed. Some of the general issues affecting the successful development and operation of the information management element are addressed.

Automated Information System (AIS) Alarm System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hunteman, W.

1997-05-01

The Automated Information Alarm System is a joint effort between Los Alamos National Laboratory, Lawrence Livermore National Laboratory, and Sandia National Laboratory to demonstrate and implement, on a small-to-medium sized local area network, an automated system that detects and automatically responds to attacks that use readily available tools and methodologies. The Alarm System will sense or detect, assess, and respond to suspicious activities that may be detrimental to information on the network or to continued operation of the network. The responses will allow stopping, isolating, or ejecting the suspicious activities. The number of sensors, the sensitivity of the sensors, themore » assessment criteria, and the desired responses may be set by the using organization to meet their local security policies.« less

Geospatial Information and Geographic Information Systems (GIS): Current Issues and Future Challenges

DTIC Science & Technology

2009-06-08

CRS Report for Congress Prepared for Members and Committees of Congress Geospatial Information and Geographic Information Systems (GIS...Geographic Information Systems (GIS): Current Issues and Future Challenges 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 Geospatial Information and Geographic Information Systems (GIS

Information Science and Information Systems: Conjunct Subjects Disjunct Disciplines.

ERIC Educational Resources Information Center

Ellis, David; Allen, David; Wilson, Tom

1999-01-01

Examines the relationship between information science and information-systems (IS) research through analysis of the subject literature of each field and by citation and co-citation analysis of highly cited researchers in each field. Subfields of user studies and information-retrieval research were selected to represent information-science…

Macrozooplankton biomass in a warm-core Gulf Stream ring: Time series changes in size structure, taxonomic composition, and vertical distribution

NASA Astrophysics Data System (ADS)

Davis, Cabell S.; Wiebe, Peter H.

1985-01-01

Macrozooplankton size structure and taxonomic composition in warm-core ring 82B was examined from a time series (March, April, June) of ring center MOCNESS (1 m) samples. Size distributions of 15 major taxonomic groups were determined from length measurements digitized from silhouette photographs of the samples. Silhouette digitization allows rapid quantification of Zooplankton size structure and taxonomic composition. Length/weight regressions, determined for each taxon, were used to partition the biomass (displacement volumes) of each sample among the major taxonomic groups. Zooplankton taxonomic composition and size structure varied with depth and appeared to coincide with the hydrographic structure of the ring. In March and April, within the thermostad region of the ring, smaller herbivorous/omnivorous Zooplankton, including copepods, crustacean larvae, and euphausiids, were dominant, whereas below this region, larger carnivores, such as medusae, ctenophores, fish, and decapods, dominated. Copepods were generally dominant in most samples above 500 m. Total macrozooplankton abundance and biomass increased between March and April, primarily because of increases in herbivorous taxa, including copepods, crustacean larvae, and larvaceans. A marked increase in total macrozooplankton abundance and biomass between April and June was characterized by an equally dramatic shift from smaller herbivores (1.0-3.0 mm) in April to large herbivores (5.0-6.0 mm) and carnivores (>15 mm) in June. Species identifications made directly from the samples suggest that changes in trophic structure resulted from seeding type immigration and subsequent in situ population growth of Slope Water zooplankton species.

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

PubMed

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

Documenting taxonomic data quality for field fish identifications: a proposal for national surveys

EPA Science Inventory

The U.S. Environmental Protection Agency is in the midst of a multiyear series of natinal surveys of water resource conditions. Because communicating ecological condition is the primary objective of the surveys, quantitative biological indicators are key. Thus, if raw taxonomic d...

Climate warming promotes species diversity, but with greater taxonomic redundancy, in complex environments

PubMed Central

Thakur, Madhav P.; Tilman, David; Purschke, Oliver; Ciobanu, Marcel; Cowles, Jane; Isbell, Forest; Wragg, Peter D.; Eisenhauer, Nico

2017-01-01

Climate warming is predicted to alter species interactions, which could potentially lead to extinction events. However, there is an ongoing debate whether the effects of warming on biodiversity may be moderated by biodiversity itself. We tested warming effects on soil nematodes, one of the most diverse and abundant metazoans in terrestrial ecosystems, along a gradient of environmental complexity created by a gradient of plant species richness. Warming increased nematode species diversity in complex (16-species mixtures) plant communities (by ~36%) but decreased it in simple (monocultures) plant communities (by ~39%) compared to ambient temperature. Further, warming led to higher levels of taxonomic relatedness in nematode communities across all levels of plant species richness. Our results highlight both the need for maintaining species-rich plant communities to help offset detrimental warming effects and the inability of species-rich plant communities to maintain nematode taxonomic distinctness when warming occur. PMID:28740868

A Distributed User Information System

DTIC Science & Technology

1990-03-01

NOE08 Department of Computer Science NOVO 8 1990 University of Maryland S College Park, MD 20742 D Abstract Current user information database technology ...Transactions on Computer Systems, May 1988. [So189] K. Sollins. A plan for internet directory services. Technical report, DDN Network Information Center...2424 A Distributed User Information System DTiC Steven D. Miller, Scott Carson, and Leo Mark DELECTE Institute for Advanced Computer Studies and

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

PubMed Central

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-01-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7–27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity. PMID:27775021

Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

NASA Astrophysics Data System (ADS)

Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

2016-10-01

Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7-27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity.

A survey of chemical information systems

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Shaikh, Aneesa Bashir

1985-01-01

A survey of the features, functions, and characteristics of a fairly wide variety of chemical information storage and retrieval systems currently in operation is given. The types of systems (together with an identification of the specific systems) addressed within this survey are as follows: patents and bibliographies (Derwent's Patent System; IFI Comprehensive Database; PULSAR); pharmacology and toxicology (Chemfile; PAGODE; CBF; HEEDA; NAPRALERT; MAACS); the chemical information system (CAS Chemical Registry System; SANSS; MSSS; CSEARCH; GINA; NMRLIT; CRYST; XTAL; PDSM; CAISF; RTECS Search System; AQUATOX; WDROP; OHMTADS; MLAB; Chemlab); spectra (OCETH; ASTM); crystals (CRYSRC); and physical properties (DETHERM). Summary characteristics and current trends in chemical information systems development are also examined.

Status of Statewide Career Information Delivery Systems.

ERIC Educational Resources Information Center

Dunn, Wynonia L.

Intended as a resource document as well as a status report on all the statewide career information delivery systems (CIDS) in operation, this report examines the status of 39 statewide information systems. (Career information delivery systems are computer-based systems that provide national, state, and local information to individuals who are in…

Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae)

PubMed Central

Chumová, Zuzana; Krejčíková, Jana; Mandáková, Terezie; Suda, Jan; Trávníček, Pavel

2015-01-01

The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x–18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus. PMID:26207824

The Arbo‑zoonet Information System.

PubMed

Di Lorenzo, Alessio; Di Sabatino, Daria; Blanda, Valeria; Cioci, Daniela; Conte, Annamaria; Bruno, Rossana; Sauro, Francesca; Calistri, Paolo; Savini, Lara

2016-06-30

The Arbo‑zoonet Information System has been developed as part of the 'International Network for Capacity Building for the Control of Emerging Viral Vector Borne Zoonotic Diseases (Arbo‑zoonet)' project. The project aims to create common knowledge, sharing data, expertise, experiences, and scientific information on West Nile Disease (WND), Crimean‑Congo haemorrhagic fever (CCHF), and Rift Valley fever (RVF). These arthropod‑borne diseases of domestic and wild animals can affect humans, posing great threat to public health. Since November 2011, when the Schmallenberg virus (SBV) has been discovered for the first time in Northern Europe, the Arbo‑zoonet Information System has been used in order to collect information on newly discovered disease and to manage the epidemic emergency. The system monitors the geographical distribution and epidemiological evolution of CCHF, RVF, and WND since 1946. More recently, it has also been deployed to monitor the SBV data. The Arbo‑zoonet Information System includes a web application for the management of the database in which data are stored and a WebGIS application to explore spatial disease distributions, facilitating the epidemiological analysis. The WebGIS application is an effective tool to show and share the information and to facilitate the exchange and dissemination of relevant data among project's participants.

Management Information System

NASA Technical Reports Server (NTRS)

1984-01-01

New Automated Management Information Center (AMIC) employs innovative microcomputer techniques to create color charts, viewgraphs, or other data displays in a fraction of the time formerly required. Developed under Kennedy Space Center's contract by Boeing Services International Inc., Seattle, WA, AMIC can produce an entirely new informational chart in 30 minutes, or an updated chart in only five minutes. AMIC also has considerable potential as a management system for business firms.

Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures.

PubMed

Aira, Manuel; Bybee, Seth; Pérez-Losada, Marcos; Domínguez, Jorge

2015-11-01

Earthworms play a key role in nutrient cycling by interacting with microorganisms thus accelerating organic matter turnover in soil systems. As detritivores, some earthworm types ingest and digest a mixture of dead organic matter and microorganisms, like animal manures (i.e. animal gut microbiomes). Here we described the earthworm cast microbiome and the role ingested bacteria play on its composition. We fed Eisenia andrei with cow, horse and pig manures and determined the taxonomic and phylogenetic composition of the these manures before and after passage through the earthworm gut. Earthworm cast microbiomes showed a smaller diversity than the manure they fed on. Manures strongly differed in their taxonomic and phylogenetic composition, but these differences were markedly reduced once transformed into earthworm cast microbiomes after passage through the earthworm gut. The core earthworm cast microbiome comprised 30 OTUs (2.6% of OTUs from cast samples), of which 10 are possibly native to the earthworm gut. Most of the core cast microbiome OTUs belonged to phyla Actinobacteria and Proteobacteria, as opposed to already described animal core gut microbiomes, which are composed mainly of Firmicutes and Bacteroidetes. Our results suggest that earthworms build up their cast microbiome by selecting from the pool of ingested bacteria. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Cross-species amplification of microsatellites reveals incongruence in the molecular variation and taxonomic limits of the Pilosocereus aurisetus group (Cactaceae).

PubMed

Moraes, Evandro M; Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Machado, Marlon C

2012-09-01

The Pilosocereus aurisetus group contains eight cactus species restricted to xeric habitats in eastern and central Brazil that have an archipelago-like distribution. In this study, 5-11 microsatellite markers previously designed for Pilosocereus machrisii were evaluated for cross-amplification and polymorphisms in ten populations from six species of the P. aurisetus group. The genotypic information was subsequently used to investigate the genetic relationships between the individuals, populations, and species analyzed. Only the Pmac101 locus failed to amplify in all of the six analyzed species, resulting in an 88 % success rate. The number of alleles per polymorphic locus ranged from 2 to 12, and the most successfully amplified loci showed at least one population with a larger number of alleles than were reported in the source species. The population relationships revealed clear genetic clustering in a neighbor-joining tree that was partially incongruent with the taxonomic limits between the P. aurisetus and P. machrisii species, a fact which parallels the problematic taxonomy of the P. aurisetus group. A Bayesian clustering analysis of the individual genotypes confirmed the observed taxonomic incongruence. These microsatellite markers provide a valuable resource for facilitating large-scale genetic studies on population structures, systematics and evolutionary history in this group.

Systems and methods for enhancing optical information

DOEpatents

DeVore, Peter Thomas Setsuda; Chou, Jason T.

2018-01-02

An Optical Information Transfer Enhancer System includes a first system for producing an information bearing first optical wave that is impressed with a first information having a first information strength wherein the first optical wave has a first shape. A second system produces a second optical wave. An information strength enhancer module receives the first and said second optical waves and impresses the first optical wave upon the second optical wave via cross-phase modulation (XPM) to produce an information-strength-enhanced second optical wave having a second information strength that is greater than the first information strength of the first optical wave. Following a center-wavelength changer by an Optical Information Transfer Enhancer System improves its performance.

BBIS: Beacon Bus Information System

NASA Astrophysics Data System (ADS)

Kasim, Shahreen; Hafit, Hanayanti; Pei Juin, Kong; Afizah Afif, Zehan; Hashim, Rathiah; Ruslai, Husni; Jahidin, Kamaruzzaman; Syafwan Arshad, Mohammad

2016-11-01

Lack of bus information for example bus timetable, status of the bus and messy advertisement on bulletin board at the bus stop will give negative impact to tourist. Therefore, a real-time update bus information bulletin board provides all information needed so that passengers can save their bus information searching time. Supported with Android or iOS, Beacon Bus Information System (BBIS) provides bus information between Batu Pahat and Kluang area. BBIS is a system that implements physical web technology and interaction on demand. It built on Backend-as-a-Service, a cloud solution and Firebase non relational database as data persistence backend and syncs between user client in the real-time. People walk through bus stop with smart device and do not require any application. Bluetooth Beacon is used to achieve smart device's best performance of data sharing. Intellij IDEA 15 is one of the tools that that used to develop the BBIS system. Multi-language included front end and backend supported Integration development environment (IDE) helped to speed up integration process.

The Intelligent Technologies of Electronic Information System

NASA Astrophysics Data System (ADS)

Li, Xianyu

2017-08-01

Based upon the synopsis of system intelligence and information services, this paper puts forward the attributes and the logic structure of information service, sets forth intelligent technology framework of electronic information system, and presents a series of measures, such as optimizing business information flow, advancing data decision capability, improving information fusion precision, strengthening deep learning application and enhancing prognostic and health management, and demonstrates system operation effectiveness. This will benefit the enhancement of system intelligence.

Evolution of microgastropods (Ellobioidea, Carychiidae): integrating taxonomic, phylogenetic and evolutionary hypotheses

PubMed Central

2013-01-01

Background Current biodiversity patterns are considered largely the result of past climatic and tectonic changes. In an integrative approach, we combine taxonomic and phylogenetic hypotheses to analyze temporal and geographic diversification of epigean (Carychium) and subterranean (Zospeum) evolutionary lineages in Carychiidae (Eupulmonata, Ellobioidea). We explicitly test three hypotheses: 1) morphospecies encompass unrecognized evolutionary lineages, 2) limited dispersal results in a close genetic relationship of geographical proximally distributed taxa and 3) major climatic and tectonic events had an impact on lineage diversification within Carychiidae. Results Initial morphospecies assignments were investigated by different molecular delimitation approaches (threshold, ABGD, GMYC and SP). Despite a conservative delimitation strategy, carychiid morphospecies comprise a great number of unrecognized evolutionary lineages. We attribute this phenomenon to historic underestimation of morphological stasis and phenotypic variability amongst lineages. The first molecular phylogenetic hypothesis for the Carychiidae (based on COI, 16S and H3) reveals Carychium and Zospeum to be reciprocally monophyletic. Geographical proximally distributed lineages are often closely related. The temporal diversification of Carychiidae is best described by a constant rate model of diversification. The evolution of Carychiidae is characterized by relatively few (long distance) colonization events. We find support for an Asian origin of Carychium. Zospeum may have arrived in Europe before extant members of Carychium. Distantly related Carychium clades inhabit a wide spectrum of the available bioclimatic niche and demonstrate considerable niche overlap. Conclusions Carychiid taxonomy is in dire need of revision. An inferred wide distribution and variable phenotype suggest underestimated diversity in Zospeum. Several Carychium morphospecies are results of past taxonomic lumping. By collecting

Taxamatch, an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases

PubMed Central

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

A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies.

PubMed

Liu, Liang; Huo, Guan-Nan; He, Hong-Bin; Zhou, Benjiang; Attwood, Stephen W

2014-02-18

The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and then China (Triculinae arising

A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies

PubMed Central

2014-01-01

Background The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. Results The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. Conclusions The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and

Information systems in dentistry.

PubMed

Masic, Fedja

2012-03-01

Almost the entire human creativity today, from the standpoint of its efficiency and expediency, is conditioned with the existence of information systems. Most information systems are oriented to the management and decision-making, including health information system. System of health and health insurance together form one of the most important segments of society and its functioning as a compact unit. Increasing requirements for reducing health care costs while preserving or improving the quality of services provided represent a difficult task for the health system. Using descriptive metods by retreiiving literature we analyzed the latest solutions in information and telecommunications technology is the basis for building an effective and efficient health system. Computerization does not have the primary objective of saving, but the rationalization of spending in health care. It is estimated that at least 20-30% of money spent in health care can be rationally utilized. Computerization should give the necessary data and indicators for this rationalization. Very important are the goals of this project and the achievement of other uses and benefits, improving overall care for patients and policyholders, increasing the speed and accuracy of diagnosis in determining treatment using electronic diagnostic and therapeutic guidelines. Computerization in dentistry began similarly as in other human activities-recording large amounts of data on digital media, and by replacing manual data processing to machine one. But specifics of the dental profession have led to the specifics of the application of information technology (IT), and continue to require special development of dental oriented and applied IT. Harmonization of dental software with global standards will enable doctors and dentists to with a few mouse clicks via the internet reach the general medical information about their patients from the central national health database. Standardization will also allow access to

Information Systems in Dentistry

PubMed Central

Masic, Fedja

2012-01-01

Introduction: Almost the entire human creativity today, from the standpoint of its efficiency and expediency, is conditioned with the existence of information systems. Most information systems are oriented to the management and decision-making, including health information system. System of health and health insurance together form one of the most important segments of society and its functioning as a compact unit. Increasing requirements for reducing health care costs while preserving or improving the quality of services provided represent a difficult task for the health system. Material and methods: Using descriptive metods by retreiiving literature we analyzed the latest solutions in information and telecommunications technology is the basis for building an effective and efficient health system. Computerization does not have the primary objective of saving, but the rationalization of spending in health care. It is estimated that at least 20-30% of money spent in health care can be rationally utilized. Computerization should give the necessary data and indicators for this rationalization. Very important are the goals of this project and the achievement of other uses and benefits, improving overall care for patients and policyholders, increasing the speed and accuracy of diagnosis in determining treatment using electronic diagnostic and therapeutic guidelines. Results and discussion: Computerization in dentistry began similarly as in other human activities–recording large amounts of data on digital media, and by replacing manual data processing to machine one. But specifics of the dental profession have led to the specifics of the application of information technology (IT), and continue to require special development of dental oriented and applied IT. Harmonization of dental software with global standards will enable doctors and dentists to with a few mouse clicks via the internet reach the general medical information about their patients from the central

Formal Specification of Information Systems Requirements.

ERIC Educational Resources Information Center

Kampfner, Roberto R.

1985-01-01

Presents a formal model for specification of logical requirements of computer-based information systems that incorporates structural and dynamic aspects based on two separate models: the Logical Information Processing Structure and the Logical Information Processing Network. The model's role in systems development is discussed. (MBR)

Forest Resource Information System (FRIS)

NASA Technical Reports Server (NTRS)

1983-01-01

The technological and economical feasibility of using multispectral digital image data as acquired from the LANDSAT satellites in an ongoing operational forest information system was evaluated. Computer compatible multispectral scanner data secured from the LANDSAT satellites were demonstrated to be a significant contributor to ongoing information systems by providing the added dimensions of synoptic and repeat coverage of the Earth's surface. Major forest cover types of conifer, deciduous, mixed conifer-deciduous and non-forest, were classified well within the bounds of the statistical accuracy of the ground sample. Further, when overlayed with existing maps, the acreage of cover type retains a high level of positional integrity. Maps were digitized by a graphics design system, overlayed and registered onto LANDSAT imagery such that the map data with associated attributes were displayed on the image. Once classified, the analysis results were converted back to map form as a cover type of information. Existing tabular information as represented by inventory is registered geographically to the map base through a vendor provided data management system. The notion of a geographical reference base (map) providing the framework to which imagery and tabular data bases are registered and where each of the three functions of imagery, maps and inventory can be accessed singly or in combination is the very essence of the forest resource information system design.

Insights into assessing water quality using taxonomic distinctness based on a small species pool of biofilm-dwelling ciliate fauna in coastal waters of the Yellow Sea, northern China.

PubMed

Zhang, Wei; Liu, Yuanyuan; Warren, Alan; Xu, Henglong

2014-12-15

The aim of this study is to determine the feasibility of using a small species pool from a raw dataset of biofilm-dwelling ciliates for bioassessment based on taxonomic diversity. Samples were collected monthly at four stations within a gradient of environmental stress in coastal waters of the Yellow Sea, northern China from August 2011 to July 2012. A 33-species subset was identified from the raw 137-species dataset using a multivariate method. The spatial patterns of this subset were significantly correlated with the changes in the nutrients and chemical oxygen demand. The taxonomic diversity indices were significantly correlated with nutrients. The pair-wise indices of average taxonomic distinctness (Δ(+)) and the taxonomic distinctness (Λ(+)) showed a clear departure from the expected taxonomic pattern. These findings suggest that this small ciliate assemblage might be used as an adequate species pool for discriminating water quality status based on taxonomic distinctness in marine ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Some Approaches to Modeling Complex Information Systems.

ERIC Educational Resources Information Center

Rao, V. Venkata; Zunde, Pranas

1982-01-01

Brief discussion of state-of-the-art of modeling complex information systems distinguishes between macrolevel and microlevel modeling of such systems. Network layout and hierarchical system models, simulation, information acquisition and dissemination, databases and information storage, and operating systems are described and assessed. Thirty-four…

Telematics and satellites. Part 1: Information systems

NASA Astrophysics Data System (ADS)

Burke, W. R.

1980-06-01

Telematic systems are identified and described. The applications are examined emphasizing the role played by satellite links. The discussion includes file transfer, examples of distributed processor systems, terminal communication, information retrieval systems, office information systems, electronic preparation and publishing of information, electronic systems for transfer of funds, electronic mail systems, record file transfer characteristics, intra-enterprise networks, and inter-enterprise networks.

Developmental Antecedents of Taxonomic and Thematic Strategies at 3 Years of Age.

ERIC Educational Resources Information Center

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.…

MIMS - MEDICAL INFORMATION MANAGEMENT SYSTEM

NASA Technical Reports Server (NTRS)

Frankowski, J. W.

1994-01-01

MIMS, Medical Information Management System is an interactive, general purpose information storage and retrieval system. It was first designed to be used in medical data management, and can be used to handle all aspects of data related to patient care. Other areas of application for MIMS include: managing occupational safety data in the public and private sectors; handling judicial information where speed and accuracy are high priorities; systemizing purchasing and procurement systems; and analyzing organizational cost structures. Because of its free format design, MIMS can offer immediate assistance where manipulation of large data bases is required. File structures, data categories, field lengths and formats, including alphabetic and/or numeric, are all user defined. The user can quickly and efficiently extract, display, and analyze the data. Three means of extracting data are provided: certain short items of information, such as social security numbers, can be used to uniquely identify each record for quick access; records can be selected which match conditions defined by the user; and specific categories of data can be selected. Data may be displayed and analyzed in several ways which include: generating tabular information assembled from comparison of all the records on the system; generating statistical information on numeric data such as means, standard deviations and standard errors; and displaying formatted listings of output data. The MIMS program is written in Microsoft FORTRAN-77. It was designed to operate on IBM Personal Computers and compatibles running under PC or MS DOS 2.00 or higher. MIMS was developed in 1987.

49 CFR 38.61 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false Public information system. 38.61 Section 38.61... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Rapid Rail Vehicles and Systems § 38.61 Public information system. (a... other passenger information. Alternative systems or devices which provide equivalent access are also...

Apoptosis Gene Information System--AGIS.

PubMed

Sakharkar, Kishore R; Clement, Marie V; Chow, Vincent T K; Pervaiz, Shazib

2006-05-01

Genes implicated in apoptosis have great relevance to biology, medicine and oncology. Here, we describe a unique resource, Apoptosis Gene Information System (AGIS) that provides data for over 2400 genes involved directly or indirectly, in apoptotic pathways of more than 350 different organisms. The organization of this information system is based on the principle of one-gene, one record. AGIS will be updated on a six monthly basis as new information becomes available. AGIS can be accessed at: http://www.cellfate.org/AGIS/.

A Perception Study of Computer Science and Information Systems Students on Bullying Prevalence in the Information Systems Profession

ERIC Educational Resources Information Center

Lawler, James; Molluzzo, John C.

2016-01-01

Bullying is considered to be omnipresent in business firms and prevalent in entrepreneurial firms in information systems and in departments of information systems in industry. Entrepreneurialism and narcissism of personalities in the information systems profession may be perceived as especially predisposed to bullying. The authors of this paper…

49 CFR 38.103 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false Public information system. 38.103 Section 38.103... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Commuter Rail Cars and Systems § 38.103 Public information system. (a... information. Alternative systems or devices which provide equivalent access are also permitted. (b) [Reserved] ...

36 CFR 1192.103 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Public information system... Commuter Rail Cars and Systems § 1192.103 Public information system. (a) Each car shall be equipped with an... speech messages, to announce stations and provide other passenger information. Alternative systems or...

36 CFR 1192.121 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Public information system... Intercity Rail Cars and Systems § 1192.121 Public information system. (a) Each car shall be equipped with a... messages, to announce stations and provide other passenger information. Alternative systems or devices...

49 CFR 38.87 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false Public information system. 38.87 Section 38.87... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Light Rail Vehicles and Systems § 38.87 Public information system. (a... information. Alternative systems or devices which provide equivalent access are also permitted. (b) [Reserved] ...

System Engineering Analysis For Improved Scout Business Information Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Slyke, D. A.

The project uses system engineering principles to address the need of Boy Scout leaders for an integrated system to facilitate advancement and awards records, leader training and planning for meetings and activities. Existing products to address needs of Scout leaders and relevant stakeholders function to support record keeping and some communication functions but opportunity exists for a better system to fully integrate these functions with training delivery and recording, activity planning along with feedback and information gathering from stakeholders. Key stakeholders for the sytem include Scouts and their families, leaders, training providers, sellers of supplies and awards, content generators andmore » facilities that serve Scout activities. Key performance parameters for the system are protection of personal information, availability of current information, information accuracy and information content that has depth. Implementation concepts considered for the system include (1) owned and operated by Boy Scouts of America, (2) Contracted out to a vendor (3) distributed system that functions with BSA managed interfaces. The selected concept is to contract out to a vendor to maximize the likelihood of successful integration and take advantage of the best technology. Development of requirements considers three key use cases (1) System facilitates planning a hike with training needed satisfied in advance and advancement recording real time (2) Scheduling and documenting in-person training, (3) Family interested in Scouting receives information and can request follow-up. Non-functional requirements are analyzed with the Quality Function Deployment tool. Requirement addressing frequency of backup, compatibility with legacy and new technology, language support, software update are developed to address system reliability and intuitive interface. System functions analyzed include update of activity database, maintenance of advancement status, archive of documents

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

USDA-ARS?s Scientific Manuscript database

Community composition data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alt...

A Personalized Health Information Retrieval System

PubMed Central

Wang, Yunli; Liu, Zhenkai

2005-01-01

Consumers face barriers when seeking health information on the Internet. A Personalized Health Information Retrieval System (PHIRS) is proposed to recommend health information for consumers. The system consists of four modules: (1) User modeling module captures user’s preference and health interests; (2) Automatic quality filtering module identifies high quality health information; (3) Automatic text difficulty rating module classifies health information into professional or patient educational materials; and (4) User profile matching module tailors health information for individuals. The initial results show that PHIRS could assist consumers with simple search strategies. PMID:16779435

NICA project management information system

NASA Astrophysics Data System (ADS)

Bashashin, M. V.; Kekelidze, D. V.; Kostromin, S. A.; Korenkov, V. V.; Kuniaev, S. V.; Morozov, V. V.; Potrebenikov, Yu. K.; Trubnikov, G. V.; Philippov, A. V.

2016-09-01

The science projects growth, changing of the efficiency criteria during the project implementation require not only increasing of the management specialization level but also pose the problem of selecting the effective planning methods, monitoring of deadlines and interaction of participants involved in research projects. This paper is devoted to choosing the project management information system for the new heavy-ion collider NICA (Nuclotron based Ion Collider fAcility). We formulate the requirements for the project management information system with taking into account the specifics of the Joint Institute for Nuclear Research (JINR, Dubna, Russia) as an international intergovernmental research organization, which is developed on the basis of a flexible and effective information system for the NICA project management.

The Oklahoma Geographic Information Retrieval System

NASA Technical Reports Server (NTRS)

Blanchard, W. A.

1982-01-01

The Oklahoma Geographic Information Retrieval System (OGIRS) is a highly interactive data entry, storage, manipulation, and display software system for use with geographically referenced data. Although originally developed for a project concerned with coal strip mine reclamation, OGIRS is capable of handling any geographically referenced data for a variety of natural resource management applications. A special effort has been made to integrate remotely sensed data into the information system. The timeliness and synoptic coverage of satellite data are particularly useful attributes for inclusion into the geographic information system.

Evolutionary dynamics of taxonomic structure

PubMed Central

Foote, Michael

2012-01-01

The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth–death model having two parameters: the rate of species extinction, μ, and the rate of genus origination, γ, each scaled as a multiple of the rate of within-genus speciation, λ. The distribution is more sensitive to γ than to μ, although μ affects the size of the largest genera. The species : genus ratio depends strongly on both γ and μ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly on γ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record. PMID:21865239

CIMS: The Cartographic Information Management System,

DTIC Science & Technology

1981-01-01

information , composites of overlays to demonstrate the decision-making possibilities and slides of the cadastral sheet. System Use After data base ...create a national soils data base that can be used in managing the soil (Johnson, 1979). Small-scale information systems can be used in planning the...maps/charts over the base map, etc.). An example of the manual phase to be found in the literature is the Overlay Information System used in Prince

Marketing in Admissions: The Information System Approach.

ERIC Educational Resources Information Center

Wofford, O. Douglas; Timmerman, Ed

1982-01-01

A marketing information system approach for college admissions is outlined that includes objectives, information needs and sources, a data collection format, and information evaluation. Coordination with other institutional information systems is recommended. (MSE)

Guest editorial. Integrated healthcare information systems.

PubMed

Li, Ling; Ge, Ri-Li; Zhou, Shang-Ming; Valerdi, Ricardo

2012-07-01

The use of integrated information systems for healthcare has been started more than a decade ago. In recent years, rapid advances in information integration methods have spurred tremendous growth in the use of integrated information systems in healthcare delivery. Various techniques have been used for probing such integrated systems. These techniques include service-oriented architecture (SOA), EAI, workflow management, grid computing, and others. Many applications require a combination of these techniques, which gives rise to the emergence of enterprise systems in healthcare. Development of the techniques originated from different disciplines has the potential to significantly improve the performance of enterprise systems in healthcare. This editorial paper briefly introduces the enterprise systems in the perspective of healthcare informatics.

DNA barcoding of Cuban freshwater fishes: evidence for cryptic species and taxonomic conflicts.

PubMed

Lara, Ariagna; Ponce de León, José Luis; Rodríguez, Rodet; Casane, Didier; Côté, Guillaume; Bernatchez, Louis; García-Machado, Erik

2010-05-01

Despite ongoing efforts to protect species and ecosystems in Cuba, habitat degradation, overuse and introduction of alien species have posed serious challenges to native freshwater fish species. In spite of the accumulated knowledge on the systematics of this freshwater ichthyofauna, recent results suggested that we are far from having a complete picture of the Cuban freshwater fish diversity. It is estimated that 40% of freshwater Cuban fish are endemic; however, this number may be even higher. Partial sequences (652 bp) of the mitochondrial gene COI (cytochrome c oxidase subunit I) were used to barcode 126 individuals, representing 27 taxonomically recognized species in 17 genera and 10 families. Analysis was based on Kimura 2-parameter genetic distances, and for four genera a character-based analysis (population aggregation analysis) was also used. The mean conspecific, congeneric and confamiliar genetic distances were 0.6%, 9.1% and 20.2% respectively. Molecular species identification was in concordance with current taxonomical classification in 96.4% of cases, and based on the neighbour-joining trees, in all but one instance, members of a given genera clustered within the same clade. Within the genus Gambusia, genetic divergence analysis suggests that there may be at least four cryptic species. In contrast, low genetic divergence and a lack of diagnostic sites suggest that Rivulus insulaepinorum may be conspecific with Rivulus cylindraceus. Distance and character-based analysis were completely concordant, suggesting that they complement species identification. Overall, the results evidenced the usefulness of the DNA barcodes for cataloguing Cuban freshwater fish species and for identifying those groups that deserve further taxonomic attention. © 2009 Blackwell Publishing Ltd.

Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

USGS Publications Warehouse

Strecker, A.L.; Olden, J.D.; Whittier, Joanna B.; Paukert, C.P.

2011-01-01

To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential tradeoffs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity;contemporary threats to biodiversity (including interactions with nonnative species);and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities;however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple

Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

USGS Publications Warehouse

Strecker, Angela L.; Olden, Julian D.; Whittier, Joanna B.; Paukert, Craig P.

2011-01-01

To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates

On Selecting Commercial Information Systems

PubMed Central

Möhr, J.R.; Sawinski, R.; Kluge, A.; Alle, W.

1984-01-01

As more commercial information systems become available, the methodology for their selection gains importance. An instances where the method employed for the selection of laboratory information systems was multilevel assessment. The method is described and the experience gained in the project is summarized and discussed. Evidence is provided that the employed method is comprehensive, reproducible, valid and economic.

A Guide to the Common Diatoms at Water Pollution Surveillance System Stations.

ERIC Educational Resources Information Center

Weber, Cornelius I.

This guide was developed by the United States Environmental Protection Agency (EPA) as a taxonomic reference for the identification of diatoms. The taxonomic information included consists of a generic key to the common genera of diatoms, a section illustrating 164 diatom species representing 43 common genera found at the Water Pollution…

Deaf and Hard of Hearing Adolescents' Processing of Pictures and Written Words for Taxonomic Categories in a Priming Task of Semantic Categorization

ERIC Educational Resources Information Center

Li, Degao; Gao, Kejuan; Wu, Xueyun; Chen, Xiaojun; Zhang, Xiaona; Li, Ling; He, Weiwei

2013-01-01

Inspired by research by Li, Yi, and Kim (2011), the authors examined Chinese deaf and hard of hearing adolescents' responses to pictures for taxonomic categories of basic level (exemplar pictures) preceded by exemplar pictures, and to written words for taxonomic categories of basic level (exemplar words) preceded by exemplar words or by written…

Gamified Android Based Academic Information System

ERIC Educational Resources Information Center

Setiana, Henry; Hansun, Seng

2017-01-01

Student is often lazy when it comes to studying, and how to motivate student was one of the problem in the educational world. To overcome the matters, we will implement the gamification method into an Academic Information System. Academic Information System is a software used for providing information and arranging administration which connected…

An integrated approach to the Taxonomic identification of prehistoric shell ornaments

USGS Publications Warehouse

Demarchi, Beatrice; O'Connor, Sonia; Ponzoni, Andre de Lima; Ponzoni, Raquel de Almeida Roch; Sheridan, Alison; Penkman, Kirsty; Hancock, Y.; Wilson, Julie

2014-01-01

Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally.

Genomic insights into the taxonomic status of the Bacillus cereus group

PubMed Central

Liu, Yang; Lai, Qiliang; Göker, Markus; Meier-Kolthoff, Jan P.; Wang, Meng; Sun, Yamin; Wang, Lei; Shao, Zongze

2015-01-01

The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments. PMID:26373441

2 CFR 200.58 - Information technology systems.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 2 Grants and Agreements 1 2014-01-01 2014-01-01 false Information technology systems. 200.58..., AND AUDIT REQUIREMENTS FOR FEDERAL AWARDS Acronyms and Definitions Acronyms § 200.58 Information technology systems. Information technology systems means computing devices, ancillary equipment, software...

Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based on rbcL and matK sequence data

PubMed Central

Häser, Annette

2016-01-01

Background Names used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae, Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed. Methods We analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential of rbcL and matK to resolve taxonomic entities within the bamboo subfamily and tribes. Results Based on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the genera Phyllostachys and Pseudosasa from the temperate “woody” bamboo tribe (Arundinarieae). Currently available rbcL and matK sequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women. PMID:27957401

Delineating species boundaries using an iterative taxonomic approach: the case of soldierless termites (Isoptera, Termitidae, Apicotermitinae).

PubMed

Bourguignon, Thomas; Šobotník, Jan; Hanus, Robert; Krasulová, Jana; Vrkoslav, Vladimír; Cvačka, Josef; Roisin, Yves

2013-12-01

Species boundaries are traditionally inferred using morphological characters, although morphology sometimes fails to correctly delineate species. To overcome this limitation, researchers have widely taken advantage of alternative methods such as DNA barcoding or analysis of cuticular hydrocarbons (CHs) profiles, but rarely use them simultaneously in an iterative taxonomic approach. Here, we follow such an approach using morphology, DNA barcoding and CHs profiles to precisely discriminate species of soldierless termites, a diversified clade constituting about one-third of the Neotropical termite species richness, but poorly resolved taxonomically due to the paucity of useful characters. We sampled soldierless termites in various forest types of the Nouragues Nature Reserve, French Guiana. Our results show that morphological species determination generally matches DNA barcoding, which only suggests the existence of three cryptic species in the 31 morphological species. Among them, Longustitermes manni is the only species whose splitting is corroborated by ecological data, other widely distributed species being supported by DNA barcoding. On the contrary, although CHs profiles provide a certain taxonomic signal, they often suggest inconsistent groupings which are not supported by other methods. Overall, our data support DNA barcoding and morphology as two efficient methods to distinguish soldierless termite species. Copyright © 2013 Elsevier Inc. All rights reserved.

Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific

PubMed Central

Larkin, Alyse A; Blinebry, Sara K; Howes, Caroline; Lin, Yajuan; Loftus, Sarah E; Schmaus, Carrie A; Zinser, Erik R; Johnson, Zackary I

2016-01-01

The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some ‘sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function. PMID:26800235

Information Systems; Modern Health Care and Medical Information.

ERIC Educational Resources Information Center

Brandejs, J. F., And Others

1975-01-01

To effectively handle changes in health policy and health information, new designs and applications of automation are explored. Increased use of computer-based information systems in health care could serve as a means of control over the costs of developing more comprehensive health service, with applications increasing not only the automation of…

Taxonomic revision of Stagmatoptera Burmeister, 1838 (Mantodea: Mantidae, Stagmatopterinae).

PubMed

Rodrigues, Henrique Miranda; Cancello, Eliana Marques

2016-11-01

Stagmatoptera Burmeister, 1838 includes medium to large-sized (49.8-98.7mm) praying mantises distributed in the Neotropical region. They are characterized for having a central, circular spot on each forewing, and 2-4 carinae in the head's frontal shield. This study is an updated revision of the genus on the basis of type and non-type material deposited in various scientific collections from Europe and the Americas. The following nomenclatural procedures were conducted: Stagmatoptera nova is a new junior synonym of Stagmatoptera pia, Stagmatoptera ignota as the junior synonym of Stagmatoptera femoralis, and Stagmatoptera flavipennis is reinstated as the junior synonym of Stagmatoptera supplicaria. Two new species are described: Stagmatoptera diana Rodrigues sp. n. from Colombia and Venezuela, and Stagmatoptera cerdai Rodrigues sp. n. from Trinidad & Tobago and Venezuela. Stagmatoptera now includes 14 species, two of which (Stagmatoptera abdominalis and Stagmatoptera indicator) are considered as species inquirenda. We provide detailed morphological descriptions of all species, a species-level identification key, in addition to abundant visual material to assist identification. Female genitalia, a structure seldom used for taxonomic purposes, was a useful character system to distinguish among species of the genus. Distribution maps for all species are also provided.

Review of Current Geographic Information Systems Technology for TxDOT Pavement Management Information System

DOT National Transportation Integrated Search

1998-05-01

A geographic information system (GIS) is a tool for effectively managing and analyzing tremendous amounts of geographic information. It employs the essential principle of geography to organize in formation and express relationships between real-world...

Establishing the Information System: An Operational Handbook. MOREL Regional Information System for Educators.

ERIC Educational Resources Information Center

Kromer, Charles; Doyle, James

This document is one of a series describing the background, functions, and utilization of the Regional Information System (RIS), developed by the Michigan-Ohio Regional Educational Laboratory (MOREL). RIS, which was developed to improve the accessibility of information for the educational practitioner, is described in this handbook. The handbook…

Information technology security system engineering methodology

NASA Technical Reports Server (NTRS)

Childs, D.

2003-01-01

A methodology is described for system engineering security into large information technology systems under development. The methodology is an integration of a risk management process and a generic system development life cycle process. The methodology is to be used by Security System Engineers to effectively engineer and integrate information technology security into a target system as it progresses through the development life cycle. The methodology can also be used to re-engineer security into a legacy system.

A polyphasic taxonomic approach in isolated strains of Cyanobacteria from thermal springs of Greece.

PubMed

Bravakos, Panos; Kotoulas, Georgios; Skaraki, Katerina; Pantazidou, Adriani; Economou-Amilli, Athena

2016-05-01

Strains of Cyanobacteria isolated from mats of 9 thermal springs of Greece have been studied for their taxonomic evaluation. A polyphasic taxonomic approach was employed which included: morphological observations by light microscopy and scanning electron microscopy, maximum parsimony, maximum likelihood and Bayesian analysis of 16S rDNA sequences, secondary structural comparisons of 16S-23S rRNA Internal Transcribed Spacer sequences, and finally environmental data. The 17 cyanobacterial isolates formed a diverse group that contained filamentous, coccoid and heterocytous strains. These included representatives of the polyphyletic genera of Synechococcus and Phormidium, and the orders Oscillatoriales, Spirulinales, Chroococcales and Nostocales. After analysis, at least 6 new taxa at the genus level provide new evidence in the taxonomy of Cyanobacteria and highlight the abundant diversity of thermal spring environments with many potential endemic species or ecotypes. Copyright © 2016 Elsevier Inc. All rights reserved.

Taxonomic etymology – in search of inspiration

PubMed Central

Jóźwiak, Piotr; Rewicz, Tomasz; Pabis, Krzysztof

2015-01-01

Abstract 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. PMID:26257573

HOPE information system review

NASA Astrophysics Data System (ADS)

Suzuki, Yoshiaki; Nishiyama, Kenji; Ono, Shuuji; Fukuda, Kouin

1992-08-01

An overview of the review conducted on H-2 Orbiting Plane (HOPE) is presented. A prototype model was constructed by inputting various technical information proposed by related laboratories. Especially operation flow which enables understanding of correlation between various analysis items, judgement criteria, technical data, and interfaces with others was constructed. Technical information data base and retrieval systems were studied. A Macintosh personal computer was selected for information shaping because of its excellent function, performance, operability, and software completeness.

CONCORDANCE OF TAXONOMIC RICHNESS PATTERNS ACROSS MULTIPLE ASSEMBLAGES IN LAKES OF THE NORTHEASTERN UNITED STATES

EPA Science Inventory

We investigated the concordance of taxonomic richness patterns and their environmental correlates for assemblages of benthic macroinvertebrates, riparian birds, sedimentary diatoms, fish, planktonic crustaceans, and planktonic rotifers in 186 northeastern U.S. lakes. Taxon counts...

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

NASA Astrophysics Data System (ADS)

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.

Clever birds are lousy: co-variation between avian innovation and the taxonomic richness of their amblyceran lice.

PubMed

Vas, Zoltán; Lefebvre, Louis; Johnson, Kevin P; Reiczigel, Jeno; Rózsa, Lajos

2011-10-01

Lice (Insecta: Phthiraptera) are ectoparasites that reduce host life expectancy and sexual attractiveness. Their taxonomic richness varies considerably among their hosts. Previous studies have already explored some important factors shaping louse diversity. An unexplored potential correlate of louse taxonomic richness is host behavioural flexibility. In this comparative study, we examine the relationship between louse generic richness, innovative capabilities (as a proxy for behavioural flexibility), and brain size while controlling for host species diversity, phylogeny, body size and research effort. Using data for 108 avian families, we found a highly significant positive relationship between host innovative capabilities and the taxonomic richness of amblyceran lice, but a lack of a similar relationship in ischnoceran lice. Host brain size had only a marginal impact on amblyceran diversity and no correlation with ischnoceran diversity. This suggests that the effect in Amblycera is not mediated by metabolic limitations due to the energetic costs of brain size and maintenance, rather directly caused by the ecological differences between hosts with differing cognitive capabilities. We propose four alternative and mutually non-exclusive hypotheses that may explain this phenomenon. Copyright © 2011 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema.

PubMed

Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper T; Bøggild, Andreas; Yang, Tingting; Kjeldsen, Kasper U; Schramm, Andreas

2016-07-01

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 exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine "Candidatus Electrothrix", with four candidate species, and the mostly freshwater "Candidatus Electronema", with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species. Copyright © 2016 The Author(s). Published by Elsevier GmbH.. All rights reserved.

Microbial phenomics information extractor (MicroPIE): a natural language processing tool for the automated acquisition of prokaryotic phenotypic characters from text sources.

PubMed

Mao, Jin; Moore, Lisa R; Blank, Carrine E; Wu, Elvis Hsin-Hui; Ackerman, Marcia; Ranade, Sonali; Cui, Hong

2016-12-13

The large-scale analysis of phenomic data (i.e., full phenotypic traits of an organism, such as shape, metabolic substrates, and growth conditions) in microbial bioinformatics has been hampered by the lack of tools to rapidly and accurately extract phenotypic data from existing legacy text in the field of microbiology. To quickly obtain knowledge on the distribution and evolution of microbial traits, an information extraction system needed to be developed to extract phenotypic characters from large numbers of taxonomic descriptions so they can be used as input to existing phylogenetic analysis software packages. We report the development and evaluation of Microbial Phenomics Information Extractor (MicroPIE, version 0.1.0). MicroPIE is a natural language processing application that uses a robust supervised classification algorithm (Support Vector Machine) to identify characters from sentences in prokaryotic taxonomic descriptions, followed by a combination of algorithms applying linguistic rules with groups of known terms to extract characters as well as character states. The input to MicroPIE is a set of taxonomic descriptions (clean text). The output is a taxon-by-character matrix-with taxa in the rows and a set of 42 pre-defined characters (e.g., optimum growth temperature) in the columns. The performance of MicroPIE was evaluated against a gold standard matrix and another student-made matrix. Results show that, compared to the gold standard, MicroPIE extracted 21 characters (50%) with a Relaxed F1 score > 0.80 and 16 characters (38%) with Relaxed F1 scores ranging between 0.50 and 0.80. Inclusion of a character prediction component (SVM) improved the overall performance of MicroPIE, notably the precision. Evaluated against the same gold standard, MicroPIE performed significantly better than the undergraduate students. MicroPIE is a promising new tool for the rapid and efficient extraction of phenotypic character information from prokaryotic taxonomic

Analysis of information systems for hydropower operations

NASA Technical Reports Server (NTRS)

Sohn, R. L.; Becker, L.; Estes, J.; Simonett, D.; Yeh, W. W. G.

1976-01-01

The operations of hydropower systems were analyzed with emphasis on water resource management, to determine how aerospace derived information system technologies can increase energy output. Better utilization of water resources was sought through improved reservoir inflow forecasting based on use of hydrometeorologic information systems with new or improved sensors, satellite data relay systems, and use of advanced scheduling techniques for water release. Specific mechanisms for increased energy output were determined, principally the use of more timely and accurate short term (0-7 days) inflow information to reduce spillage caused by unanticipated dynamic high inflow events. The hydrometeorologic models used in predicting inflows were examined to determine the sensitivity of inflow prediction accuracy to the many variables employed in the models, and the results used to establish information system requirements. Sensor and data handling system capabilities were reviewed and compared to the requirements, and an improved information system concept outlined.

Information Processing in Living Systems

NASA Astrophysics Data System (ADS)

Tkačik, Gašper; Bialek, William

2016-03-01

Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

PubMed

Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

2015-05-19

The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project.

Effectiveness of protected areas for vertebrates based on taxonomic and phylogenetic diversity.

PubMed

Quan, Qing; Che, Xianli; Wu, Yongjie; Wu, Yuchun; Zhang, Qiang; Zhang, Min; Zou, Fasheng

2018-04-01

Establishing protected areas is the primary goal and tool for preventing irreversible biodiversity loss. However, the effectiveness of protected areas that target specific species has been questioned for some time because targeting key species for conservation may impair the integral regional pool of species diversity and phylogenetic and functional diversity are seldom considered. We assessed the efficacy of protected areas in China for the conservation of phylogenetic diversity based on the ranges and phylogenies of 2279 terrestrial vertebrates. Phylogenetic and taxonomic diversity were strongly and positively correlated, and only 12.1-43.8% of priority conservation areas are currently protected. However, the patterns and coverage of phylogenetic diversity were affected when weighted by species richness. These results indicated that in China, protected areas targeting high species richness protected phylogenetic diversity well overall but failed to do so in some regions with more unique or threatened communities (e.g., coastal areas of eastern China, where severely threatened avian communities were less protected). Our results suggest that the current distribution of protected areas could be improved, although most protected areas protect both taxonomic and phylogenetic diversity. © 2017 Society for Conservation Biology.

Taxonomic revision of the genus Carasobarbus Karaman, 1971 (Actinopterygii, Cyprinidae)

PubMed Central

Borkenhagen, Kai; Krupp, Friedhelm

2013-01-01

Abstract Representatives of the fish genus Carasobarbus Karaman, 1971 (Actinopterygii: Cyprinidae) from the Middle East and North Africa were previously placed in 14 different genus-group taxa (Barbellion, Barbus, Barynotus, Capoeta, Carasobarbus, Cyclocheilichthys, Kosswigobarbus, Labeobarbus, Luciobarbus, Pseudotor, Puntius, Systomus, Tor and Varicorhinus). The generic assignment of several species changed frequently, necessitating a re-evaluation of their taxonomic status. In this study, the genus Carasobarbus is revised based on comparative morphological examinations of about 1300 preserved specimens from collections of several museums and freshly collected material. The species Carasobarbus apoensis, Carasobarbus canis, Carasobarbus chantrei, Carasobarbus exulatus, Carasobarbus fritschii, Carasobarbus harterti, Carasobarbus kosswigi, Carasobarbus luteus and Carasobarbus sublimus form a monophyletic group that shares the following combination of characters: medium-sized barbels with a smooth last unbranched dorsal-fin ray, nine or 10 branched dorsal-fin rays and six branched anal fin-rays; scales large, shield-shaped, with many parallel radii; the lateral line containing 25 to 39 scales; the pharyngeal teeth hooked, 2.3.5-5.3.2 or 2.3.4-4.3.2; one or two pairs of barbels. The species are described in detail, their taxonomic status is re-evaluated and an identification key is provided. A lectotype of Systomus luteus Heckel, 1843 is designated. Carasobarbus Karaman, 1971, Kosswigobarbus Karaman, 1971, and Pseudotor Karaman, 1971 are subjective synonyms, and acting as First Reviser we gave precedence to the name Carasobarbus. PMID:24146585

Taxonomic revision and phylogenetic analyses of rubber powdery mildew fungi.

PubMed

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.

Using citizen science to bridge taxonomic discovery with education and outreach.

PubMed

von Konrat, Matt; Campbell, Thomas; Carter, Ben; Greif, Matthew; Bryson, Mike; Larraín, Juan; Trouille, Laura; Cohen, Steve; Gaus, Eve; Qazi, Ayesha; Ribbens, Eric; Livshultz, Tatyana; Walker, Taylor J; Suwa, Tomomi; Peterson, Taylor; Rodriguez, Yarency; Vaughn, Caitlin; Yang, Christina; Aburahmeh, Selma; Carstensen, Brian; de Lange, Peter; Delavoi, Charlie; Strauss, Kalman; Drag, Justyna; Aguero, Blanka; Snyder, Chris; Martinec, Joann; Smith, Arfon

2018-02-01

Biological collections are uniquely poised to inform the stewardship of life on Earth in a time of cataclysmic biodiversity loss. Efforts to fully leverage collections are impeded by a lack of trained taxonomists and a lack of interest and engagement by the public. We provide a model of a crowd-sourced data collection project that produces quality taxonomic data sets and empowers citizen scientists through real contributions to science. Entitled MicroPlants, the project is a collaboration between taxonomists, citizen science experts, and teachers and students from universities and K-12. We developed an online tool that allows citizen scientists to measure photographs of specimens of a hyper-diverse group of liverworts from a biodiversity hotspot. Using the MicroPlants online tool, citizen scientists are generating high-quality data, with preliminary analysis indicating non-expert data can be comparable to expert data. More than 11,000 users from both the website and kiosk versions have contributed to the data set, which is demonstrably aiding taxonomists working toward establishing conservation priorities within this group. MicroPlants provides opportunities for public participation in authentic science research. The project's educational component helps move youth toward engaging in scientific thinking and has been adopted by several universities into curriculum for both biology and non-biology majors.

Spatial distribution of citizen science casuistic observations for different taxonomic groups.

PubMed

Tiago, Patrícia; Ceia-Hasse, Ana; Marques, Tiago A; Capinha, César; Pereira, Henrique M

2017-10-16

Opportunistic citizen science databases are becoming an important way of gathering information on species distributions. These data are temporally and spatially dispersed and could have limitations regarding biases in the distribution of the observations in space and/or time. In this work, we test the influence of landscape variables in the distribution of citizen science observations for eight taxonomic groups. We use data collected through a Portuguese citizen science database (biodiversity4all.org). We use a zero-inflated negative binomial regression to model the distribution of observations as a function of a set of variables representing the landscape features plausibly influencing the spatial distribution of the records. Results suggest that the density of paths is the most important variable, having a statistically significant positive relationship with number of observations for seven of the eight taxa considered. Wetland coverage was also identified as having a significant, positive relationship, for birds, amphibians and reptiles, and mammals. Our results highlight that the distribution of species observations, in citizen science projects, is spatially biased. Higher frequency of observations is driven largely by accessibility and by the presence of water bodies. We conclude that efforts are required to increase the spatial evenness of sampling effort from volunteers.

A Neurocomputational Account of Taxonomic Responding and Fast Mapping in Early Word Learning

ERIC Educational Resources Information Center

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…

Multipurpose Interactive NASA Information Systems (MINIS)

NASA Technical Reports Server (NTRS)

1977-01-01

The Multipurpose Interactive NASA Information System was developed to provide remote, interactive information retrieval capability for various types of data bases to be processed on different types of small and medium size computers. Use of the system for three different data bases is decribed: (1) LANDSAT photo look-up, (2) land use, and (3) census/socioeconomic. Each of the data base elements is shown together with other detailed information that a user would require to contact the system remotely, to transmit inquiries on commands, and to receive the results of the queries or commands.

CUAHSI Hydrologic Information Systems

NASA Astrophysics Data System (ADS)

Maidment, D.; Zaslavsky, I.; Tarboton, D.; Piasecki, M.; Goodall, J.

2006-12-01

The Consortium of Universities for the Advancement of Hydrologic Science, Inc (CUAHSI) has a Hydrologic Information System (HIS) project, which is supported by NSF to develop infrastructure and services to support the advance of hydrologic science in the United States. This paper provides an overview of the HIS project. A set of web services called WaterOneFlow is being developed to provide better access to water observations data (point measurements of streamflow, water quality, climate and groundwater levels) from government agencies and individual investigator projects. Successful partnerships have been created with the USGS National Water Information System, EPA Storet and the NCDC Climate Data Online. Observations catalogs have been created for stations in the measurement networks of each of these data systems so that they can be queried in a uniform manner through CUAHSI HIS, and data delivered from them directly to the user via web services. A CUAHSI Observations Data Model has been designed for storing individual investigator data and an equivalent set of web services created for that so that individual investigators can publish their data onto the internet in the same format CUAHSI is providing for the federal agency data. These data will be accessed through HIS Servers hosted at the national level by CUAHSI and also by research centers and academic departments for regional application of HIS. An individual user application called HIS Analyst will enable individual hydrologic scientists to access the information from the network of HIS Servers. The present focus is on water observations data but later development of this system will include weather and climate grid information, GIS data, remote sensing data and linkages between data and hydrologic simulation models.

Typification and taxonomic status re-evaluation of 15 taxon names within the species complex Cymbella affinis/tumidula/turgidula (Cymbellaceae, Bacillariophyta)

PubMed Central

da Silva, Weliton José; Jahn, Regine; Ludwig, Thelma Alvim Veiga; Hinz, Friedel; Menezes, Mariângela

2015-01-01

Abstract Specimens belonging to the Cymbella affinis / Cymbella tumidula / Cymbella turgidula species complex have many taxonomic problems, due to their high morphological variability and lack of type designations. Fifteen taxon names of this complex, distributed in five species, were re-evaluated concerning their taxonomic status, and lectotypified based on original material. In addition to light microscopy, some material was analyzed by electron microscopy. Four new combinations are proposed in order to reposition infraspecific taxa. PMID:26312038

Functioning information in the learning health system.

PubMed

Stucki, Gerold; Bickenbach, Jerome

2017-02-01

In this methodological note on applying the ICF in rehabilitation, we introduce functioning information as fundamental for the "learning health system" and the continuous improvement of the health system's response to people's functioning needs by means of the provision of rehabilitation. A learning health system for rehabilitation operates at the micro-level of the individual patient, meso-level of operational management, and the macro-level of policy that guides rehabilitation programming. All three levels rely on the capacity of the informational system of the health system for standardized documentation and coding of functioning information, and the development of national rehabilitation quality management systems. This methodological note describes how functioning information is used for the continuous improvement of functioning outcomes in a learning health system across these three levels.

NATIONAL PESTICIDE INFORMATION RETRIEVAL SYSTEM (NPIRS)

EPA Science Inventory

The National Pesticide Information Retrieval System (NPIRS) is a collection of pesticide-related databases available through subscription to the Center for Environmental and Regulatory Information Systems, CERIS. The following is a summary of data found in the databases, data sou...

36 CFR 1192.87 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Public information system... Light Rail Vehicles and Systems § 1192.87 Public information system. (a) Each vehicle shall be equipped with an interior public address system permitting transportation system personnel, or recorded or...

Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles.

PubMed

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.

Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

PubMed Central

Speller, Camilla; van den Hurk, Youri; Charpentier, Anne; Rodrigues, Ana; Gardeisen, Armelle; Wilkens, Barbara; McGrath, Krista; Rowsell, Keri; Spindler, Luke; Collins, Matthew

2016-01-01

Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species’ distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481784

Information for Successful Interaction with Autonomous Systems

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Johnson, Kathy A.

2003-01-01

Interaction in heterogeneous mission operations teams is not well matched to classical models of coordination with autonomous systems. We describe methods of loose coordination and information management in mission operations. We describe an information agent and information management tool suite for managing information from many sources, including autonomous agents. We present an integrated model of levels of complexity of agent and human behavior, which shows types of information processing and points of potential error in agent activities. We discuss the types of information needed for diagnosing problems and planning interactions with an autonomous system. We discuss types of coordination for which designs are needed for autonomous system functions.

Personal medical information system using laser card

NASA Astrophysics Data System (ADS)

Cho, Seong H.; Kim, Keun Ho; Choi, Hyung-Sik; Park, Hyun Wook

1996-04-01

The well-known hospital information system (HIS) and the picture archiving and communication system (PACS) are typical applications of multimedia to medical area. This paper proposes a personal medical information save-and-carry system using a laser card. This laser card is very useful, especially in emergency situations, because the medical information in the laser card can be read at anytime and anywhere if there exists a laser card reader/writer. The contents of the laser card include the clinical histories of a patient such as clinical chart, exam result, diagnostic reports, images, and so on. The purpose of this system is not a primary diagnosis, but emergency reference of clinical history of the patient. This personal medical information system consists of a personal computer integrated with laser card reader/writer, color frame grabber, color CCD camera and a high resolution image scanner optionally. Window-based graphical user interface was designed for easy use. The laser card has relatively sufficient capacity to store the personal medical information, and has fast access speed to restore and load the data with a portable size as compact as a credit card. Database items of laser card provide the doctors with medical data such as laser card information, patient information, clinical information, and diagnostic result information.

Classification of malignant and benign lung nodules using taxonomic diversity index and phylogenetic distance.

PubMed

de Sousa Costa, Robherson Wector; da Silva, Giovanni Lucca França; de Carvalho Filho, Antonio Oseas; Silva, Aristófanes Corrêa; de Paiva, Anselmo Cardoso; Gattass, Marcelo

2018-05-23

Lung cancer presents the highest cause of death among patients around the world, in addition of being one of the smallest survival rates after diagnosis. Therefore, this study proposes a methodology for diagnosis of lung nodules in benign and malignant tumors based on image processing and pattern recognition techniques. Mean phylogenetic distance (MPD) and taxonomic diversity index (Δ) were used as texture descriptors. Finally, the genetic algorithm in conjunction with the support vector machine were applied to select the best training model. The proposed methodology was tested on computed tomography (CT) images from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI), with the best sensitivity of 93.42%, specificity of 91.21%, accuracy of 91.81%, and area under the ROC curve of 0.94. The results demonstrate the promising performance of texture extraction techniques using mean phylogenetic distance and taxonomic diversity index combined with phylogenetic trees. Graphical Abstract Stages of the proposed methodology.

49 CFR 38.121 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false Public information system. 38.121 Section 38.121... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Intercity Rail Cars and Systems § 38.121 Public information system. (a) Each car shall be equipped with a public address system permitting transportation system personnel, or...

76 FR 76917 - Homeless Management Information Systems Requirements

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-09

...-P-01] Homeless Management Information Systems Requirements AGENCY: Office of the Assistant Secretary... for the establishment of regulations for Homeless Management Information Systems (HMIS), which are the... community development, Homeless, Information technology system, Management system, Nonprofit organizations...

Respiratory care management information systems.

PubMed

Ford, Richard M

2004-04-01

Hospital-wide computerized information systems evolved from the need to capture patient information and perform billing and other financial functions. These systems, however, have fallen short of meeting the needs of respiratory care departments regarding work load assessment, productivity management, and the level of outcome reporting required to support programs such as patient-driven protocols. The respiratory care management information systems (RCMIS) of today offer many advantages over paper-based systems and hospital-wide computer systems. RCMIS are designed to facilitate functions specific to respiratory care, including assessing work demand, assigning and tracking resources, charting, billing, and reporting results. RCMIS incorporate mobile, point-of-care charting and are highly configurable to meet the specific needs of individual respiratory care departments. Important and substantial benefits can be realized with an RCMIS and mobile, wireless charting devices. The initial and ongoing costs of an RCMIS are justified by increased charge capture and reduced costs, by way of improved productivity and efficiency. It is not unusual to recover the total cost of an RCMIS within the first year of its operation. In addition, such systems can facilitate and monitor patient-care protocols and help to efficiently manage the vast amounts of information encountered during the practitioner's workday. Respiratory care departments that invest in RCMIS have an advantage in the provision of quality care and in reducing expenses. A centralized respiratory therapy department with an RCMIS is the most efficient and cost-effective way to monitor work demand and manage the hospital-wide allocation of respiratory care services.

Information-Systems Data-Flow Diagram

NASA Technical Reports Server (NTRS)

Blosiu, J. O.

1983-01-01

Single form presents clear picture of entire system. Form giving relational review of data flow well suited to information system planning, analysis, engineering, and management. Used to review data flow for developing system or one already in use.

Performance evaluation of public hospital information systems by the information system success model.

PubMed

Cho, Kyoung Won; Bae, Sung-Kwon; Ryu, Ji-Hye; Kim, Kyeong Na; An, Chang-Ho; Chae, Young Moon

2015-01-01

This study was to evaluate the performance of the newly developed information system (IS) implemented on July 1, 2014 at three public hospitals in Korea. User satisfaction scores of twelve key performance indicators of six IS success factors based on the DeLone and McLean IS Success Model were utilized to evaluate IS performance before and after the newly developed system was introduced. All scores increased after system introduction except for the completeness of medical records and impact on the clinical environment. The relationships among six IS factors were also analyzed to identify the important factors influencing three IS success factors (Intention to Use, User Satisfaction, and Net Benefits). All relationships were significant except for the relationships among Service Quality, Intention to Use, and Net Benefits. The results suggest that hospitals should not only focus on systems and information quality; rather, they should also continuously improve service quality to improve user satisfaction and eventually reach full the potential of IS performance.

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.

PubMed

Gregor, Ivan; Dröge, Johannes; Schirmer, Melanie; Quince, Christopher; McHardy, Alice C

2016-01-01

Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into 'bins' representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies 'training' sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4-6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki.

Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae, Pucciniales) on Willows in China

PubMed Central

Zhao, Peng; Wang, Qing-Hong; Tian, Cheng-Ming; Kakishima, Makoto

2015-01-01

The species in genus Melampsora are the causal agents of leaf rust diseases on willows in natural habitats and plantations. However, the classification and recognition of species diversity are challenging because morphological characteristics are scant and morphological variation in Melampsora on willows has not been thoroughly evaluated. Thus, the taxonomy of Melampsora species on willows remains confused, especially in China where 31 species were reported based on either European or Japanese taxonomic systems. To clarify the species boundaries of Melampsora species on willows in China, we tested two approaches for species delimitation inferred from morphological and molecular variations. Morphological species boundaries were determined based on numerical taxonomic analyses of morphological characteristics in the uredinial and telial stages by cluster analysis and one-way analysis of variance. Phylogenetic species boundaries were delineated based on the generalized mixed Yule-coalescent (GMYC) model analysis of the sequences of the internal transcribed spacer (ITS1 and ITS2) regions including the 5.8S and D1/D2 regions of the large nuclear subunit of the ribosomal RNA gene. Numerical taxonomic analyses of 14 morphological characteristics recognized in the uredinial-telial stages revealed 22 morphological species, whereas the GMYC results recovered 29 phylogenetic species. In total, 17 morphological species were in concordance with the phylogenetic species and 5 morphological species were in concordance with 12 phylogenetic species. Both the morphological and molecular data supported 14 morphological characteristics, including 5 newly recognized characteristics and 9 traditionally emphasized characteristics, as effective for the differentiation of Melampsora species on willows in China. Based on the concordance and discordance of the two species delimitation approaches, we concluded that integrative taxonomy by using both morphological and molecular variations was

Customer systems group 1996 target summaries: Information systems and telecommunications. Revision 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-06-15

The target summaries give planning information on the new business systems development; customer service applications and infrastructure; and advanced information systems and telecommunications research, architecture and standards factions of Information Systems & Telecommunications.

Information pricing based on trusted system

NASA Astrophysics Data System (ADS)

Liu, Zehua; Zhang, Nan; Han, Hongfeng

2018-05-01

Personal information has become a valuable commodity in today's society. So our goal aims to develop a price point and a pricing system to be realistic. First of all, we improve the existing BLP system to prevent cascading incidents, design a 7-layer model. Through the cost of encryption in each layer, we develop PI price points. Besides, we use association rules mining algorithms in data mining algorithms to calculate the importance of information in order to optimize informational hierarchies of different attribute types when located within a multi-level trusted system. Finally, we use normal distribution model to predict encryption level distribution for users in different classes and then calculate information prices through a linear programming model with the help of encryption level distribution above.

Management Information Systems.

ERIC Educational Resources Information Center

Finlayson, Jean, Ed.

1989-01-01

This collection of papers addresses key questions facing college managers and others choosing, introducing, and living with big, complex computer-based systems. "What Use the User Requirement?" (Tony Coles) stresses the importance of an information strategy driven by corporate objectives, not technology. "Process of Selecting a…

RIMS: Resource Information Management System

NASA Technical Reports Server (NTRS)

Symes, J.

1983-01-01

An overview is given of the capabilities and functions of the resource management system (RIMS). It is a simple interactive DMS tool which allows users to build, modify, and maintain data management applications. The RIMS minimizes programmer support required to develop/maintain small data base applications. The RIMS also assists in bringing the United Information Services (UIS) budget system work inhouse. Information is also given on the relationship between the RIMS and the user community.

Is Student Performance on the Information Systems Analyst Certification Exam Affected by Form of Delivery of Information Systems Coursework?

ERIC Educational Resources Information Center

Haga, Wayne; Moreno, Abel; Segall, Mark

2012-01-01

In this paper, we compare the performance of Computer Information Systems (CIS) majors on the Information Systems Analyst (ISA) Certification Exam. The impact that the form of delivery of information systems coursework may have on the exam score is studied. Using a sample that spans three years, we test for significant differences between scores…

Cryptic diversity in the Azorean beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae): An integrative taxonomic approach with description of four new species.

PubMed

Borges, Paulo A V; Amorim, Isabel R; Terzopoulou, Sofia; Rigal, François; Emerson, Brent C; Serrano, Artur R M

2017-02-23

Recent findings based on molecular data support the occurrence in the Azores of several independently evolving lineages of the beetle genus Tarphius Erichson, 1845 (Coleoptera: Zopheridae Solier, 1834) and higher species richness masked by cryptic diversity, needing formal taxonomic description. All Tarphius from the Azores are revised using an integrative taxonomic approach, using evidence from morphology, morphometrics and molecular data to delimit species. Our results reveal that Azorean Tarphius comprise at least five phyletic lineages, two of which share a similar morphology, despite being divergent at the molecular level. A total of four new species are described grouped into two complexes: i) two new species in the "complex tornvalli" with the new taxa Tarphius relictus sp. nov. (Terceira) and Tarphius furtadoi sp. nov. (São Jorge, Faial and Pico) and; ii) two new species in the "complex azoricus-wollastoni-depressus" with the new taxa Tarphius gabrielae sp. nov. (Pico) and Tarphius floresensis sp. nov. (Flores). Descriptions, photographs of holotypes and morphological details, and remarks on diagnostic features comparing similar species are presented. Additional information on the distribution and conservation status of the 12 described species in the archipelago is also provided.

Taxonomic and nontaxonomic responses to ecological changes in an urban lowland stream through the use of Chironomidae (Diptera) larvae.

PubMed

Cortelezzi, A; Paggi, A C; Rodríguez, M; Capítulo, A Rodrigues

2011-03-01

Biotic descriptors--both taxonomic (diversity indices, species richness, and indicator species) and nontaxonomic (biomass, oxygen consumption/production, and anatomical deformities)--are useful tools for measuring a stream's ecological condition. Nontaxonomic parameters detect critical effects not reflected taxonomically. We analyzed changes in Chironomidae populations as taxonomic parameters and mentum deformities as a nontaxonomic parameter for evaluating a South-American-plains stream (Argentina). We performed samplings seasonally (March, June, September, and December; 2005) and physical and chemical measurements at three sampling sites of the stream (DC1 at river source, through DC3 downstream). The specimens collected in sediment and vegetation were analyzed to investigate mouth deformities in Chironomidae larvae. We identified a total of 9 taxa from Chironomidae and Orthocladiinae subfamilies. Shannon's diversity index for Chironomidae decreased from 1.6 bits ind⁻¹ (DC1) to 0.3 bits ind⁻¹ (DC3). The total density of the Chironomidae exhibited a great increase in abundance at site DC3, especially that of Chironomus calligraphus. Chironomidae taxonomic composition also changed among the three sites despite their spatial proximity: C. calligraphus, Goeldichironomus holoprasinus, Parachironomus longistilus, and Polypedilum were present at all three; Corynoneura and Paratanytarsu at DC1 only; Cricotopus at DC1 and DC3; Apedilum elachistus notably at DC2 and DC3; and Parametriocnemus only at DC2. C. calligraphus individuals from DC1 showed no mentum deformities; only 2 from DC2 exhibited mouth-structure alterations; while specimens from DC3 presented the most abnormalities, especially during autumn and late winter. Type-II deformities (supernumerary teeth and gaps) were the most common. Anatomical deformities are sublethal effects representing an early alert to chemically caused environmental degradation. Mentum deformities in benthic-Chironomidae larvae

ENVIRONMENTAL INFORMATION MANAGEMENT SYSTEM (EIMS)

EPA Science Inventory

The Environmental Information Management System (EIMS) organizes descriptive information (metadata) for data sets, databases, documents, models, projects, and spatial data. The EIMS design provides a repository for scientific documentation that can be easily accessed with standar...

Ionizing radiation and taxonomic, functional and evolutionary diversity of bird communities.

PubMed

Morelli, Federico; Benedetti, Yanina; Mousseau, Timothy A; Møller, Anders Pape

2018-08-15

Ionizing radiation from nuclear accidents at Chernobyl, Fukushima and elsewhere has reduced the abundance, species richness and diversity of ecosystems. Here we analyzed the taxonomic, functional and evolutionary diversity of bird communities in forested areas around Chernobyl. Species richness decreased with increasing radiation, mainly in 2007. Functional richness, but not functional evenness and divergence, decreased with increasing level of ionizing radiation. Evolutionary distinctiveness of bird communities was higher in areas with higher levels of ionizing radiation. Regression tree models revealed that species richness was higher in bird communities in areas with radiation levels lower than 0.7 μSv/h. In contrast, when radiation levels were higher than 16.67 μSv/h, bird species richness reached a minimum. Functional richness was affected by two variables: Forest cover and radiation level. Higher functional richness was found in bird communities in areas with forest cover lower than 50%. In the areas with forest cover higher than 50%, the functional richness was lower when radiation level was higher than 0.91 μSv/h. Finally, the average evolutionary distinctiveness of bird communities was higher in areas with forest cover exceeding 50%. These findings imply that level of ionizing radiation interacted with forest cover to affect species richness and its component parts, i.e. taxonomic, functional, and evolutionary diversity. Copyright © 2018 Elsevier Ltd. All rights reserved.

The information protection level assessment system implementation

NASA Astrophysics Data System (ADS)

Trapeznikov, E. V.

2018-04-01

Currently, the threat of various attacks increases significantly as automated systems become more widespread. On the basis of the conducted analysis the information protection level assessment system establishing objective was identified. The paper presents the information protection level assessment software implementation in the information system by applying the programming language C #. In conclusions the software features are identified and experimental results are represented.

The Fire Effects Information System

Treesearch

William C. Fischer

1987-01-01

Lack of information regarding fire effects is perceived by many fire and resource managers as a barrier to the effective application of prescribed fire. This lack of information, in many instances, is the result of poor diffusion of existing knowledge rather than lack of knowledge. A computerized Fire Effects Information System can make existing fire effects knowledge...

Goddard's New Approach to Information Technology: The Information Systems Center an Overview

NASA Technical Reports Server (NTRS)

Kea, Howard E.

1994-01-01

The Information Center (ISC) at Goddard was created as part of the Goddard reorganization and was located within the Applied Engineering and Technology (AET) Directorate. The creation of ISC was to: (1) focus expertise and leadership in information system development; (2) Promote organizational collaboration, partnerships, and resource sharing; (3) Stimulate design/development of seamless end-to-end flight and ground systems; (4) Enable flexibility to effectively support many simultaneous projects by improved access to critical mass of discipline expertise; (5) Enhance career growth and opportunities including multi-disciplinary opportunities; and (6) to improve communications among information system professionals. This paper presents a general overview of the Information Systems Center as well as the role of the Software Engineering Laboratory within the center.

Temporal changes in taxonomic and functional diversity of fish assemblages downstream from mountaintop mining

USGS Publications Warehouse

Hitt, Nathaniel P.; Chambers, Douglas B.

2014-01-01

Mountaintop mining (MTM) affects chemical, physical, and hydrological properties of receiving streams, but the long-term consequences for fish-assemblage structure and function are poorly understood. We sampled stream fish assemblages using electrofishing techniques in MTM exposure sites and reference sites within the Guyandotte River basin, USA, during 2010–2011. We calculated indices of taxonomic diversity (species richness, abundance, Shannon diversity) and functional diversity (functional richness, functional evenness, functional divergence) to compare exposure and reference assemblages between seasons (spring and autumn) and across years (1999–2011). We based temporal comparisons on 2 sites that were sampled during 1999–2001 by Stauffer and Ferreri (2002). Exposure assemblages had lower taxonomic and functional diversity than reference assemblages or simulated assemblages that accounted for random variation. Differences in taxonomic composition between reference and exposure assemblages were associated with conductivity and aqueous Se concentrations. Exposure assemblages had fewer species, lower abundances, and less biomass than reference assemblages across years and seasons. Green Sunfish (Lepomis cyanellus) and Creek Chub (Semotilus atromaculatus) became numerically dominant in exposure assemblages over time because of their persistence and losses of other taxa. In contrast, species richness increased over time in reference assemblages, a result that may indicate recovery from drought. Mean individual biomass increased as fish density decreased and most obligate invertivores were apparently extirpated at MTM exposure sites. Effects of MTM were not related to physical-habitat conditions but were associated with water-quality variables, which may limit quality and availability of benthic macroinvertebrate prey. Simulations revealed effects of MTM that could not be attributed to random variation in fish assemblage structure.

Information Systems Curriculum.

ERIC Educational Resources Information Center

O'Neil, Sharon Lund

This guide outlines an information systems curriculum that has been developed for postsecondary institutions in Texas. The curriculum, which is intended to help students acquire the competencies necessary to function in automated offices in business and industry, includes the following core courses: computer business applications I and II,…

Performance Information Management System (PIMS) Communication

DTIC Science & Technology

1993-12-31

34AD-A284 851 AD MIPR NO. MIPR 92MM2501 TITLE: Performance Information Management System (PIMS) Communication PRINCIPAL INVESTIGATOR: Kathryn P...93 . . ..- F •nal,. 12/1/91 - 12/31/93- ...... . ..... PIMS-Performance Information Management System Communications 92MM2501 Kathryn P. Winter Navy

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

NASA Astrophysics Data System (ADS)

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

Information Service System For Small Forestowners

NASA Astrophysics Data System (ADS)

Zhang, Shaochen; Li, Yun

Individual owned forests have boomed in the last decade in China. Hundreds of millions of private forest owners have emerged since years of afforestation practice and collective forest ownership reform. Most of those private forest owners are former peasants living in afforestation areas. They thirst for forestry information, such as technique knowledge, forestry policies, finance, marketing, etc. Unfortunately the ways they could get certain information are very limit. Before internet time, Local governments are the main channel they search helps for useful information and technique supports. State and local governments have paid much attention to provide necessary forestry technique supports to those small forest owners and provided varies training projects, issued official forestry information through their websites. While, as state government expands household contract system in the management of collective forestry land, the number of individual forest owners is bumping up in future 5 years. There is still a gap between supplying ability and requirement of forestry information. To construct an effective forestry information service system in next 3-5 year can bridge the gap. This paper discusses the framework of such an information service system.

Quality Information--Informed Choices: Advancing the Workforce Information System. Secretary of Labor's Workforce Information System Plan for Federal Fiscal Years 2001-2005.

ERIC Educational Resources Information Center

Workforce Information Council (DOL), Washington, DC.

The Workforce Investment Act of 1998 emphasizes the importance of high quality, accessible, and relevant information about the labor market for making sound decisions. In order to help both workers and employers, as well as the government agencies that serve them, the Workforce Information System was created and is being improved. The action plan…

Geographic Information System Data Analysis

NASA Technical Reports Server (NTRS)

Billings, Chad; Casad, Christopher; Floriano, Luis G.; Hill, Tracie; Johnson, Rashida K.; Locklear, J. Mark; Penn, Stephen; Rhoulac, Tori; Shay, Adam H.; Taylor, Antone;

School Management Information Systems in Primary Schools

ERIC Educational Resources Information Center

Demir, Kamile

2006-01-01

Developments in information technologies have been impacting upon educational organizations. Principals have been using management information systems to improve the efficiency of administrative services. The aim of this research is to explore principals' perceptions about management information systems and how school management information…

Educational Management Information Systems: Progress and Prospectives.

ERIC Educational Resources Information Center

Evans, John A.

An educational management information system is a network of communication channels, information sources, computer storage and retrieval devices, and processing routines that provide data to educational managers at different levels, places, and times to facilitate decisionmaking. Management information systems should be differentiated from…

Information security governance: a risk assessment approach to health information systems protection.

PubMed

Williams, Patricia A H

2013-01-01

It is no small task to manage the protection of healthcare data and healthcare information systems. In an environment that is demanding adaptation to change for all information collection, storage and retrieval systems, including those for of e-health and information systems, it is imperative that good information security governance is in place. This includes understanding and meeting legislative and regulatory requirements. This chapter provides three models to educate and guide organisations in this complex area, and to simplify the process of information security governance and ensure appropriate and effective measures are put in place. The approach is risk based, adapted and contextualized for healthcare. In addition, specific considerations of the impact of cloud services, secondary use of data, big data and mobile health are discussed.

Management Information System Project.

ERIC Educational Resources Information Center

Foley, Walter J.; Harr, Gordon G.

The Management Information System (MIS) described in this report represents a plan to utilize modern management techniques to facilitate the goal of a learner-responsive school system. The MIS component is being developed to meet the need for the coordination of the resources of staff, facilities, and time with the long range planning and…

Making the case for a clinical information system: the chief information officer view.

PubMed

Cotter, Carole M

2007-03-01

Adequate decision support for clinicians and other caregivers requires accessible and reliable patient information. Powerful societal and economic forces are moving us toward an integrated, patient-centered health care information system that will allow caregivers to exchange up-to-date patient health information quickly and easily. These forces include patient safety, potential health care cost savings, empowerment of consumers (and their subsequent demands for quality), new federal policies, and growing regional health care initiatives. Underspending on health care information technologies has gone on for many years; and the creation and implementation of a comprehensive clinical information system will entail many difficulties, particularly in regard to patients' privacy and control of their information, standardization of electronic health records, cost of adopting information technology, unbalanced financial incentives, and the varying levels of preparation across caregivers. There will also be potential effects on the physician-patient relationship. Ultimately, an integrated system will require a concerted transformation of the health care industry that is akin to what the banking industry has accomplished with electronic automation. Critical care units provide a good starting point for how information system technologies can be used and electronic patient information collected, although the robust systems designed for intensive care units are not always used to their potential.

Legal Medicine Information System using CDISC ODM.

PubMed

Kiuchi, Takahiro; Yoshida, Ken-ichi; Kotani, Hirokazu; Tamaki, Keiji; Nagai, Hisashi; Harada, Kazuki; Ishikawa, Hirono

2013-11-01

We have developed a new database system for forensic autopsies, called the Legal Medicine Information System, using the Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM). This system comprises two subsystems, namely the Institutional Database System (IDS) located in each institute and containing personal information, and the Central Anonymous Database System (CADS) located in the University Hospital Medical Information Network Center containing only anonymous information. CDISC ODM is used as the data transfer protocol between the two subsystems. Using the IDS, forensic pathologists and other staff can register and search for institutional autopsy information, print death certificates, and extract data for statistical analysis. They can also submit anonymous autopsy information to the CADS semi-automatically. This reduces the burden of double data entry, the time-lag of central data collection, and anxiety regarding legal and ethical issues. Using the CADS, various studies on the causes of death can be conducted quickly and easily, and the results can be used to prevent similar accidents, diseases, and abuse. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

49 CFR 38.35 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false Public information system. 38.35 Section 38.35... SPECIFICATIONS FOR TRANSPORTATION VEHICLES Buses, Vans and Systems § 38.35 Public information system. (a... a public address system permitting the driver, or recorded or digitized human speech messages, to...

Smart information system for gachon university gil hospital.

PubMed

Park, Dong Kyun; Jung, Eun Young; Jeong, Byung Hui; Moon, Byung Chan; Kang, Hyung Wook; Tchah, Hann; Han, Gi Seong; Cheng, Woo Sung; Lee, Young Ho

2012-03-01

In this research, the hospital information system of Gachon University Gil hospital is introduced and a future strategy for hospital information systems is proposed. This research introduces the development conditions of hospital information system at Gachon University Gil hospital, information about the development of the enterprise resource planning (ERP), a medical service process improvement system, and the personal health record (PHR) system. The medical service process and work efficiency were improved through the medical service process improvement system, which is the most common hospital information system at Gachon University Gil hospital and which includes an emergency medical service system, an online evaluation system and a round support system. Gachon University Gil hospital developed medical service improvement systems to increase work efficiency of medical team and optimized the systems to prove the availability of high-quality medical services for patients and their families. The PHR-based personalized health care solution is under development and will provide higher quality medical service for more patients in the future.

BLISS: The Bradley Library Information Support System.

ERIC Educational Resources Information Center

Hartman, Joel L.; And Others

1993-01-01

Describes the Bradley Library Information Support System (BLISS), a comprehensive local area network designed to provide library users with electronic information access and management services to support Bradley University (Illinois). System architecture is explained; and six sidebars provide more detailed information on various services, the…

Phylogenetic relationships and taxonomic revision of Paranoplocephala Lühe, 1910 sensu lato (Cestoda, Cyclophyllidea, Anoplocephalidae)

USDA-ARS?s Scientific Manuscript database

An extensive phylogenetic analysis and genus-level taxonomic revision of Paranoplocephala Lühe, 1910 -like cestodes (Cyclophyllidea, Anoplocephalidae) are presented. The phylogenetic analysis is based on DNA sequences of two partial mitochondrial genes, i.e. cytochrome c oxidase subunit 1 (cox1) and...

Data vs. information: A system paradigm

NASA Technical Reports Server (NTRS)

Billingsley, F. C.

1982-01-01

The data system designer requires data parameters, and is dependent on the user to convert information needs to these data parameters. This conversion will be done with more or less accuracy, beginning a chain of inaccuracies which propagate through the system, and which, in the end, may prevent the user from converting the data received into the information required. The concept to be pursued is that errors occur in various parts of the system, and, having occurred, propagate to the end. Modeling of the system may allow an estimation of the effects at any point and the final accumulated effect, and may prove a method of allocating an error budget among the system components. The selection of the various technical parameters which a data system must meet must be done in relation to the ability of the user to turn the cold, impersonal data into a live, personal decision or piece of information.

Advanced Approach to Information Security Management System Model for Industrial Control System

PubMed Central

2014-01-01

Organizations make use of important information in day-to-day business. Protecting sensitive information is imperative and must be managed. Companies in many parts of the world protect sensitive information using the international standard known as the information security management system (ISMS). ISO 27000 series is the international standard ISMS used to protect confidentiality, integrity, and availability of sensitive information. While an ISMS based on ISO 27000 series has no particular flaws for general information systems, it is unfit to manage sensitive information for industrial control systems (ICSs) because the first priority of industrial control is safety of the system. Therefore, a new information security management system based on confidentiality, integrity, and availability as well as safety is required for ICSs. This new ISMS must be mutually exclusive of an ICS. This paper provides a new paradigm of ISMS for ICSs, which will be shown to be more suitable than the existing ISMS. PMID:25136659

Advanced approach to information security management system model for industrial control system.

PubMed

Park, Sanghyun; Lee, Kyungho

2014-01-01

Organizations make use of important information in day-to-day business. Protecting sensitive information is imperative and must be managed. Companies in many parts of the world protect sensitive information using the international standard known as the information security management system (ISMS). ISO 27000 series is the international standard ISMS used to protect confidentiality, integrity, and availability of sensitive information. While an ISMS based on ISO 27000 series has no particular flaws for general information systems, it is unfit to manage sensitive information for industrial control systems (ICSs) because the first priority of industrial control is safety of the system. Therefore, a new information security management system based on confidentiality, integrity, and availability as well as safety is required for ICSs. This new ISMS must be mutually exclusive of an ICS. This paper provides a new paradigm of ISMS for ICSs, which will be shown to be more suitable than the existing ISMS.

Pesticide Product Information System (PPIS)

EPA Pesticide Factsheets

The Pesticide Product Information System contains information concerning all pesticide products registered in the United States. It includes registrant name and address, chemical ingredients, toxicity category, product names, distributor brand names, site/pest uses, pesticidal type, formulation code, and registration status.

Reasonable Accommodation Information Tracking System

EPA Pesticide Factsheets

The Reasonable Accommodation Information Tracking System (RAITS) is a case management system that allows the National Reasonable Accommodation Coordinator (NRAC) and the Local Reasonable Accommodation Coordinators (LORAC) to manage information related to Reasonable Accommodation (RA) requests. It provides a data base system in compliance with Executive Order 13164 and required by the Equal Employment Opportunity Commission (EEOC) Regulations and American Federation of Government Employees (AFGE) Bargaining Unit as described in the AFGE National Reasonable Accommodation Procedures. It is a tool that was internally developed in Lotus Notes to track requests for reasonable accommodation and was custom-configured to meet EPA's specific needs and infrastructure.

Corporate information systems in health organisations.

PubMed

Smith, J

1997-01-01

This paper presents an overview of the nature of corporate information systems and their applications in health organisations. It emphasises the importance of financial and human resource information in the creation of a corporate data model. The paper summarises the main features of finance and human resource systems as they are used in health organisations. It looks at a series of case studies carried out in health organisations, which were selected on the basis of their representation of different aspects of service delivery. It also discusses the theoretical and practical perspectives of the systems themselves, their roles in information management, executive and decision support, and in planning and forecasting.

Transforming Legacy Systems to Obtain Information Superiority

DTIC Science & Technology

2001-01-01

is imperative that innovative technologies be developed to enable legacy weapon systems to exploit the information revolution, achieve information ... dominance , and meet the required operational tempo. This paper presents an embedded-system architecture, open system middleware services, and a software

Implementation of Alabama Resources Information System, ARIS

NASA Technical Reports Server (NTRS)

Herring, B. E.

1978-01-01

Development of ARIS - Alabama Resources Information System is summarized. Development of data bases, system simplification for user access, and making information available to personnel having a need to use ARIS or in the process of developing ARIS type systems are discussed.

Performance Information Management System (PIMS) Communication

DTIC Science & Technology

1992-10-15

AD-A267 040 AD 14IPR NO: 92M•2501 TITLE: PERFORMANCE INFORMATION MANAGEMENT SYSTEM (PIMS) COMMUNICATION V G ,c¶• PRINCIPAL INVESTIGATOR: Kathryn P...Performance Information Management System (PIMS) MIPR No. Communication 92MM2501 6. AUTHOR(S) Kathryn P. Winter 7. PERFORMING ORGANIZATION NAME(S) AND

EOS Data and Information System (EOSDIS). [landsat satellites

NASA Technical Reports Server (NTRS)

1992-01-01

In the past decade, science and technology have reached levels that permit assessments of global environmental change. Scientific success in understanding global environmental change depends on integration and management of numerous data sources. The Global Change Data and Information System (GCDIS) must provide for the management of data, information dissemination, and technology transfer. The Earth Observing System Data and Information System (EOSDIS) is NASA's portion of this global change information system.

Developing an information systems strategy for nursing.

PubMed

Callanan, K M; Hughes, S J

1995-01-01

With the rapidly changing health care environment and information technology advances, organizations need to engage in strategic, planned change in order to allocate limited resources, achieve the organization's goals, and fulfill its mission [1]. One of the most important aspects of the organization's planned strategies for change concerns the information systems. The involvement of the nursing department in this process is critical. This poster presentation will communicate how nurses can develop an information systems strategic plan that will enable them to play an active role as contributors and vital participants in the strategic and business planning processes for information systems. This information systems strategy for nursing will: a) provide direction and purpose, b) guide nursing in identifying the kinds of information technology needed, c) assist in timely implementation of a system that supports nursing, and d) identify desired outcomes and benefits of an information system. The nursing information systems plan must be built on, and support, the organization's mission and business plan and integrate into the over-all information systems plans [2]. Components of the nursing strategic plan include the nursing mission statement and vision, an assessment of the current environment to identify supporting technology needed to achieve the nursing vision, expectations/anticipated outcomes, environmental considerations, and special staffing/expertise considerations. The nursing vision and mission statement is an articulation of the overall direction and purpose of the nursing organization. An assessment of the nursing organization, problem areas, opportunities for growth, the physical environment, existing systems, communications requirements, and resources is carried out to help identify areas where new technologies and automated methods of managing information could be applied. Special staffing and expertise not currently available in the organization, but

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

PubMed Central

Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

2015-01-01

The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project. PMID:25988396

Technical Literature Review Concerning Management Information Systems.

DTIC Science & Technology

interrelationships of the many aspects of management information systems (MIS); that is, with how analysis, design, operation, evaluation, and user considerations affect management information systems . (Author)

Use of electronic information systems in nursing management.

PubMed

Lammintakanen, Johanna; Saranto, Kaija; Kivinen, Tuula

2010-05-01

The purpose of this study is to describe nurse managers' perceptions of the use of electronic information systems in their daily work. Several kinds of software are used for administrative and information management purposes in health care organizations, but the issue has been studied less from nurse managers' perspective. The material for this qualitative study was acquired according to the principles of focus group interview. Altogether eight focus groups were held with 48 nurse managers from both primary and specialized health care organizations. The nurse managers were asked in focus groups to describe the use of information systems in their daily work in addition to some other themes. The material was analyzed by inductive content analysis using ATLAS.ti computer program. The main category "pros and cons of using information systems in nursing management" summarized the nurse managers' perceptions of using electronic information systems. The main category consisted of three sub-categories: (1) nurse managers' perceptions of the use of information technology; (2) usability of management information systems; (3) development of personnel competencies and work processes. The nurse managers made several comments on the implementation of immature electronic information systems which caused inefficiencies in working processes. However, they considered electronic information systems to be essential elements of their daily work. Furthermore, the nurse managers' descriptions of the pros and cons of using information systems reflected partly the shortcomings of strategic management and lack of coordination in health care organizations. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

36 CFR 1192.35 - Public information system.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Public information system... Buses, Vans and Systems § 1192.35 Public information system. (a) Vehicles in excess of 22 feet in length, used in multiple-stop, fixed-route service, shall be equipped with a public address system permitting...

AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

PubMed Central

Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

2014-01-01

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php. PMID:24892935

AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

PubMed

Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

2014-01-01

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.

Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda.

PubMed

Wu, Shu; Xiong, Jie; Yu, Yuhe

2015-01-01

Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.

Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda