Quantifying biological integrity by taxonomic completeness: its utility in regional and global assessments.

Science.gov (United States)

Hawkins, Charles P

2006-08-01

Water resources managers and conservation biologists need reliable, quantitative, and directly comparable methods for assessing the biological integrity of the world's aquatic ecosystems. Large-scale assessments are constrained by the lack of consistency in the indicators used to assess biological integrity and our current inability to translate between indicators. In theory, assessments based on estimates of taxonomic completeness, i.e., the proportion of expected taxa that were observed (observed/expected, O/E) are directly comparable to one another and should therefore allow regionally and globally consistent summaries of the biological integrity of freshwater ecosystems. However, we know little about the true comparability of O/E assessments derived from different data sets or how well O/E assessments perform relative to other indicators in use. I compared the performance (precision, bias, and sensitivity to stressors) of O/E assessments based on five different data sets with the performance of the indicators previously applied to these data (three multimetric indices, a biotic index, and a hybrid method used by the state of Maine). Analyses were based on data collected from U.S. stream ecosystems in North Carolina, the Mid-Atlantic Highlands, Maine, and Ohio. O/E assessments resulted in very similar estimates of mean regional conditions compared with most other indicators once these indicators' values were standardized relative to reference-site means. However, other indicators tended to be biased estimators of O/E, a consequence of differences in their response to natural environmental gradients and sensitivity to stressors. These results imply that, in some cases, it may be possible to compare assessments derived from different indicators by standardizing their values (a statistical approach to data harmonization). In situations where it is difficult to standardize or otherwise harmonize two or more indicators, O/E values can easily be derived from existing

Exploring historical trends using taxonomic name metadata

Directory of Open Access Journals (Sweden)

Schenk Ryan

2008-05-01

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

19 CFR 10.532 - Integrated Sourcing Initiative.

Science.gov (United States)

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false Integrated Sourcing Initiative. 10.532 Section 10... Trade Agreement Rules of Origin § 10.532 Integrated Sourcing Initiative. (a) For purposes of General... Sourcing Initiative if: (1) The good, in its condition as imported, is both classified in a tariff...

Dual-Source Swept-Source Optical Coherence Tomography Reconstructed on Integrated Spectrum

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Shoude Chang

2012-01-01

Full Text Available Dual-source swept-source optical coherence tomography (DS-SSOCT has two individual sources with different central wavelengths, linewidth, and bandwidths. Because of the difference between the two sources, the individually reconstructed tomograms from each source have different aspect ratio, which makes the comparison and integration difficult. We report a method to merge two sets of DS-SSOCT raw data in a common spectrum, on which both data have the same spectrum density and a correct separation. The reconstructed tomographic image can seamlessly integrate the two bands of OCT data together. The final image has higher axial resolution and richer spectroscopic information than any of the individually reconstructed tomography image.

[Taxonomic theory for non-classical systematics].

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Pavlinov, I Ia

2012-01-01

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

The nutty world of hazel names - a crtitical taxonomic checklist of the genus Corylus (Betulaceae)

OpenAIRE

Holstein, Norbert; Tamer, Sarah el; Weigend, Maximilian

2018-01-01

Hazelnuts (Corylus L.) are the source of one of the globally most important nut crops. Despite their economic and cultural importance, taxonomic knowledge is poor, even the number of species is equivocal. Weak morphological differentiation, the inconsistent taxonomic treatment of horticultural selections and cultivars, and uncritical regional treatments generated a multitude of names. The situation is further complicated by an ancient history of use (at least 10 400 years), trade (at least 40...

Charting taxonomic knowledge through ontologies and ranking algorithms

Science.gov (United States)

Huber, Robert; Klump, Jens

2009-04-01

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

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

Energy Technology Data Exchange (ETDEWEB)

Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot, Casey M.; Young, Vincent B.; Jansson, Janet K.; Fredricks, David N.; Borenstein, Elhanan; Sanchez, Laura M.

2015-12-22

Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites’ abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in

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

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Zachary S L Foster

2017-02-01

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

The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis in the grasslands of Queensland, Australia.

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Jane Melville

Full Text Available Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora, which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1 revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

Science.gov (United States)

Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

2014-01-01

Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

C-188 cobalt-60 sealed source integrity: source monitoring

International Nuclear Information System (INIS)

Defalco, G.M.; Shah, V.

1995-01-01

The integrity of C-188 cobalt-60 sealed sources used for radiation processing will be a key factor in the continued industrial acceptance and growth of gamma irradiation technology. Given the public's relatively poor understanding of most nuclear topics and the news media's tendency to sensationalize events, it is appropriate for suppliers and users of gamma technology to be vigilant and conservative regarding the application of cobalt-60 sources to industrial purposes. Nordion's recent decision to extend the optional warranty on its C-188 cobalt-60 sealed source from 15 years to 20 years is based on over 30 years of data generated from its on-going SOURCE SURVEILLANCE PROGRAM. This paper presents an overview of the C-188 SOURCE SURVEILLANCE PROGRAM. (author)

Taxonomic names, metadata, and the Semantic Web

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Roderic D. M. Page

2006-01-01

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

Integration Of Data From Heterogeneous Sources Using Etl Technology.

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Marek Macura

2014-01-01

Full Text Available Data integration is a crucial issue in environments of heterogeneous data sources. At present mentioned heterogeneity is becoming widespread. Whenever, based on various data sources, we want to gain useful information and knowledge we must solve data integration problem in order to apply appropriate analytical methods on comprehensive and uniform data. Such activity is known as knowledge discovery from data process. Therefore approaches to data integration problem are very interesting and bring us closer to the "age of information". The paper presents an architecture, which implements knowledge discovery from data process. The solution combines ETL technology and wrapper layer known from mediated systems. It also provides semantic integration through connections mechanism between data elements. The solution allows for integration of any data sources and implementation of analytical methods in one environment. The proposed environment is verified by applying it to data sources on the foundry industry.

Taxonomic chauvinism revisited: insight from parental care research.

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Zachary R Stahlschmidt

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

Taxonomic chauvinism revisited: insight from parental care research.

Science.gov (United States)

Stahlschmidt, Zachary R

2011-01-01

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

A Falsification of the Citation Impediment in the Taxonomic Literature.

Science.gov (United States)

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

2015-09-01

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

Rectangular source integral and recurrence relations

International Nuclear Information System (INIS)

Prabha, Hem

2007-01-01

In this paper Hubbell's rectangular source integral H'(a,b), which is a double integral, is expressed as a series of many converging single integrals I n (a,b). Recurrence relations relate these integrals. Once one integral I 1 is computed, recurrence relations are used to compute other integrals. I 1 (a,b) can be computed analytically. H'(a,b) is approximated by considering the first seven terms in the series and the results are found to give good results for various values of a and b. Results are presented for the values of a and b (0.1 to 20 and to 2), respectively. The rate of convergence depends on the values of a and b

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

Science.gov (United States)

Hill, Robert V

2005-08-01

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

Learning models for multi-source integration

Energy Technology Data Exchange (ETDEWEB)

Tejada, S.; Knoblock, C.A.; Minton, S. [Univ. of Southern California/ISI, Marina del Rey, CA (United States)

1996-12-31

Because of the growing number of information sources available through the internet there are many cases in which information needed to solve a problem or answer a question is spread across several information sources. For example, when given two sources, one about comic books and the other about super heroes, you might want to ask the question {open_quotes}Is Spiderman a Marvel Super Hero?{close_quotes} This query accesses both sources; therefore, it is necessary to have information about the relationships of the data within each source and between sources to properly access and integrate the data retrieved. The SIMS information broker captures this type of information in the form of a model. All the information sources map into the model providing the user a single interface to multiple sources.

ISINA: INTEGRAL Source Identification Network Algorithm

Science.gov (United States)

Scaringi, S.; Bird, A. J.; Clark, D. J.; Dean, A. J.; Hill, A. B.; McBride, V. A.; Shaw, S. E.

2008-11-01

We give an overview of ISINA: INTEGRAL Source Identification Network Algorithm. This machine learning algorithm, using random forests, is applied to the IBIS/ISGRI data set in order to ease the production of unbiased future soft gamma-ray source catalogues. First, we introduce the data set and the problems encountered when dealing with images obtained using the coded mask technique. The initial step of source candidate searching is introduced and an initial candidate list is created. A description of the feature extraction on the initial candidate list is then performed together with feature merging for these candidates. Three training and testing sets are created in order to deal with the diverse time-scales encountered when dealing with the gamma-ray sky. Three independent random forests are built: one dealing with faint persistent source recognition, one dealing with strong persistent sources and a final one dealing with transients. For the latter, a new transient detection technique is introduced and described: the transient matrix. Finally the performance of the network is assessed and discussed using the testing set and some illustrative source examples. Based on observations with INTEGRAL, an ESA project with instruments and science data centre funded by ESA member states (especially the PI countries: Denmark, France, Germany, Italy, Spain), Czech Republic and Poland, and the participation of Russia and the USA. E-mail: simo@astro.soton.ac.uk

Comparison of Sewage and Animal Fecal Microbiomes by using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

Science.gov (United States)

Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but human and other animal gut microbiota contain an array of other taxonomic groups that might serve as indicators for sources of fecal pollution. High thr...

Hacia una Taxonomía Integral: poniendo a prueba especies candidatas relacionadas a Liolaemus buergeri Werner 1907 (Iguania: Liolaemini mediante análisis morfológicos

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Avila, Luciano Javier

2012-11-01

Full Text Available La taxonomía tradicional ha estado basada en caracteres de morfología externa o interna, delimitando morfo-especies. En los últimos años comenzó a desarrollarse la denominada taxonomía integral, con el objetivo de integrar los conceptos y métodos básicos de la taxonomía tradicional con nuevos conceptos y metodologías. Dentro de esta aproximación las especies son hipótesis, y las hipótesis de especies más estables, son aquellas avaladas por diferentes tipos de caracteres independientes. Liolaemus es el género de lagartijas con más número de especies de América austral, y dentro del mismo se han propuesto varios clados y complejos. Uno de ellos es el grupo kriegi, que incluye las especies L. buergeri, L. ceii y L. kriegi. En base a tres marcadores mitocondriales, se han propuesto como especies candidatas a tres taxa cercanamente relacionados a L. buergeri: L. sp. A, L. sp. B y L. sp. C. El objetivo de este trabajo es analizar las variaciones morfológicas entre los taxa propuestos y los individuos de la localidad tipo de L. buergeri, a fin de aportar una fuente de evidencia nueva e independiente al análisis de las hipótesis de especies propuestas para este grupo. Se estudiaron individuos de toda el área de distribución de L. buergeri y de las especies candidatas. Para cada ejemplar se registraron caracteres morfométricos, de escamación y el número de poros precloacales en machos. Se encontraron diferencias significativas entre los taxa para las variables analizadas, y se hallaron diferencias en el grado de dimorfismo sexual. Los resultados de estos análisis indican que los taxa candidatos se pueden diferenciar morfológicamente y por lo tanto apoyan, de manera independiente, las hipótesis de especies planteadas por el análisis de DNA mitocondrial. Traditional taxonomy has usually been based mainly on characters of external or internal morphology to delimit morpho-species. Recent years have seen the emergence of

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

International Nuclear Information System (INIS)

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

2006-01-01

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

On Hubbell's rectangular source integral

International Nuclear Information System (INIS)

Stalker, John

2001-01-01

The integral H(a,b)=∫ 0 b ∫ 0 a dx dy/(1+x 2 +y 2 ) arises naturally in the study of radiation from a rectangular source and has been studied by many authors. This paper introduces a new series expansion which is rapidly convergent for large a and b

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

Directory of Open Access Journals (Sweden)

Luis F Aguirre

Full Text Available Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups. Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for

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

Science.gov (United States)

Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

A Source Identification Algorithm for INTEGRAL

Science.gov (United States)

Scaringi, Simone; Bird, Antony J.; Clark, David J.; Dean, Anthony J.; Hill, Adam B.; McBride, Vanessa A.; Shaw, Simon E.

2008-12-01

We give an overview of ISINA: INTEGRAL Source Identification Network Algorithm. This machine learning algorithm, using Random Forests, is applied to the IBIS/ISGRI dataset in order to ease the production of unbiased future soft gamma-ray source catalogues. The key steps of candidate searching, filtering and feature extraction are described. Three training and testing sets are created in order to deal with the diverse timescales and diverse objects encountered when dealing with the gamma-ray sky. Three independent Random Forest are built: one dealing with faint persistent source recognition, one dealing with strong persistent sources and a final one dealing with transients. For the latter, a new transient detection technique is introduced and described: the Transient Matrix. Finally the performance of the network is assessed and discussed using the testing set and some illustrative source examples.

Current Taxonomical Situation of Streptococcus suis.

Science.gov (United States)

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

2016-06-24

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

Taxonomic bias in biodiversity data and societal preferences.

Science.gov (United States)

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

2017-08-22

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

Building integrated business environments: analysing open-source ESB

Science.gov (United States)

Martínez-Carreras, M. A.; García Jimenez, F. J.; Gómez Skarmeta, A. F.

2015-05-01

Integration and interoperability are two concepts that have gained significant prominence in the business field, providing tools which enable enterprise application integration (EAI). In this sense, enterprise service bus (ESB) has played a crucial role as the underpinning technology for creating integrated environments in which companies may connect all their legacy-applications. However, the potential of these technologies remains unknown and some important features are not used to develop suitable business environments. The aim of this paper is to describe and detail the elements for building the next generation of integrated business environments (IBE) and to analyse the features of ESBs as the core of this infrastructure. For this purpose, we evaluate how well-known open-source ESB products fulfil these needs. Moreover, we introduce a scenario in which the collaborative system 'Alfresco' is integrated in the business infrastructure. Finally, we provide a comparison of the different open-source ESBs available for IBE requirements. According to this study, Fuse ESB provides the best results, considering features such as support for a wide variety of standards and specifications, documentation and implementation, security, advanced business trends, ease of integration and performance.

Tau method approximation of the Hubbell rectangular source integral

International Nuclear Information System (INIS)

Kalla, S.L.; Khajah, H.G.

2000-01-01

The Tau method is applied to obtain expansions, in terms of Chebyshev polynomials, which approximate the Hubbell rectangular source integral:I(a,b)=∫ b 0 (1/(√(1+x 2 )) arctan(a/(√(1+x 2 )))) This integral corresponds to the response of an omni-directional radiation detector situated over a corner of a plane isotropic rectangular source. A discussion of the error in the Tau method approximation follows

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

Directory of Open Access Journals (Sweden)

Olivera Savic

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

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

Science.gov (United States)

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

2017-01-01

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

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae

Directory of Open Access Journals (Sweden)

Jessica Nayara Carvalho Francisco

2018-01-01

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

Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae).

Science.gov (United States)

Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G

2018-01-01

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

Integrating source-language context into phrase-based statistical machine translation

NARCIS (Netherlands)

Haque, R.; Kumar Naskar, S.; Bosch, A.P.J. van den; Way, A.

2011-01-01

The translation features typically used in Phrase-Based Statistical Machine Translation (PB-SMT) model dependencies between the source and target phrases, but not among the phrases in the source language themselves. A swathe of research has demonstrated that integrating source context modelling

All-source Information Management and Integration for Improved Collective Intelligence Production

Science.gov (United States)

2011-06-01

Intelligence (ELINT) • Open Source Intelligence ( OSINT ) • Technical Intelligence (TECHINT) These intelligence disciplines produce... intelligence , measurement and signature intelligence , signals intelligence , and open - source data, in the production of intelligence . All- source intelligence ...All- Source Information Integration and Management) R&D Project 3 All- Source Intelligence

Integrating an Automatic Judge into an Open Source LMS

Science.gov (United States)

Georgouli, Katerina; Guerreiro, Pedro

2011-01-01

This paper presents the successful integration of the evaluation engine of Mooshak into the open source learning management system Claroline. Mooshak is an open source online automatic judge that has been used for international and national programming competitions. although it was originally designed for programming competitions, Mooshak has also…

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

Science.gov (United States)

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

2017-01-01

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

Sources of capabilities, integration and technology commercialization

DEFF Research Database (Denmark)

Zahra, Shaker A.; Nielsen, Anders

2002-01-01

In recent years, companies have increased their use of internal and external sources in pursuit of a competitive advantage through the effective and timely commercialization of new technology. Grounded in the resource-based view of the firm, this study examines the effect of a company's use...... of internal and external sources on multiple dimensions of successful technology commercialization (TC). The study also explores the moderating role of formal vs. informal integration mechanisms on these relationships. Applying a longitudinal design and data from 119 companies, the results show that internal...

A Versatile Integrated Ambient Ionization Source Platform

Science.gov (United States)

Ai, Wanpeng; Nie, Honggang; Song, Shiyao; Liu, Xiaoyun; Bai, Yu; Liu, Huwei

2018-04-01

The pursuit of high-throughput sample analysis from complex matrix demands development of multiple ionization techniques with complementary specialties. A versatile integrated ambient ionization source (iAmIS) platform is proposed in this work, based on the idea of integrating multiple functions, enhancing the efficiency of current ionization techniques, extending the applications, and decreasing the cost of the instrument. The design of the iAmIS platform combines flowing atmospheric pressure afterglow (FAPA) source/direct analysis in real time (DART), dielectric barrier discharge ionization (DBDI)/low-temperature plasma (LTP), desorption electrospray ionization (DESI), and laser desorption (LD) technique. All individual and combined ionization modes can be easily attained by modulating parameters. In particular, the FAPA/DART&DESI mode can realize the detection of polar and nonpolar compounds at the same time with two different ionization mechanisms: proton transfer and charge transfer. The introduction of LD contributes to the mass spectrometry imaging and the surface-assisted laser desorption (SALDI) under ambient condition. Compared with other individual or multi-mode ion source, the iAmIS platform provides the flexibility of choosing different ionization modes, broadens the scope of the analyte detection, and facilitates the analysis of complex samples. [Figure not available: see fulltext.

Variance Component Selection With Applications to Microbiome Taxonomic Data

Directory of Open Access Journals (Sweden)

Jing Zhai

2018-03-01

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

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

DEFF Research Database (Denmark)

Sinniger, Frédéric; Pawlowski, Jan; Harii, Saki

2016-01-01

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

Integrated Photovoltaic System Used as an Alternative Power Source

Directory of Open Access Journals (Sweden)

Ionel Laurentiu Alboteanu

2014-09-01

Full Text Available This paper presents a solution to use solar energy as an alternative source of electricity to conventional sources. The solution is to use a compact photovoltaic system integrated into a micro smart grid. The studied photovoltaic system is used into concrete application for the power supply lighting in a didactic laboratory.

Open source integrated modeling environment Delta Shell

Science.gov (United States)

Donchyts, G.; Baart, F.; Jagers, B.; van Putten, H.

2012-04-01

In the last decade, integrated modelling has become a very popular topic in environmental modelling since it helps solving problems, which is difficult to model using a single model. However, managing complexity of integrated models and minimizing time required for their setup remains a challenging task. The integrated modelling environment Delta Shell simplifies this task. The software components of Delta Shell are easy to reuse separately from each other as well as a part of integrated environment that can run in a command-line or a graphical user interface mode. The most components of the Delta Shell are developed using C# programming language and include libraries used to define, save and visualize various scientific data structures as well as coupled model configurations. Here we present two examples showing how Delta Shell simplifies process of setting up integrated models from the end user and developer perspectives. The first example shows coupling of a rainfall-runoff, a river flow and a run-time control models. The second example shows how coastal morphological database integrates with the coastal morphological model (XBeach) and a custom nourishment designer. Delta Shell is also available as open-source software released under LGPL license and accessible via http://oss.deltares.nl.

An integrative taxonomic review of the agamid genus Bronchocela (Kuhl, 1820) from Peninsular Malaysia with descriptions of new montane and insular endemics.

Science.gov (United States)

Grismer, L Lee; Wood, P L; Lee, Cheol Haeng; Quah, Evan S H; Anuar, Shahrul; Ngadi, Ehwan; Sites, Jack W

2015-04-20

An integrative taxonomic analysis is used to identify and describe two new species of the agamid genus Bronchocela (Kuhl) from Peninsular Malaysia: an upland species B. shenlong sp. nov. from Bukit Larut, Perak in the Bintang Mountain Range and Parit Falls, Cameron Highlands, Pahang in the Titiwangsa Mountain Range and an insular species, B. rayaensis sp. nov., from Pulau Langkawi, Kedah off the northwest coast on the border with Thailand. Both species are diagnosed from each other and all other species of Bronchocela on the basis of body shape, scale morphology, and color pattern. The analysis also demonstrates the remarkable genetic similarity of B. cristatella (Kuhl) throughout 1120 km of its range from northern Peninsular Malaysia to western Borneo despite its highly variable coloration and pattern. The two new species are appended to a rapidly growing list of newly described lizard species (60 to date) from Peninsular Malaysia tallied within the last decade.

Conflicting but close: Readers' integration of information sources as a function of their disagreement.

Science.gov (United States)

Saux, Gaston; Britt, Anne; Le Bigot, Ludovic; Vibert, Nicolas; Burin, Debora; Rouet, Jean-François

2017-01-01

According to the documents model framework (Britt, Perfetti, Sandak, & Rouet, 1999), readers' detection of contradictions within texts increases their integration of source-content links (i.e., who says what). This study examines whether conflict may also strengthen the relationship between the respective sources. In two experiments, participants read brief news reports containing two critical statements attributed to different sources. In half of the reports, the statements were consistent with each other, whereas in the other half they were discrepant. Participants were tested for source memory and source integration in an immediate item-recognition task (Experiment 1) and a cued recall task (Experiments 1 and 2). In both experiments, discrepancies increased readers' memory for sources. We found that discrepant sources enhanced retrieval of the other source compared to consistent sources (using a delayed recall measure; Experiments 1 and 2). However, discrepant sources failed to prime the other source as evidenced in an online recognition measure (Experiment 1). We argue that discrepancies promoted the construction of links between sources, but that integration did not take place during reading.

The Role of CHP Plants in the Integration of Fluctuating Renewable Energy Sources

DEFF Research Database (Denmark)

Lund, Henrik

2002-01-01

The paper is an Expression of Interest to the European Commission about renewable energy sources and their integration in a energy system......The paper is an Expression of Interest to the European Commission about renewable energy sources and their integration in a energy system...

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

Science.gov (United States)

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa

Science.gov (United States)

Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

2015-01-01

The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation. PMID:25978319

Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

Directory of Open Access Journals (Sweden)

Julian Martin Corbelli

Full Text Available The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD, functional (FBD and phylogenetic (PBD facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants from two contrasting biomes (subtropical forest and grassland and land uses (tree plantations and cropfields in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland, and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation.

Integrated management of waterbirds: Beyond the conventional

Science.gov (United States)

Erwin, R.M.; Parsons, Katharine C.; Brown, Stephen C.; Erwin, R. Michael; Czech, Helen A.; Coulson, John C.

2002-01-01

Integrated waterbird management over the past few decades has implicitly referred to methods for managing wetlands that usually attempt to enhance habitat for taxonomic groups such as shorebirds and wading birds, in addition to waterfowl, the traditional focus group. Here I describe five elements of integration in management: taxonomic, spatial, temporal, population and habitat, and multiple-use management objectives. Spatial integration simply expands the scale of management concern. Rather than emphasizing management on a very limited number of impoundments or wetlands in small refuges or wildlife management areas, the vision is beginning to shift to connectivity within larger landscapes on the order of many square kilometers as telemetry data on daily and seasonal movements for many species become available. Temporal integration refers to the potential for either simultaneous management for waterbirds and commercial 'crops' (e.g., crayfish and rice) or for temporally-staggered management such as row crop production in spring-summer growing seasons and waterbird management on fallow fields in the non-growing (winter) season. Integrating population dynamics with habitats has become a major research focus over the past decade. Identifying which wetlands are ?sources? or ?sinks? for specific populations provides managers with critical information about effective management. Further, the applications of spatially explicit population models place heavy demands on researchers to identify use patterns for breeding and dispersing individuals by age, sex, and reproductive class. Population viability analysis models require much the same information. Finally, multiple-use management integration refers to trying to optimize the uses of wetlands, when only one (perhaps secondary) use may include waterbird management. Depending upon the ownership and primary land use of a particular parcel of land containing wetlands and/or water bodies, managing for waterbirds may be an

Global hotspots and correlates of alien species richness across taxonomic groups

Science.gov (United States)

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

2017-01-01

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

Integrating Philips' extreme UV source in the alpha-tools

Science.gov (United States)

Pankert, Joseph; Apetz, Rolf; Bergmann, Klaus; Derra, Guenther; Janssen, Maurice; Jonkers, Jeroen; Klein, Jurgen; Kruecken, Thomas; List, Andreas; Loeken, Michael; Metzmacher, Christof; Neff, Willi; Probst, Sven; Prummer, Ralph; Rosier, Oliver; Seiwert, Stefan; Siemons, Guido; Vaudrevange, Dominik; Wagemann, Dirk; Weber, Achim; Zink, Peter; Zitzen, Oliver

2005-05-01

The paper describes recent progress in the development of the Philips's EUV source. Progress has been realized at many frontiers: Integration studies of the source into a scanner have primarily been studied on the Xe source because it has a high degree of maturity. We report on integration with a collector, associated collector lifetime and optical characteristics. Collector lifetime in excess of 1 bln shots could be demonstrated. Next, an active dose control system was developed and tested on the Xe lamp. Resulting dose stability data are less than 0.2% for an exposure window of 100 pulses. The second part of the paper reports on progress in the development of the Philips' Sn source. First, the details of the concept are described. It is based on a Laser triggered vacuum arc, which is an extension with respect to previous designs. The source is furbished with rotating electrodes that are covered with a Sn film that is constantly regenerated. Hence by the very design of the source, it is scalable to very high power levels, and moreover has fundamentally solved the notorious problem of electrode erosion. Power values of 260 W in 2p sr are reported, along with a stable, long life operation of the lamp. The paper also addresses the problem of debris generation and mitigation of the Sn-source. The problem is attacked by a combined strategy of protection of the collector by traditional means (e.g. fields, foiltraps... ), and by designing the gas atmosphere according to the principles of the well known halogen cycles in incandescent lamps. These principles have been studied in the Lighting industry for decades and rely on the excessively high vapor pressures of metal halides. Transferred to the Sn source, it allows pumping away tin residues that would otherwise irreversibly deposit on the collector.

Evaluation of integrity of radiation sources of nuclear gauges

International Nuclear Information System (INIS)

Torohate, Wiclif Francisco

2016-01-01

Nuclear equipment meters are mainly used in the industry in quality control and process control. The principle of operation consists in a shielded radioactive source together with a radiation detector such that the radiation interacts with the material to be analyzed before reaching the detector, providing real time data. Can be as their fixed and mobile mobility, the unique properties of ionizing radiation are used in three basic modes, transmission, backscatter or dispersion or induced (reactive). With the advancement and technological modernization in the world, the demand for nuclear gauges becomes increasingly larger. Currently in Brazil there are about 465 process control plants and 21 portable systems and Mozambique about 45 facilities using nuclear gauges. This font registration is done through a process called source inventory that allows also to know the category of the source, the danger or risk to human health that the source offers. The handling of this equipment requires personnel, certified, skilled and well trained in radiation protection area in accordance with the requirements of the various CNEN Rules. Due to the presence of radioactive source and because these devices are used by workers risk because there external radiation. In this context, we made the smear test in two fixed meters from the IRD industry laboratory, which determines the integrity of the source package, mandatory item in periodic integrity testing of the radiation source of this type of device. A set of procedures is made for its implementation as an evaluation of the radiological risk by radiological survey. It was intended to contribute to the learning handling and safe use of these meters. (author)

ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications.

Science.gov (United States)

Lespinats, Sylvain; Fertil, Bernard

2011-01-01

Color may be very useful to visualise complex data. As far as taxonomy is concerned, color may help observing various species' characteristics in correlation with classification. However, choosing the number of subclasses to display is often a complex task: on the one hand, assigning a limited number of colors to taxa of interest hides the structure imbedded in the subtrees of the taxonomy; on the other hand, differentiating a high number of taxa by giving them specific colors, without considering the underlying taxonomy, may lead to unreadable results since relationships between displayed taxa would not be supported by the color code. In the present paper, an automatic color coding scheme is proposed to visualise the levels of taxonomic relationships displayed as overlay on any kind of data plot. To achieve this goal, a dimensionality reduction method allows displaying taxonomic "distances" onto a Euclidean two-dimensional space. The resulting map is projected onto a 2D color space (the Hue, Saturation, Brightness colorimetric space with brightness set to 1). Proximity in the taxonomic classification corresponds to proximity on the map and is therefore materialised by color proximity. As a result, each species is related to a color code showing its position in the taxonomic tree. The so called ColorPhylo displays taxonomic relationships intuitively and can be combined with any biological result. A Matlab version of ColorPhylo is available at http://sy.lespi.free.fr/ColorPhylo-homepage.html. Meanwhile, an ad-hoc distance in case of taxonomy with unknown edge lengths is proposed.

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

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Karfidova E.A.

2018-01-01

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

Economic dispatch optimization for system integrating renewable energy sources

Science.gov (United States)

Jihane, Kartite; Mohamed, Cherkaoui

2018-05-01

Nowadays, the use of energy is growing especially in transportation and electricity industries. However this energy is based on conventional sources which pollute the environment. Multi-source system is seen as the best solution to sustainable development. This paper proposes the Economic Dispatch (ED) of hybrid renewable power system. The hybrid system is composed of ten thermal generators, photovoltaic (PV) generator and wind turbine generator. To show the importance of renewable energy sources (RES) in the energy mix we have ran the simulation for system integrated PV only and PV plus wind. The result shows that the system with renewable energy sources (RES) is more compromising than the system without RES in terms of fuel cost.

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

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Kelvin Li

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

Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.

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Vineet K Sharma

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

Avibase – a database system for managing and organizing taxonomic concepts

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Denis Lepage

2014-06-01

Full Text Available Scientific names of biological entities offer an imperfect resolution of the concepts that they are intended to represent. Often they are labels applied to entities ranging from entire populations to individual specimens representing those populations, even though such names only unambiguously identify the type specimen to which they were originally attached. Thus the real-life referents of names are constantly changing as biological circumscriptions are redefined and thereby alter the sets of individuals bearing those names. This problem is compounded by other characteristics of names that make them ambiguous identifiers of biological concepts, including emendations, homonymy and synonymy. Taxonomic concepts have been proposed as a way to address issues related to scientific names, but they have yet to receive broad recognition or implementation. Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage. We present the on-line database Avibase as one possible approach to organizing taxonomic concepts. Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years. The use of taxonomic concepts in place of scientific names, coupled with efficient resolution services, is a major step toward addressing some of the main deficiencies in the current practices of scientific name dissemination and use.

Integrating a Traveling Wave Tube into an AECR-U ion source

Energy Technology Data Exchange (ETDEWEB)

Covo, Michel Kireeff; Benitez, Janilee Y.; Ratti, Alessandro; Vujic, Jasmina L.

2011-07-01

An RF system of 500W - 10.75 to 12.75 GHz was designed and integrated into the Advanced Electron Cyclotron Resonance - Upgrade (AECR-U) ion source of the 88-Inch Cyclotron at Lawrence Berkeley National Laboratory. The AECR-U produces ion beams for the Cyclotron giving large flexibility of ion species and charge states. The broadband frequency of a Traveling Wave Tube (TWT) allows modifying the volume that couples and heats the plasma. The TWT system design and integration with the AECR-U ion source and results from commissioning are presented.

Integrating open-source software applications to build molecular dynamics systems.

Science.gov (United States)

Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

2014-04-05

Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

Partitioning taxonomic diversity of aquatic insect assemblages ...

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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

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

Data.gov (United States)

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

A taxonomic revision of Lamium (Lamiaceae)

NARCIS (Netherlands)

Mennema, J.

1989-01-01

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

Taxonomic novelties in African Dracaena (Dracaenaceae)

NARCIS (Netherlands)

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

2018-01-01

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

Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri

Science.gov (United States)

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

2017-01-01

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

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

Science.gov (United States)

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

Using geographical and taxonomic metadata to set priorities in specimen digitization

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Walter G. Berendsohn

2010-10-01

Full Text Available Digitizing the information carried by specimens in natural history collections is a key endeavor providing falsifiable information about past and present biodiversity on a global scale, for application in a variety of research fields far beyond the current application in biosystematics. Existing digitization efforts are driven by individual institutional necessities and are not coordinated on a global scale. This led to an over-all information resource that is patchy in taxonomic and geographic coverage as well as in quality. Digitizing all specimens is not an achievable aim at present, so that priorities need to be set. Most biodiversity studies are both taxonomically and geographically restricted, but access to non-digitized collection information is almost exclusively by taxon name. Creating a “Geotaxonomic Index” providing metadata on the number of specimens from a specific geographic region belonging to a specific higher taxonomic category may provide a means to attract the attention of researchers and governments towards relevant non-digitized holdings of the collections and set priorities for their digitization according to the needs of information users outside the taxonomic community.

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

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Giuseppe MORABITO

2009-02-01

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

Two new integrable couplings of the soliton hierarchies with self-consistent sources

International Nuclear Information System (INIS)

Tie-Cheng, Xia

2010-01-01

A kind of integrable coupling of soliton equations hierarchy with self-consistent sources associated with s-tilde l(4) has been presented (Yu F J and Li L 2009 Appl. Math. Comput. 207 171; Yu F J 2008 Phys. Lett. A 372 6613). Based on this method, we construct two integrable couplings of the soliton hierarchy with self-consistent sources by using the loop algebra s-tilde l(4). In this paper, we also point out that there are some errors in these references and we have corrected these errors and set up new formula. The method can be generalized to other soliton hierarchy with self-consistent sources. (general)

Multi-scale functional and taxonomic β-diversity of the macroinvertebrate communities in a Mediterranean coastal lagoon

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D. CABANA

2017-03-01

Full Text Available Benthic macroinvertebrate communities form the basis of the intricate lagoonal food web. Understanding their functional and taxonomic response, from a β-diversity perspective, is essential to disclose underlying patterns with potential applicability in conservation and management actions. Within the central lagoon of Messolonghi we studied the main environmental components structuring the macroinvertebrate community. We analyzed the β-taxonomic and β-functional diversity across the main habitats and seasons, over a year time frame. Our results outline habitat type and vegetation biomass as the major factors structuring the communities. We found environmental variability to have a positive correlation with functional β-diversity, however no correlation was found with taxonomic β-diversity. Across the seasons an asynchronous response of the functional and taxonomic β-diversity was identified. The taxonomic composition displayed significant heterogeneity during the driest period and the functional during the rainy season. Across the habitats the unvegetated presented higher taxonomic homogeneity and functionally heterogeneity, contrary the vegetated habitats present higher taxonomic variability and functional homogeneity. Across the seasons and habitats a pattern of functional redundancy and taxonomic replacement was identified. Besides high functional turnover versus low taxonomic turnover was documented in an anthropogenic organically enriched habitat We conclude that habitats display independent functional and taxonomic seasonal patterns, thus different processes may contribute to their variability. The framework presented here highlights the importance of studying both β-diversity components framed in a multiscale approach to better understand ecological processes and variability patterns. These results are important to understand macroinvertebrate community assembly processes and are valuable for conservation purposes.

Source-Based Tasks in Writing Independent and Integrated Essays

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Javad Gholami

2017-07-01

Full Text Available Integrated writing tasks have gained considerable attention in ESL and EFL writing assessment and are frequently needed and used in academic settings and daily life. However, they are very rarely practiced and promoted in writing classes. This paper explored the effects of source-based writing practice on EFL learners’ composing abilities and investigated the probable differences between those tasks and independent writing ones in improving Iranian EFL learners’ essay writing abilities. To this end, a quasi-experimental design was implemented to gauge EFL learners’ writing improvements using a pretest-posttest layout. Twenty female learners taking a TOEFL iBT preparation course were randomly divided into an only-writing group with just independent writing instruction and essay practice, and a hybrid-writing-approach group receiving instruction and practice on independent writing plus source-based essay writing for ten sessions. Based on the findings, the participants with hybrid writing practice outperformed their counterparts in integrated essay tests. Their superior performance was not observed in the case of traditional independent writing tasks. The present study calls for incorporating more source-based writing tasks in writing courses.

Open Source GIS based integrated watershed management

Science.gov (United States)

Byrne, J. M.; Lindsay, J.; Berg, A. A.

2013-12-01

Optimal land and water management to address future and current resource stresses and allocation challenges requires the development of state-of-the-art geomatics and hydrological modelling tools. Future hydrological modelling tools should be of high resolution, process based with real-time capability to assess changing resource issues critical to short, medium and long-term enviromental management. The objective here is to merge two renowned, well published resource modeling programs to create an source toolbox for integrated land and water management applications. This work will facilitate a much increased efficiency in land and water resource security, management and planning. Following an 'open-source' philosophy, the tools will be computer platform independent with source code freely available, maximizing knowledge transfer and the global value of the proposed research. The envisioned set of water resource management tools will be housed within 'Whitebox Geospatial Analysis Tools'. Whitebox, is an open-source geographical information system (GIS) developed by Dr. John Lindsay at the University of Guelph. The emphasis of the Whitebox project has been to develop a user-friendly interface for advanced spatial analysis in environmental applications. The plugin architecture of the software is ideal for the tight-integration of spatially distributed models and spatial analysis algorithms such as those contained within the GENESYS suite. Open-source development extends knowledge and technology transfer to a broad range of end-users and builds Canadian capability to address complex resource management problems with better tools and expertise for managers in Canada and around the world. GENESYS (Generate Earth Systems Science input) is an innovative, efficient, high-resolution hydro- and agro-meteorological model for complex terrain watersheds developed under the direction of Dr. James Byrne. GENESYS is an outstanding research and applications tool to address

Human impacts on functional and taxonomic homogenization of plateau fish assemblages in Yunnan, China

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Guohuan Su

2015-07-01

Full Text Available Human activities and the consequent extinctions of native species and invasions of non-native species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. However, much of the research effort to date has focused on changes in taxonomic dissimilarity (i.e. accounting for species composition whether assessments of functional dissimilarity (i.e. accounting for the diversity of biological traits are much more scarce, despite revealing important complimentary information by accounting for changes in the diversity of biological traits. Here, we assess the temporal (1950s against 2000s changes in both taxonomic and functional dissimilarities of freshwater fish assemblages across lakes from the Yunnan Plateau in China. The Jaccard index to quantify the changes in both taxonomic and functional dissimilarity. We then partitioned dissimilarity to extract its turnover component and measured the changes in the contribution of turnover to dissimilarity. We found that functional and taxonomic homogenization occurred simultaneously. However, patterns between these two processes differed for some lakes. Taxonomic and functional homogenizations were stronger when the historical level of taxonomic dissimilarity among assemblages was high. The impact of extinctions of native species and invasions of non-native species on homogenization was otherwise complex to disentangle with no significant effect of any of the studied environmental factors. In agreement with other studies, our study proved that change in taxonomic dissimilarity cannot be used to predict changes in functional dissimilarity and, as an indicator of ecosystem functioning, functional dissimilarity should be used together with taxonomic dissimilarity to attain a more holistic understanding of human impacts on natural ecosystems.

Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae with descriptions of three new species from Peru

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Cesar Aguilar

2013-12-01

Full Text Available Species delimitation studies based on integrative taxonomic approaches have received considerable attention in the last few years, and have provided the strongest hypotheses of species boundaries. We used three lines of evidence (molecular, morphological, and niche envelopes to test for species boundaries in Peruvian populations of the Liolaemus walkeri complex. Our results show that different lines of evidence and analyses are congruent in different combinations, for unambiguous delimitation of three lineages that were “hidden” within known species, and now deserve species status. Our phylogenetic analysis shows that L. walkeri, L. tacnae and the three new species are strongly separated from other species assigned to the alticolor-bibronii group. Few conventional morphological characters distinguish the new species from closely related taxa and this highlights the need to integrate other sources of data to erect strong hypothesis of species limits. A taxonomic key for known Peruvian species of the subgenus Lioalemus is provided.

Path-integral method for the source apportionment of photochemical pollutants

Science.gov (United States)

Dunker, A. M.

2015-06-01

A new, path-integral method is presented for apportioning the concentrations of pollutants predicted by a photochemical model to emissions from different sources. A novel feature of the method is that it can apportion the difference in a species concentration between two simulations. For example, the anthropogenic ozone increment, which is the difference between a simulation with all emissions present and another simulation with only the background (e.g., biogenic) emissions included, can be allocated to the anthropogenic emission sources. The method is based on an existing, exact mathematical equation. This equation is applied to relate the concentration difference between simulations to line or path integrals of first-order sensitivity coefficients. The sensitivities describe the effects of changing the emissions and are accurately calculated by the decoupled direct method. The path represents a continuous variation of emissions between the two simulations, and each path can be viewed as a separate emission-control strategy. The method does not require auxiliary assumptions, e.g., whether ozone formation is limited by the availability of volatile organic compounds (VOCs) or nitrogen oxides (NOx), and can be used for all the species predicted by the model. A simplified configuration of the Comprehensive Air Quality Model with Extensions (CAMx) is used to evaluate the accuracy of different numerical integration procedures and the dependence of the source contributions on the path. A Gauss-Legendre formula using three or four points along the path gives good accuracy for apportioning the anthropogenic increments of ozone, nitrogen dioxide, formaldehyde, and nitric acid. Source contributions to these increments were obtained for paths representing proportional control of all anthropogenic emissions together, control of NOx emissions before VOC emissions, and control of VOC emissions before NOx emissions. There are similarities in the source contributions from the

How to Integrate Variable Power Source into a Power Grid

Science.gov (United States)

Asano, Hiroshi

This paper discusses how to integrate variable power source such as wind power and photovoltaic generation into a power grid. The intermittent renewable generation is expected to penetrate for less carbon intensive power supply system, but it causes voltage control problem in the distribution system, and supply-demand imbalance problem in a whole power system. Cooperative control of customers' energy storage equipment such as water heater with storage tank for reducing inverse power flow from the roof-top PV system, the operation technique using a battery system and the solar radiation forecast for stabilizing output of variable generation, smart charging of plug-in hybrid electric vehicles for load frequency control (LFC), and other methods to integrate variable power source with improving social benefits are surveyed.

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

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Eric W. Triplett

2010-07-01

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

Developing green supply chain management strategies: A taxonomic approach

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Michael Mutingi

2013-06-01

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

Golden Ratio Versus Pi as Random Sequence Sources for Monte Carlo Integration

Science.gov (United States)

Sen, S. K.; Agarwal, Ravi P.; Shaykhian, Gholam Ali

2007-01-01

We discuss here the relative merits of these numbers as possible random sequence sources. The quality of these sequences is not judged directly based on the outcome of all known tests for the randomness of a sequence. Instead, it is determined implicitly by the accuracy of the Monte Carlo integration in a statistical sense. Since our main motive of using a random sequence is to solve real world problems, it is more desirable if we compare the quality of the sequences based on their performances for these problems in terms of quality/accuracy of the output. We also compare these sources against those generated by a popular pseudo-random generator, viz., the Matlab rand and the quasi-random generator ha/ton both in terms of error and time complexity. Our study demonstrates that consecutive blocks of digits of each of these numbers produce a good random sequence source. It is observed that randomly chosen blocks of digits do not have any remarkable advantage over consecutive blocks for the accuracy of the Monte Carlo integration. Also, it reveals that pi is a better source of a random sequence than theta when the accuracy of the integration is concerned.

IDENTIFICATIONS OF FIVE INTEGRAL SOURCES VIA OPTICAL SPECTROSCOPY

International Nuclear Information System (INIS)

Butler, Suzanne C.; Tomsick, John A.; Chaty, Sylvain; Heras, Juan A. Zurita; Rodriguez, Jerome; Walter, Roland; Kaaret, Philip; Kalemci, Emrah; Oezbey, Mehtap

2009-01-01

The International Gamma-Ray Astrophysics Laboratory (INTEGRAL) is discovering hundreds of new hard X-ray sources, many of which remain unidentified. We report on optical spectroscopy of five such sources for which X-ray observations at lower energies (∼0.5-10 keV) and higher angular resolutions than INTEGRAL have allowed for unique optical counterparts to be located. We find that INTEGRAL Gamma-Ray (IGR) J16426+6536 and IGR J22292+6647 are Type 1 Seyfert active galactic nuclei (with IGR J16426+6536 further classified as a Seyfert 1.5) which have redshifts of z = 0.323 and z = 0.113, respectively. IGR J18308-1232 is identified as a cataclysmic variable (CV), and we confirm a previous identification of IGR J19267+1325 as a magnetic CV. IGR J18214-1318 is identified as an obscured high-mass X-ray binary (HMXB), which are systems thought to have a compact object embedded in the stellar wind of a massive star. We combine Chandra fluxes with distances based on the optical observations to calculate X-ray luminosities of the HMXB and CVs, finding L 0.3-10keV = 5 x 10 36 erg s -1 for IGR J18214-1318, L 0.3-10keV = 1.3 x 10 32 erg s -1 for IGR J18308-1232, and L 0.3-10keV = 6.7 x 10 32 erg s -1 for IGR J19267+1325.

The taxlist package: managing plant taxonomic lists in R

Directory of Open Access Journals (Sweden)

Miguel Alvarez

2018-05-01

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

Total luminous flux measurement for flexible surface sources with an integrating sphere photometer

International Nuclear Information System (INIS)

Yu, Hsueh-Ling; Liu, Wen-Chun

2014-01-01

Applying an integrating sphere photometer for total luminous flux measurement is a widely used method. However, the measurement accuracy depends on the spatial uniformity of the integrating sphere, especially when the test sample has a different light distribution from that of the standard source. Therefore, spatial correction is needed to eliminate the effect caused by non-uniformity. To reduce the inconvenience of spatial correction but retain the measurement accuracy, a new type of working standard is designed for flexible and curved surface sources. Applying this new type standard source, the measurement deviation due to different orientations is reduced by an order of magnitude compared with using a naked incandescent lamp as the standard source. (paper)

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

Directory of Open Access Journals (Sweden)

Roelof Maarten evan Dijk

2016-03-01

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

Semantic integration of gene expression analysis tools and data sources using software connectors

Science.gov (United States)

2013-01-01

Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools

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

Science.gov (United States)

Haig, Susan M; Beever, Erik A; Chambers, Steven M; Draheim, Hope M; Dugger, Bruce D; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B; Kesler, Dylan C; Knaus, Brian J; Lopes, Iara F; Loschl, Pete; Mullins, Thomas D; Sheffield, Lisa M

2006-12-01

The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

Integrated societal risk assessment framework for nuclear power and renewable energy sources

International Nuclear Information System (INIS)

Lee, Sang Hun; Kang, Hyun Gook

2015-01-01

Recently, the estimation of the social cost of energy sources has been emphasized as various novel energy options become feasible in addition to conventional ones. In particular, the social cost of introducing measures to protect power-distribution systems from power-source instability and the cost of accident-risk response for various power sources must be investigated. To account for these risk factors, an integrated societal risk assessment framework, based on power-uncertainty analysis and accident-consequence analysis, is proposed. In this study, we applied the proposed framework to nuclear power plants, solar photovoltaic systems, and wind-turbine generators. The required capacity of gas-turbine power plants to be used as backup power facilities to compensate for fluctuations in the power output from the main power source was estimated based on the performance indicators of each power source. The average individual health risk per terawatt-hours (TWh) of electricity produced by each power source was quantitatively estimated by assessing accident frequency and the consequences of specific accident scenarios based on the probabilistic risk assessment methodology. This study is expected to provide insight into integrated societal risk analysis, and can be used to estimate the social cost of various power sources

Integrated societal risk assessment framework for nuclear power and renewable energy sources

Energy Technology Data Exchange (ETDEWEB)

Lee, Sang Hun; Kang, Hyun Gook [Dept. of Nuclear and Quantum Engineering, KAIST, Daejeon (Korea, Republic of)

2015-06-15

Recently, the estimation of the social cost of energy sources has been emphasized as various novel energy options become feasible in addition to conventional ones. In particular, the social cost of introducing measures to protect power-distribution systems from power-source instability and the cost of accident-risk response for various power sources must be investigated. To account for these risk factors, an integrated societal risk assessment framework, based on power-uncertainty analysis and accident-consequence analysis, is proposed. In this study, we applied the proposed framework to nuclear power plants, solar photovoltaic systems, and wind-turbine generators. The required capacity of gas-turbine power plants to be used as backup power facilities to compensate for fluctuations in the power output from the main power source was estimated based on the performance indicators of each power source. The average individual health risk per terawatt-hours (TWh) of electricity produced by each power source was quantitatively estimated by assessing accident frequency and the consequences of specific accident scenarios based on the probabilistic risk assessment methodology. This study is expected to provide insight into integrated societal risk analysis, and can be used to estimate the social cost of various power sources.

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

Science.gov (United States)

Khalturin, Konstantin; Hemmrich, Georg; Fraune, Sebastian; Augustin, René; Bosch, Thomas C G

2009-09-01

Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.

Neuronal integration of dynamic sources: Bayesian learning and Bayesian inference.

Science.gov (United States)

Siegelmann, Hava T; Holzman, Lars E

2010-09-01

One of the brain's most basic functions is integrating sensory data from diverse sources. This ability causes us to question whether the neural system is computationally capable of intelligently integrating data, not only when sources have known, fixed relative dependencies but also when it must determine such relative weightings based on dynamic conditions, and then use these learned weightings to accurately infer information about the world. We suggest that the brain is, in fact, fully capable of computing this parallel task in a single network and describe a neural inspired circuit with this property. Our implementation suggests the possibility that evidence learning requires a more complex organization of the network than was previously assumed, where neurons have different specialties, whose emergence brings the desired adaptivity seen in human online inference.

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.

Science.gov (United States)

Dryden, Michael D M; Wheeler, Aaron R

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.

Directory of Open Access Journals (Sweden)

Michael D M Dryden

Full Text Available Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat, an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously, and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.

Evaluated Rayleigh integrals for pulsed planar expanding ring sources

International Nuclear Information System (INIS)

Warshaw, S.I.

1985-01-01

Time-domain analytic and semianalytic pressure fields acoustically radiated from expanding pulsed ring sources imbedded in a planar rigid baffle have been calculated. The source functions are radially symmetric delta-function distributions whose amplitude and argument have simple functional dependencies on radius and time. Certain cases yield closed analytic results, while others result in elliptic integrals, which are evaluated to high accuracy by Gauss-Chebyshev and modified Gauss-Legendre quadrature. These results are of value for calibrating computer simulations and convolution procedures, and estimating fields from more complex planar radiators. 3 refs., 4 figs

Comparison of methods for the identification and sub-typing of O157 and non-O157 Escherichia coli serotypes and their integration into a polyphasic taxonomy approach

Directory of Open Access Journals (Sweden)

Prieto-Calvo M.A.

2016-12-01

Full Text Available Phenotypic, chemotaxonomic and genotypic data from 12 strains of Escherichia coli were collected, including carbon source utilisation profiles, ribotypes, sequencing data of the 16S–23S rRNA internal transcribed region (ITS and Fourier transform-infrared (FT-IR spectroscopic profiles. The objectives were to compare several identification systems for E. coli and to develop and test a polyphasic taxonomic approach using the four methodologies combined for the sub-typing of O157 and non-O157 E. coli. The nucleotide sequences of the 16S–23S rRNA ITS regions were amplified by polymerase chain reaction (PCR, sequenced and compared with reference data available at the GenBank database using the Basic Local Alignment Search Tool (BLAST . Additional information comprising the utilisation of carbon sources, riboprint profiles and FT-IR spectra was also collected. The capacity of the methods for the identification and typing of E. coli to species and subspecies levels was evaluated. Data were transformed and integrated to present polyphasic hierarchical clusters and relationships. The study reports the use of an integrated scheme comprising phenotypic, chemotaxonomic and genotypic information (carbon source profile, sequencing of the 16S–23S rRNA ITS, ribotyping and FT-IR spectroscopy for a more precise characterisation and identification of E. coli. The results showed that identification of E. coli strains by each individual method was limited mainly by the extension and quality of reference databases. On the contrary, the polyphasic approach, whereby heterogeneous taxonomic data were combined and weighted, improved the identification results, gave more consistency to the final clustering and provided additional information on the taxonomic structure and phenotypic behaviour of strains, as shown by the close clustering of strains with similar stress resistance patterns.

Integrated bird conservation web site in the United States

Science.gov (United States)

Roxanne Bogart; Chris Eberly; Elizabeth Martin

2005-01-01

In working towards a vision of integrated bird conservation, scientists, conservationists, land managers, and administrators are faced with a variety of scientific, managerial, administrative, and logistical challenges and complexities. The broad scope of integrated bird conservation requires organizations to work together to conserve birds across taxonomic groups,...

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

DEFF Research Database (Denmark)

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

2004-01-01

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

Korean deaf adolescents' recognition of written words for taxonomic categories of different levels.

Science.gov (United States)

Li, Degao; Yi, Kwangoh; Kim, Jung Yeon

2011-04-01

Deaf college students seem to have relatively stronger associations from words for taxonomic categories of basic (e.g., snake) to those of super-ordinate (e.g., reptiles) level than vice versa compared with hearing students in word association (Marschark, Convertino, McEvoy & Masteller, 2004). In deciding whether two sequentially presented words for taxonomic categories of different levels are conceptually related, deaf adolescents might therefore have a poorer performance when they see a category name before than when they see it after one of the corresponding exemplar words. Deaf Korean adolescents were found to recognize words for taxonomic categories of super-ordinate level with lower efficiencies than those of basic level. Their accuracy seemed to reflect a reversed typicality effect when they decided that first-presented words for taxonomic categories of basic level were conceptually related to second-presented words for those of super-ordinate level. It was argued that deaf Korean adolescents went through a temporary stage of having iconic representations of several exemplars of the category aroused in working memory before the abstract semantic representation was fully activated when they saw the word for a taxonomic category of super-ordinate level. © 2010 The Authors. Scandinavian Journal of Psychology © 2010 The Scandinavian Psychological Associations.

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

Science.gov (United States)

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

2014-04-01

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

Seasonality, distribution and taxonomic status of avian ...

African Journals Online (AJOL)

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

An integrative framework to reevaluate the Neotropical catfish genus Guyanancistrus (Siluriformes: Loricariidae) with particular emphasis on the Guyanancistrus brevispinis complex.

Science.gov (United States)

Fisch-Muller, Sonia; Mol, Jan H A; Covain, Raphaël

2018-01-01

Characterizing and naming species becomes more and more challenging due to the increasing difficulty of accurately delineating specific bounderies. In this context, integrative taxonomy aims to delimit taxonomic units by leveraging the complementarity of multiple data sources (geography, morphology, genetics, etc.). However, while the theoretical framework of integrative taxonomy has been explicitly stated, methods for the simultaneous analysis of multiple data sets are poorly developed and in many cases different information sources are still explored successively. Multi-table methods developed in the field of community ecology provide such an intregrative framework. In particular, multiple co-inertia analysis is flexible enough to allow the integration of morphological, distributional, and genetic data in the same analysis. We have applied this powerfull approach to delimit species boundaries in a group of poorly differentiated catfishes belonging to the genus Guyanancistrus from the Guianas region of northeastern South America. Because the species G. brevispinis has been claimed to be a species complex consisting of five species, particular attention was paid to taxon. Separate analyses indicated the presence of eight distinct species of Guyanancistrus, including five new species and one new genus. However, none of the preliminary analyses revealed different lineages within G. brevispinis, and the multi-table analysis revealed three intraspecific lineages. After taxonomic clarifications and description of the new genus, species and subspecies, a reappraisal of the biogeography of Guyanancistrus members was performed. This analysis revealed three distinct dispersals from the Upper reaches of Amazonian tributaries toward coastal rivers of the Eastern Guianas Ecoregion. The central role played by the Maroni River, as gateway from the Amazon basin, was confirmed. The Maroni River was also found to be a center of speciation for Guyanancistrus (with three species and

Integrated societal risk assessment framework for nuclear power and renewable energy sources

Directory of Open Access Journals (Sweden)

Sang Hun Lee

2015-06-01

Full Text Available Recently, the estimation of the social cost of energy sources has been emphasized as various novel energy options become feasible in addition to conventional ones. In particular, the social cost of introducing measures to protect power-distribution systems from power-source instability and the cost of accident-risk response for various power sources must be investigated. To account for these risk factors, an integrated societal risk assessment framework, based on power-uncertainty analysis and accident-consequence analysis, is proposed. In this study, we applied the proposed framework to nuclear power plants, solar photovoltaic systems, and wind-turbine generators. The required capacity of gas-turbine power plants to be used as backup power facilities to compensate for fluctuations in the power output from the main power source was estimated based on the performance indicators of each power source. The average individual health risk per terawatt-hours (TWh of electricity produced by each power source was quantitatively estimated by assessing accident frequency and the consequences of specific accident scenarios based on the probabilistic risk assessment methodology. This study is expected to provide insight into integrated societal risk analysis, and can be used to estimate the social cost of various power sources.

INTEGRAL discovery of a new transient source: IGR J16374-5043

DEFF Research Database (Denmark)

Pavan, L.; Terrier, R.; Bozzo, E.

2010-01-01

During the INTEGRAL observations of RX J1713.7-3946 (PI R. Terrier), performed between 2010-08-21 03:39 and 2010-08-23 12:03, a new transient source was discovered by the soft gamma-ray imager IBIS/ISGRI (17-300 keV). The source is detected at a significance level of 10 sigma in the 20-40 keV ene...

Integration of relational and textual biomedical sources. A pilot experiment using a semi-automated method for logical schema acquisition.

Science.gov (United States)

García-Remesal, M; Maojo, V; Billhardt, H; Crespo, J

2010-01-01

Bringing together structured and text-based sources is an exciting challenge for biomedical informaticians, since most relevant biomedical sources belong to one of these categories. In this paper we evaluate the feasibility of integrating relational and text-based biomedical sources using: i) an original logical schema acquisition method for textual databases developed by the authors, and ii) OntoFusion, a system originally designed by the authors for the integration of relational sources. We conducted an integration experiment involving a test set of seven differently structured sources covering the domain of genetic diseases. We used our logical schema acquisition method to generate schemas for all textual sources. The sources were integrated using the methods and tools provided by OntoFusion. The integration was validated using a test set of 500 queries. A panel of experts answered a questionnaire to evaluate i) the quality of the extracted schemas, ii) the query processing performance of the integrated set of sources, and iii) the relevance of the retrieved results. The results of the survey show that our method extracts coherent and representative logical schemas. Experts' feedback on the performance of the integrated system and the relevance of the retrieved results was also positive. Regarding the validation of the integration, the system successfully provided correct results for all queries in the test set. The results of the experiment suggest that text-based sources including a logical schema can be regarded as equivalent to structured databases. Using our method, previous research and existing tools designed for the integration of structured databases can be reused - possibly subject to minor modifications - to integrate differently structured sources.

Integration and Optimization of Alternative Sources of Energy in a Remote Region

Science.gov (United States)

Berberi, Pellumb; Inodnorjani, Spiro; Aleti, Riza

2010-01-01

In a remote coastal region supply of energy from national grid is insufficient for a sustainable development. Integration and optimization of local alternative renewable energy sources is an optional solution of the problem. In this paper we have studied the energetic potential of local sources of renewable energy (water, solar, wind and biomass). A bottom-up energy system optimization model is proposed in order to support planning policies for promoting the use of renewable energy sources. A software, based on multiple factors and constrains analysis for optimization energy flow is proposed, which provides detailed information for exploitation each source of energy, power and heat generation, GHG emissions and end-use sectors. Economical analysis shows that with existing technologies both stand alone and regional facilities may be feasible. Improving specific legislation will foster investments from Central or Local Governments and also from individuals, private companies or small families. The study is carried on the frame work of a FP6 project "Integrated Renewable Energy System."

Integrated source of broadband quadrature squeezed light

DEFF Research Database (Denmark)

Hoff, Ulrich Busk; Nielsen, Bo Melholt; Andersen, Ulrik Lund

2015-01-01

An integrated silicon nitride resonator is proposed as an ultracompact source of bright single-mode quadrature squeezed light at 850 nm. Optical properties of the device are investigated and tailored through numerical simulations, with particular attention paid to loss associated with interfacing...... the device. An asymmetric double layer stack waveguide geometry with inverse vertical tapers is proposed for efficient and robust fibre-chip coupling, yielding a simulated total loss of -0.75 dB/facet. We assess the feasibility of the device through a full quantum noise analysis and derive the output...

Taxonomically restricted genes are associated with the evolution of sociality in the honey bee

Directory of Open Access Journals (Sweden)

Tsutsui Neil D

2011-03-01

Full Text Available Abstract Background Studies have shown that taxonomically restricted genes are significant in number and important for the evolution of lineage specific traits. Social insects have gained many novel morphological and behavioral traits relative to their solitary ancestors. The task repertoire of an advanced social insect, for example, can be 40-50 tasks, about twice that of a solitary wasp or bee. The genetic basis of this expansion in behavioral repertoire is still poorly understood, and a role for taxonomically restricted genes has not been explored at the whole genome level. Results Here we present comparative genomics results suggesting that taxonomically restricted genes may have played an important role in generating the expansion of behavioral repertoire associated with the evolution of eusociality. First, we show that the current honey bee official gene set contains about 700 taxonomically restricted genes. These are split between orphans, genes found only in the Hymenoptera, and genes found only in insects. Few of the orphans or genes restricted to the Hymenoptera have been the focus of experimental work, but several of those that have are associated with novel eusocial traits or traits thought to have changed radically as a consequence of eusociality. Second, we predicted that if taxonomically restricted genes are important for generating novel eusocial traits, then they should be expressed with greater frequency in workers relative to the queen, as the workers exhibit most of the novel behavior of the honey bee relative to their solitary ancestors. We found support for this prediction. Twice as many taxonomically restricted genes were found amongst the genes with higher expression in workers compared to those with higher expression in queens. Finally, we compiled an extensive list of candidate taxonomically restricted genes involved in eusocial evolution by analyzing several caste specific gene expression data sets. Conclusions This

Integration of asynchronous knowledge sources in a novel speech recognition framework

OpenAIRE

Van hamme, Hugo

2008-01-01

Van hamme H., ''Integration of asynchronous knowledge sources in a novel speech recognition framework'', Proceedings ITRW on speech analysis and processing for knowledge discovery, 4 pp., June 2008, Aalborg, Denmark.

Carbon Sources for Polyhydroxyalkanoates and an Integrated Biorefinery

Directory of Open Access Journals (Sweden)

Guozhan Jiang

2016-07-01

Full Text Available Polyhydroxyalkanoates (PHAs are a group of bioplastics that have a wide range of applications. Extensive progress has been made in our understanding of PHAs’ biosynthesis, and currently, it is possible to engineer bacterial strains to produce PHAs with desired properties. The substrates for the fermentative production of PHAs are primarily derived from food-based carbon sources, raising concerns over the sustainability of their production in terms of their impact on food prices. This paper gives an overview of the current carbon sources used for PHA production and the methods used to transform these sources into fermentable forms. This allows us to identify the opportunities and restraints linked to future sustainable PHA production. Hemicellulose hydrolysates and crude glycerol are identified as two promising carbon sources for a sustainable production of PHAs. Hemicellulose hydrolysates and crude glycerol can be produced on a large scale during various second generation biofuels’ production. An integration of PHA production within a modern biorefinery is therefore proposed to produce biofuels and bioplastics simultaneously. This will create the potential to offset the production cost of biofuels and reduce the overall production cost of PHAs.

Carbon Sources for Polyhydroxyalkanoates and an Integrated Biorefinery.

Science.gov (United States)

Jiang, Guozhan; Hill, David J; Kowalczuk, Marek; Johnston, Brian; Adamus, Grazyna; Irorere, Victor; Radecka, Iza

2016-07-19

Polyhydroxyalkanoates (PHAs) are a group of bioplastics that have a wide range of applications. Extensive progress has been made in our understanding of PHAs' biosynthesis, and currently, it is possible to engineer bacterial strains to produce PHAs with desired properties. The substrates for the fermentative production of PHAs are primarily derived from food-based carbon sources, raising concerns over the sustainability of their production in terms of their impact on food prices. This paper gives an overview of the current carbon sources used for PHA production and the methods used to transform these sources into fermentable forms. This allows us to identify the opportunities and restraints linked to future sustainable PHA production. Hemicellulose hydrolysates and crude glycerol are identified as two promising carbon sources for a sustainable production of PHAs. Hemicellulose hydrolysates and crude glycerol can be produced on a large scale during various second generation biofuels' production. An integration of PHA production within a modern biorefinery is therefore proposed to produce biofuels and bioplastics simultaneously. This will create the potential to offset the production cost of biofuels and reduce the overall production cost of PHAs.

Taxonomic Challenges and Distribution of Gracilarioid Algae ...

African Journals Online (AJOL)

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

Compact Integrated DBR Laser Source for Absorption Lidar Instruments, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — We propose to demonstrate a compact integrated laser module that addresses the requirements of the laser source in a water vapor differential absorption lidar (DIAL)...

Taxonomic and functional composition of arthropod assemblages across contrasting Amazonian forests.

Science.gov (United States)

Lamarre, Greg P A; Hérault, Bruno; Fine, Paul V A; Vedel, Vincent; Lupoli, Roland; Mesones, Italo; Baraloto, Christopher

2016-01-01

Arthropods represent most of global biodiversity, with the highest diversity found in tropical rain forests. Nevertheless, we have a very incomplete understanding of how tropical arthropod communities are assembled. We conducted a comprehensive mass sampling of arthropod communities within three major habitat types of lowland Amazonian rain forest, including terra firme clay, white-sand and seasonally flooded forests in Peru and French Guiana. We examined how taxonomic and functional composition (at the family level) differed across these habitat types in the two regions. The overall arthropod community composition exhibited strong turnover among habitats and between regions. In particular, seasonally flooded forest habitats of both regions comprised unique assemblages. Overall, 17·7% (26 of 147) of arthropod families showed significant preferences for a particular habitat type. We present a first reproducible arthropod functional classification among the 147 taxa based on similarity among 21 functional traits describing feeding source, major mouthparts and microhabitats inhabited by each taxon. We identified seven distinct functional groups whose relative abundance contrasted strongly across the three habitats, with sap and leaf feeders showing higher abundances in terra firme clay forest. Our novel arthropod functional classification provides an important complement to link these contrasting patterns of composition to differences in forest functioning across geographical and environmental gradients. This study underlines that both environment and biogeographical processes are responsible for driving arthropod taxonomic composition while environmental filtering is the main driver of the variance in functional composition. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

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

Science.gov (United States)

Clarke, Laurence J; Soubrier, Julien; Weyrich, Laura S; Cooper, Alan

2014-11-01

Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico 90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR-amplified the blend using five primer sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers. © 2014 John Wiley & Sons Ltd.

Fuel-efficiency of hydrogen and heat storage technologies for integration of fluctuating renewable energy sources

DEFF Research Database (Denmark)

Mathiesen, Brian Vad; Lund, Henrik

2005-01-01

This paper presents the methodology and results of analysing the use of different energy storage technologies in the task of integration of fluctuating renewable energy sources (RES) into the electricity supply. The analysis is done on the complete electricity system including renewable energy...... sources as well as power plants and CHP (Combined heat and power production). Emphasis is put on the need for ancillary services. Devices to store electricity as well as devices to store heat can be used to help the integration of fluctuating sources. Electricity storage technologies can be used...... to relocate electricity production directly from the sources, while heat storage devices can be used to relocate the electricity production from CHP plants and hereby improve the ability to integrate RES. The analyses are done by advanced computer modelling and the results are given as diagrams showing...

Design of integral shutters for the beamlines at the Advanced Photon Source

International Nuclear Information System (INIS)

Chang, J.; Shu, D.; Nian, H.L.; Kuzay, T.M.; Job, P.K.

1994-01-01

An integral shutter is a device that integrates a white-beam stop, monochromatic-beam (mono-beam) shutters, a safety stop, and a collimator into one assembly to save space in the photon beamline. Various integral shutters have been developed as standard components for the beamlines at the Advanced Photon Source. The integral shutters are designed to be operated in white-beam mode or mono-beam mode. With regard to safety, each mode of operation is secured by locking certain devices in their up or down positions. Some of the components of the integral shutters share designs similar to the front-end shutters or fixed masks. Design details of the integral shutters are presented

Polyphasic taxonomic characterization of lactic acid bacteria ...

African Journals Online (AJOL)

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

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

Directory of Open Access Journals (Sweden)

Sheikh Abdul Shakoor

2014-01-01

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

A taxonomic study on the diversity of Indian Knema Lour. (Myristicaceae

Directory of Open Access Journals (Sweden)

Dipanwita Banik

2016-06-01

Full Text Available A taxonomic study on the diversity of the genus Knema Lour. belonging to the family Myristicaceae R. Br. in India revealed the distribution of the ten taxa under four series in North East and Peninsular India and Andaman and Nicobar Islands including two endemic species. Knema ser. Obovoideae W.J. de Wilde is synonymised here under ser. Knema. Series Knema is represented by two species and ser. Glaucae W.J. de Wilde by one species in North East India, while ser. Laurinae W.J. de Wilde is represented by three species and two subspecies in North East India and Andaman and Nicobar Island, and ser. Glomeratae W.J. de Wilde by 2 species in South and NE India. This is the first taxonomic study on the genus in India. All the taxa are cited with updated nomenclature, diagnostic characters, distribution, phonological data, vernacular names, line drawings, photo plates and specimens examined in various herbaria. Taxonomic keys are provided for easy identification of these taxa.

Effect of source integration on the geochemical fluxes from springs

International Nuclear Information System (INIS)

Frisbee, Marty D.; Phillips, Fred M.; White, Art F.; Campbell, Andrew R.; Liu, Fengjing

2013-01-01

Geochemical fluxes from watersheds are typically defined using mass-balance methods that essentially lump all weathering processes operative in a watershed into a single flux of solute mass measured in streamflow at the watershed outlet. However, it is important that we understand how weathering processes in different hydrological zones of a watershed (i.e., surface, unsaturated, and saturated zones) contribute to the total geochemical flux from the watershed. This capability will improve understanding of how geochemical fluxes from these different zones may change in response to climate change. Here, the geochemical flux from weathering processes occurring solely in the saturated zone is investigated. This task, however, remains exceedingly difficult due to the sparsity of subsurface sampling points, especially in large, remote, and/or undeveloped watersheds. In such cases, springflow is often assumed to be a proxy for groundwater (defined as water residing in fully saturated geologic formations). However, springflow generation may integrate different sources of water including, but not limited to, groundwater. The authors’ hypothesis is that long-term estimates of geochemical fluxes from groundwater using springflow proxies will be too large due to the integrative nature of springflow generation. Two conceptual models of springflow generation are tested using endmember mixing analyses (EMMA) on observations of spring chemistries and stable isotopic compositions in a large alpine watershed in the San Juan Mountains of southwestern Colorado. In the “total springflow” conceptual model, springflow is assumed to be 100% groundwater. In the “fractional springflow” conceptual model, springflow is assumed to be an integration of different sources of water (e.g., groundwater, unsaturated flow, preferential flow in the soil, etc.) and groundwater is only a fractional component. The results indicate that groundwater contributions in springflow range from 2% to 100

Temperature Characteristics of Monolithically Integrated Wavelength-Selectable Light Sources

International Nuclear Information System (INIS)

Han Liang-Shun; Zhu Hong-Liang; Zhang Can; Ma Li; Liang Song; Wang Wei

2013-01-01

The temperature characteristics of monolithically integrated wavelength-selectable light sources are experimentally investigated. The wavelength-selectable light sources consist of four distributed feedback (DFB) lasers, a multimode interferometer coupler, and a semiconductor optical amplifier. The oscillating wavelength of the DFB laser could be modulated by adjusting the device operating temperature. A wavelength range covering over 8.0nm is obtained with stable single-mode operation by selecting the appropriate laser and chip temperature. The thermal crosstalk caused by the lateral heat spreading between lasers operating simultaneously is evaluated by oscillating-wavelength shift. The thermal crosstalk approximately decreases exponentially as the increasing distance between lasers

Integration of renew able energy sources in smart grid: a review

International Nuclear Information System (INIS)

Zafar, S.; Nawaz, K.; Naqvi, S.A.R.; Malik, T.N.

2013-01-01

The increasing complexity of the existing power grid due to rapid population growth, development in technology, infrastructure and computational tools are the factors that contribute to the need of deployment of smart grid for secure and efficient use of electrical energy. The modernization of electric grids toward a smart grid is being carried out to improve reliability, facilitate integration of renewable energies, and improve power consumption management. Due to continuous depletion of primary fuel resources and global concern about the environmental pollution, the development of smart grids based on renewable energy resources has gained huge strategic significance now a days to resolve the energy crisis. However the intermittent and fluctuating nature of these sources makes the integration a difficult task that needs to be effectively addressed. Firstly this paper briefly discuss the emerging renewable energy resources (RERs) and Energy storage systems (EES). Secondly this work comprehensively reviews the potential challenges in integration of these sources in smart grid along with the applied control strategies for their facilitation and some practical case studies. (author)

Air source integrated heat pump simulation model for EnergyPlus

Energy Technology Data Exchange (ETDEWEB)

Shen, Bo; New, Joshua; Baxter, Van

2017-12-01

An Air Source Integrated Heat Pump (AS-IHP) is an air source, multi-functional spacing conditioning unit with water heating function (WH), which can lead to great energy savings by recovering the condensing waste heat for domestic water heating. This paper summarizes development of the EnergyPlus AS-IHP model, introducing the physics, sub-models, working modes, and control logic. Based on the model, building energy simulations were conducted to demonstrate greater than 50% annual energy savings, in comparison to a baseline heat pump with electric water heater, over 10 US cities, using the EnergyPlus quick-service restaurant template building. We assessed water heating energy saving potentials using AS-IHP versus both gas and electric baseline systems, and pointed out climate zones where AS-IHPs are promising. In addition, a grid integration strategy was investigated to reveal further energy saving and electricity cost reduction potentials, via increasing the water heating set point temperature during off-peak hours and using larger water tanks.

Generalizing human error rates: A taxonomic approach

International Nuclear Information System (INIS)

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

1989-01-01

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

Partial migration in fishes: definitions, methodologies and taxonomic distribution

DEFF Research Database (Denmark)

Chapman, B B; Skov, C; Hulthén, K

2012-01-01

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

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

Science.gov (United States)

Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

2010-02-15

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

Multi-Sensor Integration to Map Odor Distribution for the Detection of Chemical Sources

Directory of Open Access Journals (Sweden)

Xiang Gao

2016-07-01

Full Text Available This paper addresses the problem of mapping odor distribution derived from a chemical source using multi-sensor integration and reasoning system design. Odor localization is the problem of finding the source of an odor or other volatile chemical. Most localization methods require a mobile vehicle to follow an odor plume along its entire path, which is time consuming and may be especially difficult in a cluttered environment. To solve both of the above challenges, this paper proposes a novel algorithm that combines data from odor and anemometer sensors, and combine sensors’ data at different positions. Initially, a multi-sensor integration method, together with the path of airflow was used to map the pattern of odor particle movement. Then, more sensors are introduced at specific regions to determine the probable location of the odor source. Finally, the results of odor source location simulation and a real experiment are presented.

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

Science.gov (United States)

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

2016-06-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

Sources and fate of antimicrobials in integrated fish-pig and non-integrated tilapia farms.

Science.gov (United States)

Li, Kang; Liu, Liping; Zhan, Jia; Scippo, Marie-Louise; Hvidtfeldt, Kristian; Liu, Yuan; Dalsgaard, Anders

2017-10-01

Antimicrobial contamination in aquaculture products constitutes a food safety hazard, but little is known about the introduction and accumulation of antimicrobials in integrated fish-pig aquaculture. This study, conducted in 2013, aimed to determine the residues of 11 types of antimicrobials by UPLC-MS/MS analysis in fish feed (n=37), pig feed (n=9), pig manure (n=9), pond sediment (n=20), fish skin (n=20) and muscle tissue (n=20) sampled from integrated tilapia-pig farms, non-integrated tilapia farms and fish feed supply shops. There was a higher occurrence of antimicrobial residues in fish skin from both integrated and non-integrated farms, and in pig manure. Enrofloxacin (3.9-129.3μg/kg) and sulfadiazine (0.7-7.8μg/kg) were commonly detected in fish skin and muscle, pig manure and pond sediment from integrated farms, with different types of antimicrobials found in pig manure and tilapia samples. In non-integrated farms, sulfadiazine (2.5-89.9μg/kg) was the predominant antimicrobial detected in fish skin and muscle, fish feed and pond sediment. In general, antimicrobials seemed not to be commonly transmitted from pig to fish in tilapia-pig integrated farms, and fish feed, pig feed and pond sediment did not seem as important sources of the antimicrobials found in fish from both systems. The frequent findings of antimicrobial residues in fish skin compared with fish muscle was probably due to different pharmacokinetics in different tissue types, which have practical food safety implications since antimicrobial residues monitoring is usually performed analyzing mixed skin and fish muscle samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Broadband integrated mid infrared light sources as enabling technology for point of care mid-infrared spectroscopy

Science.gov (United States)

2017-08-20

AFRL-AFOSR-JP-TR-2017-0061 Broadband integrated mid-infrared light sources as enabling technology for point-of-care mid- infrared spectroscopy Alex...mid-infrared light sources as enabling technology for point-of-care mid-infrared spectroscopy 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA2386-16-1-4037...Broadband integrated mid-infrared light sources as enabling technology for point-of-care mid- infrared spectroscopy ” Date: 16th August 2017 Name

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

Directory of Open Access Journals (Sweden)

Jiang Tao

2011-10-01

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

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

Science.gov (United States)

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

2011-10-10

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

Time-domain single-source integral equations for analyzing scattering from homogeneous penetrable objects

KAUST Repository

Valdés, Felipe

2013-03-01

Single-source time-domain electric-and magnetic-field integral equations for analyzing scattering from homogeneous penetrable objects are presented. Their temporal discretization is effected by using shifted piecewise polynomial temporal basis functions and a collocation testing procedure, thus allowing for a marching-on-in-time (MOT) solution scheme. Unlike dual-source formulations, single-source equations involve space-time domain operator products, for which spatial discretization techniques developed for standalone operators do not apply. Here, the spatial discretization of the single-source time-domain integral equations is achieved by using the high-order divergence-conforming basis functions developed by Graglia alongside the high-order divergence-and quasi curl-conforming (DQCC) basis functions of Valdés The combination of these two sets allows for a well-conditioned mapping from div-to curl-conforming function spaces that fully respects the space-mapping properties of the space-time operators involved. Numerical results corroborate the fact that the proposed procedure guarantees accuracy and stability of the MOT scheme. © 2012 IEEE.

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

International Nuclear Information System (INIS)

Abid, R.; Alam, J.

2011-01-01

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

Stechiometric neodymium compounds as new materials for light sources in integrated optics

International Nuclear Information System (INIS)

Malinowski, M.

1981-01-01

Short review of physico-chemical properties of stechiometric neodymium compounds has been presented. Several constructions of minilasers as promising light sources for integrated optics devices have been described. (author)

Optical Characteristics of a Multichannel Hybrid Integrated Light Source for Ultra-High-Bandwidth Optical Interconnections

Directory of Open Access Journals (Sweden)

Takanori Shimizu

2015-11-01

Full Text Available The optical characteristics of a multi-channel hybrid integrated light source were described for an optical interconnection with a bandwidth of over 10 Tbit/s. The power uniformity of the relative intensity of a 1000-channel light source was shown, and the minimum standard deviation s of the optical power of the 200 output ports at each 25-channel laser diode (LD array was estimated to be 0.49 dB. This hybrid integrated light source is expected to be easily adaptable to a photonics-electronics convergence system for ultra-high-bandwidth interchip interconnections.

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

Science.gov (United States)

Villéger, Sébastien; Miranda, Julia Ramos; Hernandez, Domingo Flores; Mouillot, David

2012-01-01

The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395

High taxonomic variability despite stable functional structure across microbial communities.

Science.gov (United States)

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

2016-12-05

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

Revision of the genus Cuvierina Boas, 1886 based on integrative taxonomic data, including the description of a new species from the Pacific Ocean (Gastropoda, Thecosomata).

Science.gov (United States)

Burridge, Alice K; Janssen, Arie W; Peijnenburg, Katja T C A

2016-01-01

Shelled pteropods (Gastropoda, Thecosomata, Euthecosomata) are a group of holoplanktonic gastropods that occur predominantly in the surface layers of the world's oceans. Accurate species identifications are essential for tracking changes in species assemblages of planktonic gastropods, because different species are expected to have different sensitivities to ocean changes. The genus Cuvierina has a worldwide warm water distribution pattern between ~36°N and ~39°S. Based on an integrative taxonomic approach combining morphometric, genetic, and biogeographic information, the two subgenera of Cuvierina , Cuvierina s. str. and Urceolarica , are rejected. A new species is introduced: Cuvierina tsudai sp. n. , which has to date been considered the same species as Cuvierina pacifica . Cuvierina tsudai sp. n. is endemic to the Pacific Ocean and is characterised by a shell height of 7.2-8.0 mm, a moderately cylindrical shell shape, the absence of micro-ornamentation and a triangular aperture. Cuvierina pacifica is restricted to the centre of the oligotrophic southern Pacific gyre, has a shell height of 6.6-8.5 mm, a more cylindrical shell shape, no micro-ornamentation and a less triangular aperture than Cuvierina tsudai sp. n.

Computation of rectangular source integral by rational parameter polynomial method

International Nuclear Information System (INIS)

Prabha, Hem

2001-01-01

Hubbell et al. (J. Res. Nat Bureau Standards 64C, (1960) 121) have obtained a series expansion for the calculation of the radiation field generated by a plane isotropic rectangular source (plaque), in which leading term is the integral H(a,b). In this paper another integral I(a,b), which is related with the integral H(a,b) has been solved by the rational parameter polynomial method. From I(a,b), we compute H(a,b). Using this method the integral I(a,b) is expressed in the form of a polynomial of a rational parameter. Generally, a function f (x) is expressed in terms of x. In this method this is expressed in terms of x/(1+x). In this way, the accuracy of the expression is good over a wide range of x as compared to the earlier approach. The results for I(a,b) and H(a,b) are given for a sixth degree polynomial and are found to be in good agreement with the results obtained by numerically integrating the integral. Accuracy could be increased either by increasing the degree of the polynomial or by dividing the range of integration. The results of H(a,b) and I(a,b) are given for values of b and a up to 2.0 and 20.0, respectively

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

Science.gov (United States)

Zhang, Min; García Molinos, Jorge; Zhang, Xiaolin; Xu, Jun

2018-01-01

Human activities and the consequent extirpations of species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. One of the main gaps in the assessment of biodiversity change in freshwater ecosystems is our limited understanding regarding how taxonomic and functional facets of macrophyte assemblages respond to human impacts on regional scales. Here, we assess the temporal (before 1970s against after 2000s) changes in taxonomic and functional richness and compositional dissimilarities, partitioned into its turnover and nestedness components, of freshwater macrophyte assemblages across the floodplain lakes of the Yangtze River in China. We found that functional and taxonomic assemblage differentiation occurred simultaneously under increasing human impact, concomitant to a general decrease in functional and taxonomic richness. However, this effect weakened when the historical level of taxonomic dissimilarity among assemblages was high. Macrophyte species with large dispersal range and submersed life form were significantly more susceptible to extirpation. The impact of human activities on differentiation was complex but habitat loss and fishery intensity were consistently the main drivers of assemblage change in these lakes, whereas water quality (i.e., light pollution and nutrient enrichment) had weaker effects. Further, macrophyte taxonomic and functional differentiation was mainly driven by the nestedness component of dissimilarity, accounting for changes in assemblage composition related to changes in species richness independent of species replacement. This result, markedly different from previous studies on freshwater fish assemblages conducted in these lakes, represents a novel contribution toward achieving a more holistic understanding of how human impacts contribute to shape community assemblages in natural ecosystems.

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

African Journals Online (AJOL)

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

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

African Journals Online (AJOL)

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

A taxonomic synopsis of Altingiaceae with nine new combinations

Directory of Open Access Journals (Sweden)

Stefanie Ickert-Bond

2013-12-01

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

Integrating Free and Open Source Solutions into Geospatial Science Education

Directory of Open Access Journals (Sweden)

Vaclav Petras

2015-06-01

Full Text Available While free and open source software becomes increasingly important in geospatial research and industry, open science perspectives are generally less reflected in universities’ educational programs. We present an example of how free and open source software can be incorporated into geospatial education to promote open and reproducible science. Since 2008 graduate students at North Carolina State University have the opportunity to take a course on geospatial modeling and analysis that is taught with both proprietary and free and open source software. In this course, students perform geospatial tasks simultaneously in the proprietary package ArcGIS and the free and open source package GRASS GIS. By ensuring that students learn to distinguish between geospatial concepts and software specifics, students become more flexible and stronger spatial thinkers when choosing solutions for their independent work in the future. We also discuss ways to continually update and improve our publicly available teaching materials for reuse by teachers, self-learners and other members of the GIS community. Only when free and open source software is fully integrated into geospatial education, we will be able to encourage a culture of openness and, thus, enable greater reproducibility in research and development applications.

Identification and conservation application of signal, noise, and taxonomic effects in diversity patterns

Directory of Open Access Journals (Sweden)

Fleishman, E.

2005-01-01

Full Text Available Ongoing research on butterflies and birds in the Great Basin has identified biogeographic patterns while elucidating how dynamic measures of diversity (species richness and turnover affect inferences for conservation planning and adaptive management. Nested subsets analyses suggested that processes influencing predictability of assemblage composition differ among taxonomic groups, and the relative importance of those processes may vary spatially within a taxonomic group. There may be a time lag between deterministic environmental changes and a detectable faunal response, even for taxonomic groups that are known to be sensitive to changes in climate and land cover. Measures of beta diversity were sensitive to correlations between sampling resolution and local environmental heterogeneity. Temporal and spatial variation in species composition indicated that spatially extensive sampling is more effective for drawing inferences about biodiversity responses to environmental change than intensive sampling at relatively few, smaller sites.

TaxMan: a taxonomic database manager

Directory of Open Access Journals (Sweden)

Blaxter Mark

2006-12-01

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

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

Science.gov (United States)

Sachs, Olga; Weis, Susanne; Zellagui, Nadia; Huber, Walter; Zvyagintsev, Mikhail; Mathiak, Klaus; Kircher, Tilo

2008-07-07

Most current models of knowledge organization are based on hierarchical or taxonomic categories (animals, tools). Another important organizational pattern is thematic categorization, i.e. categories held together by external relations, a unifying scene or event (car and garage). The goal of this study was to compare the neural correlates of these categories under automatic processing conditions that minimize strategic influences. We used fMRI to examine neural correlates of semantic priming for category members with a short stimulus onset asynchrony (SOA) of 200 ms as subjects performed a lexical decision task. Four experimental conditions were compared: thematically related words (car-garage); taxonomically related (car-bus); unrelated (car-spoon); non-word trials (car-derf). We found faster reaction times for related than for unrelated prime-target pairs for both thematic and taxonomic categories. However, the size of the thematic priming effect was greater than that of the taxonomic. The imaging data showed signal changes for the taxonomic priming effects in the right precuneus, postcentral gyrus, middle frontal and superior frontal gyri and thematic priming effects in the right middle frontal gyrus and anterior cingulate. The contrast of neural priming effects showed larger signal changes in the right precuneus associated with the taxonomic but not with thematic priming response. We suggest that the greater involvement of precuneus in the processing of taxonomic relations indicates their reduced salience in the knowledge structure compared to more prominent thematic relations.

Taxonomical analysis of the Cancer cluster of galaxies

International Nuclear Information System (INIS)

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

1986-01-01

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

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

Science.gov (United States)

Lakhujani, Vijay; Badapanda, Chandan

2017-06-01

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

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

NARCIS (Netherlands)

Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; Vos, de Willem M.

2015-01-01

Background: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to

La confusa taxonomía de Cryptosporidium

Directory of Open Access Journals (Sweden)

Gregorio Pérez-Cordón

2006-10-01

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

A CMOS microdisplay with integrated controller utilizing improved silicon hot carrier luminescent light sources

Science.gov (United States)

Venter, Petrus J.; Alberts, Antonie C.; du Plessis, Monuko; Joubert, Trudi-Heleen; Goosen, Marius E.; Janse van Rensburg, Christo; Rademeyer, Pieter; Fauré, Nicolaas M.

2013-03-01

Microdisplay technology, the miniaturization and integration of small displays for various applications, is predominantly based on OLED and LCoS technologies. Silicon light emission from hot carrier electroluminescence has been shown to emit light visibly perceptible without the aid of any additional intensification, although the electrical to optical conversion efficiency is not as high as the technologies mentioned above. For some applications, this drawback may be traded off against the major cost advantage and superior integration opportunities offered by CMOS microdisplays using integrated silicon light sources. This work introduces an improved version of our previously published microdisplay by making use of new efficiency enhanced CMOS light emitting structures and an increased display resolution. Silicon hot carrier luminescence is often created when reverse biased pn-junctions enter the breakdown regime where impact ionization results in carrier transport across the junction. Avalanche breakdown is typically unwanted in modern CMOS processes. Design rules and process design are generally tailored to prevent breakdown, while the voltages associated with breakdown are too high to directly interact with the rest of the CMOS standard library. This work shows that it is possible to lower the operating voltage of CMOS light sources without compromising the optical output power. This results in more efficient light sources with improved interaction with other standard library components. This work proves that it is possible to create a reasonably high resolution microdisplay while integrating the active matrix controller and drivers on the same integrated circuit die without additional modifications, in a standard CMOS process.

International Requirements for Large Integration of Renewable Energy Sources

DEFF Research Database (Denmark)

Molina-Garcia, Angel; Hansen, Anca Daniela; Muljadi, Ed

2017-01-01

Most European countries have concerns about the integration of large amounts of renewable energy sources (RES) into electric power systems, and this is currently a topic of growing interest. In January 2008, the European Commission published the 2020 package, which proposes committing the European...... Union to a 20% reduction in greenhouse gas emissions, to achieve a target of deriving 20% of the European Union's final energy consumption from renewable sources, and to achieve 20% improvement in energy efficiency both by the year 2020 [1]. Member states have different individual goals to meet...... these overall objectives, and they each need to provide a detailed roadmap describing how they will meet these legally binding targets [2]. At this time, RES are an indispensable part of the global energy mix, which has been partially motivated by the continuous increases in hydropower as well as the rapid...

Open source information acquisition, analysis and integration in the IAEA Department of Safeguards

International Nuclear Information System (INIS)

Barletta, M.; Zarimpas, N.; Zarucki, R.

2010-10-01

Acquisition and analysis of open source information plays an increasingly important role in the IAEA strengthened safeguards system. The Agency's focal point for open source information collection and analysis is the Division of Safeguards Information Management (SGIM) within the IAEA Department of Safeguards. In parallel with the approval of the Model Additional Protocol in 1997, a new centre of information acquisition and analysis expertise was created within SGIM. By acquiring software, developing databases, retraining existing staff and hiring new staff with diverse analytical skills, SGIM is pro actively contributing to the future implementation of information-driven safeguards in collaboration with other Divisions within the Department of Safeguards. Open source information support is now fully integrated with core safeguards processes and activities, and has become an effective tool in the work of the Department of Safeguards. This provides and overview of progress realized through the acquisition and use of open source information in several thematic areas: evaluation of additional protocol declarations; support to the State Evaluation process; in-depth investigation of safeguards issues, including assisting inspections and complementary access; research on illicit nuclear procurement networks and trafficking; and monitoring nuclear developments. Demands for open source information have steadily grown and are likely to continue to grow in the future. Coupled with the enormous growth and accessibility in the volume and sources of information, new challenges are presented, both technical and analytical. This paper discusses actions taken and future plans for multi-source and multi-disciplinary analytic integration to strengthen confidence in safeguards conclusions - especially regarding the absence of undeclared nuclear materials and activities. (Author)

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

Science.gov (United States)

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

2011-11-01

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

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

Science.gov (United States)

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

2011-11-01

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

Time-domain single-source integral equations for analyzing scattering from homogeneous penetrable objects

KAUST Repository

Valdé s, Felipe; Andriulli, Francesco P.; Bagci, Hakan; Michielssen, Eric

2013-01-01

Single-source time-domain electric-and magnetic-field integral equations for analyzing scattering from homogeneous penetrable objects are presented. Their temporal discretization is effected by using shifted piecewise polynomial temporal basis

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

Science.gov (United States)

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.

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

African Journals Online (AJOL)

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

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

African Journals Online (AJOL)

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

Low-level radioactive waste source terms for the 1992 integrated data base

International Nuclear Information System (INIS)

Loghry, S.L.; Kibbey, A.H.; Godbee, H.W.; Icenhour, A.S.; DePaoli, S.M.

1995-01-01

This technical manual presents updated generic source terms (i.e., unitized amounts and radionuclide compositions) which have been developed for use in the Integrated Data Base (IDB) Program of the U.S. Department of Energy (DOE). These source terms were used in the IDB annual report, Integrated Data Base for 1992: Spent Fuel and Radioactive Waste Inventories, Projections, and Characteristics, DOE/RW-0006, Rev. 8, October 1992. They are useful as a basis for projecting future amounts (volume and radioactivity) of low-level radioactive waste (LLW) shipped for disposal at commercial burial grounds or sent for storage at DOE solid-waste sites. Commercial fuel cycle LLW categories include boiling-water reactor, pressurized-water reactor, fuel fabrication, and uranium hexafluoride (UF 6 ) conversion. Commercial nonfuel cycle LLW includes institutional/industrial (I/I) waste. The LLW from DOE operations is category as uranium/thorium fission product, induced activity, tritium, alpha, and open-quotes otherclose quotes. Fuel cycle commercial LLW source terms are normalized on the basis of net electrical output [MW(e)-year], except for UF 6 conversion, which is normalized on the basis of heavy metal requirement [metric tons of initial heavy metal ]. The nonfuel cycle commercial LLW source term is normalized on the basis of volume (cubic meters) and radioactivity (curies) for each subclass within the I/I category. The DOE LLW is normalized in a manner similar to that for commercial I/I waste. The revised source terms are based on the best available historical data through 1992

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

Science.gov (United States)

Mori, Akira S; Ota, Aino T; Fujii, Saori; Seino, Tatsuyuki; Kabeya, Daisuke; Okamoto, Toru; Ito, Masamichi T; Kaneko, Nobuhiro; Hasegawa, Motohiro

2015-10-01

The compositional characteristics of ecological assemblages are often simplified; this process is termed "biotic homogenization." This process of biological reorganization occurs not only taxonomically but also functionally. Testing both aspects of homogenization is essential if ecosystem functioning supported by a diverse mosaic of functional traits in the landscape is concerned. Here, we aimed to infer the underlying processes of taxonomic/functional homogenization at the local scale, which is a scale that is meaningful for this research question. We recorded species of litter-dwelling oribatid mites along a gradient of forest conversion from a natural forest to a monoculture larch plantation in Japan (in total 11 stands), and collected data on the functional traits of the recorded species to quantify functional diversity. We calculated the taxonomic and functional β-diversity, an index of biotic homogenization. We found that both the taxonomic and functional β-diversity decreased with larch dominance (stand homogenization). After further deconstructing β-diversity into the components of turnover and nestedness, which reflect different processes of community organization, a significant decrease in the response to larch dominance was observed only for the functional turnover. As a result, there was a steeper decline in the functional β-diversity than the taxonomic β-diversity. This discordance between the taxonomic and functional response suggests that species replacement occurs between species that are functionally redundant under environmental homogenization, ultimately leading to the stronger homogenization of functional diversity. The insights gained from community organization of oribatid mites suggest that the functional characteristics of local assemblages, which support the functionality of ecosystems, are of more concern in human-dominated forest landscapes.

Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16 M.

Directory of Open Access Journals (Sweden)

Aniel Jessica Leticia Brambila-Tapia

Full Text Available Many virulence genes have been detected in attenuated mutants of Brucella melitensis 16 M; nevertheless, a complete report of these genes, including the main Cluster of Orthologous Groups (COG represented as well as the taxonomical distribution among all complete bacterial and archaeal genomes, has not been analyzed. In this work a total of 160 virulence genes that have been reported in attenuated mutants in B. melitensis were included and analyzed. Additionally, we obtained 250 B. melitensis randomly selected genes as a reference group for the taxonomical comparisons. The COGs and the taxonomical distribution profile for 789 nonredundant bacterial and archaeal genomes were obtained and compared with the whole-genome COG distribution and with the 250 randomly selected genes, respectively. The main COGs associated with virulence genes corresponded to the following: intracellular trafficking, secretion and vesicular transport (U; cell motility (N; nucleotide transport and metabolism (F; transcription (K; and cell wall/membrane/envelope biogenesis (M. In addition, we found that virulence genes presented a higher proportion of orthologs in the Euryarchaeota and Proteobacteria phyla, with a significant decrease in Chlamydiae, Bacteroidetes, Tenericutes, Firmicutes and Thermotogae. In conclusion, we found that genes related to specific functions are more relevant to B. melitensis virulence, with the COG U the most significant. Additionally, the taxonomical distribution of virulence genes highlights the importance of these genes in the related Proteobacteria, being less relevant in distant groups of organisms with the exception of Euryarchaeota.

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

Science.gov (United States)

Konwar, Kishori M; Hanson, Niels W; Bhatia, Maya P; Kim, Dongjae; Wu, Shang-Ju; Hahn, Aria S; Morgan-Lang, Connor; Cheung, Hiu Kan; Hallam, Steven J

2015-10-15

Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. shallam@mail.ubc.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

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

African Journals Online (AJOL)

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

Data composition and taxonomic resolution in macroinvertebrate stream typology

NARCIS (Netherlands)

Verdonschot, P.F.M.

2006-01-01

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

Environmental quality of a stream can be better predicted by phylogenetic than by taxonomic diversity

Directory of Open Access Journals (Sweden)

Koperski Paweł

2017-01-01

Full Text Available Different indices of taxonomic diversity (TD and phylogenetic diversity (PD of the macrobenthos were compared to determine the efficient predictors of environmental quality (EQ in different types of watercourses in Poland. Archived data of 864 samples of benthic invertebrates identified to the family level were analysed on the basis of linear and non-linear multiply regression. The strengths of the correlations between two measures of EQ:BMWPpl (British Monitoring Working Party score system, Polish modification and MMI (Multimetric Macroinvertebrate Index and the values of taxonomic richness and three well-known TD indices: Shannon, Margalef and J' Evenness were compared to those for values of three PD indices, based on taxonomic distinctness. Taxonomic richness and all PD indices correlated more strongly with both measures of EQ than all TD indices. Correlations with both types of diversity indices were visibly stronger for BMWPpl when compared with MMI. We suggest that analysed indices of PD, especially MDis (mean phylogenetic distance between families in a sample, are related with EQ strongly enough to be taken into account as potential metrics in selection procedures of biological assessment.

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

International Nuclear Information System (INIS)

Gradie, J.C.; Tedesco, E.F.

1989-01-01

The distribution of asteroid taxonomic classes and, presumably, actual composition varies systematically with heliocentric distance and is seen qualitatively in the results of a variety of taxonomy methods. In general, the distribution of taxonomic classes is characterized by moderate-albedo asteroids dominant in the inner belt with low-albedo asteroids prevalent in the outer belt and beyond. If the differences in taxonomic classes are assumed to be due to differences in composition, then the asteroid belt can be divided into many compositionally distinct regions defined by peaks and troughs in the distributions of the various classes. Unfortunately, differences in the class definitions used by different classification methods are manifested in the bias-corrected distribution of the classes, which makes detailed interpretation of these trends difficult. UBV color differences among members of the moderate-albedo S class show a distribution in semimajor axis which indicates subgroups in the S class. Explanations of the causes of the overall trends range from primarily dynamical to primarily in situ arrangements of igneous, metamorphic and unaltered primitive material, but a combination of several of these factors may be more likely

Chrysomya albiceps and C. rufifacies (Diptera: Calliphoridae): contribution to an ongoing taxonomic problem.

Science.gov (United States)

Tantawi, T I; Greenberg, B

1993-05-01

Until recently, the two biologically equivalent blow flies Chrysomya albiceps (Wiedemann) and Chrysomya rufifacies (Macquart) had disjunct distributions outside the Americas; the former was Palaearctic, the latter Australasian and Oriental. The two species are now spreading throughout the Americas and coexist in Argentina. The predatory "hairy" larvae of both species are difficult to separate, which could result in taxonomic errors. New diagnostic characters are presented to differentiate the third instars of the two species. The usefulness of the prostigmatic bristle as a diagnostic taxonomic character in distinguishing adults of these species is questioned.

Open source information acquisition, analysis and integration in the IAEA Department of Safeguards

Energy Technology Data Exchange (ETDEWEB)

Barletta, M.; Zarimpas, N.; Zarucki, R., E-mail: M.Barletta@iaea.or [IAEA, Wagramerstrasse 5, P.O. Box 100, 1400 Vienna (Austria)

2010-10-15

Acquisition and analysis of open source information plays an increasingly important role in the IAEA strengthened safeguards system. The Agency's focal point for open source information collection and analysis is the Division of Safeguards Information Management (SGIM) within the IAEA Department of Safeguards. In parallel with the approval of the Model Additional Protocol in 1997, a new centre of information acquisition and analysis expertise was created within SGIM. By acquiring software, developing databases, retraining existing staff and hiring new staff with diverse analytical skills, SGIM is pro actively contributing to the future implementation of information-driven safeguards in collaboration with other Divisions within the Department of Safeguards. Open source information support is now fully integrated with core safeguards processes and activities, and has become an effective tool in the work of the Department of Safeguards. This provides and overview of progress realized through the acquisition and use of open source information in several thematic areas: evaluation of additional protocol declarations; support to the State Evaluation process; in-depth investigation of safeguards issues, including assisting inspections and complementary access; research on illicit nuclear procurement networks and trafficking; and monitoring nuclear developments. Demands for open source information have steadily grown and are likely to continue to grow in the future. Coupled with the enormous growth and accessibility in the volume and sources of information, new challenges are presented, both technical and analytical. This paper discusses actions taken and future plans for multi-source and multi-disciplinary analytic integration to strengthen confidence in safeguards conclusions - especially regarding the absence of undeclared nuclear materials and activities. (Author)

[Bibliometric analysis of literature regarding integrated schistosomiasis control strategy with emphasis on infectious source control].

Science.gov (United States)

Qian, Yi-Li; Wang, Wei; Hong, Qing-Biao; Liang, You-Sheng

2014-12-01

To evaluate the outcomes of implementation of integrated schistosomiasis control strategy with emphasis on infectious source control using a bibliometric method. The literature pertaining to integrated schistosomiasis control strategy with emphasis on infectious source control was retrieved from CNKI, Wanfangdata, VIP, PubMed, Web of Science, BIOSIS and Google Scholar, and a bibliometric analysis of literature captured was performed. During the period from January 1, 2004 through September 30, 2014, a total of 94 publications regarding integrated schistosomiasis control strategy with emphasis on infectious source control were captured, including 78 Chinese articles (82.98%) and 16 English papers (17.02%). The Chinese literature was published in 21 national journals, and Chinese Journal of Schistosomiasis Control had the largest number of publications, consisting of 37.23% of total publications; 16 English papers were published in 12 international journals, and PLoS Neglected Tropical Diseases had the largest number of publications (3 publications). There were 37 affiliations publishing these 94 articles, and National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (16 publications), Anhui Institute of Schistosomiasis Control (12 publications) and Hunan Institute of Schistosomiasis Control (9 publications) ranked top three affiliations in number of publications. A total of 157 persons were co-authored in these 94 publications, and Wang, Zhou and Zhang ranked top 3 authors in number of publications. The integrated schistosomiasis control strategy with emphasis on infectious source control has been widely implemented in China, and the achievements obtained from the implementation of this strategy should be summarized and transmitted internationally.

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

Science.gov (United States)

Törnroos, Anna; Nordström, Marie C; Bonsdorff, Erik

2013-01-01

Due to human impact, there is extensive degradation and loss of marine habitats, which calls for measures that incorporate taxonomic as well as functional and trophic aspects of biodiversity. Since such data is less easily quantifiable in nature, the use of habitats as surrogates or proxies for biodiversity is on the rise in marine conservation and management. However, there is a critical gap in knowledge of whether pre-defined habitat units adequately represent the functional and trophic structure of communities. We also lack comparisons of different measures of community structure in terms of both between- (β) and within-habitat (α) variability when accounting for species densities. Thus, we evaluated a priori defined coastal habitats as surrogates for traditional taxonomic, functional and trophic zoobenthic community structure. We focused on four habitats (bare sand, canopy-forming algae, seagrass above- and belowground), all easily delineated in nature and defined through classification systems. We analyzed uni- and multivariate data on species and trait diversity as well as stable isotope ratios of benthic macrofauna. A good fit between habitat types and taxonomic and functional structure was found, although habitats were more similar functionally. This was attributed to within-habitat heterogeneity so when habitat divisions matched the taxonomic structure, only bare sand was functionally distinct. The pre-defined habitats did not meet the variability of trophic structure, which also proved to differentiate on a smaller spatial scale. The quantification of trophic structure using species density only identified an epi- and an infaunal unit. To summarize the results we present a conceptual model illustrating the match between pre-defined habitat types and the taxonomic, functional and trophic community structure. Our results show the importance of including functional and trophic aspects more comprehensively in marine management and spatial planning.

Land use change has stronger effects on functional diversity than taxonomic diversity in tropical Andean hummingbirds.

Science.gov (United States)

Tinoco, Boris A; Santillán, Vinicio E; Graham, Catherine H

2018-03-01

Land use change modifies the environment at multiple spatial scales, and is a main driver of species declines and deterioration of ecosystem services. However, most of the research on the effects of land use change has focused on taxonomic diversity, while functional diversity, an important predictor of ecosystem services, is often neglected. We explored how local and landscape scale characteristics influence functional and taxonomic diversity of hummingbirds in the Andes Mountains in southern Ecuador. Data was collected in six landscapes along a land use gradient, from an almost intact landscape to one dominated by cattle pastures. We used point counts to sample hummingbirds from 2011 to 2012 to assessed how local factors (i.e., vegetation structure, flowering plants richness, nectar availability) and landscape factors (i.e., landscape heterogeneity, native vegetation cover) influenced taxonomic and functional diversity. Then, we analyzed environment - trait relationships (RLQ test) to explore how different hummingbird functional traits influenced species responses to these factors. Taxonomic and functional diversity of hummingbirds were positively associated with landscape heterogeneity but only functional diversity was positively related to native vegetation coverage. We found a weak response of taxonomic and functional diversity to land use change at the local scale. Environment-trait associations showed that body mass of hummingbirds likely influenced species sensitivity to land use change. In conclusion, landscape heterogeneity created by land use change can positively influence hummingbird taxonomic and functional diversity; however, a reduction of native vegetation cover could decrease functional diversity. Given that functional diversity can mediate ecosystem services, the conservation of native vegetation cover could play a key role in the maintenance of hummingbird pollination services in the tropical Andes. Moreover, there are particular functional

Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species.

Science.gov (United States)

Dahruddin, Hadi; Hutama, Aditya; Busson, Frédéric; Sauri, Sopian; Hanner, Robert; Keith, Philippe; Hadiaty, Renny; Hubert, Nicolas

2017-03-01

Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities, and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous, and the taxonomic knowledge is scattered in the literature. This study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of this study, a checklist was compiled based on online catalogues. A total of 95 sites were visited, and a library including 1046 DNA barcodes for 159 species was assembled. Nearest neighbour distance was 28-fold higher than maximum intraspecific distance on average, and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e. 24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna, and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies. © 2016 John Wiley & Sons Ltd.

An integrated approach to assess heavy metal source apportionment in peri-urban agricultural soils

International Nuclear Information System (INIS)

Huang, Ying; Li, Tingqiang; Wu, Chengxian; He, Zhenli; Japenga, Jan; Deng, Meihua; Yang, Xiaoe

2015-01-01

Highlights: • Heavy metal source apportionment was conducted in peri-urban agricultural areas. • Precise and quantified results were obtained by using isotope ratio analysis. • The integration of IRA, GIS, PCA, and CA was proved to be more reliable. • Hg pollution was from the use of organic fertilizers in this area. - Abstract: Three techniques (Isotope Ratio Analysis, GIS mapping, and Multivariate Statistical Analysis) were integrated to assess heavy metal pollution and source apportionment in peri-urban agricultural soils. The soils in the study area were moderately polluted with cadmium (Cd) and mercury (Hg), lightly polluted with lead (Pb), and chromium (Cr). GIS Mapping suggested Cd pollution originates from point sources, whereas Hg, Pb, Cr could be traced back to both point and non-point sources. Principal component analysis (PCA) indicated aluminum (Al), manganese (Mn), nickel (Ni) were mainly inherited from natural sources, while Hg, Pb, and Cd were associated with two different kinds of anthropogenic sources. Cluster analysis (CA) further identified fertilizers, waste water, industrial solid wastes, road dust, and atmospheric deposition as potential sources. Based on isotope ratio analysis (IRA) organic fertilizers and road dusts accounted for 74–100% and 0–24% of the total Hg input, while road dusts and solid wastes contributed for 0–80% and 19–100% of the Pb input. This study provides a reliable approach for heavy metal source apportionment in this particular peri-urban area, with a clear potential for future application in other regions.

An integrated approach to assess heavy metal source apportionment in peri-urban agricultural soils

Energy Technology Data Exchange (ETDEWEB)

Huang, Ying; Li, Tingqiang; Wu, Chengxian [Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058 (China); He, Zhenli [University of Florida, Institute of Food and Agricultural Sciences, Indian River Research and Education Center, Fort Pierce, FL 34945 (United States); Japenga, Jan; Deng, Meihua [Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058 (China); Yang, Xiaoe, E-mail: xeyang@zju.edu.cn [Ministry of Education Key Laboratory of Environmental Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058 (China)

2015-12-15

Highlights: • Heavy metal source apportionment was conducted in peri-urban agricultural areas. • Precise and quantified results were obtained by using isotope ratio analysis. • The integration of IRA, GIS, PCA, and CA was proved to be more reliable. • Hg pollution was from the use of organic fertilizers in this area. - Abstract: Three techniques (Isotope Ratio Analysis, GIS mapping, and Multivariate Statistical Analysis) were integrated to assess heavy metal pollution and source apportionment in peri-urban agricultural soils. The soils in the study area were moderately polluted with cadmium (Cd) and mercury (Hg), lightly polluted with lead (Pb), and chromium (Cr). GIS Mapping suggested Cd pollution originates from point sources, whereas Hg, Pb, Cr could be traced back to both point and non-point sources. Principal component analysis (PCA) indicated aluminum (Al), manganese (Mn), nickel (Ni) were mainly inherited from natural sources, while Hg, Pb, and Cd were associated with two different kinds of anthropogenic sources. Cluster analysis (CA) further identified fertilizers, waste water, industrial solid wastes, road dust, and atmospheric deposition as potential sources. Based on isotope ratio analysis (IRA) organic fertilizers and road dusts accounted for 74–100% and 0–24% of the total Hg input, while road dusts and solid wastes contributed for 0–80% and 19–100% of the Pb input. This study provides a reliable approach for heavy metal source apportionment in this particular peri-urban area, with a clear potential for future application in other regions.

Taxonomic and Thematic Organisation of Proper Name Conceptual Knowledge

Directory of Open Access Journals (Sweden)

Sebastian J. Crutch

2011-01-01

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

Taxonomic and thematic organisation of proper name conceptual knowledge.

Science.gov (United States)

Crutch, Sebastian J; Warrington, Elizabeth K

2011-01-01

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

Social Integration and Domestic Violence Support in an Indigenous Community: Women's Recommendations of Formal Versus Informal Sources of Support.

Science.gov (United States)

Gauthier, G Robin; Francisco, Sara C; Khan, Bilal; Dombrowski, Kirk

2018-05-01

Throughout North America, indigenous women experience higher rates of intimate partner violence and sexual violence than any other ethnic group, and so it is of particular importance to understand sources of support for Native American women. In this article, we use social network analysis to study the relationship between social integration and women's access to domestic violence support by examining the recommendations they would give to another woman in need. We ask two main questions: First, are less integrated women more likely to make no recommendation at all when compared with more socially integrated women? Second, are less integrated women more likely than more integrated women to nominate a formal source of support rather than an informal one? We use network data collected from interviews with 158 Canadian women residing in an indigenous community to measure their access to support. We find that, in general, less integrated women are less likely to make a recommendation than more integrated women. However, when they do make a recommendation, less integrated women are more likely to recommend a formal source of support than women who are more integrated. These results add to our understanding of how access to two types of domestic violence support is embedded in the larger set of social relations of an indigenous community.

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

Directory of Open Access Journals (Sweden)

Vikram Saini

Full Text Available BACKGROUND: Mycobacterium indicus pranii (MIP, popularly known as Mw, is a cultivable, non-pathogenic organism, which, based on its growth and metabolic properties, is classified in Runyon Group IV along with M. fortuitum, M. smegmatis and M. vaccae. The novelty of this bacterium was accredited to its immunological ability to undergo antigen driven blast transformation of leukocytes and delayed hypersensitivity skin test in leprosy patients, a disease endemic in the Indian sub-continent. Consequently, MIP has been extensively evaluated for its biochemical and immunological properties leading to its usage as an immunomodulator in leprosy and tuberculosis patients. However, owing to advances in sequencing and culture techniques, the citing of new strains with almost 100% similarity in the sequences of marker genes like 16S rRNA, has compromised the identity of MIP as a novel species. Hence, to define its precise taxonomic position, we have carried out polyphasic taxonomic studies on MIP that integrate its phenotypic, chemotaxonomic and molecular phylogenetic attributes. METHODOLOGY/PRINCIPAL FINDINGS: The comparative analysis of 16S rRNA sequence of MIP by using BLAST algorithm at NCBI (nr database revealed a similarity of > or =99% with M. intracellulare, M. arosiense, M. chimaera, M. seoulense, M. avium subsp. hominissuis, M. avium subsp. paratuberculosis and M. bohemicum. Further analysis with other widely used markers like rpoB and hsp65 could resolve the phylogenetic relationship between MIP and other closely related mycobacteria apart from M. intracellulare and M. chimaera, which shares > or =99% similarity with corresponding MIP orthologues. Molecular phylogenetic analysis, based on the concatenation of candidate orthologues of 16S rRNA, hsp65 and rpoB, also substantiated its distinctiveness from all the related organisms used in the analysis excluding M. intracellulare and M. chimaera with which it exhibited a close proximity. This

Taxonomic novelties within the genus Columnea (Gesneriaceae)

International Nuclear Information System (INIS)

Amaya Marquez, Marisol

2010-01-01

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

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

Science.gov (United States)

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

2017-05-01

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

Unified method to integrate and blend several, potentially related, sources of information for genetic evaluation.

Science.gov (United States)

Vandenplas, Jérémie; Colinet, Frederic G; Gengler, Nicolas

2014-09-30

A condition to predict unbiased estimated breeding values by best linear unbiased prediction is to use simultaneously all available data. However, this condition is not often fully met. For example, in dairy cattle, internal (i.e. local) populations lead to evaluations based only on internal records while widely used foreign sires have been selected using internally unavailable external records. In such cases, internal genetic evaluations may be less accurate and biased. Because external records are unavailable, methods were developed to combine external information that summarizes these records, i.e. external estimated breeding values and associated reliabilities, with internal records to improve accuracy of internal genetic evaluations. Two issues of these methods concern double-counting of contributions due to relationships and due to records. These issues could be worse if external information came from several evaluations, at least partially based on the same records, and combined into a single internal evaluation. Based on a Bayesian approach, the aim of this research was to develop a unified method to integrate and blend simultaneously several sources of information into an internal genetic evaluation by avoiding double-counting of contributions due to relationships and due to records. This research resulted in equations that integrate and blend simultaneously several sources of information and avoid double-counting of contributions due to relationships and due to records. The performance of the developed equations was evaluated using simulated and real datasets. The results showed that the developed equations integrated and blended several sources of information well into a genetic evaluation. The developed equations also avoided double-counting of contributions due to relationships and due to records. Furthermore, because all available external sources of information were correctly propagated, relatives of external animals benefited from the integrated

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

Science.gov (United States)

Graça, Márlon B; Morais, José W; Franklin, Elizabeth; Pequeno, Pedro A C L; Souza, Jorge L P; Bueno, Anderson Saldanha

2016-04-01

This study investigated the spatial distribution of an Amazonian fruit-feeding butterfly assemblage by linking species taxonomic and functional approaches. We hypothesized that: 1) vegetation richness (i.e., resources) and abundance of insectivorous birds (i.e., predators) should drive changes in butterfly taxonomic composition, 2) larval diet breadth should decrease with increase of plant species richness, 3) small-sized adults should be favored by higher abundance of birds, and 4) communities with eyespot markings should be able to exploit areas with higher predation pressure. Fruit-feeding butterflies were sampled with bait traps and insect nets across 25 km(2) of an Amazonian ombrophilous forest in Brazil. We measured larval diet breadth, adult body size, and wing marking of all butterflies. Our results showed that plant species richness explained most of the variation in butterfly taxonomic turnover. Also, community average diet breadth decreased with increase of plant species richness, which supports our expectations. In contrast, community average body size increased with the abundance of birds, refuting our hypothesis. We detected no influence of environmental gradients on the occurrence of species with eyespot markings. The association between butterfly taxonomic and functional composition points to a mediator role of the functional traits in the environmental filtering of butterflies. The incorporation of the functional approach into the analyses allowed for the detection of relationships that were not observed using a strictly taxonomic perspective and provided an extra insight into comprehending the potential adaptive strategies of butterflies. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

An Integrated Inductor For Parallel Interleaved Three-Phase Voltage Source Converters

DEFF Research Database (Denmark)

Gohil, Ghanshyamsinh Vijaysinh; Bede, Lorand; Teodorescu, Remus

2016-01-01

Three phase Voltage Source Converters (VSCs) are often connected in parallel to realize high current output converter system. The harmonic quality of the resultant switched output voltage can be improved by interleaving the carrier signals of these parallel connected VSCs. As a result, the line...... of the state-of-the-art filtering solution. The performance of the integrated inductor is also verified by the experimental measurements....

Does taxonomic diversity in indicator groups influence their effectiveness in identifying priority areas for species conservation?

DEFF Research Database (Denmark)

Bladt, Jesper Stentoft; Larsen, Frank Wugt; Rahbek, Carsten

2008-01-01

The identification of priority areas for biodiversity conservation is a cornerstone of systematic conservation planning. However, biodiversity, or even the distribution of all species, cannot be directly quantified, due to the inherent complexity of natural systems. Species indicator groups may...... serve as important tools for the identification of priority areas for conservation. Yet, it is unclear which factors make certain indicator groups perform better than others. In this study, using data on the Danish distribution of 847 species of plants, vertebrates and insects, we assessed whether...... the taxonomic diversity in species indicator groups influence their effectiveness in the identification of priority areas for species conservation. We tested whether indicator groups comprising a higher taxonomic diversity (i.e. indicator groups consisting of species from many different taxonomic groups...

Correlation of resource plays and biodiversity patterns: accumulation of organic-rich shale tracks taxonomic turnover

Science.gov (United States)

Eoff, Jennifer D.

2012-01-01

Similar paleogeographic and paleotectonic settings characterize most self-sourced shale hydrocarbon plays. Their deposition occurred within similar orders of magnitude of eustatic events and during geologic periods characterized by “warm” (or transitional) climates and calcitic seas. In addition, the stratigraphic occurrence of shale plays parallels certain historical patterns of marine metazoan biodiversity. Such strong agreement among several correlation tools elucidates why these resources may be limited to discrete intervals of geological time. Correlation of self-sourced shale with biodiversity trends indicates that the factors controlling the deposition of marine organic matter may not be independent of those that induced taxonomic turnover. Paleoecological changes promoted accumulation and preservation of Type II kerogen. Deposition of self-sourced shale appears to correspond to reductions in absolute biodiversity and declining percentages of bioturbating taxa, with concomitant increases in proportions of pelagic taxa relative to infaunal and epifaunal organisms. Whereas upwelling and anoxia may have contributed to the deposition of kerogen in source rocks throughout much of the sedimentary record, diminished consumption of biomass by benthic metazoans likely augmented the preservation of organic carbon during deposition of this shale type. Rapid tectonic-plate reconfiguration induced coeval events, creating basins with sufficiently high rates of accommodation creation necessary to preserve additional organic material accumulating as the heterotrophic benthos suffered in response to rapidly changing environments. Combining sea-level curves, paleogeography, climate, and seawater chemistry provides a first-order approximation of the distribution of potential self-sourced shale in the geologic record. A model that predicts the stratigraphic distribution of self-sourced-shale deposition can aid in exploration of continuous hydrocarbon accumulations in self-sourced

Laser-induced extreme UV radiation sources for manufacturing next-generation integrated circuits

International Nuclear Information System (INIS)

Borisov, V M; Vinokhodov, A Yu; Ivanov, A S; Kiryukhin, Yu B; Mishchenko, V A; Prokof'ev, A V; Khristoforov, O B

2009-01-01

The development of high-power discharge sources emitting in the 13.5±0.135-nm spectral band is of current interest because they are promising for applications in industrial EUV (extreme ultraviolet) lithography for manufacturing integrated circuits according to technological precision standards of 22 nm and smaller. The parameters of EUV sources based on a laser-induced discharge in tin vapours between rotating disc electrodes are investigated. The properties of the discharge initiation by laser radiation at different wavelengths are established and the laser pulse parameters providing the maximum energy characteristics of the EUV source are determined. The EUV source developed in the study emits an average power of 276 W in the 13.5±0.135-nm spectral band on conversion to the solid angle 2π sr in the stationary regime at a pulse repetition rate of 3000 Hz. (laser applications and other topics in quantum electronics)

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

Directory of Open Access Journals (Sweden)

Kumar Ambrish

2014-12-01

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

Photometric survey and taxonomic identifications of 92 near-Earth asteroids

Science.gov (United States)

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.

Standardizing metadata and taxonomic identification in metabarcoding studies.

Science.gov (United States)

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

2015-01-01

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

Integral migration and source term experiments on cement and bitumen waste forms

International Nuclear Information System (INIS)

Ewart, F.T.; Howse, R.M.; Sharpe, B.M.; Smith, A.J.; Thomason, H.P.; Williams, S.J.; Young, M.

1986-01-01

This is the final report of a programme of research which formed a part of the CEC joint research project into radionuclide migration in the geosphere (MIRAGE). This study addressed the aspects of integral migration and source term. The integral migration experiment simulated, in the laboratory, the intrusion of water into the repository, the leaching of radionuclides from two intermediate level wasteforms and the subsequent migration through the geosphere. The simulation consisted of a source of natural ground water which flowed over a sample of wasteform, at a controlled redox potential, and then through backfill and geological material packed in columns. The two wasteforms used here were cemented waste from the WAK plant at Karlsruhe, W. Germany and bitumenised intermediate concentrates from the Marcoule plant in France. The soluble fission products such as caesium wire rapidly released from the cemented waste but the actinides, and technetium in the reduced state, were retained in the wasteform. The release of all nuclides from the bitumenised waste was very low. (author)

Integral migration and source-term experiments on cement and bitumen waste forms

International Nuclear Information System (INIS)

Ewart, F.T.; Howse, R.M.; Sharpe, B.M.; Smith, A.J.; Thomason, H.P.; Williams, S.J.; Young, M.

1986-01-01

This is the final report of a programme of research which formed a part of the CEC joint research project into radionuclide migration in the geosphere (MIRAGE). This study addressed the aspects of integral migration and source term. The integral migration experiment simulated, in the laboratory, the intrusion of water into the repository, the leaching of radionuclides from two intermediate-level waste-forms and the subsequent migration through the geosphere. The simulation consisted of a source of natural ground water which flowed over a sample of waste-form, at a controlled redox potential, and then through backfill and geological material packed in columns. The two waste forms used here were cemented waste from the WAK plant at Karlsruhe in the Federal Republic of Germany and bitumenized intermediate concentrates from the Marcoule plant in France. The soluble fission products such as caesium were rapidly released from the cemented waste but the actinides, and technetium in the reduced state, were retained in the waste-form. The released of all nuclides from the bitumenized waste was very low

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Benjamin Stielow

2011-01-01

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

Mousetrap: An integrated, open-source mouse-tracking package.

Science.gov (United States)

Kieslich, Pascal J; Henninger, Felix

2017-10-01

Mouse-tracking - the analysis of mouse movements in computerized experiments - is becoming increasingly popular in the cognitive sciences. Mouse movements are taken as an indicator of commitment to or conflict between choice options during the decision process. Using mouse-tracking, researchers have gained insight into the temporal development of cognitive processes across a growing number of psychological domains. In the current article, we present software that offers easy and convenient means of recording and analyzing mouse movements in computerized laboratory experiments. In particular, we introduce and demonstrate the mousetrap plugin that adds mouse-tracking to OpenSesame, a popular general-purpose graphical experiment builder. By integrating with this existing experimental software, mousetrap allows for the creation of mouse-tracking studies through a graphical interface, without requiring programming skills. Thus, researchers can benefit from the core features of a validated software package and the many extensions available for it (e.g., the integration with auxiliary hardware such as eye-tracking, or the support of interactive experiments). In addition, the recorded data can be imported directly into the statistical programming language R using the mousetrap package, which greatly facilitates analysis. Mousetrap is cross-platform, open-source and available free of charge from https://github.com/pascalkieslich/mousetrap-os .

Determination of taxonomic status of chinese species of the genus clematis by using high performance liquid chromatography-mass spectrometry (HPLC-MS) technique

International Nuclear Information System (INIS)

Ishtiaq, M.; Ahmed, H.

2010-01-01

A comparative taxonomic study using chemometric and numerical taxonomic approaches on 15 populations of 12 species of major taxa of the genus Clematis, belonging to sections, Rectae, Clematis, Meclatis, Tubulosae and Viorna were analyzed by HPLC coupled with diode array detector and ESI-MS. The chemo diversity profile of saponins proved to be useful taxonomic markers for the genus and results are presented in pheno grams. The compound 'Huzhangoside D' was the most abundant in analyzed species of the genus. Numerical taxonomic study was also conducted based on phylogenetically informative characters which corroborated with chemical fingerprinting findings. The significance of chemical markers in taxonomic study as well as their correlation between morphology and chemical compound profile is also debated with its significant role in botanic drugs identification. (author)

Global Taxonomic Diversity of Living Reptiles

Science.gov (United States)

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

2013-01-01

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

Global taxonomic diversity of living reptiles.

Science.gov (United States)

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

2013-01-01

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

Global taxonomic diversity of living reptiles.

Directory of Open Access Journals (Sweden)

Daniel Pincheira-Donoso

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

Método para la construcción de una taxonomía: estructura base para riesgos en outsourcing de software

Directory of Open Access Journals (Sweden)

Gloria Piedad Gasca Hurtado

2011-01-01

Full Text Available Este artículo propone una taxonomía de riesgos enfocada en el ámbito de outsourcing de software. El objetivo es definir una estructura de clasificación de riesgos, relacionada con el proceso de outsourcing de software. La motivación está dada por la importancia que tiene la identificación de riesgos, y la ayuda que prestan las taxonomías al respecto, por lo cual se les conoce como una técnica efectiva que permite desarrollar una mejor gestión de riesgos. Este artículo incluye el método para construir la taxonomía (llamado MECT y la estructura de una taxonomía de riesgos para outsourcing de software.

Integrating renewable energy sources in the Portuguese power system

International Nuclear Information System (INIS)

Martins, Nuno; Cabral, Pedro; Azevedo, Helena

2012-01-01

The integration of large amounts of renewable energy is an important challenge for the future management of electric systems, since it affects the operation of the electric power system and the design of the transmission and distribution network infrastructure. This is specially due to the connection requirements of the renewable energy technologies, to the extension and adjustment of the grid infrastructure and to the identification of new solutions for operational reserve, in order to maintain the overall system flexibility and security. In this paper, the impact of high penetration of intermittent energy sources, expected in long term in the Portuguese Power System, is analysed and the operational reserve requirements to accomplish a reliable and reasonable electrical energy supply are identified. It was concluded that pumped storage power plants, special power plants with regulating capabilities, will have an important task to provide the operational reserve requirements of the Portuguese Power System. This technology assumes a fundamental role not only to ensure the adequate levels of security of supply but also to allow the maximum exploitation of the installed capacity in renewable energy sources. (authors)

A review of the taxonomic status and biology of the Cape Parrot ...

African Journals Online (AJOL)

A review of the taxonomic status and biology of the Cape Parrot Poicephalus robustus , with reference to the Brown-necked Parrot P. fuscicollis fuscicollis and the Grey-headed Parrot P. f. suahelicus.

Treelink: data integration, clustering and visualization of phylogenetic trees.

Science.gov (United States)

Allende, Christian; Sohn, Erik; Little, Cedric

2015-12-29

Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis. Treelink is a platform-independent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms. Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www.treelinkapp.com .

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

Science.gov (United States)

Lorenzini, Marilinda; Zapparoli, Giacomo

2016-02-01

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

The effect of source-axis distance on integral dose: implications for IMRT

International Nuclear Information System (INIS)

Keall, P.

2001-01-01

The source-axis distance (SAD) is a treatment machine design parameter that affects integral dose, dose rate and patient clearance. The aim of this work was to investigate the effect of source-axis distance on integral dose for conformal arc therapy. This work is part of a larger project to determine the ideal characteristics of a dedicated IMRT machine. The sensitivity of SAD to beam energy, PTV size, body size and PTV position were determined for conformal arc therapy. For the calculations performed here it was assumed that dose equals terma. The integral dose ratio (IDR) was used to quantify the calculation results. It was found that the IDR increases as both SAD and photon energy increase, though the dependence of IDR on SAD decreases as energy increases. The PTV size was found to have a negligible effect on the relationship between the SAD and IDR, however the body size does affect the relationship between the SAD and IDR. The position of the PTV within the body also affects the IDR. From dosimetric considerations alone, the larger the SAD, the better the possible dose distribution. The IDR for a very large SAD is increased by approximately 5% when compared with the IDR for 100 cm SAD. Similarly, the IDR for 100 cm SAD is approximately 5% higher than the IDR at 50 cm SAD. Copyright (2001) Australasian College of Physical Scientists and Engineers in Medicine

Integration of Heterogeneous Information Sources into a Knowledge Resource Management System for Lifelong Learning

NARCIS (Netherlands)

Demidova, Elena; Ternier, Stefaan; Olmedilla, Daniel; Duval, Erik; Dicerto, Michele; Stefanov, Krassen; Sacristán, Naiara

2007-01-01

Demidova, E., Ternier, S., Olmedilla, D., Duval, E., Dicerto, M., Stefanov, K., et al. (2007). Integration of Heterogeneous Information Sources into a Knowledge Resource Management System for Lifelong. TENCompetence Workshop on Service Oriented Approaches and Lifelong Competence Development

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

Science.gov (United States)

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

Science.gov (United States)

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

Uberon, an integrative multi-species anatomy ontology

Science.gov (United States)

2012-01-01

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org PMID:22293552

Taxonomic and ad hoc categorization within the two cerebral hemispheres.

Science.gov (United States)

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

2015-01-01

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

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria.

Science.gov (United States)

Hamedi, Javad; Mohammadipanah, Fatemeh

2015-02-01

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

Character Selection During Interactive Taxonomic Identification: “Best Characters”

Directory of Open Access Journals (Sweden)

Nadia Talent

2014-03-01

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

Regulatory Oversight of Radioactive Sources through the Integrated Management of Safety and Security

International Nuclear Information System (INIS)

Horvath, K.

2016-01-01

The Hungarian Atomic Energy Authority (HAEA) has full regulatory competence; its mission is to oversee the safety and security of all the peaceful applications of atomic energy. All the radioactive sources having activity above the exemption level is registered and licensed both from safety and security points of view. The Hungarian central register of radioactive sources contains about 7,000 radioactive sources and 450 license holders. In order to use its limited resources the HAEA has decided to introduce an integrated regulatory oversight programme. Accordingly, during the licensing process and inspection activities the HAEA intends to assess both safety and security aspects at the same time. The article describes the Hungarian the various applications of radioactive materials, and summarizes the preparation activities of the HAEA. (author)

PANDORA: keyword-based analysis of protein sets by integration of annotation sources.

Science.gov (United States)

Kaplan, Noam; Vaaknin, Avishay; Linial, Michal

2003-10-01

Recent advances in high-throughput methods and the application of computational tools for automatic classification of proteins have made it possible to carry out large-scale proteomic analyses. Biological analysis and interpretation of sets of proteins is a time-consuming undertaking carried out manually by experts. We have developed PANDORA (Protein ANnotation Diagram ORiented Analysis), a web-based tool that provides an automatic representation of the biological knowledge associated with any set of proteins. PANDORA uses a unique approach of keyword-based graphical analysis that focuses on detecting subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA currently supports SwissProt keywords, NCBI Taxonomy, InterPro entries and the hierarchical classification terms from ENZYME, SCOP and GO databases. The integrated study of several annotation sources simultaneously allows a representation of biological relations of structure, function, cellular location, taxonomy, domains and motifs. PANDORA is also integrated into the ProtoNet system, thus allowing testing thousands of automatically generated clusters. We illustrate how PANDORA enhances the biological understanding of large, non-uniform sets of proteins originating from experimental and computational sources, without the need for prior biological knowledge on individual proteins.

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

Science.gov (United States)

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.

JBioWH: an open-source Java framework for bioinformatics data integration.

Science.gov (United States)

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh.

Diagnostics of microdischarge-integrated plasma sources for display and materials processing

International Nuclear Information System (INIS)

Tachibana, K; Kishimoto, Y; Kawai, S; Sakaguchi, T; Sakai, O

2005-01-01

Two different types of microdischarge-integrated plasma sources have been operated at around the atmospheric pressure range. The discharge characteristics were diagnosed by optical emission spectroscopy (OES), laser absorption spectroscopy (LAS) and microwave transmission (MT) techniques. The dynamic spatiotemporal behaviour of excited atoms was analysed using OES and LAS and the temporal behaviour of the electron density was estimated using the MT method. In Ar and Xe/Ne gases, waveforms of the MT signal followed the current waveform in the rise period and lasted longer according to the recombination losses. However, in He the waveform followed the density of metastable atoms, reflecting the production of a large amount of electrons by the Penning ionization process with impurities. The estimated peak electron density in those plasma sources is of the order of 10 12 cm -3 , and the metastable atom density can reach 10 13 cm -3 . Thus, it is suggested that these sources can be potentially applied to convenient material processing tools of large area operated stably at atmospheric pressure

JBioWH: an open-source Java framework for bioinformatics data integration

Science.gov (United States)

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh PMID:23846595

A calderón-preconditioned single source combined field integral equation for analyzing scattering from homogeneous penetrable objects

KAUST Repository

Valdé s, Felipe; Andriulli, Francesco P.; Bagci, Hakan; Michielssen, Eric

2011-01-01

A new regularized single source equation for analyzing scattering from homogeneous penetrable objects is presented. The proposed equation is a linear combination of a Calderón-preconditioned single source electric field integral equation and a

An integrative taxonomic study of Pavanelliella spp. (Monogenoidea, Dactylogyridae) with the description of a new species from the nasal cavities of an Amazon pimelodid catfish.

Science.gov (United States)

Aguiar, Julio C; Maia, Antônio A M; Silva, Marcia R M; Ceccarelli, Paulo S; Domingues, Marcus V; Adriano, Edson A

2017-12-01

The present study is an integrative taxonomic analysis of Pavanelliella spp. (Monogenoidea, Dactylogyridae), and describes a new species from the nasal cavities of the Amazonian pimelodid catfish Brachyplatystoma rousseauxii (Siluriformes Pimelodidae) from the Tapajós River (Amazon Basin, Pará state, Brazil). Pavanelliella jarii sp. n. is characterized by the presence of 3-4 rings in the male copulatory organ, the absence of rings around the vaginal atrium and by its sinuous vaginal canal, which sometimes forms 0.5-1 rings in the distal portion. The sequencing of the small subunit ribosomal DNA (ssrDNA) and internal transcribed spacer 1 (ITS-1) of three species of Pavanelliella, Vancleaveus cicinnus, and an undetermined dactylogyrid allowed the phylogenetic reconstruction of these dactylogyrids. The analysis indicated that P. jarii sp. n. is closely related to Pavanelliella takemotoi and Pavanelliella pavanellii, which formed a sister clade to ancylodiscoidines parasites of siluriform fish from the Oriental and Afrotropical regions. The analysis also corroborated the non-monophyly of Ancyrocephalinae, revealing that ancylodiscoidines arose between ancyrocephalines lineages, in a sister relationship to pseudodactylogyrines+marine ancyrocephalines+ancyrocephalines parasites of afrotropical perciforms+dactylogyrines. Cladistical analysis indicates that the haptoral anchor/bar complex has been lost several times in the evolutionary history of Dactylogyridae. The analysis also indicated that Dactylogyrus is polyphyletic, as Acolpenteron ureteroecetes and Dactylogyroides longicirrus arose between the three lineages formed by Dactylogyrus spp. Copyright © 2017 Elsevier B.V. All rights reserved.

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform

Science.gov (United States)

Moutsatsos, Ioannis K.; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J.; Jenkins, Jeremy L.; Holway, Nicholas; Tallarico, John; Parker, Christian N.

2016-01-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an “off-the-shelf,” open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community. PMID:27899692

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform.

Science.gov (United States)

Moutsatsos, Ioannis K; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J; Jenkins, Jeremy L; Holway, Nicholas; Tallarico, John; Parker, Christian N

2017-03-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.

A calderón-preconditioned single source combined field integral equation for analyzing scattering from homogeneous penetrable objects

KAUST Repository

Valdés, Felipe

2011-06-01

A new regularized single source equation for analyzing scattering from homogeneous penetrable objects is presented. The proposed equation is a linear combination of a Calderón-preconditioned single source electric field integral equation and a single source magnetic field integral equation. The equation is immune to low-frequency and dense-mesh breakdown, and free from spurious resonances. Unlike dual source formulations, this equation involves operator products that cannot be discretized using standard procedures for discretizing standalone electric, magnetic, and combined field operators. Instead, the single source equation proposed here is discretized using a recently developed technique that achieves a well-conditioned mapping from div- to curl-conforming function spaces, thereby fully respecting the space mapping properties of the operators involved, and guaranteeing accuracy and stability. Numerical results show that the proposed equation and discretization technique give rise to rapidly convergent solutions. They also validate the equation\\'s resonant free character. © 2006 IEEE.

Niche differentiation in nitrogen metabolism among methanotrophs within an operational taxonomic unit.

Science.gov (United States)

Hoefman, Sven; van der Ha, David; Boon, Nico; Vandamme, Peter; De Vos, Paul; Heylen, Kim

2014-04-04

The currently accepted thesis on nitrogenous fertilizer additions on methane oxidation activity assumes niche partitioning among methanotrophic species, with activity responses to changes in nitrogen content being dependent on the in situ methanotrophic community structure Unfortunately, widely applied tools for microbial community assessment only have a limited phylogenetic resolution mostly restricted to genus level diversity, and not to species level as often mistakenly assumed. As a consequence, intragenus or intraspecies metabolic versatility in nitrogen metabolism was never evaluated nor considered among methanotrophic bacteria as a source of differential responses of methane oxidation to nitrogen amendments. We demonstrated that fourteen genotypically different Methylomonas strains, thus distinct below the level at which most techniques assign operational taxonomic units (OTU), show a versatile physiology in their nitrogen metabolism. Differential responses, even among strains with identical 16S rRNA or pmoA gene sequences, were observed for production of nitrite and nitrous oxide from nitrate or ammonium, nitrogen fixation and tolerance to high levels of ammonium, nitrate, and hydroxylamine. Overall, reduction of nitrate to nitrite, nitrogen fixation, higher tolerance to ammonium than nitrate and tolerance and assimilation of nitrite were general features. Differential responses among closely related methanotrophic strains to overcome inhibition and toxicity from high nitrogen loads and assimilation of various nitrogen sources yield competitive fitness advantages to individual methane-oxidizing bacteria. Our observations proved that community structure at the deepest phylogenetic resolution potentially influences in situ functioning.

A novel integrated approach for the hazardous radioactive dust source terms estimation in future nuclear fusion power plants.

Science.gov (United States)

Poggi, L A; Malizia, A; Ciparisse, J F; Gaudio, P

2016-10-01

An open issue still under investigation by several international entities working on the safety and security field for the foreseen nuclear fusion reactors is the estimation of source terms that are a hazard for the operators and public, and for the machine itself in terms of efficiency and integrity in case of severe accident scenarios. Source term estimation is a crucial key safety issue to be addressed in the future reactors safety assessments, and the estimates available at the time are not sufficiently satisfactory. The lack of neutronic data along with the insufficiently accurate methodologies used until now, calls for an integrated methodology for source term estimation that can provide predictions with an adequate accuracy. This work proposes a complete methodology to estimate dust source terms starting from a broad information gathering. The wide number of parameters that can influence dust source term production is reduced with statistical tools using a combination of screening, sensitivity analysis, and uncertainty analysis. Finally, a preliminary and simplified methodology for dust source term production prediction for future devices is presented.

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

Science.gov (United States)

Raia, P.; Carotenuto, F.; Passaro, F.; Piras, P.; Fulgione, D.; Werdelin, L.; Saarinen, J.; Fortelius, M.

2013-01-01

A classic question in evolutionary biology concerns the tempo and mode of lineage evolution. Considered variously in relation to resource utilization, intrinsic constraints or hierarchic level, the question of how evolutionary change occurs in general has continued to draw the attention of the field for over a century and a half. Here we use the largest species-level phylogeny of Coenozoic fossil mammals (1031 species) ever assembled and their body size estimates, to show that body size and taxonomic diversification rates declined from the origin of placentals towards the present, and very probably correlate to each other. These findings suggest that morphological and taxic diversifications of mammals occurred hierarchically, with major shifts in body size coinciding with the birth of large clades, followed by taxonomic diversification within these newly formed clades. As the clades expanded, rates of taxonomic diversification proceeded independently of phenotypic evolution. Such a dynamic is consistent with the idea, central to the Modern Synthesis, that mammals radiated adaptively, with the filling of adaptive zones following the radiation. PMID:23173207

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

Science.gov (United States)

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

A new hard X-ray source discovered by INTEGRAL: IGR J16442-554

DEFF Research Database (Denmark)

Bozzo, E.; Ferrigno, C.; Chenevez, Jérôme

2009-01-01

During a key program observation of the inner Galactic disc performed between 2009-08-30 14:04 and 2009-09-01 12:03 (UTC), a new source was discovered in the INTEGRAL/IBIS mosaic image. The best localization is RA: 251.088 DEC: -55.808, with a 90% error radius of 3.6 arcmin. The source, IGR J16442......-5548, is detected with a significance of 7 sigma in the 20-40 keV energy band and of 5 sigma in the 40-100 keV energy band. The corresponding flux is about 7 mCrab. The source is not detected in the JEM-X monitor: upper limits at 3 sigma c.l. are respectively 2 and 5 mCrab in the 3-10 keV and 10-25 keV energy bands...

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

Science.gov (United States)

Fagan, Matthew E.; Willig, Michael R.

2016-01-01

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or

Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes.

Science.gov (United States)

Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

2016-01-01

Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Variation

DNA - An integrated open-source optimization platform for thermo-fluid systems

DEFF Research Database (Denmark)

Pierobon, Leonardo; Wronski, Jorrit; Elmegaard, Brian

2014-01-01

This paper presents developments and new features added to the simulation tool Dynamic Network Analysis. This open-source software is the result of ongoing development at the Department of Mechanical Engineering, Technical University of Denmark since 1988. Ever since, it has been employed to model...... to extend the capabilities of the software, while at the same time decreasing computational time. Dynamic Network Analysis can now solve non-convex optimization problems by virtue of the fully-embedded genetic algorithm. Moreover, the thermophysical fluid property library has been extended with more than...... 110 fluids by interfacing CoolProp, a high-accuracy open-source property package for pure and pseudo-pure fluids, as well as humid air. Furthermore, the use as time integrator for other tools is demonstrated. The new features are unveiled in two case studies. The first example covers the optimization...

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

Science.gov (United States)

Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

2013-01-01

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

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

Directory of Open Access Journals (Sweden)

Benjamín Quiroz-Martínez

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

VISUALIZATION FROM INTRAOPERATIVE SWEPT-SOURCE MICROSCOPE-INTEGRATED OPTICAL COHERENCE TOMOGRAPHY IN VITRECTOMY FOR COMPLICATIONS OF PROLIFERATIVE DIABETIC RETINOPATHY.

Science.gov (United States)

Gabr, Hesham; Chen, Xi; Zevallos-Carrasco, Oscar M; Viehland, Christian; Dandrige, Alexandria; Sarin, Neeru; Mahmoud, Tamer H; Vajzovic, Lejla; Izatt, Joseph A; Toth, Cynthia A

2018-01-10

To evaluate the use of live volumetric (4D) intraoperative swept-source microscope-integrated optical coherence tomography in vitrectomy for proliferative diabetic retinopathy complications. In this prospective study, we analyzed a subgroup of patients with proliferative diabetic retinopathy complications who required vitrectomy and who were imaged by the research swept-source microscope-integrated optical coherence tomography system. In near real time, images were displayed in stereo heads-up display facilitating intraoperative surgeon feedback. Postoperative review included scoring image quality, identifying different diabetic retinopathy-associated pathologies and reviewing the intraoperatively documented surgeon feedback. Twenty eyes were included. Indications for vitrectomy were tractional retinal detachment (16 eyes), combined tractional-rhegmatogenous retinal detachment (2 eyes), and vitreous hemorrhage (2 eyes). Useful, good-quality 2D (B-scans) and 4D images were obtained in 16/20 eyes (80%). In these eyes, multiple diabetic retinopathy complications could be imaged. Swept-source microscope-integrated optical coherence tomography provided surgical guidance, e.g., in identifying dissection planes under fibrovascular membranes, and in determining residual membranes and traction that would benefit from additional peeling. In 4/20 eyes (20%), acceptable images were captured, but they were not useful due to high tractional retinal detachment elevation which was challenging for imaging. Swept-source microscope-integrated optical coherence tomography can provide important guidance during surgery for proliferative diabetic retinopathy complications through intraoperative identification of different complications and facilitation of intraoperative decision making.

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

Science.gov (United States)

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

Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

Science.gov (United States)

Guo, Xue; Zhou, Xishu; Hale, Lauren; Yuan, Mengting; Feng, Jiajie; Ning, Daliang; Shi, Zhou; Qin, Yujia; Liu, Feifei; Wu, Liyou; He, Zhili; Van Nostrand, Joy D.; Liu, Xueduan; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong

2018-01-01

Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010–2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices. PMID:29904372

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

Science.gov (United States)

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

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

NARCIS (Netherlands)

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

1999-01-01

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

NoSQL data model for semi-automatic integration of ethnomedicinal plant data from multiple sources.

Science.gov (United States)

Ningthoujam, Sanjoy Singh; Choudhury, Manabendra Dutta; Potsangbam, Kumar Singh; Chetia, Pankaj; Nahar, Lutfun; Sarker, Satyajit D; Basar, Norazah; Das Talukdar, Anupam

2014-01-01

Sharing traditional knowledge with the scientific community could refine scientific approaches to phytochemical investigation and conservation of ethnomedicinal plants. As such, integration of traditional knowledge with scientific data using a single platform for sharing is greatly needed. However, ethnomedicinal data are available in heterogeneous formats, which depend on cultural aspects, survey methodology and focus of the study. Phytochemical and bioassay data are also available from many open sources in various standards and customised formats. To design a flexible data model that could integrate both primary and curated ethnomedicinal plant data from multiple sources. The current model is based on MongoDB, one of the Not only Structured Query Language (NoSQL) databases. Although it does not contain schema, modifications were made so that the model could incorporate both standard and customised ethnomedicinal plant data format from different sources. The model presented can integrate both primary and secondary data related to ethnomedicinal plants. Accommodation of disparate data was accomplished by a feature of this database that supported a different set of fields for each document. It also allowed storage of similar data having different properties. The model presented is scalable to a highly complex level with continuing maturation of the database, and is applicable for storing, retrieving and sharing ethnomedicinal plant data. It can also serve as a flexible alternative to a relational and normalised database. Copyright © 2014 John Wiley & Sons, Ltd.

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

Science.gov (United States)

Walsh, Stephen Joseph; Meador, Michael R.

1998-01-01

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

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

Science.gov (United States)

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

2016-01-01

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

Microcontroller based implementation of fuel cell and battery integrated hybrid power source

International Nuclear Information System (INIS)

Fahad, A.; Ali, S.M.; Bhatti, A.A.; Nasir, M

2013-01-01

This paper presents the implementation of a digitally controlled hybrid power source system, composed of fuel cell and battery. Use of individual fuel cell stacks as a power source, encounters many problems in achieving the desired load characteristics. A battery integrated, digitally controlled hybrid system is proposed for high pulse requirements. The proposed hybrid power source fulfils these peak demands with efficient flow of energy as compared to individual operations of fuel cell or battery system. A dc/dc converter is applied which provides an optimal control of power flow among fuel cell, battery and load. The proposed system efficiently overcomes the electrochemical constraints like over current, battery leakage current, and over and under voltage dips. By formulation of an intelligent algorithm and incorporating a digital technology (AVR Microcontroller), an efficient control is achieved over fuel cell current limit, battery charge, voltage and current. The hybrid power source is tested and analyzed by carrying out simulations using MATLAB simulink. Along with the attainment of desired complex load profiles, the proposed design can also be used for power enhancement and optimization for different capacities. (author)

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

Science.gov (United States)

Alsop, Eric B; Raymond, Jason

2013-01-01

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

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

Directory of Open Access Journals (Sweden)

Eric B Alsop

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

A Practice Approach of Multi-source Geospatial Data Integration for Web-based Geoinformation Services

Science.gov (United States)

Huang, W.; Jiang, J.; Zha, Z.; Zhang, H.; Wang, C.; Zhang, J.

2014-04-01

Geospatial data resources are the foundation of the construction of geo portal which is designed to provide online geoinformation services for the government, enterprise and public. It is vital to keep geospatial data fresh, accurate and comprehensive in order to satisfy the requirements of application and development of geographic location, route navigation, geo search and so on. One of the major problems we are facing is data acquisition. For us, integrating multi-sources geospatial data is the mainly means of data acquisition. This paper introduced a practice integration approach of multi-source geospatial data with different data model, structure and format, which provided the construction of National Geospatial Information Service Platform of China (NGISP) with effective technical supports. NGISP is the China's official geo portal which provides online geoinformation services based on internet, e-government network and classified network. Within the NGISP architecture, there are three kinds of nodes: national, provincial and municipal. Therefore, the geospatial data is from these nodes and the different datasets are heterogeneous. According to the results of analysis of the heterogeneous datasets, the first thing we do is to define the basic principles of data fusion, including following aspects: 1. location precision; 2.geometric representation; 3. up-to-date state; 4. attribute values; and 5. spatial relationship. Then the technical procedure is researched and the method that used to process different categories of features such as road, railway, boundary, river, settlement and building is proposed based on the principles. A case study in Jiangsu province demonstrated the applicability of the principle, procedure and method of multi-source geospatial data integration.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Flexible taxonomic assignment of ambiguous sequencing reads

Directory of Open Access Journals (Sweden)

Jansson Jesper

2011-01-01

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

Integrated nanohole array surface plasmon resonance sensing device using a dual-wavelength source

International Nuclear Information System (INIS)

Escobedo, C; Vincent, S; Choudhury, A I K; Campbell, J; Gordon, R; Brolo, A G; Sinton, D

2011-01-01

In this paper, we demonstrate a compact integrated nanohole array-based surface plasmon resonance sensing device. The unit includes a LED light source, driving circuitry, CCD detector, microfluidic network and computer interface, all assembled from readily available commercial components. A dual-wavelength LED scheme was implemented to increase spectral diversity and isolate intensity variations to be expected in the field. The prototype shows bulk sensitivity of 266 pixel intensity units/RIU and a limit of detection of 6 × 10 −4 RIU. Surface binding tests were performed, demonstrating functionality as a surface-based sensing system. This work is particularly relevant for low-cost point-of-care applications, especially those involving multiple tests and field studies. While nanohole arrays have been applied to many sensing applications, and their suitability to device integration is well established, this is the first demonstration of a fully integrated nanohole array-based sensing device.

Una taxonomía de modelos de desarrollo sustentable

Directory of Open Access Journals (Sweden)

Darcy Tetreault

2004-01-01

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

Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae

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Simone Policena Rosa

2014-01-01

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

HPCAT: an integrated high-pressure synchrotron facility at the Advanced Photon Source

International Nuclear Information System (INIS)

Shen, Guoyin; Chow, Paul; Xiao, Yuming; Sinogeikin, Stanislav; Meng, Yue; Yang, Wenge; Liermann, Hans-Peter; Shebanova, Olga; Rod, Eric; Bommannavar, Arunkumar; Mao, Ho-Kwang

2008-01-01

The high pressure collaborative access team (HPCAT) was established to advance cutting edge, multidisciplinary, high-pressure (HP) science and technology using synchrotron radiation at sector 16 of the Advanced Photon Source of Argonne National Laboratory. The integrated HPCAT facility has established four operating beamlines in nine hutches. Two beamlines are split in energy space from the insertion device (16ID) line, whereas the other two are spatially divided into two fans from the bending magnet (16BM) line. An array of novel X-ray diffraction and spectroscopic techniques has been integrated with HP and extreme temperature instrumentation at HPCAT. With a multidisciplinary approach and multi-institution collaborations, the HP program at the HPCAT has been enabling myriad scientific breakthroughs in HP physics, chemistry, materials, and Earth and planetary sciences.

An integrated approach to assess heavy metal source apportionment in peri-urban agricultural soils.

Science.gov (United States)

Huang, Ying; Li, Tingqiang; Wu, Chengxian; He, Zhenli; Japenga, Jan; Deng, Meihua; Yang, Xiaoe

2015-12-15

Three techniques (Isotope Ratio Analysis, GIS mapping, and Multivariate Statistical Analysis) were integrated to assess heavy metal pollution and source apportionment in peri-urban agricultural soils. The soils in the study area were moderately polluted with cadmium (Cd) and mercury (Hg), lightly polluted with lead (Pb), and chromium (Cr). GIS Mapping suggested Cd pollution originates from point sources, whereas Hg, Pb, Cr could be traced back to both point and non-point sources. Principal component analysis (PCA) indicated aluminum (Al), manganese (Mn), nickel (Ni) were mainly inherited from natural sources, while Hg, Pb, and Cd were associated with two different kinds of anthropogenic sources. Cluster analysis (CA) further identified fertilizers, waste water, industrial solid wastes, road dust, and atmospheric deposition as potential sources. Based on isotope ratio analysis (IRA) organic fertilizers and road dusts accounted for 74-100% and 0-24% of the total Hg input, while road dusts and solid wastes contributed for 0-80% and 19-100% of the Pb input. This study provides a reliable approach for heavy metal source apportionment in this particular peri-urban area, with a clear potential for future application in other regions. Copyright © 2015 Elsevier B.V. All rights reserved.

A taxonomic survey of Saudi Arabian Red Sea octocorals (Cnidaria: Alcyonacea)

KAUST Repository

Haverkort-Yeh, Roxanne D.

2013-05-04

A preliminary survey of Saudi Arabian Alcyonacea is presented, which combines classical taxonomy, multilocus molecular barcodes, and in situ photographs. We explored 14 locations along the west coast of the Kingdom of Saudi Arabia to assess the regional taxonomic diversity of non-gorgonian alcyonaceans. We collected samples from a total of 74 colonies, distributed among four families: 18 colonies of Alcyoniidae, 14 of Nephtheidae, 9 of Tubiporidae, and 33 of Xeniidae. We sequenced the octocorals using multiple nuclear [ribosomal Internal Transcribed Spacers (ITS) and ATP Synthetase Subunit α (ATPSα)] and mitochondrial [MutS homolog (mtMutS) and Cytochrome C Oxidase subunit one (COI)] loci, providing molecular barcodes which will: (1) allow direct comparison of biodiversity from this location to others for which molecular data are available, and (2) facilitate future identifications of these taxa. Finally, this preliminary phylogeny of sampled taxa provides insights on the resolution of mitochondrial versus nuclear loci, and highlights octocoral taxa that require further taxonomic attention. © 2013 Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg.

Taxonomic and chemical assessment of exceptionally abundant rock mine biofilm

Directory of Open Access Journals (Sweden)

Karolina Tomczyk-Żak

2017-08-01

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

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

Directory of Open Access Journals (Sweden)

Peter eTóth

2016-03-01

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

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

Science.gov (United States)

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

2013-01-01

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

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

Directory of Open Access Journals (Sweden)

Elad Segev

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

Generating millimeter-wave Bessel beam with orbital angular momentum using reflective-type metasurface inherently integrated with source

Science.gov (United States)

Shen, Yizhu; Yang, Jiawei; Meng, Hongfu; Dou, Wenbin; Hu, Sanming

2018-04-01

Metasurfaces, orbital angular momenta (OAM), and non-diffractive Bessel beams have been attracting worldwide research. Combining the benefits of these three promising techniques, this paper proposes a metasurface-based reflective-type approach to generate a first-order Bessel beam carrying OAM. To validate this approach, a millimeter-wave metasurface is analyzed, designed, fabricated, and measured. Experimental results agree well with simulation. Moreover, this reflective-type metasurface, generating a Bessel beam with OAM, is inherently integrated with a planar feeding source in the same single-layer printed circuit board. Therefore, the proposed design features low profile, low cost, easy integration with front-end active circuits, and no alignment error between the feeding source and the metasurface.

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

Science.gov (United States)

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.

Comparación visual de grandes jerarquías: El caso de las de taxonomías biológicas

Directory of Open Access Journals (Sweden)

Liliana Sancho-Chavarría

2017-03-01

Full Text Available La visualización y el análisis de las taxonomías biológicas es un reto monumental: las taxonomías biológicas son voluminosas, pueden cambiar con el tiempo conforme la comunidad científica hace nuevos descubrimientos, la información taxonómica está dispersa en todo el mundo, está incompleta y existen diferentes versiones de las taxonomías ya que los científicos utilizan diferentes criterios de clasificación. Para entender y documentar mejor la biodiversidad, así como para apoyar su conservación, es necesario curar e integrar esta información. Es aquí donde la comparación de grandes jerarquías se convierte en una herramienta sumamente útil. Hasta el momento, la investigación sobre este tema incluye el estado del arte sobre la visualización de la información y técnicas de comparación de jerarquías, el desarrollo de una herramienta de visualización de jerarquías mediante la técnica de árboles de conos y la caracterización de las tareas del trabajo taxonómico que inducen cambios en las taxonomías. Se identificaron 10 tareas: identificar congruencia, identificar correcciones, identificar nuevos nodos, obtener una visión global de los cambios, resumir cambios, encontrar inconsistencias, aplicar filtros, obtener detalles, enfocarse y editar. La contribución de esta investigación es comparar y visualizar las taxonomías biológicas mediante la consideración sistemática de dicha caracterización de las tareas de los usuarios, lo cual es un enfoque novedoso para el desarrollo de propuestas de visualización en el dominio de taxonomías biológicas.

Open source projects as incubators of innovation: From niche phenomenon to integral part of the software industry

OpenAIRE

Schrape, Jan-Felix

2017-01-01

Over the last 20 years, open source development has become an integral part of the software industry and a key component of the innovation strategies of all major IT providers. Against this backdrop, this paper seeks to develop a systematic overview of open source communities and their socio-economic contexts. I begin with a reconstruction of the genesis of open source software projects and their changing relation- ships to established IT companies. This is followed by the identification of f...

Regional Integrated Tenets to Reinforce the Safety and Security of Radioactive Sources (ClearZone)

International Nuclear Information System (INIS)

Salzer, P.

2003-01-01

The EURATOM Research and Training Programme on Nuclear Energy includes 2 main fields - fusion energy research and management of radioactive waste, radiation protection and other activities of nuclear technology and safety.Seven instruments (mechanisms) for projects management are used - 'Network of Excellence' (NOE); 'Integrated Project' (IP); 'Specific Targeted Research Project' or 'Specific Targeted Training Project' (STREP); 'Co-ordination Action' (CA); Actions to Promote and Develop Human Resources and Mobility Specific Support Actions; Integrated Infrastructure Initiatives. Two consecutive sub-projects are proposed: 'small' - countries of the Visegrad four + Austrian participant -within the 6th FP 'Specific Supported Actions' and 'large' - participation of more countries in the region - more oriented to practical implementation of the 'small' project findings - intention to use the 6th Framework Programme resources to co-financing the implementation activities. The main objectives are: to create effective lines of defense (prevention -detection - categorization - transport - storage) against malicious use of radioactive sources; to achieve and maintain a high level of safety and security of radioactive sources; to arise the radioactive sources management safety and security culture at the Central European region. Consortium of 11 organisations from Czech Republic, Slovak Republic, Austria, Hungary and Poland is established for the Project implementation. The Project task are grouped in the following areas: legislation, infrastructure, practices; metallurgical industry, cross border control; instrumentation and metrology; information system

INVESTIGATING THE OPTICAL COUNTERPART CANDIDATES OF FOUR INTEGRAL SOURCES LOCALIZED WITH CHANDRA

International Nuclear Information System (INIS)

Özbey Arabacı, Mehtap; Kalemci, Emrah; Tomsick, John A.; Bodaghee, Arash; Halpern, Jules; Chaty, Sylvain; Rodriguez, Jerome; Rahoui, Farid

2012-01-01

We report on the optical spectroscopic follow-up observations of the candidate counterparts to four INTEGRAL sources: IGR J04069+5042, IGR J06552–1146, IGR J21188+4901, and IGR J22014+6034. The candidate counterparts were determined with Chandra, and the optical observations were performed with 1.5 m RTT-150 telescope (TÜBİTAK National Observatory, Antalya, Turkey) and 2.4 m Hiltner Telescope (MDM Observatory, Kitt Peak, Arizona). Our spectroscopic results show that one of the two candidates of IGR J04069+5042 and the one observed for IGR J06552–1146 could be active late-type stars in RS CVn systems. However, according to the likelihood analysis based on Chandra and INTEGRAL, two optically weaker sources in the INTEGRAL error circle of IGR J06552–1146 have higher probabilities to be the actual counterpart. The candidate counterparts of IGR J21188+4901 are classified as an active M-type star and a late-type star. Among the optical spectra of four candidates of IGR J22014+6034, two show Hα emission lines, one is a late-type star, and the other is an M type. The likelihood analysis favors a candidate with no distinguishing features in the optical spectrum. Two of the candidates classified as M-type dwarfs, are similar to some IGR candidates claimed to be symbiotic stars. However, some of the prominent features of symbiotic systems are missing in our spectra, and their NIR colors are not consistent with those expected for giants. We consider the IR colors of all IGR candidates claimed to be symbiotic systems and find that low-resolution optical spectrum may not be enough for conclusive identification.

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

NARCIS (Netherlands)

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

The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and

Dynamic pricing based on a cloud computing framework to support the integration of renewable energy sources

OpenAIRE

Rajeev Thankappan Nair; Ashok Sankar

2014-01-01

Integration of renewable energy sources into the electric grid in the domestic sector results in bidirectional energy flow from the supply side of the consumer to the grid. Traditional pricing methods are difficult to implement in such a situation of bidirectional energy flow and they face operational challenges on the application of price-based demand side management programme because of the intermittent characteristics of renewable energy sources. In this study, a dynamic pricing method usi...

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

Science.gov (United States)

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

2016-03-16

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

Particle Filter with Integrated Voice Activity Detection for Acoustic Source Tracking

Directory of Open Access Journals (Sweden)

Anders M. Johansson

2007-01-01

Full Text Available In noisy and reverberant environments, the problem of acoustic source localisation and tracking (ASLT using an array of microphones presents a number of challenging difficulties. One of the main issues when considering real-world situations involving human speakers is the temporally discontinuous nature of speech signals: the presence of silence gaps in the speech can easily misguide the tracking algorithm, even in practical environments with low to moderate noise and reverberation levels. A natural extension of currently available sound source tracking algorithms is the integration of a voice activity detection (VAD scheme. We describe a new ASLT algorithm based on a particle filtering (PF approach, where VAD measurements are fused within the statistical framework of the PF implementation. Tracking accuracy results for the proposed method is presented on the basis of synthetic audio samples generated with the image method, whereas performance results obtained with a real-time implementation of the algorithm, and using real audio data recorded in a reverberant room, are published elsewhere. Compared to a previously proposed PF algorithm, the experimental results demonstrate the improved robustness of the method described in this work when tracking sources emitting real-world speech signals, which typically involve significant silence gaps between utterances.

Support Vector Machine Based Tool for Plant Species Taxonomic Classification

OpenAIRE

Manimekalai .K; Vijaya.MS

2014-01-01

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

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

OpenAIRE

2012-01-01

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

Update of the list of QPS‐recommended biological agents intentionally added to food or feed as notified to EFSA 4: suitability of taxonomic units notified to EFSA until March 2016

OpenAIRE

EFSA Panel on Biological Hazards (BIOHAZ); Allende, Ana; Bolton, Declan; Chemaly, Marianne; Davies, Robert; Fernandez Escamez, Pablo Salvador; Girones, Rosina; Herman, Lieve; Koutsoumanis, Konstantinos; Lindqvist, Roland; Nørrung, Birgit; Ricci, Antonia; Robertson, Lucy; Ru, Giuseppe; Sanaa, Moez

2016-01-01

EFSA was requested to assess the safety of a broad range of biological agents in the context of notifications for market authorisation as sources of food and feed additives, enzymes and plant protection products. The qualified presumption of safety (QPS) assessment was developed to provide a harmonised generic preassessment to support safety risk assessments performed by EFSA's scientific Panels. The safety of unambiguously defined biological agents (at the highest taxonomic unit appropriate ...

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

Science.gov (United States)

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

2014-08-01

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

Low Power Consumption Wireless Sensor Communication System Integrated with an Energy Harvesting Power Source

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Vlad MARSIC

2013-01-01

Full Text Available This paper presents the testing results of a wireless sensor communication system with low power consumption integrated with an energy harvesting power source. The experiments focus on the system’s capability to perform continuous monitoring and to wirelessly transmit the data acquired from the sensors to a user base station, for realization of completely battery-free wireless sensor system. Energy harvesting technologies together with system design optimization for power consumption minimization ensure the system’s energy autonomous capability demonstrated in this paper by presenting the promising testing results achieved following its integration with structural health monitoring and body area network applications.

Integrative taxonomy for continental-scale terrestrial insect observations.

Directory of Open Access Journals (Sweden)

Cara M Gibson

Full Text Available Although 21(st century ecology uses unprecedented technology at the largest spatio-temporal scales in history, the data remain reliant on sound taxonomic practices that derive from 18(th century science. The importance of accurate species identifications has been assessed repeatedly and in instances where inappropriate assignments have been made there have been costly consequences. The National Ecological Observatory Network (NEON will use a standardized system based upon an integrative taxonomic foundation to conduct observations of the focal terrestrial insect taxa, ground beetles and mosquitoes, at the continental scale for a 30 year monitoring program. The use of molecular data for continental-scale, multi-decadal research conducted by a geographically widely distributed set of researchers has not been evaluated until this point. The current paper addresses the development of a reference library for verifying species identifications at NEON and the key ways in which this resource will enhance a variety of user communities.

Integrative Taxonomy for Continental-Scale Terrestrial Insect Observations

Science.gov (United States)

Gibson, Cara M.; Kao, Rebecca H.; Blevins, Kali K.; Travers, Patrick D.

2012-01-01

Although 21st century ecology uses unprecedented technology at the largest spatio-temporal scales in history, the data remain reliant on sound taxonomic practices that derive from 18th century science. The importance of accurate species identifications has been assessed repeatedly and in instances where inappropriate assignments have been made there have been costly consequences. The National Ecological Observatory Network (NEON) will use a standardized system based upon an integrative taxonomic foundation to conduct observations of the focal terrestrial insect taxa, ground beetles and mosquitoes, at the continental scale for a 30 year monitoring program. The use of molecular data for continental-scale, multi-decadal research conducted by a geographically widely distributed set of researchers has not been evaluated until this point. The current paper addresses the development of a reference library for verifying species identifications at NEON and the key ways in which this resource will enhance a variety of user communities. PMID:22666362

Integrated Wavelength-Tunable Light Source for Optical Gas Sensing Systems

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Bin Li

2015-01-01

Full Text Available A compact instrument consisting of a distributed feedback laser (DFB at 1.65 μm was developed as a light source for gas sensing systems using tunable diode laser absorption spectroscopy (TDLAS technique. The wavelength of laser is tuned by adjusting the laser working temperature and injection current, which are performed by self-developed temperature controller and current modulator respectively. Stability test shows the fluctuation of the laser temperature is within the range of ±0.02°C. For gas detection experiments, the wavelength is tuned around the gas absorption line by adjusting laser temperature and is then shifted periodically to scan across the absorption line by the laser current modulator, which generates a 10 Hz saw wave signal. In addition, the current modulator is able to generate sine wave signal for gas sensing systems using wavelength modulation spectroscopy (WMS technique involving extraction of harmonic signals. The spectrum test proves good stability that the spectrum was measured 6 times every 10 minutes at the constant temperature and current condition. This standalone instrument can be applied as a light source for detection systems of different gases by integrating lasers at corresponding wavelength.

The effect of taxonomic resolution on the assessment of ecological water quality classes

NARCIS (Netherlands)

Schmidt-Kloiber, A.; Nijboer, R.C.

2004-01-01

Within the ecological assessment of running waters based on benthic macroinvertebrates different levels of taxonomic resolution (species, genus, family and higher) are in use. Although assessment systems are often developed with detailed data on species level, water managers and other end-users

Campus and community micro grids integration of building integrated photovoltaic renewable energy sources: Case study of Split 3 area, Croatia - part A

Directory of Open Access Journals (Sweden)

Gašparović Goran

2016-01-01

Full Text Available Micro grids interconnect loads and distributed energy resources as a single controllable entity. New installations of renewable energy sources (RES in urban areas, such as Building Integrated Photovoltaic (BIPV, provide opportunities to increase energy independence and diversify energy sources in the energy system. This paper explores the integration of RES into two case study communities in an urban agglomeration to provide optimal conditions to meet a share of the electrical loads. Energy planning case studies for decentralized generation of renewable energy are conducted in H2RES energy planning software for hourly energy balances. The results indicate that BIPV and PV in the case study communities can cover about 17% of the recorded electrical demand of both areas. On a yearly basis, there will be a 0.025 GWh surplus of PV production with a maximum value of 1.25 MWh in one hour of operation unless grid storage is used. This amounts to a total investment cost of 13.36 million EUR. The results are useful for proposing future directions for the various case study communities targeting sustainable development.

A taxonomic, functional, and phylogenetic perspective on the community assembly of passerine birds along an elevational gradient in southwest China.

Science.gov (United States)

He, Xuelian; Luo, Kang; Brown, Calum; Lin, Luxiang

2018-03-01

Integrating multiple facets of biodiversity to describe spatial and temporal distribution patterns is one way of revealing the mechanisms driving community assembly. We assessed the species, functional, and phylogenetic composition and structure of passerine bird communities along an elevational gradient both in wintering and breeding seasons in the Ailao Mountains, southwest China, in order to identify the dominant ecological processes structuring the communities and how these processes change with elevation and season. Our research confirms that the highest taxonomic diversity, and distinct community composition, was found in the moist evergreen broadleaf forest at high elevation in both seasons. Environmental filtering was the dominant force at high elevations with relatively cold and wet climatic conditions, while the observed value of mean pairwise functional and phylogenetic distances of low elevation was constantly higher than expectation in two seasons, suggested interspecific competition could play the key role at low elevations, perhaps because of relative rich resource result from complex vegetation structure and human-induced disturbance. Across all elevations, there was a trend of decreasing intensity of environmental filtering whereas increasing interspecific competition from wintering season to breeding season. This was likely due to the increased resource availability but reproduction-associated competition in the summer months. In general, there is a clear justification for conservation efforts to protect entire elevational gradients in the Ailao Mountains, given the distinct taxonomic, functional, and phylogenetic compositions and also elevational migration pattern in passerine bird communities.

Analysis of hard X-ray emission from selected very high energy γ-ray sources observed with INTEGRAL

International Nuclear Information System (INIS)

Hoffmann, Agnes Irene Dorothee

2009-01-01

A few years ago, the era of very high energy γ-ray astronomy started, when the latest generation of Imaging Atmospheric Cherenkov Telescopes (IACT) like H.E.S.S. began to operate and to resolve the sources of TeV emission. Identifications via multi-wavelength studies reveal that the detected sources are supernova remnants and active galactic nuclei, but also pulsar wind nebulae and a few binaries. One widely discussed open question is, how these sources are able to accelerate particles to such high energies. The understanding of the underlying particle distribution, the acceleration processes taking place, and the knowledge of the radiation processes which produce the observed emission, is, therefore, of crucial interest. Observations in the hard X-ray domain can be a key to get information on these particle distributions and processes. Important for this thesis are the TeV and the hard X-ray range. The two instruments, H.E.S.S. and INTEGRAL, whose data were used, are, therefore, described in detail. The main part of this thesis is focused on the X-ray binary system LS 5039/RX J1826.2-1450. It was observed in several energy ranges. The nature of the compact object is still not known, and it was proposed either to be a microquasar system or a non-accreting pulsar system. The observed TeV emission is modulated with the orbital cycle. Several explanations for this variability have been discussed in recent years. The observations with INTEGRAL presented in this thesis have provided new information to solve this question. Therefore, a search for a detection in the hard X-ray range and for its orbital dependence was worthwhile. Since LS 5039 is a faint source and the sky region where it is located is crowded, a very careful, non-standard handling of the INTEGRAL data was necessary, and a cross-checking with other analysis methods was essential to provide reliable results. We found that LS 5039 is emitting in the hard X-ray energy range. A flux rate and an upper flux

Analysis of hard X-ray emission from selected very high energy {gamma}-ray sources observed with INTEGRAL

Energy Technology Data Exchange (ETDEWEB)

Hoffmann, Agnes Irene Dorothee

2009-11-13

A few years ago, the era of very high energy {gamma}-ray astronomy started, when the latest generation of Imaging Atmospheric Cherenkov Telescopes (IACT) like H.E.S.S. began to operate and to resolve the sources of TeV emission. Identifications via multi-wavelength studies reveal that the detected sources are supernova remnants and active galactic nuclei, but also pulsar wind nebulae and a few binaries. One widely discussed open question is, how these sources are able to accelerate particles to such high energies. The understanding of the underlying particle distribution, the acceleration processes taking place, and the knowledge of the radiation processes which produce the observed emission, is, therefore, of crucial interest. Observations in the hard X-ray domain can be a key to get information on these particle distributions and processes. Important for this thesis are the TeV and the hard X-ray range. The two instruments, H.E.S.S. and INTEGRAL, whose data were used, are, therefore, described in detail. The main part of this thesis is focused on the X-ray binary system LS 5039/RX J1826.2-1450. It was observed in several energy ranges. The nature of the compact object is still not known, and it was proposed either to be a microquasar system or a non-accreting pulsar system. The observed TeV emission is modulated with the orbital cycle. Several explanations for this variability have been discussed in recent years. The observations with INTEGRAL presented in this thesis have provided new information to solve this question. Therefore, a search for a detection in the hard X-ray range and for its orbital dependence was worthwhile. Since LS 5039 is a faint source and the sky region where it is located is crowded, a very careful, non-standard handling of the INTEGRAL data was necessary, and a cross-checking with other analysis methods was essential to provide reliable results. We found that LS 5039 is emitting in the hard X-ray energy range. A flux rate and an upper

Taxonomic Study of Endemic Species of Astragalus L. (Fabaceae of India

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Lal Babu Chaudhary

2007-09-01

Full Text Available The goal of the study is to provide a comprehensive taxonomic account of 12 endemic species of Astragalus occurring in India. The north-west Himalayan region harbors more endemic species (11 spp. than eastern Himalaya where only two species have been noticed from Sikkim. Jammu & Kashmir with seven species occupies first position in the list of endemic species. Five species are strictly confined to Jammu & Kashmir, while two species to Uttaranchal and one species to Sikkim. Only one species (A. tenuicaulis is found in both the Himalayas, otherwise the elements of both the Himalayas are quite distinct from each other. Most of the endemic species of Astragalus have been observed quite rare in the nature except A. uttaranchalensis. In the present investigation, A. turgidus, a newly described species from Jammu & Kashmir, has been found conspecific to A. kashmirensis. For each species nomenclature, description, distribution, phenology, taxonomic notes, list of the investigated materials, distribution map and figures are given. A new combination A. falconeri var. pilosus (Ali Chaudhary has been proposed based on A. hoffmeisteri var. pilosus Ali. A new endemic species A. nainitalensis from Kumaon Himalaya has also been described here along with illustrations.

Non point source pollution modelling in the watershed managed by Integrated Conctructed Wetlands: A GIS approach.

OpenAIRE

Vyavahare, Nilesh

2008-01-01

The non-point source pollution has been recognised as main cause of eutrophication in Ireland (EPA Ireland, 2001). Integrated Constructed Wetland (ICW) is a management practice adopted in Annestown stream watershed, located in the south county of Waterford in Ireland, used to cleanse farmyard runoff. Present study forms the annual pollution budget for the Annestown stream watershed. The amount of pollution from non-point sources flowing into the stream was simulated by using GIS techniques; u...

Methods of formation of efficiency indexes of electric power sources integration in regional electric power systems

International Nuclear Information System (INIS)

Marder, L.I.; Myzin, A.I.

1993-01-01

A methodic approach to the grounding of the integration process efficiency within the Unified electric power system is given together with the selection of a rational areal structure and concentration of power-generating source capacities. Formation of an economic functional according to alternative scenavies including the cost components taking account of the regional interests is considered. A method for estimation and distribution of the effect from electric power production integration in the power systems under new economic conditions is proposed

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

Directory of Open Access Journals (Sweden)

Nubia França da Silva Giehl

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

Testing for variation in taxonomic extinction probabilities: a suggested methodology and some results

Science.gov (United States)

Conroy, M.J.; Nichols, J.D.

1984-01-01

Several important questions in evolutionary biology and paleobiology involve sources of variation in extinction rates. In all cases of which we are aware, extinction rates have been estimated from data in which the probability that an observation (e.g., a fossil taxon) will occur is related both to extinction rates and to what we term encounter probabilities. Any statistical method for analyzing fossil data should at a minimum permit separate inferences on these two components. We develop a method for estimating taxonomic extinction rates from stratigraphic range data and for testing hypotheses about variability in these rates. We use this method to estimate extinction rates and to test the hypothesis of constant extinction rates for several sets of stratigraphic range data. The results of our tests support the hypothesis that extinction rates varied over the geologic time periods examined. We also present a test that can be used to identify periods of high or low extinction probabilities and provide an example using Phanerozoic invertebrate data. Extinction rates should be analyzed using stochastic models, in which it is recognized that stratigraphic samples are random varlates and that sampling is imperfect

PHYSICAL, PHYSICOCHEMICAL AND TAXONOMIC CHARACTERIZATION OF PSIDIUM ARAÇA RADDI

Directory of Open Access Journals (Sweden)

Maria do Rosário Fátima Padilha

2016-10-01

Full Text Available New research has stimulated a large reevaluation of species with regards to the use of fruits from native plants. Araçá (a small Brazilian guava-like fruit is found scattered in the wild in Pernambuco/Brazil. There is a scarcity of detailed studies on such regional fruit trees, especially the Psidium araçá Raddi species, whereas there is an enormous possibility to explore the potential offered by these fruits, such as in the field of gastronomy, where the search for new ingredients and exotic flavors associated with functional properties has been increasing. This article aimed to evaluate the physical, physicochemical and taxonomic characterization of araçá obtained from different agricultural regions of Pernambuco in order to investigate the possibility of developing new products from this native fruit. The taxonomic identification confirmed that all collected material belonged to the species P. araçá Raddi. An average weight of 7.45 g/fruit was observed. With respect to pH, values between 3.17 and 3.48 were found, and the acidity as a percentage of citric acid was on the order of 0.96% to 0.99%. It was shown that the P. araçá Raddi fruit has a desirable quality for the food industry, presenting excellent conditions for the development of formulations of high commercial value and promising application in the national gastronomy.

Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

Science.gov (United States)

Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

2015-02-01

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages. Copyright © 2014 Elsevier Inc. All rights reserved.

Development of an Air-Source Heat Pump Integrated with a Water Heating / Dehumidification Module

Energy Technology Data Exchange (ETDEWEB)

Rice, C Keith [ORNL; Uselton, Robert B. [Lennox Industries, Inc; Shen, Bo [ORNL; Baxter, Van D [ORNL; Shrestha, Som S [ORNL

2014-01-01

A residential-sized dual air-source integrated heat pump (AS-IHP) concept is under development in partnership between ORNL and a manufacturer. The concept design consists of a two-stage air-source heat pump (ASHP) coupled on the air distribution side with a separate novel water heating/dehumidification (WH/DH) module. The motivation for this unusual equipment combination is the forecast trend for home sensible loads to be reduced more than latent loads. Integration of water heating with a space dehumidification cycle addresses humidity control while performing double-duty. This approach can be applied to retrofit/upgrade applications as well as new construction. A WH/DH module capable of ~1.47 L/h water removal and ~2 kW water heating capacity was assembled by the manufacturer. A heat pump system model was used to guide the controls design; lab testing was conducted and used to calibrate the models. Performance maps were generated and used in a TRNSYS sub-hourly simulation to predict annual performance in a well-insulated house. Annual HVAC/WH energy savings of ~35% are predicted in cold and hot-humid U.S. climates compared to a minimum efficiency baseline.

Taxonomic assessment of seaweed community from the coastal areas of Bintulu, Sarawak, Malaysia

Directory of Open Access Journals (Sweden)

Mohd Hafizbillah Zawawi

2015-04-01

Full Text Available Basic taxonomic information forms the important basis for the documentation, resource management and utilization of marine biodiversity such as seaweeds. A taxonomic assessment of seaweeds in the coastal areas of Bintulu, Sarawak, East Malaysia, was conducted monthly from May 2011 to May 2012. Species composition was recorded following NaGISA protocols, direct observation, and SCUBA and snorkeling techniques. A total of 54 species were identified, classified into Rhodophyta (23 species, Chlorophyta (16 species and Phaeophyta (15 species. The highest abundance was recorded at Kuala Similajau (25 species while the lowest was recorded at Kuala Nyalau (12 species. As the present study was conducted by examining species collected from both rocky shores and the reef area for the first time, a higher number of species was documented compared to previous studies conducted in the same general area but focusing only on particular habitats. Thirty species found in the current survey represent new records for the locality including some with economic potentials.

On the Prospects and Concerns of Integrating Open Source Software Environment in Software Engineering Education

Science.gov (United States)

Kamthan, Pankaj

2007-01-01

Open Source Software (OSS) has introduced a new dimension in software community. As the development and use of OSS becomes prominent, the question of its integration in education arises. In this paper, the following practices fundamental to projects and processes in software engineering are examined from an OSS perspective: project management;…

An edit script for taxonomic classifications

Directory of Open Access Journals (Sweden)

Valiente Gabriel

2005-08-01

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

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

Science.gov (United States)

Dunham, Philip; Dunham, Frances

1995-01-01

Individual differences in children's conceptual strategies at 3 years of age were predicted by aspects of children's behavior and language at 13 and 24 months. Production of pointing gestures at 13 months and nouns and attributive adjectives at 24 months were positively associated with the use of a taxonomic matching strategy at 3 years of age.…

Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis.

Science.gov (United States)

Bandyopadhyay, Sanghamitra; Mallik, Saurav

2018-01-01

Identification of combinatorial markers from multiple data sources is a challenging task in bioinformatics. Here, we propose a novel computational framework for identifying significant combinatorial markers ( s) using both gene expression and methylation data. The gene expression and methylation data are integrated into a single continuous data as well as a (post-discretized) boolean data based on their intrinsic (i.e., inverse) relationship. A novel combined score of methylation and expression data (viz., ) is introduced which is computed on the integrated continuous data for identifying initial non-redundant set of genes. Thereafter, (maximal) frequent closed homogeneous genesets are identified using a well-known biclustering algorithm applied on the integrated boolean data of the determined non-redundant set of genes. A novel sample-based weighted support ( ) is then proposed that is consecutively calculated on the integrated boolean data of the determined non-redundant set of genes in order to identify the non-redundant significant genesets. The top few resulting genesets are identified as potential s. Since our proposed method generates a smaller number of significant non-redundant genesets than those by other popular methods, the method is much faster than the others. Application of the proposed technique on an expression and a methylation data for Uterine tumor or Prostate Carcinoma produces a set of significant combination of markers. We expect that such a combination of markers will produce lower false positives than individual markers.

Integrated spatiotemporal characterization of dust sources and outbreaks in Central and East Asia

Science.gov (United States)

Darmenova, Kremena T.

The potential of atmospheric dust aerosols to modify the Earth's environment and climate has been recognized for some time. However, predicting the diverse impact of dust has several significant challenges. One is to quantify the complex spatial and temporal variability of dust burden in the atmosphere. Another is to quantify the fraction of dust originating from human-made sources. This thesis focuses on the spatiotemporal characterization of sources and dust outbreaks in Central and East Asia by integrating ground-based data, satellite multisensor observations, and modeling. A new regional dust modeling system capable of operating over a span of scales was developed. The modeling system consists of a dust module DuMo, which incorporates several dust emission schemes of different complexity, and the PSU/NCAR mesoscale model MM5, which offers a variety of physical parameterizations and flexible nesting capability. The modeling system was used to perform for the first time a comprehensive study of the timing, duration, and intensity of individual dust events in Central and East Asia. Determining the uncertainties caused by the choice of model physics, especially the boundary layer parameterization, and the dust production scheme was the focus of our study. Implications to assessments of the anthropogenic dust fraction in these regions were also addressed. Focusing on Spring 2001, an analysis of routine surface meteorological observations and satellite multi-sensor data was carried out in conjunction with modeling to determine the extent to which integrated data set can be used to characterize the spatiotemporal distribution of dust plumes at a range of temporal scales, addressing the active dust sources in China and Mongolia, mid-range transport and trans-Pacific, long-range transport of dust outbreaks on a case-by-case basis. This work demonstrates that adequate and consistent characterization of individual dust events is central to establishing a reliable

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

Science.gov (United States)

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 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.

Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae)

OpenAIRE

Wagner,Warren; Krakos,Kyra; Hoch,Peter C.

2013-01-01

Abstract The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had in...

Caloplaca subpallida (Teloschistaceae, a lichen species new to Poland: distribution, ecology and taxonomic affinities

Directory of Open Access Journals (Sweden)

Katarzyna Szczepańska

2013-03-01

Full Text Available Caloplaca subpallida is reported from basic and altered ultrabasic rocks (i.e. basalt, greenstone, and serpentinite at nine sites in SW Poland. A detailed description of the species and a discussion on its taxonomic affinities are provided.

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

International Nuclear Information System (INIS)

Sharawy, S.; Karakish, E.

2015-01-01

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

Technical note: Efficient online source identification algorithm for integration within a contamination event management system

Science.gov (United States)

Deuerlein, Jochen; Meyer-Harries, Lea; Guth, Nicolai

2017-07-01

Drinking water distribution networks are part of critical infrastructures and are exposed to a number of different risks. One of them is the risk of unintended or deliberate contamination of the drinking water within the pipe network. Over the past decade research has focused on the development of new sensors that are able to detect malicious substances in the network and early warning systems for contamination. In addition to the optimal placement of sensors, the automatic identification of the source of a contamination is an important component of an early warning and event management system for security enhancement of water supply networks. Many publications deal with the algorithmic development; however, only little information exists about the integration within a comprehensive real-time event detection and management system. In the following the analytical solution and the software implementation of a real-time source identification module and its integration within a web-based event management system are described. The development was part of the SAFEWATER project, which was funded under FP 7 of the European Commission.

Commutativity of the source generation procedure and integrable semi-discretizations: the two-dimensional Leznov lattice

International Nuclear Information System (INIS)

Hu Juan; Yu Guofu; Tam, Hon-Wah

2012-01-01

The source generation procedure (SGP) is applied to a y-directional discrete version and an x-directional discrete version of the Leznov lattice. Consequently, a y-discrete Leznov lattice equation with self-consistent sources (y-discrete Leznov ESCS) and an x-discrete Leznov ESCS are presented. Also utilizing the SGP, a new type of Leznov lattice equation with self-consistent sources (new Leznov ESCS) is derived. It is interesting that the two semi-discrete Leznov ESCS produced constitute a y-discretization for the Leznov ESCS given by Wang et al (2007 J. Phys. A: Math. Theor. 40 12691) and an x-discretization for the new Leznov ESCS, respectively. This means that the commutativity of SGP and integrable semi-discretizations is valid for the two-dimensional Leznov lattice equation. (paper)

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

Science.gov (United States)

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

Integrating Gigabit ethernet cameras into EPICS at Diamond light source

International Nuclear Information System (INIS)

Cobb, T.

2012-01-01

At Diamond Light Source a range of cameras are used to provide images for diagnostic purposes in both the accelerator and photo beamlines. The accelerator and existing beamlines use Point Grey Flea and Flea2 Firewire cameras. We have selected Gigabit Ethernet cameras supporting GigE Vision for our new photon beamlines. GigE Vision is an interface standard for high speed Ethernet cameras which encourages inter-operability between manufacturers. This paper describes the challenges encountered while integrating GigE Vision cameras from a range of vendors into EPICS. GigE Vision cameras appear to be more reliable than the Firewire cameras, and the simple cabling makes much easier to move the cameras to different positions. Upcoming power over Ethernet versions of the cameras will reduce the number of cables still further

Non-native vascular plants from Canary Islands (Spain): nomenclatural and taxonomical adjustments

OpenAIRE

Verloove, F.

2013-01-01

Se propone correcciones taxonómicas y nomenclaturales respecto a 88 taxones no nativos de la lista de plantas vasculares de las Islas Canarias (España). Non-native vascular plants from Canary Islands (Spain): nomenclatural and taxonomical adjustments. Corrections and other adjustments are proposed for 88 non-native taxa from the checklist of vascular plants from the Canary Islands (Spain).

Evaluation of stormwater micropollutant source control and end-of-pipe control strategies using an uncertainty-calibrated integrated dynamic simulation model

DEFF Research Database (Denmark)

Vezzaro, Luca; Sharma, Anitha Kumari; Ledin, Anna

2015-01-01

(copper, zinc) and organic compounds (fluoranthene). MP fluxes were estimated by using an integrated dynamic model, in combination with stormwater quality measurements. MP sources were identified by using GIS land usage data, runoff quality was simulated by using a conceptual accumulation/washoff model......The estimation of micropollutant (MP) fluxes in stormwater systems is a fundamental prerequisite when preparing strategies to reduce stormwater MP discharges to natural waters. Dynamic integrated models can be important tools in this step, as they can be used to integrate the limited data provided...... by monitoring campaigns and to evaluate the performance of different strategies based on model simulation results. This study presents an example where six different control strategies, including both source-control and end-of-pipe treatment, were compared. The comparison focused on fluxes of heavy metals...

Taxonomic etymology – in search of inspiration

Directory of Open Access Journals (Sweden)

Piotr Jozwiak

2015-07-01

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

Low Power Consumption Wireless Sensor Communication System Integrated with an Energy Harvesting Power Source

OpenAIRE

Vlad MARSIC; Alessandro GIULIANO; Meiling ZHU

2013-01-01

This paper presents the testing results of a wireless sensor communication system with low power consumption integrated with an energy harvesting power source. The experiments focus on the system’s capability to perform continuous monitoring and to wirelessly transmit the data acquired from the sensors to a user base station, for realization of completely battery-free wireless sensor system. Energy harvesting technologies together with system design optimization for power consumption minimiza...

Taxonomic value of stem anatomical characters in classification of some Adonis (Ranunculaceae species in Iran

Directory of Open Access Journals (Sweden)

Majid Ghorbani Nohooji

2011-06-01

(A. aestivalis, A. flammea and A. dentata were evaluated using numerical taxonomic methods. Obtained results demonstrated that simultaneous application of both qualitative and relative characters offers a better chance in species delimitation in future researches.

The Identification, Types, Taxonomic Orders, Biodiversity and Importance of Aquatic Insects

OpenAIRE

J.F.N. Abowei; B.R. Ukoroije

2012-01-01

The identification, types, taxonomic orders, biodiversity and importance of aquatic insects was reviewed to facilitate sustainable culture fisheries management and practice. Aquatic insects contribute significantly to fresh water ecosystems, one of many groups of organisms that, together, must be considered in the study of aquatic ecology. As such their study may be a significant part of understanding the ecological state of a given ecosystem and in gauging how that ecosystem will respond to ...

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

Science.gov (United States)

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

2011-05-01

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

Electrical hubs: An effective way to integrate non-dispatchable renewable energy sources with minimum impact to the grid

International Nuclear Information System (INIS)

Perera, A.T.D.; Nik, Vahid M.; Mauree, Dasaraden; Scartezzini, Jean-Louis

2017-01-01

Highlights: • A novel method introduced to optimize Electrical Hubs. • Novel dispatch based on fuzzy control and finite state machines. • Evaluating sensitivity of three performance indices for system autonomy. • Multi objective optimization considering system autonomy-cost. • Electrical Hubs can cover above 60% of the demand using wind and Solar PV. - Abstract: A paradigm change in energy system design tools, energy market, and energy policy is required to attain the target levels in renewable energy integration and in minimizing pollutant emissions in power generation. Integrating non-dispatchable renewable energy sources such as solar and wind energy is vital in this context. Distributed generation has been identified as a promising method to integrate Solar PV (SPV) and wind energy into grid in recent literature. Distributed generation using grid-tied electrical hubs, which consist of Internal Combustion Generator (ICG), non-dispatchable energy sources (i.e., wind turbines and SPV panels) and energy storage for providing the electricity demand in Sri Lanka is considered in this study. A novel dispatch strategy is introduced to address the limitations in the existing methods in optimizing grid-integrated electrical hubs considering real time pricing of the electricity grid and curtailments in grid integration. Multi-objective optimization is conducted for the system design considering grid integration level and Levelized Energy Cost (LEC) as objective functions to evaluate the potential of electrical hubs to integrate SPV and wind energy. The sensitivity of grid curtailments, energy market, price of wind turbines and SPV panels on Pareto front is evaluated subsequently. Results from the Pareto analysis demonstrate the potential of electrical hubs to cover more than 60% of the annual electricity demand from SPV and wind energy considering stringent grid curtailments. Such a share from SPV and wind energy is quite significant when compared to direct grid

Redatuming controlled-source electromagnetic data using Stratton–Chu type integral transformations

DEFF Research Database (Denmark)

Zhdanov, Michael; Cai, Hongzhu

2016-01-01

We present a new method of analyzing controlled-source electromagnetic (CSEM) data based on redatuming of the observed data from the actual receivers into the virtual receivers. We use the Stratton–Chu type integral transform to calculate the EM field in the virtual receivers. The virtual receivers...... can be placed at any desirable position, including close to the target, which increases the sensitivity of the EM data to the target. The developed method provides an effective model-based interpolation/extrapolation tool for electromagnetic field data. This paper demonstrates that redatuming can...... be used for designing the optimized CSEM survey configuration. The numerical examples, for the Kevin Dome Electromagnetic Project Site, illustrate the practical effectiveness of the developed method....

Towards a Terahertz Room-Temperature Integrated Source

DEFF Research Database (Denmark)

Leo, Giuseppe; Gérard, Jean-Michel; Reitzenstein, Stephan

2011-01-01

We aim at a radically new continuous-wave, electrically pumped THz emitter. Compared to existing THz sources, this source will bring together several advantages that are far from being simultaneously available in any existing source today: compactness, roomtemperature operation, output power around...

Taxonomic revision and phylogenetic analyses of rubber powdery mildew fungi.

Science.gov (United States)

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

2017-04-01

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

Asian longhorned beetle complicates the relationship between taxonomic diversity and pest vulnerability in street tree assemblages

Data.gov (United States)

U.S. Environmental Protection Agency — Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to...

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

Directory of Open Access Journals (Sweden)

Ivan A. Savinov

2014-12-01

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

Taxonomía de los modelos y metodologías de desarrollo de software más utilizados

OpenAIRE

J. Cervantes Ojeda; María del Carmen Gómez Fuentes

2012-01-01

A través de una recopilación y análisis de los principales modelos de desarrollo de software existentes, proponemos una taxonomía que los integra con el fin de facilitar la e lección de un modelo apropiado para cada proyecto en particular. Una buena elección de modelo (correctamente aplicado) ahorra tiempo y mejora la calidad de los sistemas que se producen. Sin embargo, la amplia variedad de modelos y metodologías en el mundo del desarrollo de software, dificulta esta elección. La taxonomía ...

Cremastosperma (and other evolutionary digressions) : Molecular phylogenetic, biogeographic, and taxonomic studies in Neotropical Annonaceae

NARCIS (Netherlands)

Pirie, Michael David

2005-01-01

Results are presented of research on a family of flowering plants, the Annonaceae, species of which are found in tropical rainforest across the world. The project focussed on one group of species, the genus Cremastosperma, which is found in the South and Central American tropics. A taxonomic

Environmental Scanning Electron Microscopy as a Useful Tool for Taxonomical Documentation of Parasitical Helminths

Czech Academy of Sciences Publication Activity Database

Tihlaříková, Eva; Neděla, Vilém; Mašová, Š.

2016-01-01

Roč. 22, S3 (2016), s. 1178-1179 ISSN 1431-9276 R&D Projects: GA ČR(CZ) GA14-22777S Institutional support: RVO:68081731 Keywords : parasitical Helminths * ESEM * taxonomical documentation Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.891, year: 2016

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

Science.gov (United States)

Tanner, Kristie; Martí, Jose Manuel; Belliure, Josabel; Fernández-Méndez, Mar; Molina-Menor, Esther; Peretó, Juli; Porcar, Manuel

2018-02-01

Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp. and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Evaluation of integrity of radiation sources of nuclear gauges; Avaliacao da integridade de fontes radioativas de medidores nucleares

Energy Technology Data Exchange (ETDEWEB)

Torohate, Wiclif Francisco

2016-11-01

Nuclear equipment meters are mainly used in the industry in quality control and process control. The principle of operation consists in a shielded radioactive source together with a radiation detector such that the radiation interacts with the material to be analyzed before reaching the detector, providing real time data. Can be as their fixed and mobile mobility, the unique properties of ionizing radiation are used in three basic modes, transmission, backscatter or dispersion or induced (reactive). With the advancement and technological modernization in the world, the demand for nuclear gauges becomes increasingly larger. Currently in Brazil there are about 465 process control plants and 21 portable systems and Mozambique about 45 facilities using nuclear gauges. This font registration is done through a process called source inventory that allows also to know the category of the source, the danger or risk to human health that the source offers. The handling of this equipment requires personnel, certified, skilled and well trained in radiation protection area in accordance with the requirements of the various CNEN Rules. Due to the presence of radioactive source and because these devices are used by workers risk because there external radiation. In this context, we made the smear test in two fixed meters from the IRD industry laboratory, which determines the integrity of the source package, mandatory item in periodic integrity testing of the radiation source of this type of device. A set of procedures is made for its implementation as an evaluation of the radiological risk by radiological survey. It was intended to contribute to the learning handling and safe use of these meters. (author)

Large scale integration of intermittent renewable energy sources in the Greek power sector

International Nuclear Information System (INIS)

Voumvoulakis, Emmanouil; Asimakopoulou, Georgia; Danchev, Svetoslav; Maniatis, George; Tsakanikas, Aggelos

2012-01-01

As a member of the European Union, Greece has committed to achieve ambitious targets for the penetration of renewable energy sources (RES) in gross electricity consumption by 2020. Large scale integration of RES requires a suitable mixture of compatible generation units, in order to deal with the intermittency of wind velocity and solar irradiation. The scope of this paper is to examine the impact of large scale integration of intermittent energy sources, required to meet the 2020 RES target, on the generation expansion plan, the fuel mix and the spinning reserve requirements of the Greek electricity system. We perform hourly simulation of the intermittent RES generation to estimate residual load curves on a monthly basis, which are then inputted in a WASP-IV model of the Greek power system. We find that the decarbonisation effort, with the rapid entry of RES and the abolishment of the grandfathering of CO 2 allowances, will radically transform the Greek electricity sector over the next 10 years, which has wide-reaching policy implications. - Highlights: ► Greece needs 8.8 to 9.3 GW additional RES installations by 2020. ► RES capacity credit varies between 12.2% and 15.3%, depending on interconnections. ► Without institutional changes, the reserve requirements will be more than double. ► New CCGT installed capacity will probably exceed the cost-efficient level. ► Competitive pressures should be introduced in segments other than day-ahead market.

A Taxonomic Note on the Misidentification of Anemone tschernjaewii Regel. in Kashmir Himalaya

Directory of Open Access Journals (Sweden)

Aijaz Hassan Ganie

2015-03-01

Full Text Available The correct identification of Anemone tschernjaewii Regel. previously misidentified as A. biflora DC. in the Kashmir Himalaya, India is reported. In this brief report, a detailed taxonomic description and photo-plates of its diagnostic morphological and anatomical characters are provided to validate this plant record for the region and to facilitate its easier field identification.

Spectral evolution of the Atoll source 4U 1728-34 with RXTE and INTEGRAL: evidence for hard X-ray tail

NARCIS (Netherlands)

Tarana, A.; Belloni, T.; Bazzano, A.; Homan, J.; Méndez, M.; Ubertini, P.; Comastri, A.; Angelini, L.; Cappi, M.

We report the temporal and spectral results on the INTEGRAL and RXTE 2006-2007 observation campaign of the Atoll source 4U 1728-34 (GX 354-0). The source shows, more than once, spectral evolution as revealed by the hardness intensity diagram. The soft state is well described by a Comptonization with

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling.

Science.gov (United States)

Chesters, Douglas

2017-05-01

Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among

Integrating multiple data sources for malware classification

Science.gov (United States)

Anderson, Blake Harrell; Storlie, Curtis B; Lane, Terran

2015-04-28

Disclosed herein are representative embodiments of tools and techniques for classifying programs. According to one exemplary technique, at least one graph representation of at least one dynamic data source of at least one program is generated. Also, at least one graph representation of at least one static data source of the at least one program is generated. Additionally, at least using the at least one graph representation of the at least one dynamic data source and the at least one graph representation of the at least one static data source, the at least one program is classified.

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

DEFF Research Database (Denmark)

Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper Tataru

2016-01-01

Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exa...

A feasible system integrating combined heating and power system with ground-source heat pump

International Nuclear Information System (INIS)

Li, HongQiang; Kang, ShuShuo; Yu, Zhun; Cai, Bo; Zhang, GuoQiang

2014-01-01

A system integrating CHP (combined heating and power) subsystem based on natural gas and GSHP (ground-source heat pump subsystem) in series is proposed. By help of simulation software-Aspen Plus, the energy performance of a typical CHP and GSHP-S (S refers to ‘in series’) system was analyzed. The results show that the system can make a better use of waste heat in flue gas from CHP (combined heating and power subsystem). The total system energy efficiency is 123% and the COP (coefficient of performance) of GSHP (ground-source heat pump) subsystem is 5.3. A referenced CHP and GSHP-P (P refers to ‘in parallel’) system is used for comparison; its total system energy efficiency and COP of GSHP subsystem are 118.6% and 3.5 respectively. Compared with CHP and GSHP-P system with different operating parameters, the CHP and GSHP-S system can increase total system energy efficiency by 0.8–34.7%, with related output ratio of heat to power (R) from 1.9 to 18.3. Furthermore, the COP of GSHP subsystem can be increased between the range 3.6 and 6, which is much higher than that in conventional CHP and GSHP-P system. This study will be helpful for other efficient GSHP systems integrating if there is waste heat or other heat resources with low temperature. - Highlights: • CHP system based on natural gas and ground source heat pump. • The new system can make a better utilization of waste heat in flue gas by a special way. • The proposed system can realize energy saving potential from 0.8 to 34.7%. • The coefficient of performance of ground source heat pump subsystem is significantly improved from 3.5 to 3.6–6. • Warm water temperature and percentage of flue gas used to reheat are key parameters

Frost tolerance in wild potatoes : Assessing the predictivity of taxonomic, geographic and ecological factors

NARCIS (Netherlands)

Hijmans, R.J.; Jacobs, M.; Bamberg, J.B.; Spooner, D.M.

2003-01-01

The use of genetic resources could be more effective and efficient if we were able to predict the presence or absence of useful traits in different populations or accessions. We analyzed the extent to which taxonomic, geographic and ecological factors can predict the presence of frost tolerance in

Investigating The Integral Control Rod Worth Of The Miniature Neutron Source Reactor MNSR

International Nuclear Information System (INIS)

Nguyen Hoang Hai; Do Quang Binh

2011-01-01

Determining control rod characteristics is an essential problem of nuclear reactor analysis. In this research, the integral control rod worth of the miniature neutron source reactor MNSR is investigated. Some other parameters of the nuclear reactor, such as core excess reactivity, shut down margin, are also calculated. Group constants for all reactor components are generated by the WIMSD code and then are used in the CITATION code to solve the neutron diffusion equations. The maximum relative error of the calculated results compared with the measurement data is about 3.5%. (author)

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Cronn Richard

2009-12-01

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

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

Science.gov (United States)

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

2015-04-01

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

Multifunctional voltage source inverter for renewable energy integration and power quality conditioning.

Science.gov (United States)

Dai, NingYi; Lam, Chi-Seng; Zhang, WenChen

2014-01-01

In order to utilize the energy from the renewable energy sources, power conversion system is necessary, in which the voltage source inverter (VSI) is usually the last stage for injecting power to the grid. It is an economical solution to add the function of power quality conditioning to the grid-connected VSI in the low-voltage distribution system. Two multifunctional VSIs are studied in this paper, that is, inductive-coupling VSI and capacitive-coupling VSI, which are named after the fundamental frequency impedance of their coupling branch. The operation voltages of the two VSIs are compared when they are used for renewable energy integration and power quality conditioning simultaneously. The operation voltage of the capacitive-coupling VSI can be set much lower than that of the inductive-coupling VSI when reactive power is for compensating inductive loads. Since a large portion of the loads in the distribution system are inductive, the capacitive-coupling VSI is further studied. The design and control method of the multifunctional capacitive-coupling VSI are proposed in this paper. Simulation and experimental results are provided to show its validity.

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

Directory of Open Access Journals (Sweden)

Elver Luiz Mayer

2016-12-01

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

A taxonomic revision of Maurocenia (Celastraceae, a Western Cape monotypic endemic

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R. H. Archer

1998-10-01

Full Text Available A taxonomic account is given of the monotypic genus Maurocenia Mill. Maurocenia frangula Mill, has a restricted range and is endemic to the Cape Peninsula and the West Coast National Park. Western Cape. Maurocenia frangularia (L.Mill., the species name and author citation widely used in the past, is incorrect. It is characterized by. among others, pendulous ovules and gynodioecy, rare states in the Celastraceae. Maurocenia is apparently most closely related to the southern African genus Lauridia Eckl. & Zeyh.

Extrafloral nectaries in Combretaceae: morphology, anatomy and taxonomic significance

Directory of Open Access Journals (Sweden)

P. M. Tilney

2004-09-01

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

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

Science.gov (United States)

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.

Directory of Open Access Journals (Sweden)

Shu Wu

Full Text Available 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.

Integral tests of coupled multigroup neutron and gamma cross sections with fission and fusion sources

International Nuclear Information System (INIS)

Schriewer, J.; Hehn, G.; Mattes, M.; Pfister, G.; Keinert, J.

1978-01-01

Calculations were made for different benchmark experiments in order to test the coupled multigroup neutron and gamma library EURLIB-3 with 100 neutron groups and 20 gamma groups. In cooperation with EURATOM, Ispra, we produced this shielding library recently from ENDF/B-IV data for application in fission and fusion technology. Integral checks were performed for natural lithium, carbon, oxygen, and iron. Since iron is the most important structural material in nuclear technology, we started with calculations of iron benchmark experiments. Most of them are integral experiments of INR, Karlsruhe, but comparisons were also done with benchmark experiments from USA and Japan. For the experiments with fission sources we got satisfying results. All details of the resonances cannot be checked with flux measurements and multigroup cross sections used. But some averaged resonance behaviour of the measured and calculated fluxes can be compared and checked within the error limits given. We get greater differences in the calculations of benchmark experiments with 14 MeV neutron sources. For iron the group cross sections of EURLIB-3 produce an underestimation of the neutron flux in a broad energy region below the source energy. The conclusion is that the energy degradation by inelastic scattering is too strong. For fusion application the anisotropy of the inelastic scatter process must be taken into account, which isn't done by the processing codes at present. If this effect isn't enough, additional corrections have to be applied to the inelastic cross sections of iron in ENDF/B-IV. (author)

Preliminary design and integration of EPICS operation interface for the Taiwan photon source

International Nuclear Information System (INIS)

Cheng, Y.S.; Jenny Chen; Chiu, P.C.; Kuo, C.H.; Liao, C.Y.; Hsu, K.T.; Wu, C.Y.

2012-01-01

The TPS (Taiwan Photon Source) is the latest generation 3 GeV synchrotron light source which has been in construction since 2010. The EPICS (Experimental Physics and Industrial Control System) framework is adopted as control system infrastructure for the TPS. The EPICS IOCs (Input Output Controller) and various database records have been gradually implemented to control and monitor available subsystems of the TPS at this moment. The subsystem includes timing, power supply, motion controller, miscellaneous Ethernet compliant devices etc. Through EPICS PVs (Process Variables) channel access, remote access I/O data via Ethernet interface can be observed by the usable graphical tool-kits, such as the EDM (Extensible Display Manager) and MATLAB. The operation interface mainly includes the function of setting, reading, save, restore and etc. Integration of operation interfaces will depend upon properties of each subsystem. In addition, the centralized management method is utilized to serve every client from file servers in order to maintain consistent versions of related EPICS files. (authors)

Flora of the city of Podgorica, Montenegro: Taxonomic analysis

Directory of Open Access Journals (Sweden)

Stešević Danijela

2008-01-01

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

Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico.

Science.gov (United States)

Mason-Romo, Edgard David; Farías, Ariel A; Ceballos, Gerardo

2017-01-01

Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall) of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests-upland and lowland (arroyo or riparian) forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian) forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods) and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because of

Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico.

Directory of Open Access Journals (Sweden)

Edgard David Mason-Romo

Full Text Available Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests-upland and lowland (arroyo or riparian forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because

Urbanization alters the functional composition, but not taxonomic diversity, of the soil nematode community

Science.gov (United States)

Mitchell A. Pavao-Zuckerman; David C. Coleman

2007-01-01

We evaluated the response of riparian forest soil nematode community structure to the physico-chemical environment associated with urban land use. Soils were sampled seasonally between December 2000 and October 2002 along an urban-rural transect in Asheville, North Carolina. We characterized the taxonomic (to genus) and functional composition (trophic groups) of the...

Morphological variation and taxonomic interpretation in the moss genus Bryum in Antarctica

OpenAIRE

Seppelt,Rodney D.; Kanda,Hiroshi

1986-01-01

The potential for morphological variation in Antarctic species of Bryum is evaluated and related to problems associated with taxonomic interpretation based on specimens from the Soya Coast, Mac. Robertson Coast, Vestfold Hills and Knox Coast. B. argenteum HEDW. Has been positively determined for Continental Antarctica from six localities on the Soya Coast and from Ross Island, southern Victoria Land. Specimens from the Vestfold Hills and Knox Coast considered with some reservation as this spe...

Open-Source Sequence Clustering Methods Improve the State Of the Art.

Science.gov (United States)

Kopylova, Evguenia; Navas-Molina, Jose A; Mercier, Céline; Xu, Zhenjiang Zech; Mahé, Frédéric; He, Yan; Zhou, Hong-Wei; Rognes, Torbjørn; Caporaso, J Gregory; Knight, Rob

2016-01-01

Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release. IMPORTANCE Massive collections of next-generation sequencing data call for fast, accurate, and easily accessible bioinformatics algorithms to perform sequence clustering. A comprehensive benchmark is presented, including open-source tools and the popular USEARCH suite. Simulated, mock, and environmental communities were used to analyze sensitivity, selectivity, species diversity (alpha and beta), and taxonomic composition. The results demonstrate that recent clustering algorithms can significantly improve accuracy and preserve estimated diversity without the application of aggressive filtering. Moreover, these tools are all open source, apply multiple levels of multithreading, and scale to the demands of modern next-generation sequencing data, which is essential for the analysis of massive multidisciplinary studies such as the Earth Microbiome Project (EMP) (J. A. Gilbert, J. K. Jansson, and R. Knight, BMC Biol 12:69, 2014, http

Cross section measurement and integral test for several activation reactions using T + d and thick-Li + d sources

International Nuclear Information System (INIS)

Dumais, J.R.; Tanaka, S.; Odano, N.; Iwasaki, S.; Sugiyama, K.

1988-01-01

Recent activities on the area of the cross section measurement for several activation reactions at Department of Nucl. Eng., Tohoku Univ. are described. The first subject is the cross section measurement for (n,2n) reaction on aluminum using the RTNS-II neutron source. Cross sections with rather small error band were obtained for the incident neutron energies from 14 to 14.7 MeV. The second one is the status of the program for the integral experiments on several reactions using the thick Li + d source at Tohoku Fast Neutron Lab. The experimental results showed the usefullness of the source as a tool for the cross section assessment. (author)

Consumer-led health-related online sources and their impact on consumers: An integrative review of the literature.

Science.gov (United States)

Laukka, Elina; Rantakokko, Piia; Suhonen, Marjo

2017-04-01

The aim of the review was to describe consumer-led health-related online sources and their impact on consumers. The review was carried out as an integrative literature review. Quantisation and qualitative content analysis were used as the analysis method. The most common method used by the included studies was qualitative content analysis. This review identified the consumer-led health-related online sources used between 2009 and 2016 as health-related online communities, health-related social networking sites and health-related rating websites. These sources had an impact on peer support; empowerment; health literacy; physical, mental and emotional wellbeing; illness management; and relationships between healthcare organisations and consumers. The knowledge of the existence of the health-related online sources provides healthcare organisations with an opportunity to listen to their consumers' 'voice'. The sources make healthcare consumers more competent actors in relation to healthcare, and the knowledge of them is a valuable resource for healthcare organisations. Additionally, these health-related online sources might create an opportunity to reduce the need for drifting among the healthcare services. Healthcare policymakers and organisations could benefit from having a strategy of increasing their health-related online sources.

The taxonomic implication of frontal tubercles in Polypedilum subgenera diagnoses, with re-description of Polypedilum isigabeceum Sasa & Suzuki (Diptera, Chironomidae).

Science.gov (United States)

Yamamoto, Nao; Yamamoto, Masaru

2016-11-15

Polypedilum isigabeceum Sasa et Suzuki, 2000 was described as belonging to subgenus Polypedilum s. str. However, if we accept the conclusion of Sæther et al. (2010), the species might be placed into Kribionympha with P. unagiquartum Sasa, 1985 because of the presence of distinct frontal tubercles in the adult males. However, other taxonomic characters do not support their treatment. P. isigabeceum is re-described and reconfirmed to be assigned to the subgenus Polypedilum s. str. The taxonomic meaning of frontal tubercles is discussed for defining the subgeneric rankings within genus Polypedilum.

Design, fabrication, installation and shielding integrity testing of source storage container for automatic source movement system used in TLD calibration facility

International Nuclear Information System (INIS)

Subramanian, V.; Baskar, S.; Annalakshmi, O.; Jose, M.T.; Jayshree, C.P.; Choudry, Shreelatha

2012-01-01

A state-of-art TLD laboratory has been commissioned in January 2000 at Radiological Safety Division of Indira Gandhi Centre for Atomic Research (IGCAR). The laboratory provides personnel monitoring service to 2000 occupational workers from Indira Gandhi Centre for Atomic Research and Bhabha Atomic Research Centre facilities. The laboratory has been accredited by the Radiation Safety Systems Division (RSSD), Bhabha Atomic Research Centre (BARC) since year 2002. The laboratory has exclusive facility for the calibration of the TLD cards. As apart of accreditation procedure and taking into account of geometry effect, the dose rate at the card position is determined by the accreditation authorities by using graphite chamber (secondary or national standard instrument) and often re estimated by a condenser R meter (M/s Victoreen, Germany) by our laboratory. As per the regulatory requirement, the exposure protocols should be automated. Towards this an automatic source movement system has been augmented in the calibration facility. By using the system, the source will be brought to the irradiation position by pneumatically and exposures will be terminated by counter, timer and triggering system. To accomplish this task a lead container has been designed, fabricated and mounted at the beneath of the calibration table for the storage of source. As per the automation process, a lead container for the source storage has been designed and installed beneath to the Calibration Table. The container was designed to hold a 3Ci 137 Cs source, but present activity of the source is 1.2Ci. Hence, the shielding integrity was tested with higher active source (1.7Ci 60 Co). The dose rate measured outside on the circumference of the container at the middle of the source is found to be the same as calculated using QAD CGGP calculations. The top plug is so designed to avoid inadvertent upward movement of the source. Though, the shielding was not adequate on top of the top plug, however it does

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

Science.gov (United States)

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

2016-08-18

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

INTEGRAL INDEX OF OPERATION QUALITY FOR EVALUATION OF IMPACT OF DISTRIBUTIVE GENERATION SOURCES ON ELECTRIC NETWORK MODES

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Petro D. Lezhniuk

2017-06-01

Full Text Available Method of operation quality evaluation of electric network, comprising renewable sources of energy (RSE is considered. Integral index that enables to evaluate the impact of RSE on energy losses and its quality as well as balance reliability in electric network is suggested. Mathematical model is constructed, taking into account the assumption that electric network with RSE may be in various operation modes, characterized by different technical economic indices. To determine the integral index of operation quality of electric network with RSE in all possible states tools of Markov processes theory and criterial method are used.

Partitioning taxonomic diversity of aquatic insect assemblages and functional feeding groups in Neotropical Savanna headwater streams

Science.gov (United States)

Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feedin...

Comparative analyses of seven technologies to facilitate the integration of fluctuating renewable energy sources

DEFF Research Database (Denmark)

Mathiesen, Brian Vad; Lund, Henrik

2009-01-01

An analysis of seven different technologies is presented. The technologies integrate fluctuating renewable energy sources (RES) such as wind power production into the electricity supply, and the Danish energy system is used as a case. Comprehensive hour-by-hour energy system analyses are conducted...... of a complete system meeting electricity, heat and transport demands, and including RES, power plants, and combined heat and power production (CHP) for district heating and transport technologies. In conclusion, the most fuel-efficient and least-cost technologies are identified through energy system...

Quantifying the Relative Importance of Climate and Habitat on Structuring the Species and Taxonomic Diversity of Aquatic Plants in a Biodiversity Hotspot of Tropical Asia

International Nuclear Information System (INIS)

Chen, Y.

2015-01-01

It has not been well known how climate and habitat variables will influence the distribution of plant species to some extents at mesoscale. In this report, by using the distribution of aquatic plants in Western Ghats, a biodiversity hotspot in tropical Asian region, I quantify the relative importance of climate and habitat variables on structuring spatially species richness and taxonomic diversity patterns using structural equation modeling. All the sampling qudrats in the region used for the study has a spatial resolution of 0.5 latitude x 0.5 longitude. The results showed that species richness is high in both northern and southern part of the region, while low in the middle part. In contrast, taxonomic distinctiveness is relatively homogeneous over all the sampling quadrats in the region. Structural equation modeling suggested that taxonomic distinctiveness patterns of aquatic plants in the region follow temperature (partial regression coefficient=0.31, p<0.05) and elevational (partial regression coefficient=0.31, p<0.05) gradients, while richness patterns cannot be explained by any of the currently used variables. In conclusion, environmental variables that are related to taxonomic distinctiveness would not be related to richness, given the fact that these two quantities are orthogonal more or less. Both climate and habitat are equally influential on taxonomic distinctiveness patterns for aquatic plants in Western Ghats of India. (author)

Delimiting species of Protaphorura (Collembola: Onychiuridae): integrative evidence based on morphology, DNA sequences and geography.

Science.gov (United States)

Sun, Xin; Zhang, Feng; Ding, Yinhuan; Davies, Thomas W; Li, Yu; Wu, Donghui

2017-08-15

Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences. Twenty-two molecular putative species were consistently recovered across molecular and geographical analyses. Geographic criteria were was proved to be an efficient delimitation method for onychiurids. Further morphological examination, based on the combination of the number of pseudocelli, parapseudocelli and ventral mesothoracic chaetae, confirmed 18 taxa of 22 molecular units, with six of them described as new species. These characters were found to be of high taxonomical value. This study highlights the potential benefits of integrative taxonomy, particularly simultaneous use of molecular/geographical tools, as a powerful way of ascertaining the true diversity of the Onychiuridae. Our study also highlights that discovering new morphological characters remains central to achieving a full understanding of collembolan taxonomy.

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

Science.gov (United States)

Woodley, Michael A

2010-01-01

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

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

Science.gov (United States)

Skorobogatova, O. N.

2018-03-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Kobayashi, Shin

1987-02-01

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

LINKS: learning-based multi-source IntegratioN frameworK for Segmentation of infant brain images.

Science.gov (United States)

Wang, Li; Gao, Yaozong; Shi, Feng; Li, Gang; Gilmore, John H; Lin, Weili; Shen, Dinggang

2015-03-01

Segmentation of infant brain MR images is challenging due to insufficient image quality, severe partial volume effect, and ongoing maturation and myelination processes. In the first year of life, the image contrast between white and gray matters of the infant brain undergoes dramatic changes. In particular, the image contrast is inverted around 6-8months of age, and the white and gray matter tissues are isointense in both T1- and T2-weighted MR images and thus exhibit the extremely low tissue contrast, which poses significant challenges for automated segmentation. Most previous studies used multi-atlas label fusion strategy, which has the limitation of equally treating the different available image modalities and is often computationally expensive. To cope with these limitations, in this paper, we propose a novel learning-based multi-source integration framework for segmentation of infant brain images. Specifically, we employ the random forest technique to effectively integrate features from multi-source images together for tissue segmentation. Here, the multi-source images include initially only the multi-modality (T1, T2 and FA) images and later also the iteratively estimated and refined tissue probability maps of gray matter, white matter, and cerebrospinal fluid. Experimental results on 119 infants show that the proposed method achieves better performance than other state-of-the-art automated segmentation methods. Further validation was performed on the MICCAI grand challenge and the proposed method was ranked top among all competing methods. Moreover, to alleviate the possible anatomical errors, our method can also be combined with an anatomically-constrained multi-atlas labeling approach for further improving the segmentation accuracy. Copyright © 2014 Elsevier Inc. All rights reserved.

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

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Verônica M. Oliveira

2010-02-01

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

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India.

Science.gov (United States)

Patel, Vilas; Munot, Hitendra; Shah, Varun; Shouche, Yogesh S; Madamwar, Datta

2015-12-30

The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY. Copyright © 2015. Published by Elsevier Ltd.

Microscope-Integrated Intraoperative Ultrahigh-Speed Swept-Source Optical Coherence Tomography for Widefield Retinal and Anterior Segment Imaging.

Science.gov (United States)

Lu, Chen D; Waheed, Nadia K; Witkin, Andre; Baumal, Caroline R; Liu, Jonathan J; Potsaid, Benjamin; Joseph, Anthony; Jayaraman, Vijaysekhar; Cable, Alex; Chan, Kinpui; Duker, Jay S; Fujimoto, James G

2018-02-01

To demonstrate the feasibility of retinal and anterior segment intraoperative widefield imaging using an ultrahigh-speed, swept-source optical coherence tomography (SS-OCT) surgical microscope attachment. A prototype post-objective SS-OCT using a 1,050-nm wavelength, 400 kHz A-scan rate, vertical cavity surface-emitting laser (VCSEL) light source was integrated to a commercial ophthalmic surgical microscope after the objective. Each widefield OCT data set was acquired in 3 seconds (1,000 × 1,000 A-scans, 12 × 12 mm 2 for retina and 10 × 10 mm 2 for anterior segment). Intraoperative SS-OCT was performed in 20 eyes of 20 patients. In six of seven membrane peels and five of seven rhegmatogenous retinal detachment repair surgeries, widefield retinal imaging enabled evaluation pre- and postoperatively. In all seven cataract cases, anterior imaging evaluated the integrity of the posterior lens capsule. Ultrahigh-speed SS-OCT enables widefield intraoperative viewing in the posterior and anterior eye. Widefield imaging visualizes ocular structures and pathology without requiring OCT realignment. [Ophthalmic Surg Lasers Imaging Retina. 2018;49:94-102.]. Copyright 2018, SLACK Incorporated.

Asian longhorned beetle complicates the relationship between taxonomic diversity and pest vulnerability in street tree assemblages

Science.gov (United States)

Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven c...

Contrasting taxonomic and functional responses of a tropical tree community to selective logging

OpenAIRE

Baraloto, C.; Hérault, B.; Paine, C. E. T.; Massot, H.; Blanc, L.; Bonal, D.; Molino, Jean-François; Nicolini, E. A.; Sabatier, Daniel

2012-01-01

1. Considerable debate surrounds the extent to which tropical forests can be managed for resource extraction while conserving biodiversity and ecosystem properties, which depend on functional composition. Here we evaluate the compatibility of these aims by examining the effects of logging on taxonomic and functional diversity and composition in a tropical forest. 2. Twenty years after selective logging, we inventoried 4140 stems regenerating in logging gaps and adjacent undisturbed areas, and...

Differences in Processing of Taxonomic and Sequential Relations in Semantic Memory: An fMRI Investigation

Science.gov (United States)

Kuchinke, Lars; van der Meer, Elke; Krueger, Frank

2009-01-01

Conceptual knowledge of our world is represented in semantic memory in terms of concepts and semantic relations between concepts. We used functional magnetic resonance imaging (fMRI) to examine the cortical regions underlying the processing of sequential and taxonomic relations. Participants were presented verbal cues and performed three tasks:…

Método para la construcción de una taxonomía: estructura base para riesgos en outsourcing de software

OpenAIRE

Gloria Piedad Gasca Hurtado; Bell Manrique Losada

2011-01-01

Este artículo propone una taxonomía de riesgos enfocada en el ámbito de outsourcing de software. El objetivo es definir una estructura de clasificación de riesgos, relacionada con el proceso de outsourcing de software. La motivación está dada por la importancia que tiene la identificación de riesgos, y la ayuda que prestan las taxonomías al respecto, por lo cual se les conoce como una técnica efectiva que permite desarrollar una mejor gestión de riesgos. Este artículo incluye el método para c...

Integrative response of plant mitochondrial electron transport chain to nitrogen source.

Science.gov (United States)

Hachiya, Takushi; Noguchi, Ko

2011-02-01

Nitrogen (N) availability is widely known as a determinant of plant growth and respiration rate. However, less attention has been paid to the effect of the type of N source (nitrate, nitrite or ammonium) on the respiratory system. This review summarizes the latest findings on this topic, with an emphasis on the effect of ammonium and nitric oxide (NO) on the respiratory system, and the physiological role of alternative oxidase (AOX). First, concentrated ammonium has been found to increase plant respiration rate (ammonium-dependent respiratory increase, ARI). We will introduce two hypotheses to explain ARI, futile ammonium cycling and excess reducing equivalents, and verify the validity of each hypothesis. We suggest that these two hypotheses are not necessarily mutually exclusive. Second, gene expression of AOX is suppressed when N is predominately available as nitrate instead of ammonium. We will discuss possible signaling pathways leading to this expression pattern. Third, while AOX expression is induced by NO, AOX activity itself is insensitive to NO. In contrast, activity of cytochrome c oxidase (COX) is sensitive to NO. We outline the NO production pathway, focusing on nitrite-dependent NO production, and discuss the physiological significance of the fact that AOX activity is insensitive to NO. Finally, this review aims to build an integrated scheme of the respiratory response to the type of N source, considering leaves in high light conditions or hypoxic roots.

Taxonomic study on Navicula sensu lato from inland waters in the Arctic

Directory of Open Access Journals (Sweden)

Hiroshi Fukushima

2013-07-01

Full Text Available Very few comparative taxonomic studies on Arctic and circumboreal diatoms have been conducted in recent years. During the period of Aug. 1996 to 1999 (table 1, we visited a number of island within the Arctic Circle (Baf?n Island, Coburg Island, Beechey Island, Devon Island, Cornwallis Island, Spitsbergen, Greenland and collected specimens of 20 algal taxa (identi?ed by micrograph observations of Navicula sensu lato (Chamaepinnularia: 6 taxa, Geissleria: 1 taxon, Luticola: 1 taxon, Navicula: 11 taxa, Placoneis: 1 taxon.

Developing an open source-based spatial data infrastructure for integrated monitoring of mining areas

Science.gov (United States)

Lahn, Florian; Knoth, Christian; Prinz, Torsten; Pebesma, Edzer

2014-05-01

In all phases of mining campaigns, comprehensive spatial information is an essential requirement in order to ensure economically efficient but also safe mining activities as well as to reduce environmental impacts. Earth observation data acquired from various sources like remote sensing or ground measurements is important e.g. for the exploration of mineral deposits, the monitoring of mining induced impacts on vegetation or the detection of ground subsidence. The GMES4Mining project aims at exploring new remote sensing techniques and developing analysis methods on various types of sensor data to provide comprehensive spatial information during mining campaigns (BENECKE et al. 2013). One important task in this project is the integration of the data gathered (e.g. hyperspectral images, spaceborne radar data and ground measurements) as well as results of the developed analysis methods within a web-accessible data source based on open source software. The main challenges here are to provide various types and formats of data from different sensors and to enable access to analysis and processing techniques without particular software or licensing requirements for users. Furthermore the high volume of the involved data (especially hyperspectral remote sensing images) makes data transfer a major issue in this use case. To engage these problems a spatial data infrastructure (SDI) including a web portal as user frontend is being developed which allows users to access not only the data but also several analysis methods. The Geoserver software is used for publishing the data, which is then accessed and visualized in a JavaScript-based web portal. In order to perform descriptive statistics and some straightforward image processing techniques on the raster data (e.g. band arithmetic or principal component analysis) the statistics software R is implemented on a server and connected via Rserve. The analysis is controlled and executed directly by the user through the web portal and

Delaunay Tetrahedralization of the Heart Based on Integration of Open Source Codes

International Nuclear Information System (INIS)

Pavarino, E; Neves, L A; Machado, J M; Momente, J C; Zafalon, G F D; Pinto, A R; Valêncio, C R; Godoy, M F de; Shiyou, Y; Nascimento, M Z do

2014-01-01

The Finite Element Method (FEM) is a way of numerical solution applied in different areas, as simulations used in studies to improve cardiac ablation procedures. For this purpose, the meshes should have the same size and histological features of the focused structures. Some methods and tools used to generate tetrahedral meshes are limited mainly by the use conditions. In this paper, the integration of Open Source Softwares is presented as an alternative to solid modeling and automatic mesh generation. To demonstrate its efficiency, the cardiac structures were considered as a first application context: atriums, ventricles, valves, arteries and pericardium. The proposed method is feasible to obtain refined meshes in an acceptable time and with the required quality for simulations using FEM

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

Science.gov (United States)

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.

Capability Maturity Model Integration (CMMISM), Version 1.1 CMMISM for Systems Engineering, Software Engineering, Integrated Product and Process Development, and Supplier Sourcing (CMMI-SE/SW/IPPD/SS, V1.1). Staged Representation

National Research Council Canada - National Science Library

2002-01-01

.... Concepts covered by this model include systems engineering, software engineering, integrated product and process development, and supplier sourcing as well as traditional CMM concepts such as process...

Global Sourcing and Firm Selection

DEFF Research Database (Denmark)

Kohler, Wilhelm; Smolka, Marcel

2014-01-01

We analyze the sourcing strategies of firms active in the Spanish manufacturing sector. We show that firms that select strategies of vertical integration and of foreign sourcing ex post tend to have been more productive, ex ante, than other firms.......We analyze the sourcing strategies of firms active in the Spanish manufacturing sector. We show that firms that select strategies of vertical integration and of foreign sourcing ex post tend to have been more productive, ex ante, than other firms....

Taxonomic key for the genera of Elmidae (Coleoptera, Byrrhoidea occurring in Goiás State, Brazil, including new records and distributional notes

Directory of Open Access Journals (Sweden)

Felipe F. Barbosa

2013-06-01

Full Text Available A taxonomic key for the genera of Elmidae (Coleoptera, Byrrhoidea occurring in Goiás State, Brazil, including new records and distributional notes. Despite their great diversity and high abundance in Neotropical aquatic environments, the fauna of Elmidae remains practically unknown in some areas and even entire biomes in this region. In this work we bring, for the first time, faunistic data for the Elmidae of central Brazil. The aim of this work was to inventory the Elmidae fauna in central, southwestern and southeastern Goiás State, Brazil and to produce a taxonomic key, at genus level, for adults from the studied region. The taxonomic key presented herein offers means for the identification of all the 13 genera known to occur in Goiás, 11 of them being new records for the State. Moreover, the number of named species registered for Goiás increased from one to nine.

An integrated and open source GIS environmental management system for a protected area in the south of Portugal

Science.gov (United States)

Teodoro, A.; Duarte, L.; Sillero, N.; Gonçalves, J. A.; Fonte, J.; Gonçalves-Seco, L.; Pinheiro da Luz, L. M.; dos Santos Beja, N. M. R.

2015-10-01

Herdade da Contenda (HC), located in Moura municipality, Beja district (Alentejo province) in the south of Portugal (southwestern Iberia Peninsula), is a national hunting area with 5270ha. The development of an integrated system that aims to make the management of the natural and cultural heritage resources will be very useful for an effective management of this area. This integrated system should include the physical characterization of the territory, natural conservation, land use and land management themes, as well the cultural heritage resources. This paper presents a new tool for an integrated environmental management system of the HC, which aims to produce maps under a GIS open source environment (QGIS). The application is composed by a single button which opens a window. The window is composed by twelve menus (File, DRASTIC, Forest Fire Risk, Revised Universal Soil Loss Equation (RUSLE), Bioclimatic Index, Cultural Heritage, Fauna and Flora, Ortofoto, Normalizes Difference Vegetation Index (NDVI), Digital Elevation Model (DEM), Land Use Land Cover Cover (LULC) and Help. Several inputs are requires to generate these maps, e.g. DEM, geologic information, soil map, hydraulic conductivity information, LULC map, vulnerability and economic information, NDVI. Six buttons were added to the toolbar which allows to manipulate the information in the map canvas: Zoom in, Zoom out, Pan, Print/Layout and Clear. This integrated and open source GIS environment management system was developed for the HC area, but could be easily adapted to other natural or protected area. Despite the lack of data, the methodology presented fulfills the objectives.

How to deal with cryptic species in Enchytraeidae, with recommendations on taxonomical descriptions

Directory of Open Access Journals (Sweden)

Schmelz, R. M.

2017-11-01

Full Text Available During the 12th International Symposium on Enchytraeidae, held in Tihany, Hungary (27–29 June 2016, the participants discussed cryptic species, i.e., species that are morphologically so similar that they are classified as the same species (Bickford et al. 2007, and how to deal with them taxonomically. Here we summarise the discussion together with a few additional comments, and we give recommendations for species descriptions in Enchytraeidae.

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

Science.gov (United States)

Harrison, Terry; Msuya, Charles P.

2005-04-01

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

Revision of the taxonomic status of Aphis floridanae Tissot (Hemiptera:Aphididae) using morphological and molecular insight

Science.gov (United States)

Three Aphis species are involved in this study. Aphis floridanae Tissot, 1933 and A. nasturtii Kaltenbach, 1843 are currently treated as synonym, and A. impatientis Thomas, 1878 has a valid taxonomic status. Morphological and cytochrome oxidase 1 (Cox1) data show that Aphis floridanae is not synonym...

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

Science.gov (United States)

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

Taxonomic and nomenclatural rearrangements in Artemisia subgen. Tridentatae, including a redefinition of Sphaeromeria (Asteraceae, Anthemideae)

Science.gov (United States)

Sonia Garcia; Teresa Garnatje; E. Durant McArthur; Jaume Pellicer; Stewart C. Sanderson; Joan Valles

2011-01-01

A recent molecular phylogenetic study of all members of Artemisia subgenus Tridentatae, as well as most of the other New World endemic Artemisia and the allied genera Sphaeromeria and Picrothamnus, raised the necessity of revising the taxonomic framework of the North American endemic Artemisia. Composition of the subgenus Tridentatae is enlarged to accommodate other...

Integrated source-risk model for radon: A definition study

International Nuclear Information System (INIS)

Laheij, G.M.H.; Aldenkamp, F.J.; Stoop, P.

1993-10-01

The purpose of a source-risk model is to support policy making on radon mitigation by comparing effects of various policy options and to enable optimization of counter measures applied to different parts of the source-risk chain. There are several advantages developing and using a source-risk model: risk calculations are standardized; the effects of measures applied to different parts of the source-risk chain can be better compared because interactions are included; and sensitivity analyses can be used to determine the most important parameters within the total source-risk chain. After an inventory of processes and sources to be included in the source-risk chain, the models presently available in the Netherlands are investigated. The models were screened for completeness, validation and operational status. The investigation made clear that, by choosing for each part of the source-risk chain the most convenient model, a source-risk chain model for radon may be realized. However, the calculation of dose out of the radon concentrations and the status of the validation of most models should be improved. Calculations with the proposed source-risk model will give estimations with a large uncertainty at the moment. For further development of the source-risk model an interaction between the source-risk model and experimental research is recommended. Organisational forms of the source-risk model are discussed. A source-risk model in which only simple models are included is also recommended. The other models are operated and administrated by the model owners. The model owners execute their models for a combination of input parameters. The output of the models is stored in a database which will be used for calculations with the source-risk model. 5 figs., 15 tabs., 7 appendices, 14 refs

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks.

Science.gov (United States)

Haibe-Kains, Benjamin; Olsen, Catharina; Djebbari, Amira; Bontempi, Gianluca; Correll, Mick; Bouton, Christopher; Quackenbush, John

2012-01-01

Genomics provided us with an unprecedented quantity of data on the genes that are activated or repressed in a wide range of phenotypes. We have increasingly come to recognize that defining the networks and pathways underlying these phenotypes requires both the integration of multiple data types and the development of advanced computational methods to infer relationships between the genes and to estimate the predictive power of the networks through which they interact. To address these issues we have developed Predictive Networks (PN), a flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these 'known' interactions together with gene expression data to infer robust gene networks. The PN web application is accessible from http://predictivenetworks.org. The PN code base is freely available at https://sourceforge.net/projects/predictivenets/.

Sources and fate of antimicrobials in integrated fish-pig and non-integrated tilapia farms

DEFF Research Database (Denmark)

Li, Kang; Liu, Liping; Zhan, Jia

2017-01-01

residues in fish skin from both integrated and non-integrated farms, and in pig manure. Enrofloxacin (3.9–129.3 μg/kg) and sulfadiazine (0.7–7.8 μg/kg) were commonly detected in fish skin and muscle, pig manure and pond sediment from integrated farms, with different types of antimicrobials found in pig...

Temporal and spatial differences between taxonomic and trait biodiversity in a large marine ecosystem: Causes and consequences

DEFF Research Database (Denmark)

Dencker, Tim Spaanheden; Pécuchet, Lauréne; Beukhof, Esther

2017-01-01

Biodiversity is a multifaceted concept, yet most biodiversity studies have taken a taxonomic approach, implying that all species are equally important. However, species do not contribute equally to ecosystem processes and differ markedly in their responses to changing environments. This recogniti...

The concentration of 137Cs and stable Cs in zooplankton in the western North Pacific in relation to their taxonomic composition

International Nuclear Information System (INIS)

Kaeriyama, Hideki; Watabe, Teruhisa; Kusakabe, Masashi

2008-01-01

The objective of this study is to obtain information on the background level of 137 Cs in zooplankton in the waters close to Rokkasho-mura in Aomori Prefecture, Japan, where a large-scale project has been progressively promoted to establish the nuclear fuel cycle. Prior to the full-scale operation of the spent nuclear fuel reprocessing plant, zooplankton samples were collected in May and October 2005, June 2006, and June 2007 from the surface water (0-5 m depth). The samples were analyzed to determine the concentrations of 137 Cs and stable Cs in relation to taxonomic composition. The numerical abundance of the plankton varied from 253 to 1514 inds. m -3 . Taxonomic composition differed between the two sampling periods. Although copepods formed the most abundant taxonomic group during both seasons, gelatinous plankton (chaetognaths, siphonophores, appendicularians and doliolids) were more abundant in October 2005 than in June 2006 and June 2007. The concentration of 137 Cs in zooplankton varied from 11 to 24 mBq kg-WW -1 . At the same station, the 137 Cs concentration in zooplankton in October 2005 was almost twice as much as that in June 2006, although the concentration of 137 Cs in seawater did not show a difference. The concentration of stable Cs was measured for each taxonomic group: that in gelatinous zooplankton (chaetognaths) was higher than that in crustacean zooplankton (copepods, euphausiids and amphipods). These results suggest that the concentration of 137 Cs in zooplankton is affected by the occurrence of gelatinous zooplankton. (author)

Meteorite Source Regions as Revealed by the Near-Earth Object Population

Science.gov (United States)

Binzel, Richard P.; DeMeo, Francesca E.; Burt, Brian J.; Polishook, David; Burbine, Thomas H.; Bus, Schelte J.; Tokunaga, Alan; Birlan, Mirel

2014-11-01

Spectroscopic and taxonomic information is now available for 1000 near-Earth objects, having been obtained through both targeted surveys (e.g. [1], [2], [3]) or resulting from all-sky surveys (e.g. [4]). We determine their taxonomic types in the Bus-DeMeo system [5] [6] and subsequently examine meteorite correlations based on spectral analysis (e.g. [7],[8]). We correlate our spectral findings with the source region probabilities calculated using the methods of Bottke et al. [9]. In terms of taxonomy, very clear sources are indicated: Q-, Sq-, and S-types most strongly associated with ordinary chondrite meteorites show clear source signatures through the inner main-belt. V-types are relatively equally balanced between nu6 and 3:1 resonance sources, consistent with the orbital dispersion of the Vesta family. B- and C-types show distinct source region preferences for the outer belt and for Jupiter family comets. A Jupiter family comet source predominates for the D-type near-Earth objects, implying these "asteroidal" bodies may be extinct or dormant comets [10]. Similarly, near-Earth objects falling in the spectrally featureless "X-type" category also show a strong outer belt and Jupiter family comet source region preference. Finally the Xe-class near-Earth objects, which most closely match the spectral properties of enstatite achondrite (aubrite) meteorites seen in the Hungaria region[11], show a source region preference consistent with a Hungaria origin by entering near-Earth space through the Mars crossing and nu6 resonance pathways. This work supported by the National Science Foundation Grant 0907766 and NASA Grant NNX10AG27G.[1] Lazzarin, M. et al. (2004), Mem. S. A. It. Suppl. 5, 21. [2] Thomas, C. A. et al. (2014), Icarus 228, 217. [3] Tokunaga, A. et al. (2006) BAAS 38, 59.07. [4] Hasselmann, P. H., Carvano, J. M., Lazzaro, D. (2011) NASA PDS, EAR-A-I0035-5-SDSSTAX-V1.0. [5] Bus, S.J., Binzel, R.P. (2002). Icarus 158, 146. [6] DeMeo, F.E. et al. (2009), Icarus

ON THE NEAR-INFRARED IDENTIFICATION OF THE INTEGRAL SOURCE IGR J16328–4726

Energy Technology Data Exchange (ETDEWEB)

Persi, P.; Fiocchi, M.; Bazzano, A.; Ubertini, P.; Parisi, P. [INAF/IAPS-Roma, Via fosso del cavaliere, 100, I-00133 Roma (Italy); Tapia, M. [Instituto de Astronomía, Universidad Nacional Autónoma de México, Ensenada, B.C. (Mexico); Roth, M., E-mail: paolo.persi@iaps.inaf.it [Las Campanas Observatory, Carnegie Institution of Washington, La Serena (Chile)

2015-07-15

The aim of this work is to identify the infrared (IR) counterpart of the Galactic high-mass X-ray binary IGR J16328–4726 discovered by the INTEGRAL satellite, and to derive the extinction and distance to the system. We present new deep sub-arcsecond JHK{sub s} imaging and low-resolution near-IR spectroscopy in the 1.5 and 2.4 μm range of IGR J16328–4726. We report the presence of two near-IR stellar sources separated by about 1.″8 at the location of the unresolved 2MASS source J16323791–4723409, previously considered to be the near-IR counterpart of the X-ray source. From the analysis of their near-IR colors and spectra as well as accurate positions, we uniquely identify the true IR counterpart of IGR J16328–4726. Our 1.5–2.4 μm spectrum of this star is consistent with the published classification O8Iafpe. Assuming this, and in combination with new JHK{sub s} photometry, a reddening A{sub V} = 23.6 ± 0.7 and a distance of 7.2 ± 0.3 kpc from the Sun are derived.

Micro/Nano Fabricated Solid-State Thermoelectric Generator Devices for Integrated High Voltage Power Sources

Science.gov (United States)

Fleurial, J.-P.; Ryan, M. A.; Snyder, G. J.; Huang, C.-K.; Whitacre, J. F.; Patel, J.; Lim, J.; Borshchevsky, A.

2002-01-01

Deep space missions have a strong need for compact, high power density, reliable and long life electrical power generation and storage under extreme temperature conditions. Except for electrochemical batteries and solar cells, there are currently no available miniaturized power sources. Conventional power generators devices become inefficient in extreme environments (such as encountered in Mars, Venus or outer planet missions) and rechargeable energy storage devices can only be operated in a narrow temperature range thereby limiting mission duration. The planned development of much smaller spacecrafts incorporating a variety of micro/nanodevices and miniature vehicles will require novel, reliable power technologies. It is also expected that such micro power sources could have a wide range of terrestrial applications, in particular when the limited lifetime and environmental limitations of batteries are key factors. Advanced solid-state thermoelectric combined with radioisotope or waste heat sources and low profile energy storage devices are ideally suited for these applications. The Jet Propulsion Laboratory has been actively pursuing the development of thermoelectric micro/nanodevices that can be fabricated using a combination of electrochemical deposition and integrated circuit processing techniques. Some of the technical challenges associated with these micro/nanodevice concepts, their expected level of performance and experimental fabrication and testing results to date are presented and discussed.

Classification of Pinus patula, P. tecunumanii, P. oocarpa, P. caribaea var. hondurensis, and Related Taxonomic Entities

Science.gov (United States)

A.E. Squillace; Jesse P. Perry

1992-01-01

Stem xylem terpenes of 75 pine populations were studied to determine relationships among taxonomic entities. Typical Pinus patula populations occurring in areas north and west of Oaxaca, Mexico, had very high proportions of 3-phellandrene and low proportions of other constituents. Terpene compositions of populations of variety longipeduncalatain...

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

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Kaczmarczyk Paweł

2017-12-01

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

Computing the Taxonomic, Morphological and Sexual Variations of Bornean Hornbills (family: Bucerotidae)

Science.gov (United States)

Laman, Charlie J. M.; Kho, Angel

Bornean Hornbills (Family Bucerotidae) are omnivorous creatures, distinguished for their large size and large bill. In our study, only five out of eight species of Bornean hornbills were available. Our aims were to determine the taxonomic, morphological and sexual variations, among the species. Nine morphological features were measured from 83 specimens. Canonical Discriminant and Cluster analyses showed that the data were successfully clustered into 5 species. Logistic regression analyses showed that the diagnostic character differentiation is total length. Further results showed that males tend to be bigger than females.

Alternative energy sources or integrated alternative energy systems? Oil as a modern lance of Peleus for the energy transition

International Nuclear Information System (INIS)

Szklo, Alexandre; Schaeffer, Roberto

2006-01-01

In this viewpoint, we discuss the importance of consorting alternative energy sources with oil, and not of opposing them. That is why we introduce the concept of alternative energy systems, which we feel is broader-ranging and more effective than alternative energy sources, as this deals with the actual transformation process of the global energy system. Alternative energy systems integrate oil with other energy sources and pave the way for new systems, which will benefit from what we call the 'virtues of oil'. They produce energy carriers for multi-fuel and multi-product strategies, where flexibility is a key target, allied to other co-benefits, especially those related to the increased use of renewable energy sources. The concept of alternative energy systems can bring a new light to the oil transition era discussion and might also influence energy policies for promoting renewables

System and method for integrating and accessing multiple data sources within a data warehouse architecture

Science.gov (United States)

Musick, Charles R [Castro Valley, CA; Critchlow, Terence [Livermore, CA; Ganesh, Madhaven [San Jose, CA; Slezak, Tom [Livermore, CA; Fidelis, Krzysztof [Brentwood, CA

2006-12-19

A system and method is disclosed for integrating and accessing multiple data sources within a data warehouse architecture. The metadata formed by the present method provide a way to declaratively present domain specific knowledge, obtained by analyzing data sources, in a consistent and useable way. Four types of information are represented by the metadata: abstract concepts, databases, transformations and mappings. A mediator generator automatically generates data management computer code based on the metadata. The resulting code defines a translation library and a mediator class. The translation library provides a data representation for domain specific knowledge represented in a data warehouse, including "get" and "set" methods for attributes that call transformation methods and derive a value of an attribute if it is missing. The mediator class defines methods that take "distinguished" high-level objects as input and traverse their data structures and enter information into the data warehouse.

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

Science.gov (United States)

Brown-Elliott, Barbara A; Wallace, Richard J

2002-10-01

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

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

Directory of Open Access Journals (Sweden)

Jonas Zimmermann

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

Open-Source Integrated Design-Analysis Environment For Nuclear Energy Advanced Modeling & Simulation Final Scientific/Technical Report

Energy Technology Data Exchange (ETDEWEB)

O' Leary, Patrick [Kitware, Inc., Clifton Park, NY (United States)

2017-01-30

The framework created through the Open-Source Integrated Design-Analysis Environment (IDAE) for Nuclear Energy Advanced Modeling & Simulation grant has simplify and democratize advanced modeling and simulation in the nuclear energy industry that works on a range of nuclear engineering applications. It leverages millions of investment dollars from the Department of Energy's Office of Nuclear Energy for modeling and simulation of light water reactors and the Office of Nuclear Energy's research and development. The IDEA framework enhanced Kitware’s Computational Model Builder (CMB) while leveraging existing open-source toolkits and creating a graphical end-to-end umbrella guiding end-users and developers through the nuclear energy advanced modeling and simulation lifecycle. In addition, the work deliver strategic advancements in meshing and visualization for ensembles.

Homoplastic evolution and host association of Eriophyoidea (Acari, Prostigmata) conflict with the morphological-based taxonomic system.

Science.gov (United States)

Li, Hao-Sen; Xue, Xiao-Feng; Hong, Xiao-Yue

2014-09-01

The superfamily Eriophyoidea is exceptionally diverse and its members are highly host-specific. Currently, the taxonomy of this group is based on morphology only. However, phylogenetic relationships in this group could be incorrect if the diagnostic morphological characters are homoplastic. Therefore, the phylogeny of 112 representative taxa of Eriophyoidea from China was determined using 18S, 28S D2-5 and D9-10 rRNA. Phylogenetic relationships were inferred through Bayesian, maximum likelihood and maximum parsimony methods, and then a number of clades or major clades were defined according to robust phylogenetic topologies combined with morphological comparison. Tests of monophyly showed that two of three families of Eriophyoidea as well as one subfamily and four tribes were not monophyletic. Ancestral character state reconstruction (ACSR) showed that five diagnostic morphological characters evolved several times, confounding the current taxonomy. Additionally, reconstruction of the history of host plant colonization suggested host switching occurred in a limited range of host plants. The host association data made it possible to determine taxonomic relationships more accurately. These results show that by integrating morphological and molecular information and host plant choice, it is possible to obtain a more accurate taxonomy and a deeper phylogenetic understanding of Eriophyoidea. Copyright © 2014 Elsevier Inc. All rights reserved.

Taxonomic Diversity of Fungi Associated with Some PCN Populations from Serbia

Directory of Open Access Journals (Sweden)

Violeta Oro

2012-01-01

Full Text Available Increased content of pesticides in food chain resulted in using microorganisms asagents of biological control. The potato cyst nematodes (PCN - Globodera pallida and G.rostochiensis belong to the group of the most important parasites - the quarantine organisms.The external and internal area of a cyst harbor numerous fungal and bacterial species.The aim of this study was to identify antagonistic fungi associated with some PCN populationsfrom Serbia. Fungal antagonists of potato cyst nematodes have not been previouslyinvestigated in our country. The diversity of PCN fungal antagonists is not reflected only atthe species level but also at the level of higher taxonomic categories.

CITOGENÉTICA COMO HERRAMIENTA TAXONÓMICA EN PECES I CYTOGENETICS AS A TAXONOMIC TOOL IN FISH

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Mauro Nircho

2018-04-01

Full Text Available This document presents a general overview on the basic and molecular techniques more commonly employed for the study of chromosomes in fi shes, with examples that demonstrate the usefulness of cytogenetics to resolve taxonomic problems, particularly when meristic or morphometric characteristic do not result in a clear differentiation between species.

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

Science.gov (United States)

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.

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

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Alan Bonner

2017-03-01

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

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

Science.gov (United States)

Santos, Cláudia Portes; Moravec, Frantisek

2009-02-01

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

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

Directory of Open Access Journals (Sweden)

Cláudia Portes Santos

2009-02-01

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

Detection of the Nitrate Pollution Sources in Shallow Aquifer, Using Integration of RS&GIS with Stable Isotopes Technologies

Science.gov (United States)

Shakak, N. B. I.

2018-04-01

Geographical information system (GIS) and remote sensing technique is a tool which is used for acquiring data from space, storing, analyzing and displaying spatial data, also can use for investigating source of environmental pollution which is affect health. Sudan landsat mosaic image which acquired in 2013 was used in this study to develop land use and land cover maps for tow selected study area, Khartoum urban area, and Bara locality in North kordofan state western Sudan. The main objective to assess the source of Nitrate pollution in shallow aquifer. ERDAS software was used to create land cover-land use maps for the study areas. For Khartoum town we used land sat mosaic image which acquire in 2013, and used supervised classification which more closely controlled than unsupervised. In this process, we select pixel that represent patterns you recognized or can identify with help from knowledge of the data, the classes desired, and the algorithm to be used is required. In this paper we integrated the (GIS&RS), and stable isotopes methods for fingerprinting Nitrate sources in shallow boreholes. The global positioning system (GPS), used in the field to identify the shallow boreholes location in a three dimensional coordinate (Latitude, longitude, and altitude), Water samples were collected from 19 shallow boreholes in the study areas according to the standard sampling method send to laboratory to measure stable nitrogen (δ15Nnitrate), and Nitrate-oxygen (δ18Onitrate) isotopes. Analysis were conducted by using isotope ratio mass spectrometry (IRMS). We can conclude that, special distribution and integration of GIs & RS help to identify the source of nitrate pollution.

DETECTION OF THE NITRATE POLLUTION SOURCES IN SHALLOW AQUIFER, USING INTEGRATION OF RS&GIS WITH STABLE ISOTOPES TECHNOLOGIES

Directory of Open Access Journals (Sweden)

N. B. I. Shakak

2018-04-01

Full Text Available Geographical information system (GIS and remote sensing technique is a tool which is used for acquiring data from space, storing, analyzing and displaying spatial data, also can use for investigating source of environmental pollution which is affect health. Sudan landsat mosaic image which acquired in 2013 was used in this study to develop land use and land cover maps for tow selected study area, Khartoum urban area, and Bara locality in North kordofan state western Sudan. The main objective to assess the source of Nitrate pollution in shallow aquifer. ERDAS software was used to create land cover-land use maps for the study areas. For Khartoum town we used land sat mosaic image which acquire in 2013, and used supervised classification which more closely controlled than unsupervised. In this process, we select pixel that represent patterns you recognized or can identify with help from knowledge of the data, the classes desired, and the algorithm to be used is required. In this paper we integrated the (GIS&RS, and stable isotopes methods for fingerprinting Nitrate sources in shallow boreholes. The global positioning system (GPS, used in the field to identify the shallow boreholes location in a three dimensional coordinate (Latitude, longitude, and altitude, Water samples were collected from 19 shallow boreholes in the study areas according to the standard sampling method send to laboratory to measure stable nitrogen (δ15Nnitrate, and Nitrate-oxygen (δ18Onitrate isotopes. Analysis were conducted by using isotope ratio mass spectrometry (IRMS. We can conclude that, special distribution and integration of GIs & RS help to identify the source of nitrate pollution.

An Image Matching Algorithm Integrating Global SRTM and Image Segmentation for Multi-Source Satellite Imagery

Directory of Open Access Journals (Sweden)

Xiao Ling

2016-08-01

Full Text Available This paper presents a novel image matching method for multi-source satellite images, which integrates global Shuttle Radar Topography Mission (SRTM data and image segmentation to achieve robust and numerous correspondences. This method first generates the epipolar lines as a geometric constraint assisted by global SRTM data, after which the seed points are selected and matched. To produce more reliable matching results, a region segmentation-based matching propagation is proposed in this paper, whereby the region segmentations are extracted by image segmentation and are considered to be a spatial constraint. Moreover, a similarity measure integrating Distance, Angle and Normalized Cross-Correlation (DANCC, which considers geometric similarity and radiometric similarity, is introduced to find the optimal correspondences. Experiments using typical satellite images acquired from Resources Satellite-3 (ZY-3, Mapping Satellite-1, SPOT-5 and Google Earth demonstrated that the proposed method is able to produce reliable and accurate matching results.

Modeling the effects of integrating larval habitat source reduction and insecticide treated nets for malaria control.

Directory of Open Access Journals (Sweden)

Laith Yakob

Full Text Available Integrated vector management for malaria control has received a lot of recent interest. Attacking multiple points in the transmission cycle is hoped to act synergistically and improve upon current single-tool interventions based on the use of insecticide-treated bed nets (ITNs. In the present study, we theoretically examined the application of larval habitat source reduction with ITNs in reducing malaria transmission. We selected this type of environmental management to complement ITNs because of a potential secondary mode of action that both control strategies share. In addition to increasing vector mortality, ITNs reduce the rate at which female mosquitoes locate human hosts for blood feeding, thereby extending their gonotrophic cycle. Similarly, while reducing adult vector emergence and abundance, source reduction of larval habitats may prolong the cycle duration by extending delays in locating oviposition sites. We found, however, that source reduction of larval habitats only operates through this secondary mode of action when habitat density is below a critical threshold. Hence, we illustrate how this strategy becomes increasingly effective when larval habitats are limited. We also demonstrate that habitat source reduction is better suited to human populations of higher density and in the presence of insecticide resistance or when the insecticidal properties of ITNs are depleted.

Silicon photonic integrated circuit swept-source optical coherence tomography receiver with dual polarization, dual balanced, in-phase and quadrature detection.

Science.gov (United States)

Wang, Zhao; Lee, Hsiang-Chieh; Vermeulen, Diedrik; Chen, Long; Nielsen, Torben; Park, Seo Yeon; Ghaemi, Allan; Swanson, Eric; Doerr, Chris; Fujimoto, James

2015-07-01

Optical coherence tomography (OCT) is a widely used three-dimensional (3D) optical imaging method with many biomedical and non-medical applications. Miniaturization, cost reduction, and increased functionality of OCT systems will be critical for future emerging clinical applications. We present a silicon photonic integrated circuit swept-source OCT (SS-OCT) coherent receiver with dual polarization, dual balanced, in-phase and quadrature (IQ) detection. We demonstrate multiple functional capabilities of IQ polarization resolved detection including: complex-conjugate suppressed full-range OCT, polarization diversity detection, and polarization-sensitive OCT. To our knowledge, this is the first demonstration of a silicon photonic integrated receiver for OCT. The integrated coherent receiver provides a miniaturized, low-cost solution for SS-OCT, and is also a key step towards a fully integrated high speed SS-OCT system with good performance and multi-functional capabilities. With further performance improvement and cost reduction, photonic integrated technology promises to greatly increase penetration of OCT systems in existing applications and enable new applications.

Post-Disturbance Stability of Fish Assemblages Measured at Coarse Taxonomic Resolution Masks Change at Finer Scales.

Science.gov (United States)

Ceccarelli, Daniela M; Emslie, Michael J; Richards, Zoe T

2016-01-01

Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events.

Determination of a source term for a time fractional diffusion equation with an integral type over-determining condition

Directory of Open Access Journals (Sweden)

Timurkhan S. Aleroev

2013-12-01

Full Text Available We consider a linear heat equation involving a fractional derivative in time, with a nonlocal boundary condition. We determine a source term independent of the space variable, and the temperature distribution for a problem with an over-determining condition of integral type. We prove the existence and uniqueness of the solution, and its continuous dependence on the data.

Large Scale Integration of Renewable Power Sources into the Vietnamese Power System

Science.gov (United States)

Kies, Alexander; Schyska, Bruno; Thanh Viet, Dinh; von Bremen, Lueder; Heinemann, Detlev; Schramm, Stefan

2017-04-01

The Vietnamese Power system is expected to expand considerably in upcoming decades. Power capacities installed are projected to grow from 39 GW in 2015 to 129.5 GW by 2030. Installed wind power capacities are expected to grow to 6 GW (0.8 GW 2015) and solar power capacities to 12 GW (0.85 GW 2015). This goes hand in hand with an increase of the renewable penetration in the power mix from 1.3% from wind and photovoltaics (PV) in 2015 to 5.4% by 2030. The overall potential for wind power in Vietnam is estimated to be around 24 GW. Moreover, the up-scaling of renewable energy sources was formulated as one of the priorized targets of the Vietnamese government in the National Power Development Plan VII. In this work, we investigate the transition of the Vietnamese power system towards high shares of renewables. For this purpose, we jointly optimise the expansion of renewable generation facilities for wind and PV, and the transmission grid within renewable build-up pathways until 2030 and beyond. To simulate the Vietnamese power system and its generation from renewable sources, we use highly spatially and temporally resolved historical weather and load data and the open source modelling toolbox Python for Power System Analysis (PyPSA). We show that the highest potential of renewable generation for wind and PV is observed in southern Vietnam and discuss the resulting need for transmission grid extensions in dependency of the optimal pathway. Furthermore, we show that the smoothing effect of wind power has several considerable beneficial effects and that the Vietnamese hydro power potential can be efficiently used to provide balancing opportunities. This work is part of the R&D Project "Analysis of the Large Scale Integration of Renewable Power into the Future Vietnamese Power System" (GIZ, 2016-2018).

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

Science.gov (United States)

2011-01-01

Background Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. Results To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350

LabKey Server: An open source platform for scientific data integration, analysis and collaboration

Directory of Open Access Journals (Sweden)

Lum Karl

2011-03-01

Full Text Available Abstract Background Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. Results To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i Submitting specimens requests across collaborating organizations (ii Graphically defining new experimental data types, metadata and wizards for data collection (iii Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v Interacting dynamically with external data sources (vi Tracking study participants and cohorts over time (vii Developing custom interfaces using client libraries (viii Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36

LabKey Server: an open source platform for scientific data integration, analysis and collaboration.

Science.gov (United States)

Nelson, Elizabeth K; Piehler, Britt; Eckels, Josh; Rauch, Adam; Bellew, Matthew; Hussey, Peter; Ramsay, Sarah; Nathe, Cory; Lum, Karl; Krouse, Kevin; Stearns, David; Connolly, Brian; Skillman, Tom; Igra, Mark

2011-03-09

Broad-based collaborations are becoming increasingly common among disease researchers. For example, the Global HIV Enterprise has united cross-disciplinary consortia to speed progress towards HIV vaccines through coordinated research across the boundaries of institutions, continents and specialties. New, end-to-end software tools for data and specimen management are necessary to achieve the ambitious goals of such alliances. These tools must enable researchers to organize and integrate heterogeneous data early in the discovery process, standardize processes, gain new insights into pooled data and collaborate securely. To meet these needs, we enhanced the LabKey Server platform, formerly known as CPAS. This freely available, open source software is maintained by professional engineers who use commercially proven practices for software development and maintenance. Recent enhancements support: (i) Submitting specimens requests across collaborating organizations (ii) Graphically defining new experimental data types, metadata and wizards for data collection (iii) Transitioning experimental results from a multiplicity of spreadsheets to custom tables in a shared database (iv) Securely organizing, integrating, analyzing, visualizing and sharing diverse data types, from clinical records to specimens to complex assays (v) Interacting dynamically with external data sources (vi) Tracking study participants and cohorts over time (vii) Developing custom interfaces using client libraries (viii) Authoring custom visualizations in a built-in R scripting environment. Diverse research organizations have adopted and adapted LabKey Server, including consortia within the Global HIV Enterprise. Atlas is an installation of LabKey Server that has been tailored to serve these consortia. It is in production use and demonstrates the core capabilities of LabKey Server. Atlas now has over 2,800 active user accounts originating from approximately 36 countries and 350 organizations. It tracks

Pulseq-Graphical Programming Interface: Open source visual environment for prototyping pulse sequences and integrated magnetic resonance imaging algorithm development.

Science.gov (United States)

Ravi, Keerthi Sravan; Potdar, Sneha; Poojar, Pavan; Reddy, Ashok Kumar; Kroboth, Stefan; Nielsen, Jon-Fredrik; Zaitsev, Maxim; Venkatesan, Ramesh; Geethanath, Sairam

2018-03-11

To provide a single open-source platform for comprehensive MR algorithm development inclusive of simulations, pulse sequence design and deployment, reconstruction, and image analysis. We integrated the "Pulseq" platform for vendor-independent pulse programming with Graphical Programming Interface (GPI), a scientific development environment based on Python. Our integrated platform, Pulseq-GPI, permits sequences to be defined visually and exported to the Pulseq file format for execution on an MR scanner. For comparison, Pulseq files using either MATLAB only ("MATLAB-Pulseq") or Python only ("Python-Pulseq") were generated. We demonstrated three fundamental sequences on a 1.5 T scanner. Execution times of the three variants of implementation were compared on two operating systems. In vitro phantom images indicate equivalence with the vendor supplied implementations and MATLAB-Pulseq. The examples demonstrated in this work illustrate the unifying capability of Pulseq-GPI. The execution times of all the three implementations were fast (a few seconds). The software is capable of user-interface based development and/or command line programming. The tool demonstrated here, Pulseq-GPI, integrates the open-source simulation, reconstruction and analysis capabilities of GPI Lab with the pulse sequence design and deployment features of Pulseq. Current and future work includes providing an ISMRMRD interface and incorporating Specific Absorption Ratio and Peripheral Nerve Stimulation computations. Copyright © 2018 Elsevier Inc. All rights reserved.

Gram-positive bacteria of marine origin: a numerical taxonomic study on Mediterranean isolates.

Science.gov (United States)

Ortigosa, M; Garay, E; Pujalte, M J

1997-12-01

A numerical taxonomic study was performed on 65 Gram-positive wild strains of heterotrophic, aerobic, marine bacteria, and 9 reference strains. The isolates were obtained from oysters and seawater sampled monthly over one year, by direct plating on Marine Agar. The strains were characterized by 96 morphological, biochemical, physiological and nutritional tests. Clustering yielded 13 phena at 0.62 similarity level (Sl coefficient). Only one of the seven phena containing wild isolates could be identified (Bacillus marinus). A pronounced salt requirement was found in most isolates.

Three reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Grant's gazelles

DEFF Research Database (Denmark)

Lorenzen, Eline Deidre; Arctander, Peter; Siegismund, Hans Redlef

2008-01-01

are discussed in reference to the four currently recognised subspecies. We suggest Grant's gazelles be raised to the superspecies Nanger (granti) comprising three taxonomic units corresponding to the three mtDNA lineages. There was no evidence of gene flow between the notata and granti lineages, despite...... their geographic proximity, suggesting reproductive isolation. These constitute evolutionary significant units within the adaptive evolutionary framework. Due to its restricted geographic distribution and genetic and morphological distinctiveness, we suggest the petersii lineage be raised to the species Nanger...

Taxonomic Review of the Genus Euodynerus (Hymenoptera: Vespidae: Eumeninae in the Korean Peninsula

Directory of Open Access Journals (Sweden)

Jeong-Kyu Kim

2012-07-01

Full Text Available Korean species of the genus Euodynerus Dalla Torre were taxonomically reviewed. Four species were confirmed: E. trilobus, E. dantici violaceipennis, E. nipanicus nipanicus, and E. quadrifasciatus atripes. The specimens previously identified as E. dantici brachyotomus and E. notatus pubescence form North Korea were re-examined, and corrected to E. dantici violaceipennis and E. nipanicus nipanicus, respectively. Euodynerus quadrifasciatus atripes was re-described for future researchers. After careful reading previous descriptions, Euodynerus seuli Radoszkowski was tentatively supposed to be conspecific with E. nipanicus.

Effects of land use on taxonomic and functional diversity

DEFF Research Database (Denmark)

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

2016-01-01

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

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

Science.gov (United States)

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

2017-01-15

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

Seed morphology and its taxonomic significance in the family malvaceae

International Nuclear Information System (INIS)

Abid, R.; Ather, A.

2016-01-01

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

Integrating intermittent energy sources in liberalized electricity markets: from technical costs to economic penalties as a result of market rules

International Nuclear Information System (INIS)

Menanteau, Ph.; Finon, D.; Lamy, M.L.

2003-06-01

With the aim of preventing climatic change and ensuring the security of energy supplies, the recent European Directive on renewable energy production sources is aimed at bringing about a very substantial increase in electricity production from renewable sources in Europe by the 2010 horizon. Generally speaking, production of electricity from renewable sources will be assured by biomass and wind, and to a lesser extent by micro hydro, technologies whose characteristics are very different from the point of view of their integration into the electricity system. Their inclusion in the electricity systems will cause problems because of the intermittent nature of the production, a factor that does not enter into the paradigms of producers, system operators or regulators. The problems raised by the integration of intermittent production are technical in nature (risk of non-availability in peak periods, the need for additional reserves) and will incur adjustment costs, but the way in which the electricity markets function will impose economic penalties generally more substantial than the added technical costs. In this paper are examined in succession: (i) the additional costs raised by intermittence; (ii) the economic penalties imposed by the operating rules of de-regulated electricity markets with electricity production from renewable sources included, with particular reference to the case of the British and Nordic markets; and (iii) an analysis of the options that could limit the gap between the additional cost of intermittent production for the system and the adjustment surcharges imposed by the electricity markets, with the aim of reducing the tension between the deregulation of the electricity market and promoting the development of renewable energy sources. (A.L.B.)

The Protein Identifier Cross-Referencing (PICR service: reconciling protein identifiers across multiple source databases

Directory of Open Access Journals (Sweden)

Leinonen Rasko

2007-10-01

Full Text Available Abstract Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR service, a web application that provides interactive and programmatic (SOAP and REST access to a mapping algorithm that uses the UniProt Archive (UniParc as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV or Microsoft Excel (XLS files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR

LASER APPLICATIONS AND OTHER TOPICS IN QUANTUM ELECTRONICS: Laser-induced extreme UV radiation sources for manufacturing next-generation integrated circuits

Science.gov (United States)

Borisov, V. M.; Vinokhodov, A. Yu; Ivanov, A. S.; Kiryukhin, Yu B.; Mishchenko, V. A.; Prokof'ev, A. V.; Khristoforov, O. B.

2009-10-01

The development of high-power discharge sources emitting in the 13.5±0.135-nm spectral band is of current interest because they are promising for applications in industrial EUV (extreme ultraviolet) lithography for manufacturing integrated circuits according to technological precision standards of 22 nm and smaller. The parameters of EUV sources based on a laser-induced discharge in tin vapours between rotating disc electrodes are investigated. The properties of the discharge initiation by laser radiation at different wavelengths are established and the laser pulse parameters providing the maximum energy characteristics of the EUV source are determined. The EUV source developed in the study emits an average power of 276 W in the 13.5±0.135-nm spectral band on conversion to the solid angle 2π sr in the stationary regime at a pulse repetition rate of 3000 Hz.

Review of the cyanobacterial genera implaying planktic species after recent taxonomic revisions according to polyphasic methods: state as of 2014.

Czech Academy of Sciences Publication Activity Database

Komárek, Jiří

2016-01-01

Roč. 764, č. 1 (2016), s. 259-270 ISSN 0018-8158 Institutional support: RVO:67985939 Keywords : cyanobacteria * plankton * taxonomic revisions Subject RIV: EH - Ecology, Behaviour Impact factor: 2.056, year: 2016

ViCTree: An automated framework for taxonomic classification from protein sequences.

Science.gov (United States)

Modha, Sejal; Thanki, Anil; Cotmore, Susan F; Davison, Andrew J; Hughes, Joseph

2018-02-20

The increasing rate of submission of genetic sequences into public databases is providing a growing resource for classifying the organisms that these sequences represent. To aid viral classification, we have developed ViCTree, which automatically integrates the relevant sets of sequences in NCBI GenBank and transforms them into an interactive maximum likelihood phylogenetic tree that can be updated automatically. ViCTree incorporates ViCTreeView, which is a JavaScript-based visualisation tool that enables the tree to be explored interactively in the context of pairwise distance data. To demonstrate utility, ViCTree was applied to subfamily Densovirinae of family Parvoviridae. This led to the identification of six new species of insect virus. ViCTree is open-source and can be run on any Linux- or Unix-based computer or cluster. A tutorial, the documentation and the source code are available under a GPL3 license, and can be accessed at http://bioinformatics.cvr.ac.uk/victree_web/. sejal.modha@glasgow.ac.uk.

Advanced RF and microwave functions based on an integrated optical frequency comb source.

Science.gov (United States)

Xu, Xingyuan; Wu, Jiayang; Nguyen, Thach G; Shoeiby, Mehrdad; Chu, Sai T; Little, Brent E; Morandotti, Roberto; Mitchell, Arnan; Moss, David J

2018-02-05

We demonstrate advanced transversal radio frequency (RF) and microwave functions based on a Kerr optical comb source generated by an integrated micro-ring resonator. We achieve extremely high performance for an optical true time delay aimed at tunable phased array antenna applications, as well as reconfigurable microwave photonic filters. Our results agree well with theory. We show that our true time delay would yield a phased array antenna with features that include high angular resolution and a wide range of beam steering angles, while the microwave photonic filters feature high Q factors, wideband tunability, and highly reconfigurable filtering shapes. These results show that our approach is a competitive solution to implementing reconfigurable, high performance and potentially low cost RF and microwave signal processing functions for applications including radar and communication systems.

Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA

Directory of Open Access Journals (Sweden)

Arthur Gusman

2016-12-01

Full Text Available There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA in the animal kingdom: a system named doubly uniparental inheritance (DUI, which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI in two bivalve species, i.e., the nuculanoid Yoldia hyperborea(Gould, 1841and the veneroid Scrobicularia plana(Da Costa,1778, increasing the number of families in which DUI has been found by two. An update on the taxonomic distribution of DUI in the Bivalvia is also presented.

Critical Taxonomic Appraisal of Some Taxa of Pedicularis from Indian Himalayas Belonging to Section Siphonanthae

Directory of Open Access Journals (Sweden)

Arti Garg

2009-06-01

Full Text Available The existing confusion on the taxonomic status of five taxa of Pedicularis viz. P. punctata Decne, P. siphonantha D. Don, P. hookeriana Wall. ex Benth., P. megalantha D. Don and P. hoffmeisteri Kl. ex Kl. & Garcke is resolved on the basis of critical morphological study. These taxa belong to section Siphonanthae, subgenus Longirostres. Pennell’s view of segregating these taxa into distinct species is defended and upheld.

Elaiophores: their taxonomic distribution, morphology and functions

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Clivia Carolina Fiorilo Possobom

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

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

International Nuclear Information System (INIS)

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

2010-01-01

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

Integrated watershed- and farm-scale modeling framework for targeting critical source areas while maintaining farm economic viability.

Science.gov (United States)

Ghebremichael, Lula T; Veith, Tamie L; Hamlett, James M

2013-01-15

Quantitative risk assessments of pollution and data related to the effectiveness of mitigating best management practices (BMPs) are important aspects of nonpoint source pollution control efforts, particularly those driven by specific water quality objectives and by measurable improvement goals, such as the total maximum daily load (TMDL) requirements. Targeting critical source areas (CSAs) that generate disproportionately high pollutant loads within a watershed is a crucial step in successfully controlling nonpoint source pollution. The importance of watershed simulation models in assisting with the quantitative assessments of CSAs of pollution (relative to their magnitudes and extents) and of the effectiveness of associated BMPs has been well recognized. However, due to the distinct disconnect between the hydrological scale in which these models conduct their evaluation and the farm scale at which feasible BMPs are actually selected and implemented, and due to the difficulty and uncertainty involved in transferring watershed model data to farm fields, there are limited practical applications of these tools in the current nonpoint source pollution control efforts by conservation specialists for delineating CSAs and planning targeting measures. There are also limited approaches developed that can assess impacts of CSA-targeted BMPs on farm productivity and profitability together with the assessment of water quality improvements expected from applying these measures. This study developed a modeling framework that integrates farm economics and environmental aspects (such as identification and mitigation of CSAs) through joint use of watershed- and farm-scale models in a closed feedback loop. The integration of models in a closed feedback loop provides a way for environmental changes to be evaluated with regard to the impact on the practical aspects of farm management and economics, adjusted or reformulated as necessary, and revaluated with respect to effectiveness of

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci.

Science.gov (United States)

Cornman, R Scott; Otto, Clint R V; Iwanowicz, Deborah; Pettis, Jeffery S

2015-01-01

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5' of ITS1 and the 3' of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower "read2" quality, further

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

Science.gov (United States)

Smith, B Eugene; Johnston, Mark K; Lücking, Robert

2016-01-01

Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of

A new integral experiment on copper with DT neutron source at JAEA/FNS

Energy Technology Data Exchange (ETDEWEB)

Kwon, Saerom, E-mail: kwon.saerom@jaea.go.jp; Sato, Satoshi; Ohta, Masayuki; Ochiai, Kentaro; Konno, Chikara

2016-11-01

Highlights: • Integral experiment on copper with DT neutron was performed under small influence of background neutrons which were efficiently absorbed in the Li{sub 2}O layers. • The experimental analyses were carried out using MCNP5-1.40 and the recent nuclear data libraries. • The underestimation issue of the reaction rates related to lower energy neutrons is focused on. • The combination of the {sup 63}Cu data in JEFF-3.2 and {sup 65}Cu data in JENDL-4.0 gave the best C/E. • The specific cross section data of copper should be reassessed. - Abstract: In order to validate copper nuclear data, an integral experiment on copper with the DT neutron source at JAEA/FNS had been performed over 20 years ago. The experiment had showed that ratios of the calculated values to the experimental ones (C/Es) related to lower energy neutrons had been drastically smaller than unity. In order to reveal reasons of the small C/Es, we newly performed the integral experiment on copper with the DT neutron source at JAEA/FNS. A quasi-cylindrical copper assembly of 315 mm in radius and 608 mm in depth was covered with Li{sub 2}O blocks of 51 mm in thickness for the front and side parts and 153 mm in thickness for the rear part to exclude background neutrons which might affect the measured data. We measured reaction rates with 5 activation foils and fission rates with 2 micro fission chambers at the center of the assembly. The experiment was analyzed by using MCNP5-1.40 with the recent nuclear data libraries, ENDF/B-VII.1, JEFF-3.2 and JENDL-4.0. As a result, the C/E of the reaction rate of the {sup 197}Au(n,γ){sup 198}Au reaction improved by 10% from the previous result and the combination of the {sup 63}Cu data in JEFF-3.2 and {sup 65}Cu data in JENDL-4.0 increased the C/E by more 10% because of the resonance data of the {sup 63}Cu in JEFF-3.2. Moreover, the calculated result with the {sup 63}Cu data in JEFF-3.2 and {sup 65}Cu data in JENDL-4.0 with 10% larger elastic

Taxonomic and geographic novelties in the genus Plantago (Plantaginaceae) in Chile, including the description of a new species

DEFF Research Database (Denmark)

Hassemer, Gustavo; Shipunov, Alexey; Rønsted, Nina

2018-01-01

We present taxonomic and geographic novelties in the genus Plantago from Chile. More specifically, we describe P. nebularis, a new species endemic to Cerro Moreno, Antofagasta region, and propose P. zoellneriana, a new name for P. sericea subsp. araucana. We also lectotypify the name P. sericea, ...

Polyphasic taxonomic approach in the description of Alishewanella fetalis gen. nov., sp nov., isolated from a human foetus

DEFF Research Database (Denmark)

Vogel, Birte Fonnesbech; Venkateswaran, K.; Christensen, H.

2000-01-01

A taxonomically unique bacterium is described on the basis of a physiological and biochemical characterization, fatty acid profiling and sequence analyses of 16S rRNA and gyrase B (gyrB) genes. This non-motile, non-fermentative bacterium was isolated from a human foetus in Uppsala, Sweden...

The source apportionment of carbonaceous combustion products by micro-radiocarbon measurements for the integrated air cancer project (IACP)

International Nuclear Information System (INIS)

Klouda, G.A.; Currie, L.A.; Sheffield, A.E.; Wise, S.A.; Benner, B.A.; Stevens, R.K.; Merrill, R.G.

1987-01-01

Atmospheric particle samples were collected during the winter of 1984-1985 in Albuquerque, NM and Raleigh, NC by the EPA for the Integrated Air Cancer Project (IACP). Selected chemical fractions were analyzed for /sup 14/C to apportion mobile (motor vehicles) and stationary (residential wood combustion) sources. In addition, these results were used to validate the EPA Single Tracer Regression Model (STRM), also a technique for the source apportionment of aerosols. Preliminary /sup 14/C results for the Albuquerque residential site at night showed 79% Contemporary Carbon (CC) compared to 95% CC for Raleight at night for the total carbon; 88% and 94% of the total-C was organic, respectively. The Albuquerque traffic site during the day showed 1.4 to 3.9 times less CC compared to the daytime residential site for total-C. The elemental carbon fraction in all cases showed a lower percentage of contemporary carbon than the total carbon, which indicates that this chemical fraction may be an excellent tracer of mobile sources. These results are consistent with a daytime mobile source at the traffic site and a nighttime Residential Wood Combustion (RWC) source at the residential site. Also, the results from the EPA STRM technique for this study were in good agreement with those obtained by the /sup 14/C Direct Tracer (/sup 14/C-DT) technique for source apportionment of these aerosols

XML schemas and mark-up practices of taxonomic literature.

Science.gov (United States)

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

2011-01-01

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

HARVESTING, INTEGRATING AND DISTRIBUTING LARGE OPEN GEOSPATIAL DATASETS USING FREE AND OPEN-SOURCE SOFTWARE

Directory of Open Access Journals (Sweden)

R. Oliveira

2016-06-01

Full Text Available Federal, State and Local government agencies in the USA are investing heavily on the dissemination of Open Data sets produced by each of them. The main driver behind this thrust is to increase agencies’ transparency and accountability, as well as to improve citizens’ awareness. However, not all Open Data sets are easy to access and integrate with other Open Data sets available even from the same agency. The City and County of Denver Open Data Portal distributes several types of geospatial datasets, one of them is the city parcels information containing 224,256 records. Although this data layer contains many pieces of information it is incomplete for some custom purposes. Open-Source Software were used to first collect data from diverse City of Denver Open Data sets, then upload them to a repository in the Cloud where they were processed using a PostgreSQL installation on the Cloud and Python scripts. Our method was able to extract non-spatial information from a ‘not-ready-to-download’ source that could then be combined with the initial data set to enhance its potential use.

Vertical integration as a source of market power

Energy Technology Data Exchange (ETDEWEB)

Phelps, J.H.

1981-11-01

This paper has put forward a theory of vertial integration where the ability of a group of firms to engage in noncompetitive pricing is increased by altering conjectural variations. An analysis of conditions faced by major oil companies at refining indicated little likelihood of market power, short of a complex, secret price fixing agreement. Vertical integration to branded retail outlets appears to have created the ability to price noncompetitively without overt collusion. More interesting for vertical policy are the results on non price rivalry where excess profits appear to have been turned into social costs.

A taxonomic review of the dry-fruited species of Anemone (Ranunculaceae in southern Africa

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J. C. Manning

2013-01-01

Full Text Available The three dry-fruited species of Anemone sect. Pulsatilloides subsect. Alchemillifoliae (Ranunculaceae from southern Africa are reviewed, with full descriptions and nomenclature, including complete synonomy, taxonomic history with nomenclatural corrections, ecological notes, and distribution. A. tenuifolia (L.f. DC. from the Cape Floristic Region is segregated as ser. Pinnatifoliae from the two summer rainfall species, A. caffra (Eckl. & Zeyh. Harv. and A. fanninnii Harv. ex Masters, which remain in ser. Alchemillifoliae, emphasising the strong vegetative differences between the two series.

Colombian coca plants. A critical discussion on taxonomic aspects of cultivated Erythroxylum species (Erythroxylaceae)

International Nuclear Information System (INIS)

Galindo Bonilla, Aida; Fernandez Alonzo, Jose Luis

2010-01-01

Forensic botany is in high demand in Colombia in connection with plant material, mainly coca from illicit crops. The taxonomic study of the two species and four varieties of Erythroxylum P. Browne (Erythroxylaceae) cultivated in Colombia was carried out. Hybridization between E. coca and E. novogranatense and between the two varieties of E. coca is suggested, and important changes in the geographic distribution of all taxa are described. Both, hybridization and changes in distribution patterns are due to anthropic intervention.

Towards Utilization of Neurofuzzy Systems for Taxonomic Identification Using Psittacines as a Case Study

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Shahram Rahimi

2016-01-01

Full Text Available Demonstration of the neurofuzzy application to the task of psittacine (parrot taxonomic identification is presented in this paper. In this work, NEFCLASS-J neurofuzzy system is utilized for classification of parrot data for 141 and 183 groupings, using 68 feature points or qualities. The reported results display classification accuracies of above 95%, which is strongly tied to the setting of certain parameters of the neurofuzzy system. Rule base sizes were in the range of 1,750 to 1,950 rules.

ERP correlates of source memory: Unitized source information increases familiarity-based retrieval

OpenAIRE

Diana, Rachel A.; Van den Boom, Wijnand; Yonelinas, Andrew P.; Ranganath, Charan

2010-01-01

Source memory tests typically require subjects to make decisions about the context in which an item was encoded and are thought to depend on recollection of details from the study episode. Although it is generally believed that familiarity does not contribute to source memory, recent behavioral studies have suggested that familiarity may also support source recognition when item and source information are integrated, or “unitized”, during study (Diana, Yonelinas, and Ranganath 2008). However,...

Taxonomic study of Festuca L. subgenus Schedonorus (P. Beauv. Peterm. in Iran

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Sayed Zabihollah Hosseini

2013-11-01

Full Text Available This study was based upon a taxonomic review of the subgenus Schedonorus in Iran. A collection of 30 specimens belonging to the herbaria: W, B and HUI (herbarium of the University of Isfahan were studied. Based on the results of this study, this subgenus included three species: Festuca arundinacea, F. gigantea and F. pratensis in Iran. Furthermore, this study showed that F. arundinacea, occured in this country with two subspecies: orientalis (Hack. Tzvelev and fenas (Lag. Arcang. with the greatest area of distribution compared to the other two species. Our examination of the type specimen of F. elatior subsp. pratensis var. elbursiana confirmed its synonymy with F. arundinacea.

Data Integration The Relational Logic Approach

CERN Document Server

Genesereth, Michael

2010-01-01

Data integration is a critical problem in our increasingly interconnected but inevitably heterogeneous world. There are numerous data sources available in organizational databases and on public information systems like the World Wide Web. Not surprisingly, the sources often use different vocabularies and different data structures, being created, as they are, by different people, at different times, for different purposes. The goal of data integration is to provide programmatic and human users with integrated access to multiple, heterogeneous data sources, giving each user the illusion of a sin

Data integration for plant genomics--exemplars from the integration of Arabidopsis thaliana databases.

Science.gov (United States)

Lysenko, Artem; Lysenko, Atem; Hindle, Matthew Morritt; Taubert, Jan; Saqi, Mansoor; Rawlings, Christopher John

2009-11-01

The development of a systems based approach to problems in plant sciences requires integration of existing information resources. However, the available information is currently often incomplete and dispersed across many sources and the syntactic and semantic heterogeneity of the data is a challenge for integration. In this article, we discuss strategies for data integration and we use a graph based integration method (Ondex) to illustrate some of these challenges with reference to two example problems concerning integration of (i) metabolic pathway and (ii) protein interaction data for Arabidopsis thaliana. We quantify the degree of overlap for three commonly used pathway and protein interaction information sources. For pathways, we find that the AraCyc database contains the widest coverage of enzyme reactions and for protein interactions we find that the IntAct database provides the largest unique contribution to the integrated dataset. For both examples, however, we observe a relatively small amount of data common to all three sources. Analysis and visual exploration of the integrated networks was used to identify a number of practical issues relating to the interpretation of these datasets. We demonstrate the utility of these approaches to the analysis of groups of coexpressed genes from an individual microarray experiment, in the context of pathway information and for the combination of coexpression data with an integrated protein interaction network.

Source-Message-Receiver in Integrated Marketing Communication

Science.gov (United States)

Broussard, Sharee LeBlanc

2011-01-01

This is an abbreviation of the author's dissertation. Because integrated marketing communication (IMC) research has traditionally been problematic, this study used an existing scale to determine that higher educational institutional advancement (alumni, marketing-communications, development) is an appropriate venue to study the process model of…

Air-Source Integrated Heat Pump System Development – Final Report

Energy Technology Data Exchange (ETDEWEB)

Baxter, Van D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Rice, C. Keith [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Munk, Jeffrey D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ally, Moonis R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Shen, Bo [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Uselton, R. B. [Lennox Industries, Inc., Knoxville, TN (United States)

2017-07-01

Between October 2007 and September 2017, Oak Ridge National Laboratory (ORNL) and Lennox Industries, Inc. (Lennox) engaged in a Cooperative Research and Development Agreement (CRADA) to develop an air-source integrated heat pump (AS-IHP) system for the US residential market. The Lennox AS-IHP concept consisted of a high-efficiency air-source heat pump (ASHP) for space heating and cooling services and a separate heat pump water heater/dehumidifier (WH/DH) module for domestic water heating and dehumidification (DH) services. A key feature of this system approach with the separate WH/DH is capability to pretreat (i.e., dehumidify) ventilation air and dedicated whole-house DH independent of the ASHP. Two generations of laboratory prototype WH/DH units were designed, fabricated, and lab tested. Performance maps for the system were developed using the latest research version of the US Department of Energy/ORNL heat pump design model (Rice 1992; Rice and Jackson 2005; Shen et al. 2012) as calibrated against the lab test data. These maps served as the input to TRNSYS (Solar Energy Laboratory et al. 2010) to predict annual performance relative to a baseline suite of equipment meeting minimum efficiency standards in effect in 2006 (i.e., a combination of an ASHP with a seasonal energy efficiency ratio (SEER) of 13 and resistance water heater with an energy factor (EF) of 0.9). Predicted total annual energy savings (based on use of a two-speed ASHP and the second-generation WH/DH prototype for the AS-IHP), while providing space conditioning, water heating, and dehumidification for a tight, well-insulated 2600 ft2 (242 m2) house at three US locations, ranged from 33 to 36%, averaging 35%, relative to the baseline system. The lowest savings were seen at the cold-climate Chicago location. Predicted energy use for water heating was reduced by about 50 to 60% relative to a resistance WH.

The taxonomic identity of Heliconius melpomene f. pyritosa var. fumigata Zikán (Lepidoptera: Nymphalidae

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André Victor Lucci Freitas

2015-06-01

Full Text Available The taxonomic identity of the butterfly Heliconius melpomene f. pyritosa var. fumigata Zikán, 1937 (Nymphalidae: Heliconiinae is discussed based on the discovery of the specimen based on which this name was assigned. The specimen is not a variation of Eueides tales surdus Stichel, 1903, as previously stated, but is in fact a variation of H. melpomene f. pyritosa, which is a synonym of Heliconius erato amalfreda Riffarth, 1901.

dena grid study II. Integration of renewable energy sources into the German power supply system until 2020; dena - Netzstudie II. Integration erneuerbarer Energien in die deutsche Stromversorgung bis 2020

Energy Technology Data Exchange (ETDEWEB)

Agricola, Annegret C.; Seidl, Hannes; Zoch, Immo (comps.)

2010-12-15

With its broad system approach, dena Grid Study II describes new ways of developing Germany's integrated grid with regard to the expansion of renewable energy sources and taking not only an economically optimised conventional power generation system but also European power trading into account. Basis for detailed grid planning. Having investigated many different transmission technologies, grid management measures and options for increasing flexibility on both the supply and demand side, the study does much more than simply identify grid expansion requirements, it shows the path towards overall optimisation of the energy supply system. In addition to robustly identifying grid expansion requirements, dena Grid Study II provides a very sound basis for further detailed grid planning and the identification of specific power routes in the German power transmission grid. Increasing grid expansion requirements. dena Grid Study II investigates the expansion of electricity generation from renewable energy sources to 39 percent by 2020. However, this is just an interim goal. By as soon as 2030, the German Federal Government is planning to raise the proportion of renewable electricity generation to 50 percent. This shows that even after 2020, further adaptation of grid infrastructure will still be necessary. Practical action required. If the grid expansion required to integrate renewable energy sources is to be achieved rapidly, there is an urgent need to back up the grid expansion scenarios presented in dena Grid Study II with practical action. (orig.)

Low-loss integrated electrical surface plasmon source with ultra-smooth metal film fabricated by polymethyl methacrylate ‘bond and peel’ method

Science.gov (United States)

Liu, Wenjie; Hu, Xiaolong; Zou, Qiushun; Wu, Shaoying; Jin, Chongjun

2018-06-01

External light sources are mostly employed to functionalize the plasmonic components, resulting in a bulky footprint. Electrically driven integrated plasmonic devices, combining ultra-compact critical feature sizes with extremely high transmission speeds and low power consumption, can link plasmonics with the present-day electronic world. In an effort to achieve this prospect, suppressing the losses in the plasmonic devices becomes a pressing issue. In this work, we developed a novel polymethyl methacrylate ‘bond and peel’ method to fabricate metal films with sub-nanometer smooth surfaces on semiconductor wafers. Based on this method, we further fabricated a compact plasmonic source containing a metal-insulator-metal (MIM) waveguide with an ultra-smooth metal surface on a GaAs-based light-emitting diode wafer. An increase in propagation length of the SPP mode by a factor of 2.95 was achieved as compared with the conventional device containing a relatively rough metal surface. Numerical calculations further confirmed that the propagation length is comparable to the theoretical prediction on the MIM waveguide with perfectly smooth metal surfaces. This method facilitates low-loss and high-integration of electrically driven plasmonic devices, thus provides an immediate opportunity for the practical application of on-chip integrated plasmonic circuits.

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

Directory of Open Access Journals (Sweden)

R. Henrik Nilsson

2018-01-01

Full Text Available 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.

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

Science.gov (United States)

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

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

Directory of Open Access Journals (Sweden)

Jian-Wei Zhang

2018-04-01

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

Grid Integration of Single Stage Solar PV System using Three-level Voltage Source Converter

Science.gov (United States)

Hussain, Ikhlaq; Kandpal, Maulik; Singh, Bhim

2016-08-01

This paper presents a single stage solar PV (photovoltaic) grid integrated power generating system using a three level voltage source converter (VSC) operating at low switching frequency of 900 Hz with robust synchronizing phase locked loop (RS-PLL) based control algorithm. To track the maximum power from solar PV array, an incremental conductance algorithm is used and this maximum power is fed to the grid via three-level VSC. The use of single stage system with three level VSC offers the advantage of low switching losses and the operation at high voltages and high power which results in enhancement of power quality in the proposed system. Simulated results validate the design and control algorithm under steady state and dynamic conditions.

Loveridge’s Angolan geckos, Afroedura karroica bogerti and Pachydactylus scutatus angolensis (Sauria, Gekkonidae: new distribution records, comments on type localities and taxonomic status

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William R. Branch

2017-03-01

Full Text Available In 1944 Loveridge described two new geckos from Angola Afroedura karroica bogerti and Pachydactylus scutatus angolensis. The descriptions of both species have vague and confusing type localities and refinements are suggested based on early expedition reports historical accounts from the region and a review of cartographic material. Numerous new distribution records are reported for both species from expeditions undertaken from 1956–2016 by the authors or their colleagues. The taxonomic status of both species has changed but new material from diverse habitats altitudes and geological substrates indicates that further taxonomic adjustments are likely in order to reflect additional cryptic diversity.

La depresión en la infancia desde la perspectiva de las taxonomías empíricas

OpenAIRE

López Soler, Concepción; López Pina, José Antonio

1998-01-01

En este trabajo se analiza la depresión infantil desde el modelo de taxonomías empíricas propuesto por Achenbach y Edelbrock. Se revisan algunos aspectos diferenciales en el diagnóstico de la depresión en menores y adultos. La parte empírica se cent

Information Integration; The process of integration, evolution and versioning

NARCIS (Netherlands)

de Keijzer, Ander; van Keulen, Maurice

2005-01-01

At present, many information sources are available wherever you are. Most of the time, the information needed is spread across several of those information sources. Gathering this information is a tedious and time consuming job. Automating this process would assist the user in its task. Integration

Taxonomic diversity dynamics of early cretaceous brachiopods and gastropods in the Azerbaijanian domains of the Lesser Caucasus (Neo-Tethys Ocean

Directory of Open Access Journals (Sweden)

Ruban Dmitry A.