WorldWideScience

Sample records for evaluating taxon sampling

  1. Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

    OpenAIRE

    Passamonti Marco; Ferrucci Ronald R; Plazzi Federico

    2010-01-01

    Abstract Background Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup), or even a well-established phylogeny itself; these data are not always available in ge...

  2. Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies.

    Science.gov (United States)

    Plazzi, Federico; Ferrucci, Ronald R; Passamonti, Marco

    2010-04-27

    Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup), or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. We propose a new method to assess taxon sampling developing Clarke and Warwick statistics. This method aims to measure the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, our method also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses we describe in this paper. We show that this method is sensitive and allows direct discrimination between representative and unrepresentative samples. It is also informative about the addition of taxa to improve taxonomic coverage of the ingroup. Provided that the investigators' expertise is mandatory in this field, phylogenetic representativeness makes up an objective touchstone in planning phylogenetic studies.

  3. Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

    Directory of Open Access Journals (Sweden)

    Passamonti Marco

    2010-04-01

    Full Text Available Abstract Background Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. Results We propose a new method to assess taxon sampling developing Clarke and Warwick statistics. This method aims to measure the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, our method also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses we describe in this paper. Conclusions We show that this method is sensitive and allows direct discrimination between representative and unrepresentative samples. It is also informative about the addition of taxa to improve taxonomic coverage of the ingroup. Provided that the investigators' expertise is mandatory in this field, phylogenetic representativeness makes up an objective touchstone in planning phylogenetic studies.

  4. Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships.

    Science.gov (United States)

    Pick, K S; Philippe, H; Schreiber, F; Erpenbeck, D; Jackson, D J; Wrede, P; Wiens, M; Alié, A; Morgenstern, B; Manuel, M; Wörheide, G

    2010-09-01

    Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes.

  5. How taxonomic diversity, community structure, and sample size determine the reliability of higher taxon surrogates.

    Science.gov (United States)

    Neeson, Thomas M; Van Rijn, Itai; Mandelik, Yael

    2013-07-01

    Ecologists and paleontologists often rely on higher taxon surrogates instead of complete inventories of biological diversity. Despite their intrinsic appeal, the performance of these surrogates has been markedly inconsistent across empirical studies, to the extent that there is no consensus on appropriate taxonomic resolution (i.e., whether genus- or family-level categories are more appropriate) or their overall usefulness. A framework linking the reliability of higher taxon surrogates to biogeographic setting would allow for the interpretation of previously published work and provide some needed guidance regarding the actual application of these surrogates in biodiversity assessments, conservation planning, and the interpretation of the fossil record. We developed a mathematical model to show how taxonomic diversity, community structure, and sampling effort together affect three measures of higher taxon performance: the correlation between species and higher taxon richness, the relative shapes and asymptotes of species and higher taxon accumulation curves, and the efficiency of higher taxa in a complementarity-based reserve-selection algorithm. In our model, higher taxon surrogates performed well in communities in which a few common species were most abundant, and less well in communities with many equally abundant species. Furthermore, higher taxon surrogates performed well when there was a small mean and variance in the number of species per higher taxa. We also show that empirically measured species-higher-taxon correlations can be partly spurious (i.e., a mathematical artifact), except when the species accumulation curve has reached an asymptote. This particular result is of considerable practical interest given the widespread use of rapid survey methods in biodiversity assessment and the application of higher taxon methods to taxa in which species accumulation curves rarely reach an asymptote, e.g., insects.

  6. Likelihood inference of non-constant diversification rates with incomplete taxon sampling.

    Directory of Open Access Journals (Sweden)

    Sebastian Höhna

    Full Text Available Large-scale phylogenies provide a valuable source to study background diversification rates and investigate if the rates have changed over time. Unfortunately most large-scale, dated phylogenies are sparsely sampled (fewer than 5% of the described species and taxon sampling is not uniform. Instead, taxa are frequently sampled to obtain at least one representative per subgroup (e.g. family and thus to maximize diversity (diversified sampling. So far, such complications have been ignored, potentially biasing the conclusions that have been reached. In this study I derive the likelihood of a birth-death process with non-constant (time-dependent diversification rates and diversified taxon sampling. Using simulations I test if the true parameters and the sampling method can be recovered when the trees are small or medium sized (fewer than 200 taxa. The results show that the diversification rates can be inferred and the estimates are unbiased for large trees but are biased for small trees (fewer than 50 taxa. Furthermore, model selection by means of Akaike's Information Criterion favors the true model if the true rates differ sufficiently from alternative models (e.g. the birth-death model is recovered if the extinction rate is large and compared to a pure-birth model. Finally, I applied six different diversification rate models--ranging from a constant-rate pure birth process to a decreasing speciation rate birth-death process but excluding any rate shift models--on three large-scale empirical phylogenies (ants, mammals and snakes with respectively 149, 164 and 41 sampled species. All three phylogenies were constructed by diversified taxon sampling, as stated by the authors. However only the snake phylogeny supported diversified taxon sampling. Moreover, a parametric bootstrap test revealed that none of the tested models provided a good fit to the observed data. The model assumptions, such as homogeneous rates across species or no rate shifts, appear

  7. The importance of taxon sampling in genomic studies: an example from the cyclooxygenases of teleost fishes.

    Science.gov (United States)

    Havird, Justin C; Miyamoto, Michael M

    2010-07-01

    Comparative genomic studies must often rely on single model species and exemplars to represent the genetic variation both within and among different major groups, because of technological, financial, and time constraints. This study of the cyclooxygenases from teleost fishes serves as a reminder that caution is required in these cases, since such incomplete taxon sampling can lead to errors in the interpretation and prediction of genome evolution, function, and structure. Copyright 2010 Elsevier Inc. All rights reserved.

  8. Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?

    Science.gov (United States)

    Vandergast, Amy; Weissman, David B; Wood, Dustin; Rentz, David C F; Bazelet, Corinna S; Ueshima, Norihiro

    2017-01-01

    The relationships among and within the families that comprise the orthopteran superfamily Stenopelmatoidea (suborder Ensifera) remain poorly understood. We developed a phylogenetic hypothesis based on Bayesian analysis of two nuclear ribosomal and one mitochondrial gene for 118 individuals (84 de novo and 34 from GenBank). These included Gryllacrididae from North, Central, and South America, South Africa and Madagascar, Australia and Papua New Guinea; Stenopelmatidae from North and Central America and South Africa; Anostostomatidae from North and Central America, Papua New Guinea, New Zealand, Australia, and South Africa; members of the Australian endemic Cooloola (three species); and a representative of Lezina from the Middle East. We also included representatives of all other major ensiferan families: Prophalangopsidae, Rhaphidophoridae, Schizodactylidae, Tettigoniidae, Gryllidae, Gryllotalpidae and Myrmecophilidae and representatives of the suborder Caelifera as outgroups. Bayesian analyses of concatenated sequence data supported a clade of Stenopelmatoidea inclusive of all analyzed members of Gryllacrididae, Stenopelmatidae, Anostostomatidae, Lezina and Cooloola. We found Gryllacrididae worldwide to be monophyletic, while we did not recover a monophyletic Stenopelmatidae nor Anostostomatidae. Australian Cooloola clustered in a clade composed of Australian, New Zealand, and some (but not all) North American Anostostomatidae. Lezina was included in a clade of New World Anostostomatidae. Finally, we compiled and compared karyotypes and sound production characteristics for each supported group. Chromosome number, centromere position, drumming, and stridulation differed among some groups, but also show variation within groups. This preliminary trait information may contribute toward future studies of trait evolution. Despite greater taxon sampling within Stenopelmatoidea than previous efforts, some relationships among the families examined continue to remain elusive.

  9. Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling.

    Directory of Open Access Journals (Sweden)

    Alexis Crête-Lafrenière

    Full Text Available Considerable research efforts have focused on elucidating the systematic relationships among salmonid fishes; an understanding of these patterns of relatedness will inform conservation- and fisheries-related issues, as well as provide a framework for investigating evolutionary mechanisms in the group. However, uncertainties persist in current Salmonidae phylogenies due to biological and methodological factors, and a comprehensive phylogeny including most representatives of the family could provide insight into the causes of these difficulties. Here we increase taxon sampling by including nearly all described salmonid species (n = 63 to present a time-calibrated and more complete portrait of Salmonidae using a combination of molecular markers and analytical techniques. This strategy improved resolution by increasing the signal-to-noise ratio and helped discriminate methodological and systematic errors from sources of difficulty associated with biological processes. Our results highlight novel aspects of salmonid evolution. First, we call into question the widely-accepted evolutionary relationships among sub-families and suggest that Thymallinae, rather than Coregoninae, is the sister group to the remainder of Salmonidae. Second, we find that some groups in Salmonidae are older than previously thought and that the mitochondrial rate of molecular divergence varies markedly among genes and clades. We estimate the age of the family to be 59.1 MY (CI: 63.2-58.1 MY old, which likely corresponds to the timing of whole genome duplication in salmonids. The average, albeit highly variable, mitochondrial rate of molecular divergence was estimated as ~0.31%/MY (CI: 0.27-0.36%/MY. Finally, we suggest that some species require taxonomic revision, including two monotypic genera, Stenodus and Salvethymus. In addition, we resolve some relationships that have been notoriously difficult to discern and present a clearer picture of the evolution of the group. Our

  10. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?

    Directory of Open Access Journals (Sweden)

    Rice Danny W

    2004-09-01

    Full Text Available Abstract Background Numerous studies, using in aggregate some 28 genes, have achieved a consensus in recognizing three groups of plants, including Amborella, as comprising the basal-most grade of all other angiosperms. A major exception is the recent study by Goremykin et al. (2003; Mol. Biol. Evol. 20:1499–1505, whose analyses of 61 genes from 13 sequenced chloroplast genomes of land plants nearly always found 100% support for monocots as the deepest angiosperms relative to Amborella, Calycanthus, and eudicots. We hypothesized that this conflict reflects a misrooting of angiosperms resulting from inadequate taxon sampling, inappropriate phylogenetic methodology, and rapid evolution in the grass lineage used to represent monocots. Results We used two main approaches to test this hypothesis. First, we sequenced a large number of chloroplast genes from the monocot Acorus and added these plus previously sequenced Acorus genes to the Goremykin et al. (2003 dataset in order to explore the effects of altered monocot sampling under the same analytical conditions used in their study. With Acorus alone representing monocots, strongly supported Amborella-sister trees were obtained in all maximum likelihood and parsimony analyses, and in some distance-based analyses. Trees with both Acorus and grasses gave either a well-supported Amborella-sister topology or else a highly unlikely topology with 100% support for grasses-sister and paraphyly of monocots (i.e., Acorus sister to "dicots" rather than to grasses. Second, we reanalyzed the Goremykin et al. (2003 dataset focusing on methods designed to account for rate heterogeneity. These analyses supported an Amborella-sister hypothesis, with bootstrap support values often conflicting strongly with cognate analyses performed without allowing for rate heterogeneity. In addition, we carried out a limited set of analyses that included the chloroplast genome of Nymphaea, whose position as a basal angiosperm was

  11. Snake mitochondrial genomes: phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution

    Science.gov (United States)

    2010-01-01

    alethinophidians. Conclusions Mitochondrial gene sequence data alone may not be able to robustly resolve basal divergences among alethinophidian snakes. Taxon sampling plays an important role in identifying mitogenomic evolutionary events within snakes, and in testing hypotheses explaining their origin. Dramatic rate shifts in mitogenomic evolution occur within Scolecophidia as well as Alethinophidia, thus falsifying the hypothesis that these shifts in snakes are associated exclusively with evolution of a non-burrowing lifestyle, macrostomatan feeding ecology and/or duplication of the control region, both restricted to alethinophidians among living snakes. PMID:20055998

  12. Evaluating and interpreting cross-taxon congruence: Potential pitfalls and solutions

    Science.gov (United States)

    Gioria, Margherita; Bacaro, Giovanni; Feehan, John

    2011-05-01

    Characterizing the relationship between different taxonomic groups is critical to identify potential surrogates for biodiversity. Previous studies have shown that cross-taxa relationships are generally weak and/or inconsistent. The difficulties in finding predictive patterns have often been attributed to the spatial and temporal scales of these studies and on the differences in the measure used to evaluate such relationships (species richness versus composition). However, the choice of the analytical approach used to evaluate cross-taxon congruence inevitably represents a major source of variation. Here, we described the use of a range of methods that can be used to comprehensively assess cross-taxa relationships. To do so, we used data for two taxonomic groups, wetland plants and water beetles, collected from 54 farmland ponds in Ireland. Specifically, we used the Pearson correlation and rarefaction curves to analyse patterns in species richness, while Mantel tests, Procrustes analysis, and co-correspondence analysis were used to evaluate congruence in species composition. We compared the results of these analyses and we described some of the potential pitfalls associated with the use of each of these statistical approaches. Cross-taxon congruence was moderate to strong, depending on the choice of the analytical approach, on the nature of the response variable, and on local and environmental conditions. Our findings indicate that multiple approaches and measures of community structure are required for a comprehensive assessment of cross-taxa relationships. In particular, we showed that selection of surrogate taxa in conservation planning should not be based on a single statistic expressing the degree of correlation in species richness or composition. Potential solutions to the analytical issues associated with the assessment of cross-taxon congruence are provided and the implications of our findings in the selection of surrogates for biodiversity are discussed.

  13. Multiple continental radiations and correlates of diversification in Lupinus (Leguminosae): testing for key innovation with incomplete taxon sampling.

    Science.gov (United States)

    Drummond, Christopher S; Eastwood, Ruth J; Miotto, Silvia T S; Hughes, Colin E

    2012-05-01

    Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth-death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18-0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48-1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89-3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36-1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations" in the sense of convergent morphological and ecological trajectories among species in different clades, these

  14. How to handle speciose clades? Mass taxon-sampling as a strategy towards illuminating the natural history of Campanula (Campanuloideae.

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    Guilhem Mansion

    Full Text Available BACKGROUND: Speciose clades usually harbor species with a broad spectrum of adaptive strategies and complex distribution patterns, and thus constitute ideal systems to disentangle biotic and abiotic causes underlying species diversification. The delimitation of such study systems to test evolutionary hypotheses is difficult because they often rely on artificial genus concepts as starting points. One of the most prominent examples is the bellflower genus Campanula with some 420 species, but up to 600 species when including all lineages to which Campanula is paraphyletic. We generated a large alignment of petD group II intron sequences to include more than 70% of described species as a reference. By comparison with partial data sets we could then assess the impact of selective taxon sampling strategies on phylogenetic reconstruction and subsequent evolutionary conclusions. METHODOLOGY/PRINCIPAL FINDINGS: Phylogenetic analyses based on maximum parsimony (PAUP, PRAP, Bayesian inference (MrBayes, and maximum likelihood (RAxML were first carried out on the large reference data set (D680. Parameters including tree topology, branch support, and age estimates, were then compared to those obtained from smaller data sets resulting from "classification-guided" (D088 and "phylogeny-guided sampling" (D101. Analyses of D088 failed to fully recover the phylogenetic diversity in Campanula, whereas D101 inferred significantly different branch support and age estimates. CONCLUSIONS/SIGNIFICANCE: A short genomic region with high phylogenetic utility allowed us to easily generate a comprehensive phylogenetic framework for the speciose Campanula clade. Our approach recovered 17 well-supported and circumscribed sub-lineages. Knowing these will be instrumental for developing more specific evolutionary hypotheses and guide future research, we highlight the predictive value of a mass taxon-sampling strategy as a first essential step towards illuminating the detailed

  15. Can Sample-Specific Simulations Help Detect Low Base-Rate Taxonicity?

    Science.gov (United States)

    Beach, Steven R. H.; Amir, Nader; Bau, Jinn Jonp

    2005-01-01

    The authors examined the role of the sample-specific simulations (SSS; A. M. Ruscio & J. Ruscio, 2002; J. Ruscio & A. M. Ruscio, 2004) procedure in detecting low base-rate taxa that might otherwise prove elusive. The procedure preserved key distributional characteristics for moderate to high base-rate taxa, but it performed inadequately for low…

  16. Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling.

    Science.gov (United States)

    Stamatakis, Alexandros; Göker, Markus; Grimm, Guido W

    2010-05-24

    The constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number of base pairs, phylogenomic alignments) as well as vertical (number of taxa) dimension. Put aside the ongoing controversial discussion about appropriate models, partitioning schemes, and assembly methods for phylogenomic alignments, coupled with the high computational cost to infer these, for many organismic groups, a sufficient number of taxa is often exclusively available from one or just a few genes (e.g., rbcL, matK, rDNA). In this paper we address scalability of Maximum-Likelihood-based phylogeny reconstruction with respect to the number of taxa by example of several large nested single-gene rbcL alignments comprising 400 up to 3,491 taxa. In order to test the effect of taxon sampling, we employ an appropriately adapted taxon jackknifing approach. In contrast to standard jackknifing, this taxon subsampling procedure is not conducted entirely at random, but based on drawing subsamples from empirical taxon-groups which can either be user-defined or determined by using taxonomic information from databases. Our results indicate that, despite an unfavorable number of sequences to number of base pairs ratio, i.e., many relatively short sequences, Maximum Likelihood tree searches and bootstrap analyses scale well on single-gene rbcL alignments with a dense taxon sampling up to several thousand sequences. Moreover, the newly implemented taxon subsampling procedure can be beneficial for inferring higher level relationships and interpreting bootstrap support from comprehensive analysis.

  17. Resolving the question of trypanosome monophyly: a comparative genomics approach using whole genome data sets with low taxon sampling.

    Science.gov (United States)

    Leonard, Guy; Soanes, Darren M; Stevens, Jamie R

    2011-07-01

    Since the first attempts to classify the evolutionary history of trypanosomes, there have been conflicting reports regarding their true phylogenetic relationships and, in particular, their relationships with other vertebrate trypanosomatids, e.g. Leishmania sp., as well as with the many insect parasitising trypanosomatids. Perhaps the issue that has provided most debate is that concerning the monophyly (or otherwise) of genus Trypanosoma and, even with the advent of molecular methods, the findings of numerous studies have varied significantly depending on the gene sequences analysed, number of taxa included, choice of outgroup and phylogenetic methodology. While of arguably limited applied importance, resolution of the question as to whether or not trypanosomes are monophyletic is critical to accurate evaluation of competing, mutually exclusive evolutionary scenarios for these parasites, namely the 'vertebrate-first' or 'insect-first' hypotheses. Therefore, a new approach, which could overcome previous limitations was needed. At its most simple, the problem can be defined within the framework of a trifurcated tree with three hypothetical positions at which the root can be placed. Using BLASTp and whole-genome gene-by-gene phylogenetic analyses of Trypanosoma brucei, Trypanosoma cruzi, Leishmania major and Naegleria gruberi, we have identified 599 gene markers--putative homologues--that were shared between the genomes of these four taxa. Of these, 75 homologous gene families that demonstrate monophyly of the kinetoplastids were identified. We then used these data sets in combination with an additional outgroup, Euglena gracilis, coupled with large-scale gene concatenation and diverse phylogenetic techniques to investigate the relative branching order of T. brucei, T. cruzi and L. major. Our findings confirm the monophyly of genus Trypanosoma and demonstrate that <1% of the analysed gene markers shared between the genomes of T. brucei, T. cruzi and L. major reject

  18. Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment.

    Science.gov (United States)

    Pepato, A R; Klimov, P B

    2015-09-02

    Acariformes is the most species-rich and morphologically diverse radiation of chelicerate arthropods, known from the oldest terrestrial ecosystems. It is also a key lineage in understanding the evolution of this group, with the most vexing question whether mites, or Acari (Parasitiformes and Acariformes) is monophyletic. Previous molecular studies recovered Acari either as monophyletic or non-monophyletic, albeit with a limited taxon sampling. Similarly, relationships between basal acariform groups (include little-known, deep-soil 'endeostigmatan' mites) and major lineages of Acariformes (Sarcoptiformes, Prostigmata) are virtually unknown. We infer phylogeny of chelicerate arthropods, using a large and representative dataset, comprising all main in- and outgroups (228 taxa). Basal diversity of Acariformes is particularly well sampled. With this dataset, we conduct a series of phylogenetically explicit tests of chelicerate and acariform relationships and present a phylogenetic framework for internal relationships of acariform mites. Our molecular data strongly support a diphyletic Acari, with Acariformes as the sister group to Solifugae (PP =1.0; BP = 100), the so called Poecilophysidea. Among Acariformes, some representatives of the basal group Endeostigmata (mainly deep-soil mites) were recovered as sister-groups to the remaining Acariformes (i. e., Trombidiformes + and most of Sarcoptiformes). Desmonomatan oribatid mites (soil and litter mites) were recovered as the monophyletic sister group of Astigmata (e. g., stored product mites, house dust mites, mange mites, feather and fur mites). Trombidiformes (Sphaerolichida + Prostigmata) is strongly supported (PP =1.0; BP = 98-100). Labidostommatina was inferred as the basal lineage of Prostigmata. Eleutherengona (e. g., spider mites) and Parasitengona (e. g., chiggers, fresh water mites) were recovered as monophyletic. By contrast, Eupodina (e. g., snout mites and relatives) was not. Marine mites (Halacaridae) were

  19. Roadway sampling evaluation.

    Science.gov (United States)

    2014-09-01

    The Florida Department of Transportation (FDOT) has traditionally required that all sampling : and testing of asphalt mixtures be at the Contractors production facility. With recent staffing cuts, as : well as budget reductions, FDOT has been cons...

  20. Sampling for Machine Translation Evaluation

    OpenAIRE

    de la Fuente, Rubén

    2014-01-01

    Aquest article pretén oferir una visió general de les millors pràctiques desenvolupades a PayPal per al disseny i preparació de mostres per a diferents tasques incloses en el procés d'avaluació de la traducció automàtica. This paper intends to provide an overview of best practices developed within PayPal for designing and preparing samples for different tasks included in the process of machine translation evaluation. Este artículo pretende ofrecer una visión general de las mejores práct...

  1. Macrosystematics of eutherian mammals combining HTS data to expand taxon coverage.

    Science.gov (United States)

    Feijoo, M; Parada, A

    2017-08-01

    In the last few years high-throughput sequencing technologies have permitted significant advances in mammalian phylogenetic studies from a genomic perspective. However, these studies have been restricted to a sparse number of species with available reference genomes. Thus, several issues inside the eutherian mammals phylogeny remain unresolved. This may be due in part to limited taxon sampling, as taxonomic density is known to affect phylogenetic resolution. In this context, we present a protocol to increase taxon coverage using high-throughput sequencing data (RNA or DNA) generated for other biological studies and available in public databases. Following this procedure we addressed pending or controversial issues concerning the phylogenetic position of Dermoptera, Pholidota and Chiroptera, considering multiple and independent loci. Also for Chiroptera and Arctoidea we evaluated the relationships of the lineages that compose it. Although the maximum number of genes used is moderate (95), in some cases taxon coverage doubles that of previous related studies. Globally, all coalescent-based (STAR, MP-EST and ASTRAL) and concatenated (IQ-TREE and BEAST2) methods used for species tree reconstruction were consistent to each other and most of interrogated nodes received high statistical support. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Evaluation of diesel particulate matter sampling techniques

    CSIR Research Space (South Africa)

    Pretorius, CJ

    2011-09-01

    Full Text Available The study evaluated diesel particulate matter (DPM) sampling methods used in the South African mining industry. The three-piece cassette respirable, open face and stopper sampling methods were compared with the SKC DPM cassette method to find a...

  3. Quality evaluation of processed clay soil samples.

    Science.gov (United States)

    Steiner-Asiedu, Matilda; Harrison, Obed Akwaa; Vuvor, Frederick; Tano-Debrah, Kwaku

    2016-01-01

    This study assessed the microbial quality of clay samples sold on two of the major Ghanaian markets. The study was a cross-sectional assessing the evaluation of processed clay and effects it has on the nutrition of the consumers in the political capital town of Ghana. The items for the examination was processed clay soil samples. Staphylococcus spp and fecal coliforms including Klebsiella, Escherichia, and Shigella and Enterobacterspp were isolated from the clay samples. Samples from the Kaneshie market in Accra recorded the highest total viable counts 6.5 Log cfu/g and Staphylococcal count 5.8 Log cfu/g. For fecal coliforms, Madina market samples had the highest count 6.5 Log cfu/g and also recorded the highest levels of yeast and mould. For Koforidua, total viable count was highest in the samples from the Zongo market 6.3 Log cfu/g. Central market samples had the highest count of fecal coliforms 4.6 Log cfu/g and yeasts and moulds 6.5 Log cfu/g. "Small" market recorded the highest staphylococcal count 6.2 Log cfu/g. The water activity of the clay samples were low, and ranged between 0.65±0.01 and 0.66±0.00 for samples collected from Koforidua and Accra respectively. The clay samples were found to contain Klebsiella spp. Escherichia, Enterobacter, Shigella spp. staphylococcus spp., yeast and mould. These have health implications when consumed.

  4. Ribosomes in the sea: a window on taxon-specific lysis

    Science.gov (United States)

    Suttle, C.; Zhong, X.; Wirth, J.

    2016-02-01

    Microbes are estimated to comprise more than 90% of the biomass in the world's oceans, are major drivers of biogeochemical cycles, and have turnover rates ranging from hours to days. Despite the central role that microbes play in marine ecosystems, there is no robust method to evaluate taxon-specific mortality rates. Here, we report a method that employs extracellular free-ribosomes as a proxy to evaluate taxon-specific microbial lysis. The method was validated with laboratory cultures of the marine heterotrophic bacterium Vibrio natriegens strain PWH3a and the photoautotroph Synechococcus strain DC2, with and without grazers or viruses, to identify the origin and fate of the extracellular free-ribosomes. Our results showed both viral lysis and programmed-cell-death (PCD) contribute to free-ribosome production. Ribosomes were not released when cells were grazed, but grazers could consume free-ribosomes. We show that extracellular free-ribosomes can be used to evaluate microbial mortality caused by viral lysis and PCD. This approach was applied to environmental samples by examining the taxonomic composition and relative abundance of free 16S-ribosomes in seawater samples collected from the Strait of Georgia and Saanich Inlet, British Columbia, Canada. Based on the presence of free ribosomes, lysis was detected in 2198 out of 4013 prokaryotic taxa, representing 22 bacterial and three archaeal phyla. Of these, lysis of 140 taxa could be detected in all nine samples. Based on the ratio of free ribosomes to cellular ribosomes, some taxa associated with specific ecological niches appeared to be subject to high rates of lysis, including the genera Achromobacter, Chryseobacterium, Clostridium, Delftia, Ferruginibacter, Lactobacillus, Marinomonas, Massilia, Microbacterium, Ochrobactrum, Paenibacillus, Phyllobacterium, Pseudomonas, Rhodobacter, and Stenotrophomonas. Our results showed high-lysis coupled with low-abundance, suggesting that taxa in lower abundance are subject

  5. Taxonicity of anxiety sensitivity: a multi-national analysis.

    Science.gov (United States)

    Bernstein, Amit; Zvolensky, Michael J; Kotov, Roman; Arrindell, Willem A; Taylor, Steven; Sandin, Bonifacio; Cox, Brian J; Stewart, Sherry H; Bouvard, Martine; Cardenas, Samuel Jurado; Eifert, Georg H; Schmidt, Norman B

    2006-01-01

    Taxometric coherent cut kinetic analyses were used to test the latent structure of anxiety sensitivity in samples from North America (Canada and United States of America), France, Mexico, Spain, and The Netherlands (total n = 2741). Anxiety sensitivity was indexed by the 36-item Anxiety Sensitivity Index--Revised (ASI-R; [J. Anxiety Disord. 12(5) (1998) 463]). Four manifest indicators of anxiety sensitivity were constructed using the ASI-R: fear of cardiovascular symptoms, fear of respiratory symptoms, fear of publicly observable anxiety reactions, and fear of mental incapacitation. Results from MAXCOV-HITMAX, internal consistency tests, analyses of simulated Monte Carlo data, and a MAMBAC external consistency test indicated that the latent structure of anxiety sensitivity was taxonic in each of the samples. The estimated base rate of the anxiety sensitivity taxon differed slightly between nations, ranging from 11.5 to 21.5%. In general, the four ASI-R based manifest indicators showed high levels of validity. Results are discussed in relation to the conceptual understanding of anxiety sensitivity, with specific emphasis on theoretical refinement of the construct.

  6. The influence of taxonomic resolution of Oligochaeta on the evaluation of water quality in an urban stream in Minas Gerais, Brazil A influência da resolução taxonômica de Oligochaeta na avaliação da qualidade da água em um córrego urbano em Minas Gerais, Brasil

    Directory of Open Access Journals (Sweden)

    Gabriela Linhares Frizzera

    2012-12-01

    Full Text Available OBJECTIVE: The objective of this study was to verify the identification of specimens of the Oligochaeta in different taxonomic levels (family and species has the same potential for assessing the water quality of an urban stream in Minas Gerais, Brazil. METHODS: Oligochaeta specimens were collected from eight sampling stations in July 2007. Four stations were located in rural areas and the other four in urban areas. Were measured concentrations of dissolved oxygen, phosphorus and total nitrogen, pH, electrical conductivity and BOD. To evaluate the influence of taxonomic level, Oligochaeta specimens were identified at the family and species. We performed a principal component analysis (PCA to determine which abiotic variables best explained the distribution of Oligochaeta along the sampling stations. Cluster analysis was performed with the abundance of Oligochaeta in the family and species levels, separately, to assess the degree of similarity between the stations and check the level of identification of organisms could interfere with the associations formed. RESULTS: In general, the sampling stations located in urban areas had high pH, BOD and total nitrogen and phosphorus, while rural stations had a higher concentration of oxygen. Three families of Oligochaeta were found: Tubificidae, Naididae and Enchytraeidae. Tubificidae and Limnodrilus hoffmeisteri were the family and the species with the highest density, respectively, especially at those stations located in urban areas. Both the PCA analysis and cluster analysis showed that the sampling stations in urban areas and rural areas have different characteristics that separate CONCLUSIONS: The studied environment presents two distinct regions: the urban region with a high degree of organic pollution and high density Tubificidae and L. hoffmeisteri, and rural, with less human influence and low density of organisms Oligochaeta. These features made the use of the taxonomic level of family allow a

  7. Brine Sampling and Evaluation Program, 1990 report

    Energy Technology Data Exchange (ETDEWEB)

    Deal, D.E.; Abitz, R.J.; Myers, J.; Case, J.B.; Martin, M.L.; Roggenthen, W.M. [International Technology Corp., Albuquerque, NM (United States); Belski, D.S. [Westinghouse Electric Corp., Carlsbad, NM (United States). Waste Isolation Div.

    1991-08-01

    The data presented in this report are the result of Brine Sampling and Evaluation Program (BSEP) activities at the Waste Isolation Pilot Plant (WIPP) during 1990. When excavations began in 1982, small brine seepages (weeps) were observed on the walls. These brine occurrences were initially described as part of the Site Validation Program. Brine studies were formalized in 1985. The BSEP activities document and investigate the origins, hydraulic characteristics, extent, and composition of brine occurrences in the Permian Salado Formation and seepage of that brine into the excavations at the WIPP. The brine chemistry is important because it assists in understanding the origin of the brine and because it may affect possible chemical reactions in the buried waste after sealing the repository. The volume of brine and the hydrologic system that drives the brine seepage also need to be understood to assess the long-term performance of the repository. After more than eight years of observations (1982--1990), no credible evidence exists to indicate that enough naturally occurring brine will seep into the WIPP excavations to be of practical concern. The detailed observations and analyses summarized herein and in previous BSEP reports confirm the evidence apparent during casual visits to the underground workings -- that the excavations are remarkably dry.

  8. Brine Sampling and Evaluation Program, 1991 report

    Energy Technology Data Exchange (ETDEWEB)

    Deal, D.E.; Abitz, R.J.; Myers, J.; Martin, M.L.; Milligan, D.J.; Sobocinski, R.W.; Lipponer, P.P.J. [International Technology Corp., Albuquerque, NM (United States); Belski, D.S. [Westinghouse Electric Corp., Carlsbad, NM (United States). Waste Isolation Div.

    1993-09-01

    The data presented in this report are the result of Brine Sampling and Evaluation Program (BSEP) activities at the Waste Isolation Pilot Plan (WIPP) during 1991. These BSEP activities document and investigate the origins, hydraulic characteristics, extent, and composition of brine occurrences in the Permian Salado Formation and seepage of that brine into the excavations at the WIPP. When excavations began at the WIPP in 1982, small brine seepages (weeps) were observed on the walls. Brine studies began as part of the Site Validation Program and were formalized as a program in its own right in 1985. During nine years of observations (1982--1991), evidence has mounted that the amount of brine seeping into the WIPP excavations is limited, local, and only a small fraction of that required to produce hydrogen gas by corroding the metal in the waste drums and waste inventory. The data through 1990 is discussed in detail and summarized by Deal and others (1991). The data presented in this report describes progress made during the calendar year 1991 and focuses on four major areas: (1) quantification of the amount of brine seeping across vertical surfaces in the WIPP excavations (brine ``weeps); (2) monitoring of brine inflow, e.g., measuring brines recovered from holes drilled downward from the underground drifts (downholes), upward from the underground drifts (upholes), and from subhorizontal holes; (3) further characterization of brine geochemistry; and (4) preliminary quantification of the amount of brine that might be released by squeezing the underconsolidated clays present in the Salado Formation.

  9. Taxon- and Site-Specific Melatonin Catabolism

    Directory of Open Access Journals (Sweden)

    Rüdiger Hardeland

    2017-11-01

    Full Text Available Melatonin is catabolized both enzymatically and nonenzymatically. Nonenzymatic processes mediated by free radicals, singlet oxygen, other reactive intermediates such as HOCl and peroxynitrite, or pseudoenzymatic mechanisms are not species- or tissue-specific, but vary considerably in their extent. Higher rates of nonenzymatic melatonin metabolism can be expected upon UV exposure, e.g., in plants and in the human skin. Additionally, melatonin is more strongly nonenzymatically degraded at sites of inflammation. Typical products are several hydroxylated derivatives of melatonin and N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK. Most of these products are also formed by enzymatic catalysis. Considerable taxon- and site-specific differences are observed in the main enzymatic routes of catabolism. Formation of 6-hydroxymelatonin by cytochrome P450 subforms are prevailing in vertebrates, predominantly in the liver, but also in the brain. In pineal gland and non-mammalian retina, deacetylation to 5-methoxytryptamine (5-MT plays a certain role. This pathway is quantitatively prevalent in dinoflagellates, in which 5-MT induces cyst formation and is further converted to 5-methoxyindole-3-acetic acid, an end product released to the water. In plants, the major route is catalyzed by melatonin 2-hydroxylase, whose product is tautomerized to 3-acetamidoethyl-3-hydroxy-5-methoxyindolin-2-one (AMIO, which exceeds the levels of melatonin. Formation and properties of various secondary products are discussed.

  10. Sample evaluation of ontology-matching systems

    NARCIS (Netherlands)

    Hage, W.R. van; Isaac, A.; Aleksovski, Z.

    2007-01-01

    Ontology matching exists to solve practical problems. Hence, methodologies to find and evaluate solutions for ontology matching should be centered on practical problems. In this paper we propose two statistically-founded evaluation techniques to assess ontology-matching performance that are based on

  11. Tissue Sampling and Processing for Histopathology Evaluation.

    Science.gov (United States)

    Slaoui, Mohamed; Bauchet, Anne-Laure; Fiette, Laurence

    2017-01-01

    Histological procedures aim at providing good-quality sections that can be used for a light microscopic evaluation of tissue. These are applicable to identify either spontaneous or diseases-induced changes. Routinely, tissues are fixed with neutral formalin 10%, embedded in paraffin, and manually sectioned with a microtome to obtain 4-5 μm thick paraffin sections. Dewaxed sections are then stained with HE&S (hematoxylin-eosin and saffron) or can be used for other purposes (special stains, immunohistochemistry, in situ hybridization, etc.). During this processing, many steps and procedures are critical to ensure standard and interpretable sections. This chapter provides key recommendations to efficiently achieve this objective.

  12. Taxon ordering in phylogenetic trees by means of evolutionary algorithms

    Directory of Open Access Journals (Sweden)

    Cerutti Francesco

    2011-07-01

    Full Text Available Abstract Background In in a typical "left-to-right" phylogenetic tree, the vertical order of taxa is meaningless, as only the branch path between them reflects their degree of similarity. To make unresolved trees more informative, here we propose an innovative Evolutionary Algorithm (EA method to search the best graphical representation of unresolved trees, in order to give a biological meaning to the vertical order of taxa. Methods Starting from a West Nile virus phylogenetic tree, in a (1 + 1-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius next taxa. After having set the radius to the best performance, we evolved the trees with (λ + μ-EAs to study the influence of population on the algorithm. Results The (1 + 1-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (λ + μ-EAs performed as well as the (1 + 1, except the larger population (1000 + 1000. Conclusions The trees after the evolution showed an improvement both of the fitness (based on a genetic distance matrix, then close taxa are actually genetically close, and of the biological interpretation. Samples collected in the same state or year moved close each other, making the tree easier to interpret. Biological relationships between samples are also easier to observe.

  13. Evaluation of alternative macroinvertebrate sampling techniques for use in a new tropical freshwater bioassessment scheme

    Directory of Open Access Journals (Sweden)

    Isabel Eleanor Moore

    2015-06-01

    Full Text Available Aim: The study aimed to determine the effectiveness of benthic macroinvertebrate dredge net sampling procedures as an alternative method to kick net sampling in tropical freshwater systems, specifically as an evaluation of sampling methods used in the Zambian Invertebrate Scoring System (ZISS river bioassessment scheme. Tropical freshwater ecosystems are sometimes dangerous or inaccessible to sampling teams using traditional kick-sampling methods, so identifying an alternative procedure that produces similar results is necessary in order to collect data from a wide variety of habitats.MethodsBoth kick and dredge nets were used to collect macroinvertebrate samples at 16 riverine sites in Zambia, ranging from backwaters and floodplain lagoons to fast flowing streams and rivers. The data were used to calculate ZISS, diversity (S: number of taxa present, and Average Score Per Taxon (ASPT scores per site, using the two sampling methods to compare their sampling effectiveness. Environmental parameters, namely pH, conductivity, underwater photosynthetically active radiation (PAR, temperature, alkalinity, flow, and altitude, were also recorded and used in statistical analysis. Invertebrate communities present at the sample sites were determined using multivariate procedures.ResultsAnalysis of the invertebrate community and environmental data suggested that the testing exercise was undertaken in four distinct macroinvertebrate community types, supporting at least two quite different macroinvertebrate assemblages, and showing significant differences in habitat conditions. Significant correlations were found for all three bioassessment score variables between results acquired using the two methods, with dredge-sampling normally producing lower scores than did the kick net procedures. Linear regression models were produced in order to correct each biological variable score collected by a dredge net to a score similar to that of one collected by kick net

  14. Taxon lists for studies of modern nannoplankton

    DEFF Research Database (Denmark)

    Jordan, R.W.; Broerse, A.T.C.; Hagino, K.

    2000-01-01

    Six studies in this special issue dealt with modern nannoplankton assemblages. In total during these studies 552 samples were analysed and about 180,000 specimens identified, from 152 species. This paper provides a unified list of taxa from these studies, records the presence/absence of each spec...

  15. Choice of Sample Split in Out-of-Sample Forecast Evaluation

    DEFF Research Database (Denmark)

    Hansen, Peter Reinhard; Timmermann, Allan

    Out-of-sample tests of forecast performance depend on how a given data set is split into estimation and evaluation periods, yet no guidance exists on how to choose the split point. Empirical forecast evaluation results can therefore be difficult to interpret, particularly when several values......, while conversely the power of forecast evaluation tests is strongest with long out-of-sample periods. To deal with size distortions, we propose a test statistic that is robust to the effect of considering multiple sample split points. Empirical applications to predictabil- ity of stock returns...... and inflation demonstrate that out-of-sample forecast evaluation results can critically depend on how the sample split is determined....

  16. Evaluation of sampling strategies to estimate crown biomass

    Directory of Open Access Journals (Sweden)

    Krishna P Poudel

    2015-01-01

    Full Text Available Background Depending on tree and site characteristics crown biomass accounts for a significant portion of the total aboveground biomass in the tree. Crown biomass estimation is useful for different purposes including evaluating the economic feasibility of crown utilization for energy production or forest products, fuel load assessments and fire management strategies, and wildfire modeling. However, crown biomass is difficult to predict because of the variability within and among species and sites. Thus the allometric equations used for predicting crown biomass should be based on data collected with precise and unbiased sampling strategies. In this study, we evaluate the performance different sampling strategies to estimate crown biomass and to evaluate the effect of sample size in estimating crown biomass. Methods Using data collected from 20 destructively sampled trees, we evaluated 11 different sampling strategies using six evaluation statistics: bias, relative bias, root mean square error (RMSE, relative RMSE, amount of biomass sampled, and relative biomass sampled. We also evaluated the performance of the selected sampling strategies when different numbers of branches (3, 6, 9, and 12 are selected from each tree. Tree specific log linear model with branch diameter and branch length as covariates was used to obtain individual branch biomass. Results Compared to all other methods stratified sampling with probability proportional to size estimation technique produced better results when three or six branches per tree were sampled. However, the systematic sampling with ratio estimation technique was the best when at least nine branches per tree were sampled. Under the stratified sampling strategy, selecting unequal number of branches per stratum produced approximately similar results to simple random sampling, but it further decreased RMSE when information on branch diameter is used in the design and estimation phases. Conclusions Use of

  17. Development and evaluation of the photoload sampling technique

    Science.gov (United States)

    Robert E. Keane; Laura J. Dickinson

    2007-01-01

    Wildland fire managers need better estimates of fuel loading so they can accurately predict potential fire behavior and effects of alternative fuel and ecosystem restoration treatments. This report presents the development and evaluation of a new fuel sampling method, called the photoload sampling technique, to quickly and accurately estimate loadings for six common...

  18. Trochiscia (Chlorococcales) a new taxon from Central Anatolian ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    Jun 3, 2009 ... Gazi University, Department of Biology Education, 06500 Teknikokullar/Ankara, Turkey. E-mail: tahir@gazi.edu.tr. Tel: +90 312 2028208. Fax: +90 312 ... Light microscopes indicate a clear relationship with species in the genus Trochiscia. Some of the characteristic features of the new taxon include a spines ...

  19. Field evaluation of personal sampling methods for multiple bioaerosols.

    Directory of Open Access Journals (Sweden)

    Chi-Hsun Wang

    Full Text Available Ambient bioaerosols are ubiquitous in the daily environment and can affect health in various ways. However, few studies have been conducted to comprehensively evaluate personal bioaerosol exposure in occupational and indoor environments because of the complex composition of bioaerosols and the lack of standardized sampling/analysis methods. We conducted a study to determine the most efficient collection/analysis method for the personal exposure assessment of multiple bioaerosols. The sampling efficiencies of three filters and four samplers were compared. According to our results, polycarbonate (PC filters had the highest relative efficiency, particularly for bacteria. Side-by-side sampling was conducted to evaluate the three filter samplers (with PC filters and the NIOSH Personal Bioaerosol Cyclone Sampler. According to the results, the Button Aerosol Sampler and the IOM Inhalable Dust Sampler had the highest relative efficiencies for fungi and bacteria, followed by the NIOSH sampler. Personal sampling was performed in a pig farm to assess occupational bioaerosol exposure and to evaluate the sampling/analysis methods. The Button and IOM samplers yielded a similar performance for personal bioaerosol sampling at the pig farm. However, the Button sampler is more likely to be clogged at high airborne dust concentrations because of its higher flow rate (4 L/min. Therefore, the IOM sampler is a more appropriate choice for performing personal sampling in environments with high dust levels. In summary, the Button and IOM samplers with PC filters are efficient sampling/analysis methods for the personal exposure assessment of multiple bioaerosols.

  20. DOE methods for evaluating environmental and waste management samples.

    Energy Technology Data Exchange (ETDEWEB)

    Goheen, S C; McCulloch, M; Thomas, B L; Riley, R G; Sklarew, D S; Mong, G M; Fadeff, S K [eds.; Pacific Northwest Lab., Richland, WA (United States)

    1994-04-01

    DOE Methods for Evaluating Environmental and Waste Management Samples (DOE Methods) provides applicable methods in use by. the US Department of Energy (DOE) laboratories for sampling and analyzing constituents of waste and environmental samples. The development of DOE Methods is supported by the Laboratory Management Division (LMD) of the DOE. This document contains chapters and methods that are proposed for use in evaluating components of DOE environmental and waste management samples. DOE Methods is a resource intended to support sampling and analytical activities that will aid in defining the type and breadth of contamination and thus determine the extent of environmental restoration or waste management actions needed, as defined by the DOE, the US Environmental Protection Agency (EPA), or others.

  1. Decreased Taxon-Specific IgA Response in Relation to the Changes of Gut Microbiota Composition in the Elderly.

    Science.gov (United States)

    Sugahara, Hirosuke; Okai, Shinsaku; Odamaki, Toshitaka; Wong, Chyn B; Kato, Kumiko; Mitsuyama, Eri; Xiao, Jin-Zhong; Shinkura, Reiko

    2017-01-01

    Gut microbiota is known to change with aging; however, the underlying mechanisms have not been well elucidated. Immunoglobulin A (IgA) is the dominant class of antibody secreted by the intestinal mucosa, and are thought to play a key role in the regulation of the gut microbiota. T cells regulate the magnitude and nature of microbiota-specific IgA responses. However, it is also known that T cells become senescent in elderly people. Therefore, we speculated that the age-related changes of IgA response against the gut microbiota might be one of the mechanisms causing the age-associated changes of gut microbiota composition. To prove our hypothesis, fecal samples from 40 healthy subjects (adult group: n = 20, an average of 35 years old; elderly group: n = 20, an average of 76 years old) were collected, and the gut microbiota composition and the response of IgA to gut microbiota were investigated. The relative abundance of Bifidobacteriaceae was significantly lower, whereas those of Clostridiaceae , Clostridiales ;f__ and Enterobacteriaceae were significantly higher in the elderly group than in the adult group. There was no significant difference in the fecal IgA concentration between the adult and elderly groups. However, the taxon-specific IgA response to some bacterial taxa was different between the adult and elderly groups. To evaluate inter-group differences in the taxon-specific IgA response to each bacterial taxon, the IgA-indices were calculated, and the IgA-indices of Clostridiaceae and Enterobacteriaceae were found to be significantly lower in the elderly group than the adult group. In addition, Clostridiales ;f__ and Enterobacteriaceae were significantly enriched in the IgA + fraction in the adult group but not in the elderly group, whereas Clostridiaceae was significantly enriched in the IgA - fraction in the elderly group but not in the adult group. Some species assigned to Clostridiaceae or Enterobacteriaceae are known to be pathogenic bacteria. Our

  2. The Taxonic Latent Structure and Taxometrics in Forensic Mental Health.

    Science.gov (United States)

    Maraun, Michael D; Hart, Stephen D

    2016-10-01

    Recently, researchers in the field of forensic mental health have attempted to address the technical, empirical question of whether important clinical problems, such as psychopathy or malingering, constitute taxa (i.e., discrete conditions). In this paper, we provide a detailed elucidation of the foundational logic of the quantitative methods employed to answer this question, focusing on the taxometric procedures developed by Paul Meehl and colleagues. We attempt to demonstrate that research on taxonicity is hampered by (a) researchers' unfamiliarity with or misunderstanding of the logic underlying latent variable technologies and (b) the fundamental incapacity of Meehlian procedures to provide a test of taxonicity. We conclude by discussing the utility of taxometric procedures to research in forensic mental health and, more broadly, in the field of applied psychological measurement. © The Author(s) 2016.

  3. Quality evaluation of processed clay soil samples | Steiner-Asiedu ...

    African Journals Online (AJOL)

    Introduction: This study assessed the microbial quality of clay samples sold on two of the major Ghanaian markets. Methods: The study was a cross-sectional assessing the evaluation of processed clay and effects it has on the nutrition of the consumers in the political capital town of Ghana. The items for the examination was ...

  4. Comparative Evaluation of Cheese samples treated with Honey and ...

    African Journals Online (AJOL)

    A study was conducted to evaluate the efficacy of honey and thyme solutions in extending the shelf life and enhancing the nutritional and sensory qualities of Wara, the West African soft cheese. The control treatment (A) was cheese kept in the whey, while Treatments B and C were cheese samples kept in Thyme and Honey ...

  5. Acacia polyphylla var. rhytidocarpa (Leguminosae: Mimosoideae, un nuevo taxon de Bolivia y Brasil

    Directory of Open Access Journals (Sweden)

    Rico Arce, María de Lourdes

    2006-06-01

    Full Text Available Acacia polyphylla var. rhytidocarpa, a new taxon for Bolivia and Brazil is described and illustrated.Se describe e ilustra Acacia polyphylla var. rhytidocarpa, taxon nuevo para Bolivia y Brasil.

  6. Global metabolite analysis of yeast: evaluation of sample preparation methods

    DEFF Research Database (Denmark)

    Villas-Bôas, Silas Granato; Højer-Pedersen, Jesper; Åkesson, Mats Fredrik

    2005-01-01

    Sample preparation is considered one of the limiting steps in microbial metabolome analysis. Eukaryotes and prokaryotes behave very differently during the several steps of classical sample preparation methods for analysis of metabolites. Even within the eukaryote kingdom there is a vast diversity...... of cell structures that make it imprudent to blindly adopt protocols that were designed for a specific group of microorganisms. We have therefore reviewed and evaluated the whole sample preparation procedures for analysis of yeast metabolites. Our focus has been on the current needs in metabolome analysis......, which is the analysis of a large number of metabolites with very diverse chemical and physical properties. This work reports the leakage of intracellular metabolites observed during quenching yeast cells with cold methanol solution, the efficacy of six different methods for the extraction...

  7. ACS sampling system: design, implementation, and performance evaluation

    Science.gov (United States)

    Di Marcantonio, Paolo; Cirami, Roberto; Chiozzi, Gianluca

    2004-09-01

    By means of ACS (ALMA Common Software) framework we designed and implemented a sampling system which allows sampling of every Characteristic Component Property with a specific, user-defined, sustained frequency limited only by the hardware. Collected data are sent to various clients (one or more Java plotting widgets, a dedicated GUI or a COTS application) using the ACS/CORBA Notification Channel. The data transport is optimized: samples are cached locally and sent in packets with a lower and user-defined frequency to keep network load under control. Simultaneous sampling of the Properties of different Components is also possible. Together with the design and implementation issues we present the performance of the sampling system evaluated on two different platforms: on a VME based system using VxWorks RTOS (currently adopted by ALMA) and on a PC/104+ embedded platform using Red Hat 9 Linux operating system. The PC/104+ solution offers, as an alternative, a low cost PC compatible hardware environment with free and open operating system.

  8. Sensory evaluation of commercial samples of condensed milk

    Directory of Open Access Journals (Sweden)

    Ana Laís Andrade Gaspardi

    2017-02-01

    Full Text Available The Brazil stands out for the huge production and consumption of condensed milk, industries rely on high-tech production, offering products with high added value and enabling the consumer to purchase products from different brands, prices and quality. This job aimed to verify if there is sensory difference at the 5% level of significance as the acceptance of 6 samples of commercial condensed milk. The samples were evaluated by 120 consumers, recruited voluntarily for the acceptance test. The results of ANOVA showed that the samples C, D, E and F were significantly higher acceptance (p = 0.05 in the other hedonic scale. While the sample A had lower acceptance for all the attributes listed on the hedonic scale. The purchase intention test showed that the C and F samples achieved the highest frequencies of positive purchase intention. The internal preference mapping confirmed the results of the ANOVA and purchase intention test indicating a greater preference of tasters by C and F samples. Acquired samples were made with the same ingredients, it is assumed that the sensory differences occurred due to the quality of raw material and to product development processes in each company. It is necessary to identify the importance of quality of the raw material and the type of process used to obtain the product enabling the improvement of brands less accepted in its production, increasing the acceptance and quality of their own product. The quality along with the standardization of the final product is a key factor for maintaining competitiveness and increasing productivity in the market.

  9. DOE methods for evaluating environmental and waste management samples

    Energy Technology Data Exchange (ETDEWEB)

    Goheen, S.C.; McCulloch, M.; Thomas, B.L.; Riley, R.G.; Sklarew, D.S.; Mong, G.M.; Fadeff, S.K. [eds.

    1994-10-01

    DOE Methods for Evaluating Environmental and Waste Management Samples (DOE Methods) is a resource intended to support sampling and analytical activities for the evaluation of environmental and waste management samples from U.S. Department of Energy (DOE) sites. DOE Methods is the result of extensive cooperation from all DOE analytical laboratories. All of these laboratories have contributed key information and provided technical reviews as well as significant moral support leading to the success of this document. DOE Methods is designed to encompass methods for collecting representative samples and for determining the radioisotope activity and organic and inorganic composition of a sample. These determinations will aid in defining the type and breadth of contamination and thus determine the extent of environmental restoration or waste management actions needed, as defined by the DOE, the U.S. Environmental Protection Agency, or others. The development of DOE Methods is supported by the Analytical Services Division of DOE. Unique methods or methods consolidated from similar procedures in the DOE Procedures Database are selected for potential inclusion in this document. Initial selection is based largely on DOE needs and procedure applicability and completeness. Methods appearing in this document are one of two types, {open_quotes}Draft{close_quotes} or {open_quotes}Verified{close_quotes}. {open_quotes}Draft{close_quotes} methods that have been reviewed internally and show potential for eventual verification are included in this document, but they have not been reviewed externally, and their precision and bias may not be known. {open_quotes}Verified{close_quotes} methods in DOE Methods have been reviewed by volunteers from various DOE sites and private corporations. These methods have delineated measures of precision and accuracy.

  10. Evaluation of a Smartphone App for Forest Sample Plot Measurements

    Directory of Open Access Journals (Sweden)

    Mikko Vastaranta

    2015-04-01

    Full Text Available We evaluated a smartphone app (TRESTIMATM for forest sample plot measurements. The app interprets imagery collected from the sample plots using the camera in the smartphone and then estimates forest inventory attributes, including species-specific basal areas (G as well as the diameter (DgM and height (HgM of basal area median trees. The estimates from the smartphone app were compared to forest inventory attributes derived from tree-wise measurements using calipers and a Vertex height measurement device. The data consist of 2169 measured trees from 25 sample plots (32 m × 32 m, dominated by Scots pine and Norway spruce from southern Finland. The root-mean-square errors (RMSEs in the basal area varied from 19.7% to 29.3% and the biases from 11.4% to 18.4% depending on the number of images per sample plot and image shooting location. DgM measurement bias varied from −1.4% to 3.1% and RMSE from 5.2% to 11.6% depending on the tree species. Respectively, HgM bias varied from 5.0% to 8.3% and RMSE 10.0% to 13.6%. In general, four images captured toward the center of the plot provided more accurate results than four images captured away from the plot center. Increasing the number of captured images per plot to the analyses yielded only marginal improvement to the results.

  11. 'Candidatus Phytoplasma pini', a novel taxon from Pinus silvestris and Pinus halepensis.

    Science.gov (United States)

    Schneider, Bernd; Torres, Ester; Martín, María P; Schröder, Manfred; Behnke, Heinz-Dietmar; Seemüller, Erich

    2005-01-01

    Pinus silvestris and Pinus halepensis trees grown in Germany and Spain, respectively, showing abnormal shoot branching, dwarfed needles and other symptoms were examined for the presence of plant-pathogenic mollicutes (phytoplasmas). While phytoplasmas could not be detected unambiguously with microscopical methods, PCR amplification using universal phytoplasma primers yielded positive results. Samples collected from symptomatic and non-symptomatic plant parts of both symptomatic Pinus silvestris and Pinus halepensis trees tested positive. Also, surrounding non-symptomatic trees proved to be phytoplasma-infected. Comparisons revealed that the 16S rRNA gene sequences of the phytoplasmas identified in Pinus silvestris and Pinus halepensis were nearly identical. However, the pine phytoplasma is only distantly related to other phytoplasmas. The closest relatives are members of the palm lethal yellowing and rice yellow dwarf groups and 'Candidatus Phytoplasma castaneae', which share between 94.5 and 96.6 % 16S rRNA gene sequence similarity. From these data it can be concluded that the phytoplasmas identified in the two Pinus species represent a coherent but discrete taxon; it is proposed that this taxon be distinguished at putative species level under the name 'Candidatus Phytoplasma pini'.

  12. ACTINIDE REMOVAL PROCESS SAMPLE ANALYSIS, CHEMICAL MODELING, AND FILTRATION EVALUATION

    Energy Technology Data Exchange (ETDEWEB)

    Martino, C.; Herman, D.; Pike, J.; Peters, T.

    2014-06-05

    Filtration within the Actinide Removal Process (ARP) currently limits the throughput in interim salt processing at the Savannah River Site. In this process, batches of salt solution with Monosodium Titanate (MST) sorbent are concentrated by crossflow filtration. The filtrate is subsequently processed to remove cesium in the Modular Caustic Side Solvent Extraction Unit (MCU) followed by disposal in saltstone grout. The concentrated MST slurry is washed and sent to the Defense Waste Processing Facility (DWPF) for vitrification. During recent ARP processing, there has been a degradation of filter performance manifested as the inability to maintain high filtrate flux throughout a multi-batch cycle. The objectives of this effort were to characterize the feed streams, to determine if solids (in addition to MST) are precipitating and causing the degraded performance of the filters, and to assess the particle size and rheological data to address potential filtration impacts. Equilibrium modelling with OLI Analyzer{sup TM} and OLI ESP{sup TM} was performed to determine chemical components at risk of precipitation and to simulate the ARP process. The performance of ARP filtration was evaluated to review potential causes of the observed filter behavior. Task activities for this study included extensive physical and chemical analysis of samples from the Late Wash Pump Tank (LWPT) and the Late Wash Hold Tank (LWHT) within ARP as well as samples of the tank farm feed from Tank 49H. The samples from the LWPT and LWHT were obtained from several stages of processing of Salt Batch 6D, Cycle 6, Batch 16.

  13. Soil Gas Sample Handling: Evaluation of Water Removal and Sample Ganging

    Energy Technology Data Exchange (ETDEWEB)

    Fritz, Brad G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Abrecht, David G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hayes, James C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mendoza, Donaldo P. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-10-31

    Soil gas sampling is currently conducted in support of Nuclear Test Ban treaty verification. Soil gas samples are collected and analyzed for isotopes of interest. Some issues that can impact sampling and analysis of these samples are excess moisture and sample processing time. Here we discuss three potential improvements to the current sampling protocol; a desiccant for water removal, use of molecular sieve to remove CO2 from the sample during collection, and a ganging manifold to allow composite analysis of multiple samples.

  14. Field evaluation of broiler gait score using different sampling methods

    Directory of Open Access Journals (Sweden)

    AFS Cordeiro

    2009-09-01

    Full Text Available Brazil is today the world's largest broiler meat exporter; however, in order to keep this position, it must comply with welfare regulations while maintaining low production costs. Locomotion problems restrain bird movements, limiting their access to drinking and feeding equipment, and therefore their survival and productivity. The objective of this study was to evaluate locomotion deficiency in broiler chickens reared under stressful temperature conditions using three different sampling methods of birds from three different ages. The experiment consisted in determining the gait score of 28, 35, 42 and 49-day-old broilers using three different known gait scoring methods: M1, birds were randomly selected, enclosed in a circle, and then stimulated to walk out of the circle; M2, ten birds were randomly selected and gait scored; and M3, birds were randomly selected, enclosed in a circle, and then observed while walking away from the circle without stimulus to walking. Environmental temperature, relative humidity, and light intensity inside the poultry houses were recorded. No evidence of interaction between scoring method and age was found however, both method and age influenced gait score. Gait score was found to be lower at 28 days of age. The evaluation using the ten randomly selected birds within the house was the method that presented the less reliable results. Gait score results when birds were stimulated to walk were lower than when they were not simulated, independently of age. The gait scores obtained with the three tested methods and ages were higher than those considered acceptable. The highest frequency of normal gait score (0 represented 50% of the flock. These results may be related to heat stress during rearing. Average gait score incresead with average ambient temperature, relative humidity, and light intensity. The evaluation of gait score to detect locomotion problems of broilers under rearing conditions seems subjective and

  15. Sampling pig farms at the abattoir in a cross-sectional study - Evaluation of a sampling method.

    Science.gov (United States)

    Birkegård, Anna Camilla; Halasa, Tariq; Toft, Nils

    2017-09-15

    A cross-sectional study design is relatively inexpensive, fast and easy to conduct when compared to other study designs. Careful planning is essential to obtaining a representative sample of the population, and the recommended approach is to use simple random sampling from an exhaustive list of units in the target population. This approach is rarely feasible in practice, and other sampling procedures must often be adopted. For example, when slaughter pigs are the target population, sampling the pigs on the slaughter line may be an alternative to on-site sampling at a list of farms. However, it is difficult to sample a large number of farms from an exact predefined list, due to the logistics and workflow of an abattoir. Therefore, it is necessary to have a systematic sampling procedure and to evaluate the obtained sample with respect to the study objective. We propose a method for 1) planning, 2) conducting, and 3) evaluating the representativeness and reproducibility of a cross-sectional study when simple random sampling is not possible. We used an example of a cross-sectional study with the aim of quantifying the association of antimicrobial resistance and antimicrobial consumption in Danish slaughter pigs. It was not possible to visit farms within the designated timeframe. Therefore, it was decided to use convenience sampling at the abattoir. Our approach was carried out in three steps: 1) planning: using data from meat inspection to plan at which abattoirs and how many farms to sample; 2) conducting: sampling was carried out at five abattoirs; 3) evaluation: representativeness was evaluated by comparing sampled and non-sampled farms, and the reproducibility of the study was assessed through simulated sampling based on meat inspection data from the period where the actual data collection was carried out. In the cross-sectional study samples were taken from 681 Danish pig farms, during five weeks from February to March 2015. The evaluation showed that the sampling

  16. Phylogeny of the taxon Paralaophontodes Lang (Copepoda, Harpacticoida, Laophontodinae, including species descriptions, chorological remarks, and a key to species

    Directory of Open Access Journals (Sweden)

    Kai Horst George

    2017-03-01

    Full Text Available A detailed phylogenetic analysis of the taxon Paralaophontodes Lang (Copepoda, Harpacticoida, Laophontodinae Lang based on morphological characters is presented. The monophylum Paralaophontodes is supported by 16 unambiguous autapomorphies such as the presence of characteristic dorsal processes on cephalothorax and body somites, a 5-segmented male antennule, the loss of the syncoxal seta on the maxilliped, and the endopodal strengthening of the first swimming leg. The corresponding extensive phylogenetic evaluation includes the description of Paralaophontodes anjae sp. n. from a beach on Chiloé Island (Chile, the re-description of Laophontodes armatus Lang, and the re-establishment of Paralaophontodes robustus (Bŏzić, the displacement of Laophontodes armatus, L. hedgpethi Lang and L. psammophilus Soyer to Paralaophontodes, a discussion on relationships within that taxon, remarks on its geographical distribution, and a key to the species.

  17. Spinopelvic parameters evaluation in a Brazilian population sample.

    Science.gov (United States)

    Jacob, C J; Cardoso, I M; Batista, J L J; Maia, T C; Roncaglio, B

    2015-07-01

    The morphology of the spine is variable within a population, and its maintenance in appropriate values implies a decrease in the energy expended. We need to know their normal values in population. This study aims to carry out a literature review and evaluate published papers on spinopelvic parameters in a Brazilian population sample. Eleven potentially eligible papers were initially identified for inclusion in this review: three papers from PubMed and eight from Medicine. Out of these, only five papers contained methodology and relevant significance level, and therefore, they were included in the final analytical run. According to a Brazilian study, Pratali mentions no significant difference in the average values of spinopelvic balance in the Brazilian population and those found in the literature; there was also no significant difference comparing Brazilian and Korean population; however, a difference was found in comparison with European population regarding PI parameters and SS, but the latter with higher values. According to Kulcheski (Column/Columna 12:224-227, 2013), the values of pelvic tilt in the Brazilian population evaluated in his research were 19° (10°-35°) and the sacral inclination was 38° (30°-55°), presenting similar values concerning the European population. In another Brazilian paper, Oliveira (Rev Bras Ort 49:189-193, 2014) reports that the research population had PI average of 45° (41.9°-48.1°). The values obtained are relatively minor when compared to the European population. However, all of these are within the normal margin considered in the worldwide literature.

  18. A simple capacitive method to evaluate ethanol fuel samples

    Science.gov (United States)

    Vello, Tatiana P.; de Oliveira, Rafael F.; Silva, Gustavo O.; de Camargo, Davi H. S.; Bufon, Carlos C. B.

    2017-02-01

    Ethanol is a biofuel used worldwide. However, the presence of excessive water either during the distillation process or by fraudulent adulteration is a major concern in the use of ethanol fuel. High water levels may cause engine malfunction, in addition to being considered illegal. Here, we describe the development of a simple, fast and accurate platform based on nanostructured sensors to evaluate ethanol samples. The device fabrication is facile, based on standard microfabrication and thin-film deposition methods. The sensor operation relies on capacitance measurements employing a parallel plate capacitor containing a conformational aluminum oxide (Al2O3) thin layer (15 nm). The sensor operates over the full range water concentration, i.e., from approximately 0% to 100% vol. of water in ethanol, with water traces being detectable down to 0.5% vol. These characteristics make the proposed device unique with respect to other platforms. Finally, the good agreement between the sensor response and analyses performed by gas chromatography of ethanol biofuel endorses the accuracy of the proposed method. Due to the full operation range, the reported sensor has the technological potential for use as a point-of-care analytical tool at gas stations or in the chemical, pharmaceutical, and beverage industries, to mention a few.

  19. Sampling of plant in coffee for evaluation of nutritional status

    OpenAIRE

    Cintra, Antonio Carlos de Oliveira; Universidade Estadual Paulista "Júlio de Mesquita Filho"; Rozane, Danilo Eduardo; Universidade Estadual Paulista "Júlio de Mesquita Filho"; Natale, William; Universidade Estadual Paulista "Júlio de Mesquita Filho; Silva, Silvia Helena Modenese Gorla da; Universidade Estadual Paulista "Júlio de Mesquita Filho; Barbosa, José Carlos; Universidade Estadual Paulista "Júlio de Mesquita Filho; Lopes, Marcelo Domingos Chamma; Universidade Estadual Paulista "Júlio de Mesquita Filho

    2015-01-01

    The foliar fertilization assists programs in order to obtain higher yields, however, it is essential to know the ideal number of plants to be sampled. The study aimed to determine in commercial coffee plantations, subjected to two water regimes, the number of plants to be sampled and estimate the sample error for the diagnosis of nutritional status of that culture. The work consisted of two studies where samples of leaves were collected in rainfed and irrigated farming. For both studies the c...

  20. Towards Standardization of Sampling Methodology for Evaluation of ...

    African Journals Online (AJOL)

    This article proposes the procedure that may be adopted for comparable, representative and cost effective, soil sampling, and thereafter explores the policy issues regarding standardization of sampling activities and analytical process as it relates to soil pollution in Nigeria. Standardized sampling and analytical data for soil ...

  1. Towards Standardization of Sampling Methodology for Evaluation of ...

    African Journals Online (AJOL)

    MICHAEL

    ABSTRACT: This article proposes the procedure that may be adopted for comparable, representative and cost effective, soil sampling, and thereafter explores the policy issues regarding standardization of sampling activities and analytical process as it relates to soil pollution in Nigeria. Standardized sampling and analytical.

  2. Evaluation of common methods for sampling invertebrate pollinator assemblages: net sampling out-perform pan traps.

    Directory of Open Access Journals (Sweden)

    Tony J Popic

    Full Text Available Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km(2 area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service.

  3. The Latent Taxonicity of Schizotypy in Biological Siblings of Probands With Schizophrenia

    NARCIS (Netherlands)

    Linscott, Richard J.; Morton, Sarah E.; Alizadeh, Berhooz Z.; Bartels-Velthuis, Agna A.; van Beveren, Nico J.; Bruggeman, Richard; Cahn, Wiepke; de Haan, Lieuwe; Delespaul, Philippe; Meijer, Carin J.; Myin-Germeys, Inez; Kahn, Rene S.; Schirmbeck, Frederike; Simons, Claudia J. P.; van Haren, Neeltje E.; van Os, Jim; van Winkel, Ruud

    2017-01-01

    If schizotypy is a taxonic liability for schizophrenia with a general population prevalence of ~10%, it should also be taxonic among biological siblings of probands with schizophrenia. Moreover, assuming this is so, siblings' schizotypy class membership should be predicted by probands' familial load

  4. Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ....18908/lsdba.nbdc01194-02-006.V002 Version V2 10.18908/lsdba.nbdc01194-02-006.V002 Update History V1 10.1890...ower taxon Next infrageneric taxon About This Database Database Description Download License Update History

  5. Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ....18908/lsdba.nbdc01194-02-003.V002 Version V2 10.18908/lsdba.nbdc01194-02-003.V002 Update History V1 10.1890...ower taxon Next infrageneric taxon About This Database Database Description Download License Update History

  6. Evaluating Composite Sampling Methods of Bacillus spores at Low Concentrations

    Energy Technology Data Exchange (ETDEWEB)

    Hess, Becky M.; Amidan, Brett G.; Anderson, Kevin K.; Hutchison, Janine R.

    2016-10-13

    Restoring facility operations after the 2001 Amerithrax attacks took over three months to complete, highlighting the need to reduce remediation time. The most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite: a single cellulose sponge samples multiple coupons; 2) single medium multi-pass composite: a single cellulose sponge is used to sample multiple coupons; and 3) multi-medium post-sample composite: a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155CFU/cm2, respectively). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p-value < 0.0001) and coupon material (p-value = 0.0008). Recovery efficiency (RE) was higher overall using the post-sample composite (PSC) method compared to single medium composite from both clean and grime coated materials. RE with the PSC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, painted wall board, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but significantly lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when

  7. An Evaluation of Stratified Sampling of Microarchitecture Simulations

    OpenAIRE

    Wunderlich, Roland E.; Wenisch, Thomas F.; Falsafi, Babak; Hoe, James C.

    2004-01-01

    Recent research advocates applying sampling to accelerate microarchitecture simulation. Simple random sampling offers accurate performance estimates (with a high quantifiable confidence) by taking a large number (e.g., 10,000) of short performance measurements over the full length of a benchmark. Simple random sampling does not exploit the often repetitive behaviors of benchmarks, collecting many redundant measurements. By identifying repetitive behaviors, we can apply stratified rand...

  8. Viscous oil dynamics evaluation for better fluid sampling

    Energy Technology Data Exchange (ETDEWEB)

    Canas, J.A.; Low, S.; Adur, N.; Teixeira, V. [Society of Petroleum Engineers, Richardson, TX (United States)]|[Schlumberger, Sugar Land, TX (United States)

    2005-11-01

    The benefits that heavy oil producers can gain by sampling formation fluid early in the life of a well were discussed. Sampling provides the necessary information for reservoir completion planning and decision making, which is important in areas where flow assurance is a key concern. Most sampling problems are attributed to a sudden pressure change and the associated surge of fluids. The increased flow rate mobilizes sand grains and fines, which can plug flow lines, cause erosion of drilling parts and prevent proper operation of mechanical components in tools. In addition to the extremely low flow rates that are generally required for sampling highly viscous oils in unconsolidated sands, other factors should also be considered for optimum sampling, such as reservoir permeability, anisotropy, nearby upper and lower impermeable barriers, and location of the wireline formation tester (WFT) or modular formation tester (MDT) relative to the formation being samples. This paper presented the results of a study of near wellbore fluid flow during cleanup prior to sampling with a large diameter probe, a new extra large diameter probe, dual packer formation testers with customized gravel pack screens, an extra high-pressure displacement unit pump for low flow rates, advanced downhole flow analysis monitoring and special sampling methods. The intent of the study was to predict cleanup time with respect to viscous oils and the variables which make sampling feasible with respect to quality, operational time and reduction of associated risks. 11 refs., 32 figs.

  9. Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building.

    Science.gov (United States)

    Cui, Hong; Xu, Dongfang; Chong, Steven S; Ramirez, Martin; Rodenhausen, Thomas; Macklin, James A; Ludäscher, Bertram; Morris, Robert A; Soto, Eduardo M; Koch, Nicolás Mongiardino

    2016-11-17

    Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self-contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the

  10. Summary Report for Evaluation of Compost Sample Drying Methods

    National Research Council Canada - National Science Library

    Frye, Russell

    1994-01-01

    .... Previous work in Support of these efforts developed a compost sample preparation scheme, consisting of air drying followed by milling, to reduce analytical variability in the heterogeneous compost matrix...

  11. DSM-IV antisocial personality disorder and conduct disorder: evidence for taxonic structures among individuals with and without substance use disorders in the general population.

    Science.gov (United States)

    Kerridge, Bradley T; Saha, Tulshi D; Hasin, Deborah S

    2014-05-01

    The categorical-dimensional status of DSM-IV (Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition) conduct disorder (CD) and antisocial personality disorder (ASPD) is a source of controversy. This study examined whether the underlying structure of DSM-IV CD and ASPD was dimensional or categorical (taxonic) among individuals with and without substance use disorders. Using a national large representative survey of U.S. adults (n = 43,093), taxometric analyses of DSM-IV CD and ASPD diagnostic criteria were conducted on the total sample and among those with and without substance use disorders. Results of three taxometric procedures were consistent in showing that the structures underlying DSM-IV CD and ASPD were clearly taxonic in the total sample and among individuals with and without substance use disorders. Comparison curve fit indices exceeded 0.57 for each model. Taxonic findings of the present study were in contrast to the dimensional results of prior taxometric research among incarcerated samples with substantial comorbidity of antisocial syndromes and substance use disorders. Results supported the categorical representation and diagnostic thresholds of ASPD and CD as defined in DSM-IV and DSM-5. That the structure of ASPD and CD may be taxonic suggests that further research on these disorders use group comparative designs in which samples with and without these disorders are compared in terms of sociodemographic and clinical correlates, comorbidity, and treatment utilization. The taxonic structure of ASPD and CD may contribute to future research on causal processes through which these antisocial syndromes develop.

  12. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  13. Evaluation of Sampling and Sample Preparation Modifications for Soil Containing Metallic Residues

    Science.gov (United States)

    2012-01-01

    representation of the overall experimental design. Soil samples were transported to CRREL and air-dried on alumi - num trays. Once air-dried, each...60 s and then spread out onto an alumi - num cookie sheet. Digestion generally followed USEPA Method 3050B with the following exceptions. Two grams of

  14. Comparative Evaluation of Gari Samples Produced from Fresh ...

    African Journals Online (AJOL)

    Gari was produced from fresh cassava roots and dried cassava chips from four cassava cultivars; (TMS 98/2101, TMS 97/4779, TMS 91/02324 and NR87184). The gari samples were analyzed for chemical properties and sensory qualities. Results showed that gari obtained from the chips compared favourably with gari ...

  15. Screening and evaluation of fruit samples for four pesticide residues.

    Science.gov (United States)

    Blasco, Cristina; Font, Guillermina; Mañes, Jordi; Picó, Yolanda

    2005-01-01

    The occurrence of 4 pesticide residues, imidacloprid, carbendazim, methiocarb, and hexythiazox, was assessed in several fruits (oranges, tangerines, watermelons, and date plums) from the Valencian Community (Spain). A total of 227 samples--56 oranges, 134 tangerines, 13 watermelons, and 24 date plums--were taken from an agricultural cooperative representative of the area studied during 2001. The pesticides were determined by liquid chromatography/mass spectrometry after sample extraction with ethyl acetate and anhydrous sodium sulfate. Recoveries of 4 pesticides at 2 fortification levels (0.02 and 0.2 mg/kg), the lower of which was the quantification limit, ranged from 60 to 108%. Concentrations of imidacloprid, carbendazim, methiocarb, and hexythiazox ranged from 0.02 to 0.75 mg/kg in 184 samples (54 oranges, 119 tangerines, 3 watermelons, and 8 date plums). Nineteen samples contained methiocarb or hexythiazox residues that exceeded the maximum residue limits. Calculation of the estimated daily intakes of the 4 pesticides studied and their comparison with the Acceptable Daily Intakes established by the Food and Agriculture Organization of the World Health Organization demonstrated the safety of fruit consumption and showed the importance of monitoring for pesticide residues.

  16. Evaluation of sampling techniques for millipedes | Inyang | Moor ...

    African Journals Online (AJOL)

    Techniques (ii), (iii) and (iv) appeared appropriate for wet season sampling as the millipedes prefer the top soil during this period to avoid waterlogged condition or excessive moisture. The four techniques derived from the natural habitat, food needs, suitable conditions of temperature and moisture dictated by time of ...

  17. Technical Evaluation of Sample-Processing, Collection, and Preservation Methods

    Science.gov (United States)

    2014-07-01

    enhanced situational awareness of biological threats to the environment, human health, agriculture , and food supplies. Specifically mentioned is the...preparing for the possibility of biologically based attacks on military, civilian, or agricultural targets. To be fully prepared for this...from the various collected samples was extracted using an identical process—the Blood and Tissue Midi Preparation Kit (Qiagen, Inc.; Valencia , CA)—and

  18. Fluorimetric screening assay for protein carbonyl evaluation in biological samples.

    Science.gov (United States)

    Stocker, P; Ricquebourg, E; Vidal, N; Villard, C; Lafitte, D; Sellami, L; Pietri, S

    2015-08-01

    Many assays are available for the detection of protein carbonyls (PCs). Currently, the measurement of PC groups after their derivatization with 2,4-dinitrophenol hydrazine (DNPH) is widely used for measuring protein oxidation in biological samples. However, this method includes several washing steps. In this context, we have developed a rapid, sensitive, and accurate fluorimetric method adapted to 96-well microplates for the convenient assessment of protein carbonyl level in biological samples. The method reported here is based on the reaction of carbonyl content in proteins with 7-hydrazino-4-nitrobenzo-2,1,3-oxadiazole (NBDH) to form highly fluorescent derivatives via hydrazone formation. PCs were determined using the DNPH and NBDH assays in fully reduced bovine serum albumin (BSA) and plasma and liver homogenates obtained from healthy control rats up the addition of various amounts of HOCl-oxidized BSA (OxBSA). Using the NBDH assay, PC concentrations as low as 0.2 nmol/mg were detected with precision as low as 5%. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectroscopy was used to successfully identify the formation of the NBDH adducts after derivatization with standard oxidized peptides. Finally, the two methods were further used for PC determination in plasma and liver samples from diabetic and normal rats, showing that the NBDH assay can be reliably used in biological experiments. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Evaluating sampling strategies for larval cisco (Coregonus artedi)

    Science.gov (United States)

    Myers, J.T.; Stockwell, J.D.; Yule, D.L.; Black, J.A.

    2008-01-01

    To improve our ability to assess larval cisco (Coregonus artedi) populations in Lake Superior, we conducted a study to compare several sampling strategies. First, we compared density estimates of larval cisco concurrently captured in surface waters with a 2 x 1-m paired neuston net and a 0.5-m (diameter) conical net. Density estimates obtained from the two gear types were not significantly different, suggesting that the conical net is a reasonable alternative to the more cumbersome and costly neuston net. Next, we assessed the effect of tow pattern (sinusoidal versus straight tows) to examine if propeller wash affected larval density. We found no effect of propeller wash on the catchability of larval cisco. Given the availability of global positioning systems, we recommend sampling larval cisco using straight tows to simplify protocols and facilitate straightforward measurements of volume filtered. Finally, we investigated potential trends in larval cisco density estimates by sampling four time periods during the light period of a day at individual sites. Our results indicate no significant trends in larval density estimates during the day. We conclude estimates of larval cisco density across space are not confounded by time at a daily timescale. Well-designed, cost effective surveys of larval cisco abundance will help to further our understanding of this important Great Lakes forage species.

  20. Evaluation of sampling strategies to estimate crown biomass

    Science.gov (United States)

    Krishna P Poudel; Hailemariam Temesgen; Andrew N Gray

    2015-01-01

    Depending on tree and site characteristics crown biomass accounts for a significant portion of the total aboveground biomass in the tree. Crown biomass estimation is useful for different purposes including evaluating the economic feasibility of crown utilization for energy production or forest products, fuel load assessments and fire management strategies, and wildfire...

  1. Biological richness of a large urban cemetery in Berlin. Results of a multi-taxon approach.

    Science.gov (United States)

    Buchholz, Sascha; Blick, Theo; Hannig, Karsten; Kowarik, Ingo; Lemke, Andreas; Otte, Volker; Scharon, Jens; Schönhofer, Axel; Teige, Tobias; von der Lippe, Moritz; Seitz, Birgit

    2016-01-01

    Urban green spaces can harbor a considerable species richness of plants and animals. A few studies on single species groups indicate important habitat functions of cemeteries, but this land use type is clearly understudied compared to parks. Such data are important as they (i) illustrate habitat functions of a specific, but ubiquitous urban land-use type and (ii) may serve as a basis for management approaches. We sampled different groups of plants and animals in the Weißensee Jewish Cemetery in Berlin (WJC) which is one of the largest Jewish cemeteries in Europe. With a total of 608 species of plants and animals, this first multi-taxon survey revealed a considerable biological richness in the WJC. In all, 363 wild-growing vascular plant, 72 lichen and 26 bryophyte taxa were recorded. The sampling also yielded 34 bird and 5 bat species as well as 39 ground beetle, 5 harvestman and 64 spider species. Some species are new records for Berlin.

  2. Evaluation of samples comprising minute amounts of DNA.

    Science.gov (United States)

    Benschop, Corina C G; Haned, Hinda; Yoo, Seong Yeon; Sijen, Titia

    2015-09-01

    Minute amounts of DNA representing only few diploid cells, may be interrogated using enhanced DNA profiling, which will be accompanied by stochastic amplification effects. Notwithstanding, a weight of evidence statistic may be calculated using current interpretation software. In this study, we profiled single donor, two- and three-person samples having only 3 pg to 12 pg of DNA per contributor using both standard and enhanced capillary electrophoresis (CE) injection settings. Likelihood ratios (LRs) were computed using LRmix Studio, compared for both types of profiles and examined in relation to the amount of DNA, drop-out level, number of detected alleles, peak heights and reproducibility of alleles. Especially for DNA profiles that were generated using enhanced CE, the obtained LRs could indicate strong evidence in favour of the prosecution (log10(LR)>6), also when the amount of DNA represented about half of a diploid cell equivalent in the amplification. These results illustrate that an assessment of the criminalistic relevance of a sample carrying minute amounts of DNA is essential prior to applying enhanced interrogation techniques and/or calculating a weight of evidence statistic. Copyright © 2015 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

  3. [Pasteurella] caballi infection not limited to horses - a closer look at taxon 42 of Bisgaard

    DEFF Research Database (Denmark)

    Christensen, Henrik; Hommez, J.; Olsen, John Elmerdahl

    2006-01-01

    Aim To investigate if taxon 42 of Bisgaard isolated from pigs represents genuine [Pasteurella] caballi which has previously only been isolated from horses. Methods and Results A total of 15 field isolates from horses and pigs from 5 different countries representing three continents were to subjec......Aim To investigate if taxon 42 of Bisgaard isolated from pigs represents genuine [Pasteurella] caballi which has previously only been isolated from horses. Methods and Results A total of 15 field isolates from horses and pigs from 5 different countries representing three continents were...... to subjected extended phenotypical characterization. Although minor differences were observed between taxon 42 and [P.] caballi, these differences did not allow phenotypic separation. Ribotyping based on HindIII digestion showed five profiles based on 9 band positions. One [P.] caballi strain and two taxon 42...... strains shared the same profile. Ribotyping using HpaII gave a higher diversity with 9 profiles based on 10 band positions. While no profiles were shared between the Taxon 42 and [P.] caballi strains, pattern analysis showed that two of the Taxon 42 isolates were most similar (91 % similarity) with a [P...

  4. The evaluation of homophobia in an Italian sample.

    Science.gov (United States)

    Lingiardi, Vittorio; Falanga, Simona; D'Augelli, Anthony R

    2005-02-01

    Homophobia has not been systematically studied by Italian social scientists. This study was an initial investigation of the nature of homophobia among Italians, using an Italian version of a scale measuring the construct, and investigated personality and other factors related to homophobia. We examined (1) whether a male military personnel group had more homophobic attitudes than a group of comparably aged male university students; (2) whether personal characteristics and personality factors were correlated with homophobia; and (3) whether there were gender differences in homophobia between male and female university students. Male officers of the Italian Marine Corps were compared to male university students of the same age with respect to homophobia and personality characteristics. In addition, a sample of male university students was compared to female students. The instruments used were the Italian versions of the Modern Homophobia Scale (MHS) and the 16 Personality Factor Inventory (16 PF). Results showed significantly higher homophobia among the military personnel than among male students. Consistent with previous research, male university students demonstrated more negative attitudes towards gay and lesbian people than female students.

  5. Reliability of a higher-taxon approach to richness, rarity, and composition assessments at the local scale.

    Science.gov (United States)

    Mandelik, Yael; Dayan, Tamar; Chikatunov, Vladimir; Kravchenko, Vasiliy

    2007-12-01

    A promising shortcut for quantifying species patterns is to use genera and families as surrogates of species. At large spatial scales, concurrence between patterns of richness, rarity, and composition of species and higher taxa is generally high. Only a few researchers, however, have examined this relationship at the local scale, which is frequently the relevant scale in land-use conflicts. We investigated the reliability of the higher-taxon approach in assessing patterns of species richness, rarity, and composition at the local scale. We studied diversity patterns of three commonly used surrogate taxa: vascular plants, ground-dwelling beetles, and moths. We conducted year-round field surveys for these taxa in the Jerusalem Mountains and the Judean foothills, Israel. Richness and composition of species were highly correlated with richness and composition of genera for all taxa. At the family level, correlations with richness and composition of species were much lower. Excluding monotypic genera and families did not affect these relations. Rarity representation based on higher taxa varied considerably depending on the taxon, and rarity scale and was weaker compared with richness and composition representation. Cumulative richness curves of species and genera showed similar patterns, leveling off at equivalent sampling efforts. Genus-level assessments were a reliable surrogate for local patterns of species richness, rarity, and composition, but family-level assessments performed poorly. The advantage of using coarse taxonomic scales in local diversity surveys is that it may decrease identification time and the need for experts, but it will not reduce sampling effort.

  6. Sampling and energy evaluation challenges in ligand binding protein design

    Science.gov (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr. Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L.

    2017-01-01

    Abstract The steroid hormone 17α‐hydroxylprogesterone (17‐OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17‐OHP containing an extended, nonpolar, shape‐complementary binding pocket for the four‐ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17‐OHP with micromolar affinity. A co‐crystal structure of one of the designs revealed that 17‐OHP is rotated 180° around a pseudo‐two‐fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same “flipped” orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two‐fold symmetry of the molecule. PMID:28980354

  7. Sampling and energy evaluation challenges in ligand binding protein design.

    Science.gov (United States)

    Dou, Jiayi; Doyle, Lindsey; Jr Greisen, Per; Schena, Alberto; Park, Hahnbeom; Johnsson, Kai; Stoddard, Barry L; Baker, David

    2017-12-01

    The steroid hormone 17α-hydroxylprogesterone (17-OHP) is a biomarker for congenital adrenal hyperplasia and hence there is considerable interest in development of sensors for this compound. We used computational protein design to generate protein models with binding sites for 17-OHP containing an extended, nonpolar, shape-complementary binding pocket for the four-ring core of the compound, and hydrogen bonding residues at the base of the pocket to interact with carbonyl and hydroxyl groups at the more polar end of the ligand. Eight of 16 designed proteins experimentally tested bind 17-OHP with micromolar affinity. A co-crystal structure of one of the designs revealed that 17-OHP is rotated 180° around a pseudo-two-fold axis in the compound and displays multiple binding modes within the pocket, while still interacting with all of the designed residues in the engineered site. Subsequent rounds of mutagenesis and binding selection improved the ligand affinity to nanomolar range, while appearing to constrain the ligand to a single bound conformation that maintains the same "flipped" orientation relative to the original design. We trace the discrepancy in the design calculations to two sources: first, a failure to model subtle backbone changes which alter the distribution of sidechain rotameric states and second, an underestimation of the energetic cost of desolvating the carbonyl and hydroxyl groups of the ligand. The difference between design model and crystal structure thus arises from both sampling limitations and energy function inaccuracies that are exacerbated by the near two-fold symmetry of the molecule. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  8. An evaluation of adhesive sample holders for advanced crystallographic experiments

    Science.gov (United States)

    Mazzorana, Marco; Sanchez-Weatherby, Juan; Sandy, James; Lobley, Carina M. C.; Sorensen, Thomas

    2014-01-01

    The hydration state of macromolecular crystals often affects their overall order and, ultimately, the quality of the X-ray diffraction pattern that they produce. Post-crystallization techniques that alter the solvent content of a crystal may induce rearrangement within the three-dimensional array making up the crystal, possibly resulting in more ordered packing. The hydration state of a crystal can be manipulated by exposing it to a stream of air at controlled relative humidity in which the crystal can equilibrate. This approach provides a way of exploring crystal hydration space to assess the diffraction capabilities of existing crystals. A key requirement of these experiments is to expose the crystal directly to the dehydrating environment by having the minimum amount of residual mother liquor around it. This is usually achieved by placing the crystal on a flat porous support (Kapton mesh) and removing excess liquid by wicking. Here, an alternative approach is considered whereby crystals are harvested using adhesives that capture naked crystals directly from their crystallization drop, reducing the process to a one-step procedure. The impact of using adhesives to ease the harvesting of different types of crystals is presented together with their contribution to background scattering and their usefulness in dehydration experiments. It is concluded that adhesive supports represent a valuable tool for mounting macromolecular crystals to be used in humidity-controlled experiments and to improve signal-to-noise ratios in diffraction experiments, and how they can protect crystals from modifications in the sample environment is discussed. PMID:25195752

  9. [DOE method for evaluating environmental and waste management samples: Revision 1, Addendum 1

    Energy Technology Data Exchange (ETDEWEB)

    Goheen, S.C.

    1995-04-01

    The US Dapartment of Energy`s (DOE`s) environmental and waste management (EM) sampling and analysis activities require that large numbers of samples be analyzed for materials characterization, environmental surveillance, and site-remediation programs. The present document, DOE Methods for Evaluating Environmental and Waste Management Samples (DOE Methods), is a supplemental resource for analyzing many of these samples.

  10. Revisión taxonómica de la familia Celastraceae para la flora de Colombia Revisión taxonómica de la familia Celastraceae para la flora de Colombia

    Directory of Open Access Journals (Sweden)

    Fernandez Alonso José Luis

    2000-06-01

    Full Text Available ABSTRACTTaxonomic processing of the Celastraceae was made based on morphological characters andpollen from exsiccates pertaining to the different herbaria from Colombia an some fromoutside: MO, NY y US, along with characters taken directly from plants in the field,concatenating with the distributions patterns. Besides the taxonomical study, a review of thisplant group nomenclature was made, in order to establish the valid names, those ones whichare synonymous, and species location. The characters established in the descriptions of thespecies were compared with the observed ones in the study material. The study of pollen tookinto account grain type, opening of the pores, presence of rims and ribs ambit, exine, sexine andnexine, reticulation and measurements including equatorial and polar axis and the ratio long-width of pores and colpes. Fourteen pollen samples were analyzed, belonging to 8 nativegenera, revealing that palinology makes valuable contributions in the boundary of taxons,providing valid characters, that they are complemented with the other morphologic characters.The taxonomic description of the family fits with the Colombian constituent taxons.Dichotomizing keys were made in order to identify genera and species, and descriptions of eachone of the species, as well as their distribution, citation studied material of each taxon and insome cases illustrations of the species, were drawn at least one for each genus. Eigth native and1 cultivated genera were found: Celastrus 4, andean and subandean woody scandent species.Crossopetalum: 2 species of islands of Tintipán and San Andrés and Providencia. Goupia: 1species from equatorial rain forest. Gymnosporia: 2 species, one of forest of the median valleyof Magdalena and the other of the andean and subandean forest. Maytenus considered aspreliminary synopsis, with 26 species coming of different habitats. Perrottetia with 10 species,4 of these new; 1 species from piedemonte, the rest live in

  11. A macrophyte bioassessment approach linking taxon-specific tolerance and abundance in north temperate lakes.

    Science.gov (United States)

    Mikulyuk, Alison; Barton, Martha; Hauxwell, Jennifer; Hein, Catherine; Kujawa, Ellen; Minahan, Kristi; Nault, Michelle E; Oele, Daniel L; Wagner, Kelly I

    2017-09-01

    Bioassessment methods are critically needed to evaluate and monitor lake ecological condition. Aquatic macrophytes are good candidate indicators, but few lake bioassessment methods developed in North America use them. The few macrophyte bioassessment methods that do exist suffer from problems related to subjectivity and discernibility along disturbance gradients. We developed and tested a bioassessment approach for 462 north temperate lakes. The approach links macrophyte abundance to lake ecological condition via estimates of taxon-specific abundance-weighted tolerance to anthropogenic disturbance. Using variables related to eutrophication, urban development and agriculture, we calculated abundance-weighted tolerance ranges for 59 macrophyte taxa and clustered them according to their tolerance to anthropogenic disturbance. We also created a composite index of anthropogenic disturbance using 20 variables related to population density, land cover and water chemistry. We used a statistical approach to set ecological condition thresholds based on the observed abundance of sensitive, moderately tolerant and tolerant taxa in each lake. The resulting lake condition categories were usually stable across multiple survey events and largely agreed with condition rankings assigned using expert judgment. We suggest using this macrophyte bioassessment method for federal water quality reports, restoration and management on north temperate lakes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Evaluation of alternative macroinvertebrate sampling techniques for use in a new tropical freshwater bioassessment scheme

    OpenAIRE

    Moore, Isabel Eleanor; Murphy, Kevin Joseph

    2015-01-01

    Aim: The study aimed to determine the effectiveness of benthic macroinvertebrate dredge net sampling procedures as an alternative method to kick net sampling in tropical freshwater systems, specifically as an evaluation of sampling methods used in the Zambian Invertebrate Scoring System (ZISS) river bioassessment scheme. Tropical freshwater ecosystems are sometimes dangerous or inaccessible to sampling teams using traditional kick-sampling methods, so identifying an alternative procedure that...

  13. The evolutionary diversification of parrots supports a taxon pulse model with multiple trans-oceanic dispersal events and local radiations.

    Science.gov (United States)

    Schweizer, Manuel; Seehausen, Ole; Güntert, Marcel; Hertwig, Stefan T

    2010-03-01

    Vicariance is thought to have played a major role in the evolution of modern parrots. However, as the relationships especially of the African taxa remained mostly unresolved, it has been difficult to draw firm conclusions about the roles of dispersal and vicariance. Our analyses using the broadest taxon sampling of old world parrots ever based on 3219bp of three nuclear genes revealed well-resolved and congruent phylogenetic hypotheses. Agapornis of Africa and Madagascar was found to be the sister group to Loriculus of Australasia and Indo-Malayasia and together they clustered with the Australasian Loriinae, Cyclopsittacini and Melopsittacus. Poicephalus and Psittacus from mainland Africa formed the sister group of the Neotropical Arini and Coracopsis from Madagascar and adjacent islands may be the closest relative of Psittrichas from New Guinea. These biogeographic relationships are best explained by independent colonization of the African continent via trans-oceanic dispersal from Australasia and Antarctica in the Paleogene following what may have been vicariance events in the late Cretaceous and/or early Paleogene. Our data support a taxon pulse model for the diversification of parrots whereby trans-oceanic dispersal played a more important role than previously thought and was the prerequisite for range expansion into new continents. Copyright 2009 Elsevier Inc. All rights reserved.

  14. 'Candidatus Phytoplasma tamaricis', a novel taxon discovered in witches'-broom-diseased salt cedar (Tamarix chinensis Lour.).

    Science.gov (United States)

    Zhao, Yan; Sun, Qingrong; Wei, Wei; Davis, Robert E; Wu, Wei; Liu, Qingzhong

    2009-10-01

    Salt cedar trees with pronounced witches'-broom symptoms were observed in their natural habitat in China. 16S rRNA gene sequences unique to phytoplasmas were detected in every DNA sample extracted from stem and leaf tissues of the symptomatic trees, revealing a direct association between phytoplasma infection and the salt cedar witches'-broom (SCWB) disease. Phylogenetic analysis of the SCWB phytoplasma 16S rRNA gene sequence indicated that the SCWB phytoplasma belonged to a subclade consisting of several mutually distinct 'Candidatus Phytoplasma' taxa including 'Ca. Phytoplasma prunorum', 'Ca. Phytoplasma mali', 'Ca. Phytoplasma pyri' and 'Ca. Phytoplasma spartii'. Pairwise sequence similarity scores calculated from an alignment of near full-length 16S rRNA genes revealed that SCWB phytoplasma shared 96.6 % or less sequence similarity with each previously described or proposed 'Ca. Phytoplasma' taxon, justifying the recognition of SCWB phytoplasma as a novel taxon, 'Candidatus Phytoplasma tamaricis'. The distinct virtual RFLP pattern derived from the SCWB phytoplasma 16S rRNA gene sequence, together with its lower-than-threshold similarity coefficient values with RFLP patterns of any of the 29 previously established groups, supported the recognition of a new 16Sr group, designated 16SrXXX, salt cedar witches'-broom phytoplasma group.

  15. Improved evaluation of measurement uncertainty from sampling by inclusion of between-sampler bias using sampling proficiency testing.

    Science.gov (United States)

    Ramsey, Michael H; Geelhoed, Bastiaan; Wood, Roger; Damant, Andrew P

    2011-04-07

    A realistic estimate of the uncertainty of a measurement result is essential for its reliable interpretation. Recent methods for such estimation include the contribution to uncertainty from the sampling process, but they only include the random and not the systematic effects. Sampling Proficiency Tests (SPTs) have been used previously to assess the performance of samplers, but the results can also be used to evaluate measurement uncertainty, including the systematic effects. A new SPT conducted on the determination of moisture in fresh butter is used to exemplify how SPT results can be used not only to score samplers but also to estimate uncertainty. The comparison between uncertainty evaluated within- and between-samplers is used to demonstrate that sampling bias is causing the estimates of expanded relative uncertainty to rise by over a factor of two (from 0.39% to 0.87%) in this case. General criteria are given for the experimental design and the sampling target that are required to apply this approach to measurements on any material. © The Royal Society of Chemistry 2011

  16. Evaluation of standard methods for collecting and processing fuel moisture samples

    Science.gov (United States)

    Sally M. Haase; José Sánchez; David R. Weise

    2016-01-01

    A variety of techniques for collecting and processing samples to determine moisture content of wildland fuels in support of fire management activities were evaluated. The effects of using a chainsaw or handsaw to collect samples of largediameter wood, containers for storing and transporting collected samples, and quick-response ovens for estimating moisture content...

  17. Evaluation of Carpet Steam and Heat Cleaners as Biological Sampling Devices

    Science.gov (United States)

    2016-05-01

    Final 3. DATES COVERED (From - To) Mar 2010 – Dec 2012 4. TITLE AND SUBTITLE Evaluation of Carpet Steam and Heat Cleaners as Biological Sampling...such as Bacillus anthracis spores. Residential, commercial, and industrial carpet cleaners were compared for their effectiveness in sampling...TERMS Carpet steam and heat cleaners Biological sampling Re-aerosolization Aerosol deposition Carpet Bacillus globigii spores 16. SECURITY

  18. Inventario taxonómico de drosophilidae (Diptera) en el Parque Nacional Yasuni, Amazonia Ecuatoriana

    OpenAIRE

    Acurio,Andrea Elizabeth; Rafael,Violeta Lily

    2009-01-01

    En el Parque Nacional Yasuní, reconocido como un sector de alto endemismo y biodiversidad, ubicado al noroeste de la Amazonía Ecuatoriana se realizó el inventario taxonómico de la familia Drosophilidae. Para la captura de los individuos se utilizaron trampas con atrayente de banano y solución de levadura de cerveza. La identificación taxonómica se realizó usando caracteres morfológicos y la terminalia de los machos. En total se colectaron 7425 individuos clasificados en 34 especies de los gén...

  19. Estudio de frutos y semillas en Parentucellia Viv. (Scrophulariaceae) y sus implicaciones taxonómicas

    OpenAIRE

    Pastor Díaz, Julio E.; Fernández, Inmaculada; Juan, Rocío

    1998-01-01

    Estudio de frutos y semillas en Parentucellia Viv. (Scrophulariaceae) y sus implicaciones taxonómicas. Se estudia la morfología y anatomía de frutos y semillas en las dos especies europeas de Parentucellia. Los resultados muestran el valor taxonómico para este género de los caracteres morfoanatómicos. Las dos especies, P. viscosa (L.) Caruel y P. latifolia (L.) Caruel pueden distinguirse por los caracteres de frutos y semillas. Por último se hace un breve comentario sobre el sistema de disper...

  20. Novidades taxonômicas em Maytenus (Celastraceae para a flora da Argentina

    Directory of Open Access Journals (Sweden)

    Leonardo Biral

    2014-01-01

    Full Text Available No decorrer dos estudos taxonômicos de Maytenus Molina desenvolvidos pelo autor para a América do Sul, novidades taxonômicas para a flora argentina são apresentadas. Essas novidades incluem três sinonimizações, cinco lectotipificações e um novo registro de ocorrência no país. Dessa forma objetiva-se atualizar as informações disponíveis sobre o presente táxon na Argentina.

  1. A cross-taxon analysis of insect-associated bacterial diversity.

    Science.gov (United States)

    Jones, Ryan Thomas; Sanchez, Leticia Gonzales; Fierer, Noah

    2013-01-01

    Although it is well known that plants and animals harbor microbial symbionts that can influence host traits, the factors regulating the structure of these microbial communities often remain largely undetermined. This is particularly true for insect-associated microbial communities, as few cross-taxon comparisons have been conducted to date. To address this knowledge gap and determine how host phylogeny and ecology affect insect-associated microbial communities, we collected 137 insect specimens representing 39 species, 28 families, and 8 orders, and characterized the bacterial communities associated with each specimen via 16S rRNA gene sequencing. Bacterial taxa within the phylum Proteobacteria were dominant in nearly all insects sampled. On average, the insect-associated bacterial communities were not very diverse, with individuals typically harboring fewer than 8 bacterial phylotypes. Bacterial communities also tended to be dominated by a single phylotype; on average, the most abundant phylotype represented 54.7% of community membership. Bacterial communities were significantly more similar among closely related insects than among less-related insects, a pattern driven by within-species community similarity but detected at every level of insect taxonomy tested. Diet was a poor predictor of bacterial community composition. Individual insect species harbored remarkably unique communities: the distribution of 69.0% of bacterial phylotypes was limited to unique insect species, whereas only 5.7% of phylotypes were detected in more than five insect species. Together these results suggest that host characteristics strongly regulate the colonization and assembly of bacterial communities across insect lineages, patterns that are driven either by co-evolution between insects and their symbionts or by closely related insects sharing conserved traits that directly select for similar bacterial communities.

  2. Molecular evidence for sequential colonization and taxon cycling in freshwater decapod shrimps on a Caribbean island

    Science.gov (United States)

    Benjamin D. Cook; Catherine M. Pringle; Jane M. Hughes

    2008-01-01

    Taxon cycling, i.e. sequential phases of expansions and contractions in species’ distributions associated with ecological or morphological shifts, are postulated to characterize dynamic biogeographic histories in various island faunas. The Caribbean freshwater shrimp assemblage is mostly widespread and sympatric throughout the region, although one species (Atyidae:...

  3. Taxon-specific PCR primers to detect two inconspicuous arbuscular mycorrhizal fungi from temperate agricultural grassland

    NARCIS (Netherlands)

    Gamper, H.A.; Leuchtmann, A.

    2007-01-01

    Taxon-specific polymerase chain reaction (PCR) primers enable detection of arbuscular mycorrhizal fungi (AMF, Glomeromycota) in plant roots where the fungi lack discriminative morphological and biochemical characters. We designed and validated pairs of new PCR primers targeted to the flanking

  4. Are marketed topical metronidazole creams bioequivalent? Evaluation by in vivo microdialysis sampling and tape stripping methodology

    DEFF Research Database (Denmark)

    Garcia Ortiz, Patricia Elodia; Hansen, S H; Shah, Surendra P.

    2011-01-01

    To evaluate the bioequivalence of 3 marketed topical metronidazole formulations by simultaneous dermal microdialysis and stratum corneum sampling by the tape stripping methodology, and to compare the techniques as tools for the determination of bioequivalence....

  5. [Basic evaluation of sampling step angle and spatial resolution in continuous rotating acquisition with SPECT].

    Science.gov (United States)

    Kangai, Yoshiharu; Nagaki, Akio; Matsutomo, Norikazu; Sugino, Shuichi; Ohata, Yasushi; Mimura, Hiroaki; Onishi, Hideo

    2011-01-01

    In the data sampling in single photon emission computed tomography (SPECT), the continuous rotating acquisition method has high clinical utility. There have been various reports about the optimum sampling step angle for continuous rotating acquisition. Objective evaluation was performed visually and by measuring spatial resolution with a column phantom to find the optimum sampling step angle for continuous rotating acquisition. In locations far from the rotation center, a large sampling step angle produced artificial images with tangential elongation. The spatial resolution was 11.58 ± 0.19 mm full width half maximum (FWHM) as measured at a sampling step angle of 3 degrees and at 10 cm away from the rotation center. Increasing the sampling step angle to more than 3 degrees resulted in an increase of FWHM in the tangential direction. The optimum sampling step angle for continuous rotating acquisition in SPECT needs to be below that calculated from the sampling theorem.

  6. Are marketed topical metronidazole creamas bioequivalent ? Evaluation by in vivo microdialysis sampling and tape stripping methodology

    DEFF Research Database (Denmark)

    Ortiz, P. Garcia; Hansen, Steen Honore'; Shah, V. P.

    2011-01-01

    To evaluate the bioequivalence of 3 marketed topical metronidazole formulations by simultaneous dermal microdialysis and stratum corneum sampling by the tape stripping methodology, and to compare the techniques as tools for the determination of bioequivalence.......To evaluate the bioequivalence of 3 marketed topical metronidazole formulations by simultaneous dermal microdialysis and stratum corneum sampling by the tape stripping methodology, and to compare the techniques as tools for the determination of bioequivalence....

  7. Long-term strategic asset allocation: An out-of-sample evaluation

    NARCIS (Netherlands)

    Diris, B.F.; Palm, F.C.; Schotman, P.C.

    We evaluate the out-of-sample performance of a long-term investor who follows an optimized dynamic trading strategy. Although the dynamic strategy is able to benefit from predictability out-of-sample, a short-term investor using a single-period market timing strategy would have realized an almost

  8. Evaluation of the Frequency for Gas Sampling for the High Burnup Confirmatory Data Project

    Energy Technology Data Exchange (ETDEWEB)

    Stockman, Christine T. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Alsaed, Halim A. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Bryan, Charles R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Marschman, Steven C. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Scaglione, John M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-05-01

    This report provides a technically based gas sampling frequency strategy for the High Burnup (HBU) Confirmatory Data Project. The evaluation of: 1) the types and magnitudes of gases that could be present in the project cask and, 2) the degradation mechanisms that could change gas compositions culminates in an adaptive gas sampling frequency strategy. This adaptive strategy is compared against the sampling frequency that has been developed based on operational considerations.

  9. Sample Size Requirements for Structural Equation Models: An Evaluation of Power, Bias, and Solution Propriety

    OpenAIRE

    Wolf, Erika J.; Harrington, Kelly M.; Shaunna L Clark; Miller, Mark W.

    2013-01-01

    Determining sample size requirements for structural equation modeling (SEM) is a challenge often faced by investigators, peer reviewers, and grant writers. Recent years have seen a large increase in SEMs in the behavioral science literature, but consideration of sample size requirements for applied SEMs often relies on outdated rules-of-thumb. This study used Monte Carlo data simulation techniques to evaluate sample size requirements for common applied SEMs. Across a series of simulations, we...

  10. Revisión taxonómica de la Familia Iridaceae para Colombia Revisión taxonómica de la Familia Iridaceae para Colombia

    OpenAIRE

    Betancur Betancur Julio César; Celis Pachecho Marcela

    2000-01-01

    RESUMENSe presenta la revisión taxonómica de la familia Iridaceaepara Colombia que incluye descripcionesmorfológicas de la familia, los géneros y las especies. Se presentan claves dicotómicas paraidentificar los géneros y las especies y un análisis de la distribución geográfica y altitudinal de lasmismas. En Sisyrinchiumse incluye, asi mismo, una clave sinóptica. Se encontraron 24 especies,distribuidas en 10 géneros, de las cuales dos son naturalizadas (Crocosmia x crocosmiifloray Tigridiapav...

  11. Diversidad y distinción taxonómica de la macrofauna en fondos blandos de la plataforma norte y suroccidental cubana

    Directory of Open Access Journals (Sweden)

    Gema Hidalgo

    2015-11-01

    Full Text Available Se evaluó la diversidad de la macrofauna en fondos blandos de la plataforma marina cubana norte y suroccidental. Se utilizaron índices de variación taxonómica que aportan una nueva dimensión en la interpretación de la diversidad de las comunidades, que son independientes del tipo de hábitat y del esfuerzo de muestreo, y tienen respuesta monotónica ante las perturbaciones del ambiente. La heterogeneidad de taxones fue significativamente mayor en los biotopos areno-fangoso con vegetación, arenoso con vegetación y arenoso con vegetación sobre fondo duro. La diversidad por biotopos reflejó un gradiente de menor a mayor tamaño de partícula y de ausencia a presencia de vegetación. La distinción taxonómica promedio (Δ+ esperada en estas zonas de la plataforma cubana es de 92,5, con límites de confianza de 95% entre 76,7 y 100. Las estaciones con distinción taxonómica promedio <92,5 y fuera del límite de confianza inferior, se pueden considerar con condiciones ambientales de deterioro o que favorecen la diversidad de algún grupo en particular. Los grupos dominantes en esta fracción del bentos son crustáceos y poliquetos, como ocurre en otras regiones tropicales y templadas. Estos resultados sirven de base para la evaluación y monitoreo ambiental del macrozoobentos como componente clave del funcionamiento de ecosistemas marinos en fondos blandos de Cuba.

  12. Evaluation of correlation between physical properties and ultrasonic pulse velocity of fired clay samples.

    Science.gov (United States)

    Özkan, İlker; Yayla, Zeliha

    2016-03-01

    The aim of this study is to establish a correlation between physical properties and ultrasonic pulse velocity of clay samples fired at elevated temperatures. Brick-making clay and pottery clay were studied for this purpose. The physical properties of clay samples were assessed after firing pressed clay samples separately at temperatures of 850, 900, 950, 1000, 1050 and 1100 °C. A commercial ultrasonic testing instrument (Proceq Pundit Lab) was used to evaluate the ultrasonic pulse velocity measurements for each fired clay sample as a function of temperature. It was observed that there became a relationship between physical properties and ultrasonic pulse velocities of the samples. The results showed that in consequence of increasing densification of the samples, the differences between the ultrasonic pulse velocities were higher with increasing temperature. These findings may facilitate the use of ultrasonic pulse velocity for the estimation of physical properties of fired clay samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Draft evaluation of the frequency for gas sampling for the high burnup confirmatory data project

    Energy Technology Data Exchange (ETDEWEB)

    Stockman, Christine T. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Alsaed, Halim A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Bryan, Charles R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-03-26

    This report fulfills the M3 milestone M3FT-15SN0802041, “Draft Evaluation of the Frequency for Gas Sampling for the High Burn-up Storage Demonstration Project” under Work Package FT-15SN080204, “ST Field Demonstration Support – SNL”. This report provides a technically based gas sampling frequency strategy for the High Burnup (HBU) Confirmatory Data Project. The evaluation of: 1) the types and magnitudes of gases that could be present in the project cask and, 2) the degradation mechanisms that could change gas compositions culminates in an adaptive gas sampling frequency strategy. This adaptive strategy is compared against the sampling frequency that has been developed based on operational considerations. Gas sampling will provide information on the presence of residual water (and byproducts associated with its reactions and decomposition) and breach of cladding, which could inform the decision of when to open the project cask.

  14. Elasticity Evaluation of Regenerating Cartilage Sample Based on Laser Doppler Measurement of Ultrasonic Particle Velocity

    Science.gov (United States)

    Nitta, Naotaka; Misawa, Masaki; Homma, Kazuhiro; Shiina, Tsuyoshi

    2012-07-01

    It is important for regenerative medicine to evaluate the maturity of regenerating tissue. In the maturity evaluation of regenerating cartilage, it is useful to measure the temporal change of elasticity because the maturity of regenerating tissue is closely related to its elasticity. In this study, an elasticity evaluation method for the extracted regenerating cartilage sample, which is based on the laser Doppler measurement of ultrasonic particle velocity, was experimentally investigated using agar-based phantoms with different elastic moduli and the regenerating cartilage samples extracted from beagles in animal experiments. In addition, the experimentally-obtained elasticity was compared with the result of a static compression test. These results verified the feasibility of the proposed method in the elasticity evaluation of regenerating cartilage samples.

  15. Method validation and uncertainty evaluation of organically bound tritium analysis in environmental sample.

    Science.gov (United States)

    Huang, Yan-Jun; Zeng, Fan; Zhang, Bing; Chen, Chao-Feng; Qin, Hong-Juan; Wu, Lian-Sheng; Guo, Gui-Yin; Yang, Li-Tao; Shang-Guan, Zhi-Hong

    2014-08-01

    The analytical method for organically bound tritium (OBT) was developed in our laboratory. The optimized operating conditions and parameters were established for sample drying, special combustion, distillation, and measurement on a liquid scintillation spectrometer (LSC). Selected types of OBT samples such as rice, corn, rapeseed, fresh lettuce and pork were analyzed for method validation of recovery rate reproducibility, the minimum detection concentration, and the uncertainty for typical low level environmental sample was evaluated. The combustion water recovery rate of different dried environmental sample was kept at about 80%, the minimum detection concentration of OBT ranged from 0.61 to 0.89 Bq/kg (dry weight), depending on the hydrogen content. It showed that this method is suitable for OBT analysis of environmental sample with stable recovery rate, and the combustion water yield of a sample with weight about 40 g would provide sufficient quantity for measurement on LSC. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Evaluation of the Chemical Composition of Brazilian Commercial Cymbopogon citratus (D.C. Stapf Samples

    Directory of Open Access Journals (Sweden)

    Evandro de Castro Melo

    2008-08-01

    Full Text Available Abstract: The concentration and the chemical composition of the essential oils obtained from different samples of Cymbopogon citratus were evaluated. Among the 12 samples investigated (11 dried leaf samples and fresh plant leaves, seven presented essential oil concentrations within the threshold established by the Brazilian legislation. The moisture content was also determined and the majority of the samples presented humidity contents near 12%. The GC and GC/MS analyses of the essential oils led to identification of 22 compounds, with neral and geranial as the two major components. The total percentage of these two compounds varied within the investigated sample oils from 40.7% to 75.4%. In addition, a considerable variation in the chemical composition of the analyzed samples was observed. The process of grinding the leaves significantly decreased (by up to 68% the essential oil content, as well as the percentage of myrcene in the oils.

  17. Evaluation of the chemical composition of Brazilian commercial Cymbopogon citratus (D.C.) stapf samples.

    Science.gov (United States)

    Barbosa, Luiz Cláudio Almeida; Pereira, Ulisses Alves; Martinazzo, Ana Paula; Maltha, Célia Regina Alvares; Teixeira, Róbson Ricardo; Melo, Evandro de Castro

    2008-08-27

    The concentration and the chemical composition of the essential oils obtained from different samples of Cymbopogon citratus were evaluated. Among the 12 samples investigated (11 dried leaf samples and fresh plant leaves), seven presented essential oil concentrations within the threshold established by the Brazilian legislation. The moisture content was also determined and the majority of the samples presented humidity contents near 12%. The GC and GC/MS analyses of the essential oils led to identification of 22 compounds, with neral and geranial as the two major components. The total percentage of these two compounds varied within the investigated sample oils from 40.7% to 75.4%. In addition, a considerable variation in the chemical composition of the analyzed samples was observed. The process of grinding the leaves significantly decreased (by up to 68%) the essential oil content, as well as the percentage of myrcene in the oils.

  18. Evaluation of various conventional methods for sampling weeds in potato and spinach crops

    Directory of Open Access Journals (Sweden)

    David Jamaica

    2014-04-01

    Full Text Available This study aimed to evaluate (at an exploratory level, some of the different conventional sampling designs in a section of a potato crop and in a commercial crop of spinach. Weeds were sampled in a 16 x 48 m section of a potato crop with a set grid of 192 sections. The cover and density of the weeds were registered in squares of from 0.25 to 64 m². The results were used to create a database that allowed for the simulation of different sampling designs: variables and square size. A second sampling was carried out with these results in a spinach crop of 1.16 ha with a set grid of 6 x 6 m cells, evaluating the cover in 4 m² squares. Another database was created with this information, which was used to simulate other sampling designs such as distribution and quantity of sampling squares. According to the obtained results, a good method for approximating the quantity of squares for diverse samples is 10-12 squares (4 m² for richness per ha and 18 or more squares for abundance per hectare. This square size is optimal since it allows for a sampling of more area without losing sight of low-profile species, with the cover variable best representing the abundance of the weeds.

  19. Development of color micro optical-CT: evaluation using phantom and biological samples

    Science.gov (United States)

    Murata, C.; Teramoto, A.; Kaneko, C.; Fujita, H.

    2015-03-01

    Micro-optical computed tomography (MOCT) is a method for performing image reconstruction using microscopic images to obtain tomographic images of small samples. Compared with conventional observation methods, it offers the possibility to obtain tomograpic images without distortion, and create three-dimensional images. However, MOCT system which developed previously outputs monochrome images, while useful color information could not be obtained from the analysis of the sample. Therefore, we focused on the features that simplify the wavelength measurement of visible light, and developed a color MOCT system that can obtain color tomographic images. In this study, we acquired tomographic images of phantom and biological samples, and evaluated its usefulness. In this system, a digital single-lens reflex camera was used as a detector that was connected to a stereoscopic microscope, and projection images were obtained by rotating the sample. The sample was fixed in the test tube by carrageenan. The projection images were obtained from various projection angles followed by decomposing the R, G and B components. Subsequently, we performed image reconstruction for each component using filtered back projection. Finally, color tomographic image was obtained by combining the three-color component images. In the experiments, we scanned a color phantom and biological samples and evaluated the color and shape reproducibility. As a result, it was found that the color and shape of the tomographic images were similar to those of the samples. These results indicate that the proposed system may be useful to obtain the three-dimensional color structure of biological samples.

  20. Comparative Genomics of Bifidobacterium animalis subsp. lactis Reveals a Strict Monophyletic Bifidobacterial Taxon

    Science.gov (United States)

    Milani, Christian; Duranti, Sabrina; Lugli, Gabriele Andrea; Bottacini, Francesca; Strati, Francesco; Arioli, Stefania; Foroni, Elena; Turroni, Francesca; van Sinderen, Douwe

    2013-01-01

    Strains of Bifidobacterium animalis subsp. lactis are extensively exploited by the food industry as health-promoting bacteria, although the genetic variability of members belonging to this taxon has so far not received much scientific attention. In this article, we describe the complete genetic makeup of the B. animalis subsp. lactis Bl12 genome and discuss the genetic relatedness of this strain with other sequenced strains belonging to this taxon. Moreover, a detailed comparative genomic analysis of B. animalis subsp. lactis genomes was performed, which revealed a closely related and isogenic nature of all currently available B. animalis subsp. lactis strains, thus strongly suggesting a closed pan-genome structure of this bacterial group. PMID:23645200

  1. Higher-taxon richness as a surrogate for species richness in chemosynthetic communities

    Science.gov (United States)

    Doerries, M. B.; Van Dover, C. L.

    2003-06-01

    Estimations of biodiversity and species richness in deep-sea marine ecosystems are impeded by time-consuming methods of species identification. In conservation biology, in environmental monitoring, and in paleontology, a higher-taxon approach (e.g., identification to genera or families) can be used as a surrogate for species richness. We applied a higher-taxon approach to well-documented chemosynthetic communities associated with seep and vent mussel beds to test its applicability in these systems. Significant positive correlations between cumulative number of species and cumulative number of higher taxa were found at the generic, family, and order levels. The number of these higher taxa can be used to predict species richness in vent and seep mussel beds.

  2. Method of evaluation of process of red blood cell sedimentation based on photometry of droplet samples.

    Science.gov (United States)

    Aristov, Alexander; Nosova, Ekaterina

    2017-04-01

    The paper focuses on research aimed at creating and testing a new approach to evaluate the processes of aggregation and sedimentation of red blood cells for purpose of its use in clinical laboratory diagnostics. The proposed method is based on photometric analysis of blood sample formed as a sessile drop. The results of clinical approbation of this method are given in the paper. Analysis of the processes occurring in the sample in the form of sessile drop during the process of blood cells sedimentation is described. The results of experimental studies to evaluate the effect of the droplet sample focusing properties on light radiation transmittance are presented. It is shown that this method significantly reduces the sample volume and provides sufficiently high sensitivity to the studied processes.

  3. Psychometric evaluation of the authenticity scale on the sample of students in Serbia

    Directory of Open Access Journals (Sweden)

    Grijak Đurđa

    2017-01-01

    Full Text Available The aim of this study, conducted at two time points, was to evaluate the psychometric properties of the Serbian translation of the Authenticity Scale on the sample of students. The paper presents the results of testing the validity construct of the Authenticity Scale by confirmatory factor analysis at two time points, on the initial sample of 706 students and on the test-retest sample of 206 students within a 10-week interval. The model in which there are three separate, mutually related dimensions with the superordinate factor of authenticity best describes the scale structure. The test-retest sample was used to test the convergent validity of the Authenticity Scale by evaluating its relation to the measures of both positive and negative affect, self-esteem, psychological distress and psychological well-being and mental health index. The results showed that the Serbian translation of the Authenticity Scale represents a reliable and valid measure of authenticity.

  4. (Sample) size matters! An examination of sample size from the SPRINT trial study to prospectively evaluate reamed intramedullary nails in patients with tibial fractures

    NARCIS (Netherlands)

    Bhandari, Mohit; Tornetta, Paul; Rampersad, Shelly-Ann; Sprague, Sheila; Heels-Ansdell, Diane; Sanders, David W.; Schemitsch, Emil H.; Swiontkowski, Marc; Walter, Stephen; Guyatt, Gordon; Buckingham, Lisa; Leece, Pamela; Viveiros, Helena; Mignott, Tashay; Ansell, Natalie; Sidorkewicz, Natalie; Agel, Julie; Bombardier, Claire; Berlin, Jesse A.; Bosse, Michael; Browner, Bruce; Gillespie, Brenda; O'Brien, Peter; Poolman, Rudolf; Macleod, Mark D.; Carey, Timothy; Leitch, Kellie; Bailey, Stuart; Gurr, Kevin; Konito, Ken; Bartha, Charlene; Low, Isolina; MacBean, Leila V.; Ramu, Mala; Reiber, Susan; Strapp, Ruth; Tieszer, Christina; Kreder, Hans; Stephen, David J. G.; Axelrod, Terry S.; Yee, Albert J. M.; Richards, Robin R.; Finkelstein, Joel; Holtby, Richard M.; Cameron, Hugh; Cameron, John; Gofton, Wade; Murnaghan, John; Schatztker, Joseph; Bulmer, Beverly; Conlan, Lisa; Laflamme, Yves; Berry, Gregory; Beaumont, Pierre; Ranger, Pierre; Laflamme, Georges-Henri; Jodoin, Alain; Renaud, Eric; Gagnon, Sylvain; Maurais, Gilles; Malo, Michel; Fernandes, Julio; Latendresse, Kim; Poirier, Marie-France; Daigneault, Gina; McKee, Michael M.; Waddell, James P.; Bogoch, Earl R.; Daniels, Timothy R.; McBroom, Robert R.; Vicente, Milena R.; Storey, Wendy; Wild, Lisa M.; McCormack, Robert; Perey, Bertrand; Goetz, Thomas J.; Pate, Graham; Penner, Murray J.; Panagiotopoulos, Kostas; Pirani, Shafique; Dommisse, Ian G.; Loomer, Richard L.; Stone, Trevor; Moon, Karyn; Zomar, Mauri; Webb, Lawrence X.; Teasdall, Robert D.; Birkedal, John Peter; Martin, David Franklin; Ruch, David S.; Kilgus, Douglas J.; Pollock, David C.; Harris, Mitchel Brion; Wiesler, Ethan Ron; Ward, William G.; Shilt, Jeffrey Scott; Koman, Andrew L.; Poehling, Gary G.; Kulp, Brenda; Creevy, William R.; Stein, Andrew B.; Bono, Christopher T.; Einhorn, Thomas A.; Brown, T. Desmond; Pacicca, Donna; Sledge, John B.; Foster, Timothy E.; Voloshin, Ilva; Bolton, Jill; Carlisle, Hope; Shaughnessy, Lisa; Ombremsky, William T.; LeCroy, C. Michael; Meinberg, Eric G.; Messer, Terry M.; Craig, William L.; Dirschl, Douglas R.; Caudle, Robert; Harris, Tim; Elhert, Kurt; Hage, William; Jones, Robert; Piedrahita, Luis; Schricker, Paul O.; Driver, Robin; Godwin, Jean; Hansley, Gloria; Obremskey, William Todd; Kregor, Philip James; Tennent, Gregory; Truchan, Lisa M.; Sciadini, Marcus; Shuler, Franklin D.; Driver, Robin E.; Nading, Mary Alice; Neiderstadt, Jacky; Vap, Alexander R.; Vallier, Heather A.; Patterson, Brendan M.; Wilber, John H.; Wilber, Roger G.; Sontich, John K.; Moore, Timothy Alan; Brady, Drew; Cooperman, Daniel R.; Davis, John A.; Cureton, Beth Ann; Mandel, Scott; Orr, R. Douglas; Sadler, John T. S.; Hussain, Tousief; Rajaratnam, Krishan; Petrisor, Bradley; Drew, Brian; Bednar, Drew A.; Kwok, Desmond C. H.; Pettit, Shirley; Hancock, Jill; Cole, Peter A.; Smith, Joel J.; Brown, Gregory A.; Lange, Thomas A.; Stark, John G.; Levy, Bruce; Swiontkowski, Marc F.; Garaghty, Mary J.; Salzman, Joshua G.; Schutte, Carol A.; Tastad, Linda Toddie; Vang, Sandy; Seligson, David; Roberts, Craig S.; Malkani, Arthur L.; Sanders, Laura; Gregory, Sharon Allen; Dyer, Carmen; Heinsen, Jessica; Smith, Langan; Madanagopal, Sudhakar; Coupe, Kevin J.; Tucker, Jeffrey J.; Criswell, Allen R.; Buckle, Rosemary; Rechter, Alan Jeffrey; Sheth, Dhiren Shaskikant; Urquart, Brad; Trotscher, Thea; Anders, Mark J.; Kowalski, Joseph M.; Fineberg, Marc S.; Bone, Lawrence B.; Phillips, Matthew J.; Rohrbacher, Bernard; Stegemann, Philip; Mihalko, William M.; Buyea, Cathy; Augustine, Stephen J.; Jackson, William Thomas; Solis, Gregory; Ero, Sunday U.; Segina, Daniel N.; Berrey, Hudson B.; Agnew, Samuel G.; Fitzpatrick, Michael; Campbell, Lakina C.; Derting, Lynn; McAdams, June; Goslings, J. Carel; Ponsen, Kees Jan; Luitse, Jan; Kloen, Peter; Joosse, Pieter; Winkelhagen, Jasper; Duivenvoorden, Raphaël; Teague, David C.; Davey, Joseph; Sullivan, J. Andy; Ertl, William J. J.; Puckett, Timothy A.; Pasque, Charles B.; Tompkins, John F.; Gruel, Curtis R.; Kammerlocher, Paul; Lehman, Thomas P.; Puffinbarger, William R.; Carl, Kathy L.; Weber, Donald W.; Jomha, Nadr M.; Goplen, Gordon R.; Masson, Edward; Beaupre, Lauren A.; Greaves, Karen E.; Schaump, Lori N.; Jeray, Kyle J.; Goetz, David R.; Westberry, Davd E.; Broderick, J. Scott; Moon, Bryan S.; Tanner, Stephanie L.; Powell, James N.; Buckley, Richard E.; Elves, Leslie; Connolly, Stephen; Abraham, Edward P.; Eastwood, Donna; Steele, Trudy; Ellis, Thomas; Herzberg, Alex; Brown, George A.; Crawford, Dennis E.; Hart, Robert; Hayden, James; Orfaly, Robert M.; Vigland, Theodore; Vivekaraj, Maharani; Bundy, Gina L.; Miclau, Theodore; Matityahu, Amir; Coughlin, R. Richard; Kandemir, Utku; McClellan, R. Trigg; Lin, Cindy Hsin-Hua; Karges, David; Cramer, Kathryn; Watson, J. Tracy; Moed, Berton; Scott, Barbara; Beck, Dennis J.; Orth, Carolyn; Puskas, David; Clark, Russell; Jones, Jennifer; Egol, Kenneth A.; Paksima, Nader; France, Monet; Wai, Eugene K.; Johnson, Garth; Wilkinson, Ross; Gruszczynski, Adam T.; Vexler, Liisa

    2013-01-01

    Inadequate sample size and power in randomized trials can result in misleading findings. This study demonstrates the effect of sample size in a large clinical trial by evaluating the results of the Study to Prospectively evaluate Reamed Intramedullary Nails in Patients with Tibial fractures (SPRINT)

  5. A New Taxon of Basal Ceratopsian from China and the Early Evolution of Ceratopsia

    OpenAIRE

    Fenglu Han; Catherine A Forster; Clark, James M.; Xing Xu

    2015-01-01

    Ceratopsia is one of the best studied herbivorous ornithischian clades, but the early evolution of Ceratopsia, including the placement of Psittacosaurus, is still controversial and unclear. Here, we report a second basal ceratopsian, Hualianceratops wucaiwanensis gen. et sp. nov., from the Upper Jurassic (Oxfordian) Shishugou Formation of the Junggar Basin, northwestern China. This new taxon is characterized by a prominent caudodorsal process on the subtemporal ramus of the jugal, a robust qu...

  6. Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms

    Directory of Open Access Journals (Sweden)

    Hilu Khidir W

    2009-03-01

    Full Text Available Abstract Background Phylogenetic analyses of angiosperm relationships have used only a small percentage of available sequence data, but phylogenetic data matrices often can be augmented with existing data, especially if one allows missing characters. We explore the effects on phylogenetic analyses of adding 378 matK sequences and 240 26S rDNA sequences to the complete 3-gene, 567-taxon angiosperm phylogenetic matrix of Soltis et al. Results We performed maximum likelihood bootstrap analyses of the complete, 3-gene 567-taxon data matrix and the incomplete, 5-gene 567-taxon data matrix. Although the 5-gene matrix has more missing data (27.5% than the 3-gene data matrix (2.9%, the 5-gene analysis resulted in higher levels of bootstrap support. Within the 567-taxon tree, the increase in support is most evident for relationships among the 170 taxa for which both matK and 26S rDNA sequences were added, and there is little gain in support for relationships among the 119 taxa having neither matK nor 26S rDNA sequences. The 5-gene analysis also places the enigmatic Hydrostachys in Lamiales (BS = 97% rather than in Cornales (BS = 100% in 3-gene analysis. The placement of Hydrostachys in Lamiales is unprecedented in molecular analyses, but it is consistent with embryological and morphological data. Conclusion Adding available, and often incomplete, sets of sequences to existing data sets can be a fast and inexpensive way to increase support for phylogenetic relationships and produce novel and credible new phylogenetic hypotheses.

  7. Technical Note : Evaluation of between-sample memory effects in the analysis of ?2H and ?18O of water samples measured by laser spectroscopes

    NARCIS (Netherlands)

    Penna, D.; Stenni, B.; Sanda, M.; Wrede, S.; Bogaard, T.A.; Michelini, M.; Fischer, B.M.C.; Gobbi, A.; Mantese, N.; Zuecco, G.; Borga, M.; Bonazza, M.; Sobotkova, M.; Cejkova, B.; Wassenaar, L.I.

    2012-01-01

    This study evaluated between-sample memory in isotopic measurements of ?2H and ?18O in water samples by laser spectroscopy. Ten isotopically depleted water samples spanning a broad range of oxygen and hydrogen isotopic compositions were measured by three generations of offaxis integrated cavity

  8. Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.

    Science.gov (United States)

    Bowler, Matthew W; Guijarro, Matias; Petitdemange, Sebastien; Baker, Isabel; Svensson, Olof; Burghammer, Manfred; Mueller-Dieckmann, Christoph; Gordon, Elspeth J; Flot, David; McSweeney, Sean M; Leonard, Gordon A

    2010-08-01

    Crystals of biological macromolecules often exhibit considerable inter-crystal and intra-crystal variation in diffraction quality. This requires the evaluation of many samples prior to data collection, a practice that is already widespread in macromolecular crystallography. As structural biologists move towards tackling ever more ambitious projects, new automated methods of sample evaluation will become crucial to the success of many projects, as will the availability of synchrotron-based facilities optimized for high-throughput evaluation of the diffraction characteristics of samples. Here, two examples of the types of advanced sample evaluation that will be required are presented: searching within a sample-containing loop for microcrystals using an X-ray beam of 5 microm diameter and selecting the most ordered regions of relatively large crystals using X-ray beams of 5-50 microm in diameter. A graphical user interface developed to assist with these screening methods is also presented. For the case in which the diffraction quality of a relatively large crystal is probed using a microbeam, the usefulness and implications of mapping diffraction-quality heterogeneity (diffraction cartography) are discussed. The implementation of these techniques in the context of planned upgrades to the ESRF's structural biology beamlines is also presented.

  9. Characterization of specimens obtained by different sampling methods for evaluation of periodontal bacteria.

    Science.gov (United States)

    Okada, Ayako; Sogabe, Kaoru; Takeuchi, Hiroaki; Okamoto, Masaaki; Nomura, Yoshiaki; Hanada, Nobuhiro

    2017-11-17

    Quantitative analysis of periodontal bacteria is considered useful for clinical diagnosis, evaluation and assessment of the risk of periodontal disease. The purpose of this study was to compare the effectiveness of sampling of saliva, supragingival and subgingival plaque for evaluation of periodontal bacteria. From each of 12 subjects, i) subgingival plaque was collected from the deepest pocket using a sterile paper point, ii) stimulated whole saliva was collected after chewing gum, and iii) supragingival plaque was collected using a tooth brush. These samples were sent to the medical examination laboratory for quantitative analysis of the counts of three periodontal bacterial species: Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. The proportions of these bacteria in subgingival plaque were higher than those in saliva or supragingival plaque, but lower in subgingival plaque than in saliva or supragingival plaque. In several cases, periodontal bacteria were below the levels of detection in subgingival plaque. We concluded that samples taken from subgingival plaque may be more useful for evaluating the proportion of periodontal bacteria in deep pockets than is the case for other samples. Therefore, for evaluation of periodontal bacteria, clinicians should consider the characteristics of the specimens obtained using different sampling methods.

  10. Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

    Directory of Open Access Journals (Sweden)

    Mungall Christopher J

    2010-10-01

    Full Text Available Abstract Background The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation. Results We have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology. Conclusions Detection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at https://sourceforge.net/tracker/?atid=605890&group_id=36855.

  11. Evaluating leaf litter beetle data sampled by Winkler extraction from Atlantic forest sites in southern Brazil

    Directory of Open Access Journals (Sweden)

    Philipp Werner Hopp

    2011-06-01

    Full Text Available Evaluating leaf litter beetle data sampled by Winkler extraction from Atlantic forest sites in southern Brazil. To evaluate the reliability of data obtained by Winkler extraction in Atlantic forest sites in southern Brazil, we studied litter beetle assemblages in secondary forests (5 to 55 years after abandonment and old-growth forests at two seasonally different points in time. For all regeneration stages, species density and abundance were lower in April compared to August; but, assemblage composition of the corresponding forest stages was similar in both months. We suggest that sampling of small litter inhabiting beetles at different points in time using the Winkler technique reveals identical ecological patterns, which are more likely to be influenced by sample incompleteness than by differences in their assemblage composition. A strong relationship between litter quantity and beetle occurrences indicates the importance of this variable for the temporal species density pattern. Additionally, the sampled beetle material was compared with beetle data obtained with pitfall traps in one old-growth forest. Over 60% of the focal species captured with pitfall traps were also sampled by Winkler extraction in different forest stages. Few beetles with a body size too large to be sampled by Winkler extraction were only sampled with pitfall traps. This indicates that the local litter beetle fauna is dominated by small species. Hence, being aware of the exclusion of large beetles and beetle species occurring during the wet season, the Winkler method reveals a reliable picture of the local leaf litter beetle community.

  12. Evaluation of Primary Immunization Coverage of Infants Under Universal Immunization Programme in an Urban Area of Bangalore City Using Cluster Sampling and Lot Quality Assurance Sampling Techniques

    Science.gov (United States)

    K, Punith; K, Lalitha; G, Suman; BS, Pradeep; Kumar K, Jayanth

    2008-01-01

    Research Question: Is LQAS technique better than cluster sampling technique in terms of resources to evaluate the immunization coverage in an urban area? Objective: To assess and compare the lot quality assurance sampling against cluster sampling in the evaluation of primary immunization coverage. Study Design: Population-based cross-sectional study. Study Setting: Areas under Mathikere Urban Health Center. Study Subjects: Children aged 12 months to 23 months. Sample Size: 220 in cluster sampling, 76 in lot quality assurance sampling. Statistical Analysis: Percentages and Proportions, Chi square Test. Results: (1) Using cluster sampling, the percentage of completely immunized, partially immunized and unimmunized children were 84.09%, 14.09% and 1.82%, respectively. With lot quality assurance sampling, it was 92.11%, 6.58% and 1.31%, respectively. (2) Immunization coverage levels as evaluated by cluster sampling technique were not statistically different from the coverage value as obtained by lot quality assurance sampling techniques. Considering the time and resources required, it was found that lot quality assurance sampling is a better technique in evaluating the primary immunization coverage in urban area. PMID:19876474

  13. Tapentadol abuse potential: a postmarketing evaluation using a sample of individuals evaluated for substance abuse treatment.

    Science.gov (United States)

    Butler, Stephen F; McNaughton, Emily C; Black, Ryan A

    2015-01-01

    Abuse of prescription opioid pain relievers continues to be a serious public health concern. In contrast to opioids such as oxycodone or morphine, tapentadol, a prescription analgesic, has two mechanisms of action: μ-opioid receptor agonism and norepinephrine reuptake inhibition. As a result of differences in its receptor pharmacology, there may be differences in its abuse profile. As an initial step toward testing this hypothesis, we present a postmarketing examination of tapentadol's abuse liability relative to comparators. A sentinel sample of 113,914 individuals assessed for substance abuse treatment as part of the NAVIPPRO ASI-MV(®) surveillance system at 624 facilities in 38 states from January 2011 to September 2012 was examined for prevalence and prescription-adjusted prevalence of past 30-day abuse of tapentadol as a compound and its immediate-release (IR) and extended-release (ER) formulations with oxymorphone, hydromorphone, hydrocodone, morphine, fentanyl, oxycodone, tramadol, and buprenorphine as comparators. Tapentadol abuse was reported significantly less often (P Tapentadol IR abuse prevalence was significantly lower than all comparators except fentanyl IR, which had the next lowest unadjusted abuse prevalence. Prevalence of tapentadol ER abuse was lower than comparators except hydromorphone ER. Low prescription-adjusted estimates were observed for tapentadol as a compound as well as its IR and ER formulations, which were among the lowest observed and the lowest of the Schedule II comparators. Prescription-adjusted risk for tapentadol ER was less than comparators except hydromorphone ER (P = 0.06). Tapentadol abuse was seen infrequently in this study and, on a prescription basis, was less likely to be abused than most of the examined Schedule II analgesics. Wiley Periodicals, Inc.

  14. WOODSTOVE EMISSION SAMPLING METHODS COMPARABILITY ANALYSIS AND IN-SITU EVALUATION OF NEW TECHNOLOGY WOODSTOVES

    Science.gov (United States)

    This report compares simultaneous results from three woodstove sampling methods and evaluates particulate emission rates of conventional and Oregon-certified catalytic and noncatalytic woodstoves in six Portland, OR, houses. EPA Methods 5G and 5H and the field emission sampler (A...

  15. Multi-Factor Policy Evaluation and Selection in the One-Sample Situation

    NARCIS (Netherlands)

    C.M. Chen (Chien-Ming)

    2008-01-01

    textabstractFirms nowadays need to make decisions with fast information obsolesce. In this paper I deal with one class of decision problems in this situation, called the “one-sample” problems: we have finite options and one sample of the multiple criteria with which we use to evaluate those options.

  16. Performance Evaluation and Parameter Optimization of Wavelength Division Multiplexing Networks with Importance Sampling Techniques

    NARCIS (Netherlands)

    Remondo Bueno, D.; Srinivasan, R.; Nicola, V.F.; van Etten, Wim; Tattje, H.E.P.

    1998-01-01

    In this paper new adaptive importance sampling techniques are applied to the performance evaluation and parameter optimization of wavelength division multiplexing (WDM) network impaired by crosstalk in an optical cross-connect. Worst-case analysis is carried out including all the beat noise terms

  17. Evaluation of HDPE water sample bottles and PVC sampler tubing used in herbicide dissipation studies.

    Science.gov (United States)

    J. B. Fischer; J. L. Michael; H. L. Gibbs

    2009-01-01

    The recovery of six herbicides (triclopyr, triclopyr ester, sulfometuron methyl, metsulfuron methyl, imazapyr, and hexazinone) was evaluated in two stream water samples, one from Weogufka Creek in the Alabama Piedmont and one from a stagnant stream in the Escambia Experimental Forest near Florida. Simulated field study conditions were...

  18. Evaluation of the Bacterial Status of Water Samples at Umudike Abia ...

    African Journals Online (AJOL)

    The bacteriological status of different water samples (borehole, sachet, bottled, stream and rain) from Umudike, Abia State, Nigeria and its environs was evaluated. The total viable count (TVC) for the borehole I (MOUAU) and borehole II (Umuwaya) were 14.7x102 and 15.7x102 cfu/ml respectively, while the sachet water ...

  19. Phytochemical analysis and biological evaluation of selected African propolis samples from Cameroon and Congo

    NARCIS (Netherlands)

    Papachroni, D.; Graikou, K.; Kosalec, I.; Damianakos, H.; Ingram, V.J.; Chinou, I.

    2015-01-01

    The objective of this study was the chemical analysis of four selected samples of African propolis (Congo and Cameroon) and their biological evaluation. Twenty-one secondary metabolites belonging to four different chemical groups were isolated from the 70% ethanolic extracts of propolis and their

  20. [Sample size calculation in clinical post-marketing evaluation of traditional Chinese medicine].

    Science.gov (United States)

    Fu, Yingkun; Xie, Yanming

    2011-10-01

    In recent years, as the Chinese government and people pay more attention on the post-marketing research of Chinese Medicine, part of traditional Chinese medicine breed has or is about to begin after the listing of post-marketing evaluation study. In the post-marketing evaluation design, sample size calculation plays a decisive role. It not only ensures the accuracy and reliability of post-marketing evaluation. but also assures that the intended trials will have a desired power for correctly detecting a clinically meaningful difference of different medicine under study if such a difference truly exists. Up to now, there is no systemic method of sample size calculation in view of the traditional Chinese medicine. In this paper, according to the basic method of sample size calculation and the characteristic of the traditional Chinese medicine clinical evaluation, the sample size calculation methods of the Chinese medicine efficacy and safety are discussed respectively. We hope the paper would be beneficial to medical researchers, and pharmaceutical scientists who are engaged in the areas of Chinese medicine research.

  1. Clinical evaluation of Statstrip(R) Lactate for use in fetal scalp blood sampling

    NARCIS (Netherlands)

    Heinis, A.M.F.; Dillen, J. van; Oosting, J.D.; Rhose, S.; Vandenbussche, F.P.; Drongelen, J. van

    2017-01-01

    INTRODUCTION: Point-of-care testing of fetal scalp blood lactate is used as an alternative to pH analysis in fetal scalp blood sampling (FBS) during labor. Lactate measurements are not standardized and values vary with each device used. The aim of this study was to evaluate StatStrip(R) Lactate

  2. Bottle Traps and Dipnetting: Evaluation of two Sampling Techniques for Assessing Macroinvertebrate Biodiversity in Depressional Wetlands.

    Science.gov (United States)

    Serieyssol, C. A.; Bouchard, R. W.; Sealock, A. W.; Rufer, M. M.; Chirhart, J.; Genet, J.; Ferrington, L. C.

    2005-05-01

    Dipnet (DN) sampling is routinely employed for macroinvertebrate bioassessments, however it has been shown that some taxa are more effectively sampled with activity traps, commonly called Bottle Traps (BT). In 2001, the Minnesota Pollution Control Agency used both DN and BT sampling in nine depressional wetlands in the North Central Hardwood Forest Ecoregion to evaluate macroinvertebrate biodiversity for the purpose of assessing water quality and developing biological criteria. Both methods, consisting of five bottle trap samples and two dip net samples per wetland, were collected from each of two sites in each wetland. To determine the performance of each method in documenting biodiversity, we compared taxa and their abundances by wetland, for each type of sample. DN sampling was more effective, with 44 of 140 macroinvertebrate taxa only identified from DN, compared to 14 only from BT. By contrast, BT more effectively collected leeches and beetles, especially active swimmers such as Tropisternus and several genera of Dytiscidae. However, taxa richness patterns for BT and DN were not strongly correlated. Consequently, we conclude these two sampling methods complement each other, providing a better overall picture of macroinvertebrate biodiversity, and should be used jointly when investigating macroinvertebrate biodiversity in depressional wetlands.

  3. STATISTICAL EVALUATION OF SMALL SCALE MIXING DEMONSTRATION SAMPLING AND BATCH TRANSFER PERFORMANCE - 12093

    Energy Technology Data Exchange (ETDEWEB)

    GREER DA; THIEN MG

    2012-01-12

    The ability to effectively mix, sample, certify, and deliver consistent batches of High Level Waste (HLW) feed from the Hanford Double Shell Tanks (DST) to the Waste Treatment and Immobilization Plant (WTP) presents a significant mission risk with potential to impact mission length and the quantity of HLW glass produced. DOE's Tank Operations Contractor, Washington River Protection Solutions (WRPS) has previously presented the results of mixing performance in two different sizes of small scale DSTs to support scale up estimates of full scale DST mixing performance. Currently, sufficient sampling of DSTs is one of the largest programmatic risks that could prevent timely delivery of high level waste to the WTP. WRPS has performed small scale mixing and sampling demonstrations to study the ability to sufficiently sample the tanks. The statistical evaluation of the demonstration results which lead to the conclusion that the two scales of small DST are behaving similarly and that full scale performance is predictable will be presented. This work is essential to reduce the risk of requiring a new dedicated feed sampling facility and will guide future optimization work to ensure the waste feed delivery mission will be accomplished successfully. This paper will focus on the analytical data collected from mixing, sampling, and batch transfer testing from the small scale mixing demonstration tanks and how those data are being interpreted to begin to understand the relationship between samples taken prior to transfer and samples from the subsequent batches transferred. An overview of the types of data collected and examples of typical raw data will be provided. The paper will then discuss the processing and manipulation of the data which is necessary to begin evaluating sampling and batch transfer performance. This discussion will also include the evaluation of the analytical measurement capability with regard to the simulant material used in the demonstration tests. The

  4. Evaluating the suitability of different environmental samples for tracing atmospheric pollution in industrial areas.

    Science.gov (United States)

    Francová, Anna; Chrastný, Vladislav; Šillerová, Hana; Vítková, Martina; Kocourková, Jana; Komárek, Michael

    2017-01-01

    Samples of lichens, snow and particulate matter (PM10, 24 h) are used for the source identification of air pollution in the heavily industrialized region of Ostrava, Upper Silesia, Czech Republic. An integrated approach that uses different environmental samples for metal concentration and Pb isotope analyses was applied. The broad range of isotope ratios in the samples indicates a combination of different pollution sources, the strongest among them being the metallurgical industry, bituminous coal combustion and traffic. Snow samples are proven as the most relevant indicator for tracing metal(loid)s and recent local contamination in the atmosphere. Lichens can be successfully used as tracers of the long-term activity of local and remote sources of contamination. The combination of PM10 with snow can provide very useful information for evaluation of current pollution sources. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. A contribution to reduce sampling variability in the evaluation of deoxynivalenol contamination of organic wheat grain.

    Science.gov (United States)

    Hallier, Arnaud; Celette, Florian; Coutarel, Julie; David, Christophe

    2013-01-01

    Fusarium head blight caused by different varieties of Fusarium species is one of the major serious worldwide diseases found in wheat production. It is therefore important to be able to quantify the deoxynivalenol concentration in wheat. Unfortunately, in mycotoxin quantification, due to the uneven distribution of mycotoxins within the initial lot, it is difficult, or even impossible, to obtain a truly representative analytical sample. In previous work we showed that the sampling step most responsible for variability was grain sampling. In this paper, it is more particularly the step scaling down from a laboratory sample of some kilograms to an analytical sample of a few grams that is investigated. The naturally contaminated wheat lot was obtained from an organic field located in the southeast of France (Rhône-Alpes) from the year 2008-2009 cropping season. The deoxynivalenol level was found to be 50.6 ± 2.3 ng g⁻¹. Deoxynivalenol was extracted with a acetonitrile-water mix and quantified by gas chromatography-electron capture detection (GC-ECD). Three different grain sampling techniques were tested to obtain analytical samples: a technique based on manually homogenisation and division, a second technique based on the use of a rotating shaker and a third on the use of compressed air. Both the rotating shaker and the compressed air techniques enabled a homogeneous laboratory sample to be obtained, from which representative analytical samples could be taken. Moreover, the techniques did away with many repetitions and grinding. This study, therefore, contributes to sampling variability reduction in the evaluation of deoxynivalenol contamination of organic wheat grain, and then, at a reasonable cost.

  6. Evaluation of Legionella Air Contamination in Healthcare Facilities by Different Sampling Methods: An Italian Multicenter Study

    Directory of Open Access Journals (Sweden)

    Maria Teresa Montagna

    2017-06-01

    Full Text Available Healthcare facilities (HF represent an at-risk environment for legionellosis transmission occurring after inhalation of contaminated aerosols. In general, the control of water is preferred to that of air because, to date, there are no standardized sampling protocols. Legionella air contamination was investigated in the bathrooms of 11 HF by active sampling (Surface Air System and Coriolis®μ and passive sampling using settling plates. During the 8-hour sampling, hot tap water was sampled three times. All air samples were evaluated using culture-based methods, whereas liquid samples collected using the Coriolis®μ were also analyzed by real-time PCR. Legionella presence in the air and water was then compared by sequence-based typing (SBT methods. Air contamination was found in four HF (36.4% by at least one of the culturable methods. The culturable investigation by Coriolis®μ did not yield Legionella in any enrolled HF. However, molecular investigation using Coriolis®μ resulted in eight HF testing positive for Legionella in the air. Comparison of Legionella air and water contamination indicated that Legionella water concentration could be predictive of its presence in the air. Furthermore, a molecular study of 12 L. pneumophila strains confirmed a match between the Legionella strains from air and water samples by SBT for three out of four HF that tested positive for Legionella by at least one of the culturable methods. Overall, our study shows that Legionella air detection cannot replace water sampling because the absence of microorganisms from the air does not necessarily represent their absence from water; nevertheless, air sampling may provide useful information for risk assessment. The liquid impingement technique appears to have the greatest capacity for collecting airborne Legionella if combined with molecular investigations.

  7. Evaluation of Legionella Air Contamination in Healthcare Facilities by Different Sampling Methods: An Italian Multicenter Study.

    Science.gov (United States)

    Montagna, Maria Teresa; De Giglio, Osvalda; Cristina, Maria Luisa; Napoli, Christian; Pacifico, Claudia; Agodi, Antonella; Baldovin, Tatjana; Casini, Beatrice; Coniglio, Maria Anna; D'Errico, Marcello Mario; Delia, Santi Antonino; Deriu, Maria Grazia; Guida, Marco; Laganà, Pasqualina; Liguori, Giorgio; Moro, Matteo; Mura, Ida; Pennino, Francesca; Privitera, Gaetano; Romano Spica, Vincenzo; Sembeni, Silvia; Spagnolo, Anna Maria; Tardivo, Stefano; Torre, Ida; Valeriani, Federica; Albertini, Roberto; Pasquarella, Cesira

    2017-06-22

    Healthcare facilities (HF) represent an at-risk environment for legionellosis transmission occurring after inhalation of contaminated aerosols. In general, the control of water is preferred to that of air because, to date, there are no standardized sampling protocols. Legionella air contamination was investigated in the bathrooms of 11 HF by active sampling (Surface Air System and Coriolis(®)μ) and passive sampling using settling plates. During the 8-hour sampling, hot tap water was sampled three times. All air samples were evaluated using culture-based methods, whereas liquid samples collected using the Coriolis(®)μ were also analyzed by real-time PCR. Legionella presence in the air and water was then compared by sequence-based typing (SBT) methods. Air contamination was found in four HF (36.4%) by at least one of the culturable methods. The culturable investigation by Coriolis(®)μ did not yield Legionella in any enrolled HF. However, molecular investigation using Coriolis(®)μ resulted in eight HF testing positive for Legionella in the air. Comparison of Legionella air and water contamination indicated that Legionella water concentration could be predictive of its presence in the air. Furthermore, a molecular study of 12 L. pneumophila strains confirmed a match between the Legionella strains from air and water samples by SBT for three out of four HF that tested positive for Legionella by at least one of the culturable methods. Overall, our study shows that Legionella air detection cannot replace water sampling because the absence of microorganisms from the air does not necessarily represent their absence from water; nevertheless, air sampling may provide useful information for risk assessment. The liquid impingement technique appears to have the greatest capacity for collecting airborne Legionella if combined with molecular investigations.

  8. Preservation of urine samples for metabolic evaluation of stone-forming patients.

    Science.gov (United States)

    Ferraz, Renato Ribeiro Nogueira; Baxmann, Alessandra Calábria; Ferreira, Larissa Gorayb; Nishiura, José Luiz; Siliano, Priscila Reina; Gomes, Samirah Abreu; Moreira, Silvia Regina Silva; Heilberg, Ita Pfeferman

    2006-10-01

    Metabolic evaluation of stone-forming (SF) patients is based on the determination of calcium, oxalate, citrate, uric acid and other parameters in 24-h urine samples under a random diet. A reliable measurement of urinary oxalate requires the collection of urine in a receptacle containing acid preservative. However, urinary uric acid cannot be determined in the same sample under this condition. Therefore, we tested the hypothesis that the addition of preservatives (acid or alkali) after urine collection would not modify the results of those lithogenic parameters. Thirty-four healthy subjects (HS) were submitted to two non-consecutive collections of 24-h urine. The first sample was collected in a receptacle containing hydrochloric acid (HCl 6 N) and the second in a dry plastic container, with HCl being added as soon as the urine sample was received at the laboratory. Additionally, 34 HS and 34 SF patients collected a spot urine sample that was divided into four aliquots, one containing HCl, another containing sodium bicarbonate (NaHCO(3 )5 g/l), and two others in which these two preservative agents were added 24 h later. Urinary oxalate, calcium, magnesium, citrate, creatinine and uric acid were determined. Urinary parameters were also evaluated in the presence of calcium oxalate or uric acid crystals. Mean values of all urinary parameters obtained from previously acidified 24-h urine samples did not differ from those where acid was added after urine collection. The same was true for spot urine samples, with the exception of urinary citrate that presented a slight albeit significant change of 5.9% between samples in HS and 3.1% in SF. Uric acid was also not different between pre- and post-alkalinized spot urine samples. The presence of crystals did not alter these results. We concluded that post-delivery acidification or alkalinization of urine samples does not modify the measured levels of urinary oxalate, calcium, magnesium, creatinine and uric acid, and that the

  9. Sampling pig farms at the abattoir in a cross-sectional study − Evaluation of a sampling method

    DEFF Research Database (Denmark)

    Birkegård, Anna Camilla; Hisham Beshara Halasa, Tariq; Toft, Nils

    2017-01-01

    A cross-sectional study design is relatively inexpensive, fast and easy to conduct when compared to other study designs. Careful planning is essential to obtaining a representative sample of the population, and the recommended approach is to use simple random sampling from an exhaustive list of u...

  10. Estimation after classification using lot quality assurance sampling: corrections for curtailed sampling with application to evaluating polio vaccination campaigns.

    Science.gov (United States)

    Olives, Casey; Valadez, Joseph J; Pagano, Marcello

    2014-03-01

    To assess the bias incurred when curtailment of Lot Quality Assurance Sampling (LQAS) is ignored, to present unbiased estimators, to consider the impact of cluster sampling by simulation and to apply our method to published polio immunization data from Nigeria. We present estimators of coverage when using two kinds of curtailed LQAS strategies: semicurtailed and curtailed. We study the proposed estimators with independent and clustered data using three field-tested LQAS designs for assessing polio vaccination coverage, with samples of size 60 and decision rules of 9, 21 and 33, and compare them to biased maximum likelihood estimators. Lastly, we present estimates of polio vaccination coverage from previously published data in 20 local government authorities (LGAs) from five Nigerian states. Simulations illustrate substantial bias if one ignores the curtailed sampling design. Proposed estimators show no bias. Clustering does not affect the bias of these estimators. Across simulations, standard errors show signs of inflation as clustering increases. Neither sampling strategy nor LQAS design influences estimates of polio vaccination coverage in 20 Nigerian LGAs. When coverage is low, semicurtailed LQAS strategies considerably reduces the sample size required to make a decision. Curtailed LQAS designs further reduce the sample size when coverage is high. Results presented dispel the misconception that curtailed LQAS data are unsuitable for estimation. These findings augment the utility of LQAS as a tool for monitoring vaccination efforts by demonstrating that unbiased estimation using curtailed designs is not only possible but these designs also reduce the sample size. © 2014 John Wiley & Sons Ltd.

  11. Evaluation of denuder sampling for a mixture of three common gaseous diisocyanates.

    Science.gov (United States)

    Nordqvist, Y; Nilsson, U; Colmsjö, A

    2003-03-01

    A denuder sampler has been evaluated for a mixture of three gaseous diisocyanates, i.e. toluene diisocyanate (TDI), hexamethylene diisocyanate (HDI) and isophorone diisocyanate (IPDI). Sampling was performed at a total concentration of diisocyanates close to the Swedish occupational exposure limit (OEL), which is 10 ppbv (69-92 microg m(-3)), for a 5-min period. The denuder tube was coated with a chemosorptive stationary phase consisting of SE-30 (polydimethylsiloxane) and the derivatising reagent dibutylamine (DBA). It was shown that the denuder has a collection efficiency for HDI and IPDI comparable to that of an impinger method, while sampling of TDI resulted in an 8% lower concentration. Both short-term (15 min) and long-term (8 h) sampling periods were shown to yield reproducible results. For 8-h measurements, a sampling flow rate of 5 mL min(-1) was shown to be suitable for the investigated concentration range, i.e. 10-100 ppbv (69-921 microg m(-3)). A flow rate of 25 mL min(-1) or higher resulted in breakthrough after 8 h due to chromatography of the compounds in the adsorbent. The limit of detection (LOD) for the air sampling method is nearly 500 times lower than the OEL. The denuder tubes can be prepared at least 10 days prior to sampling without degradation of performance. Furthermore, they can be stored up to 6 days in a freezer after sampling without significant loss of analytes.

  12. Performance Evaluation of Commercial Dengue Diagnostic Tests for Early Detection of Dengue in Clinical Samples

    Directory of Open Access Journals (Sweden)

    Tuan Nur Akmalina Mat Jusoh

    2017-01-01

    Full Text Available The shattering rise in dengue virus infections globally has created a need for an accurate and validated rapid diagnostic test for this virus. Rapid diagnostic test (RDT and reverse transcription-polymerase chain reaction (RT-PCR diagnostic detection are useful tools for diagnosis of early dengue infection. We prospectively evaluated the diagnostic performance of nonstructural 1 (NS1 RDT and real-time RT-PCR diagnostic kits in 86 patient serum samples. Thirty-six samples were positive for dengue NS1 antigen while the remaining 50 were negative when tested with enzyme-linked immunosorbent assay (ELISA. Commercially available RDTs for NS1 detection, RTK ProDetect™, and SD Bioline showed high sensitivity of 94% and 89%, respectively, compared with ELISA. GenoAmp® Trioplex Real-Time RT-PCR and RealStar® Dengue RT-PCR tests presented a comparable kappa agreement with 0.722. The result obtained from GenoAmp® Real-Time RT-PCR Dengue test showed that 14 samples harbored dengue virus type 1 (DENV-1, 8 samples harbored DENV-2, 2 samples harbored DENV-3, and 1 sample harbored DENV-4. 1 sample had a double infection with DENV-1 and DENV-2. The NS1 RDTs and real-time RT-PCR tests were found to be a useful diagnostic for early and rapid diagnosis of acute dengue and an excellent surveillance tool in our battle against dengue.

  13. Diagnosing intramammary infections: evaluation of definitions based on a single milk sample.

    Science.gov (United States)

    Dohoo, I R; Smith, J; Andersen, S; Kelton, D F; Godden, S

    2011-01-01

    Criteria for diagnosing intramammary infections (IMI) have been debated for many years. Factors that may be considered in making a diagnosis include the organism of interest being found on culture, the number of colonies isolated, whether or not the organism was recovered in pure or mixed culture, and whether or not concurrent evidence of inflammation existed (often measured by somatic cell count). However, research using these criteria has been hampered by the lack of a "gold standard" test (i.e., a perfect test against which the criteria can be evaluated) and the need for very large data sets of culture results to have sufficient numbers of quarters with infections with a variety of organisms. This manuscript used 2 large data sets of culture results to evaluate several definitions (sets of criteria) for classifying a quarter as having, or not having an IMI by comparing the results from a single culture to a gold standard diagnosis based on a set of 3 milk samples. The first consisted of 38,376 milk samples from which 25,886 triplicate sets of milk samples taken 1 wk apart were extracted. The second consisted of 784 quarters that were classified as infected or not based on a set of 3 milk samples collected at 2-d intervals. From these quarters, a total of 3,136 additional samples were evaluated. A total of 12 definitions (named A to L) based on combinations of the number of colonies isolated, whether or not the organism was recovered in pure or mixed culture, and the somatic cell count were evaluated for each organism (or group of organisms) with sufficient data. The sensitivity (ability of a definition to detect IMI) and the specificity (Sp; ability of a definition to correctly classify noninfected quarters) were both computed. For all species, except Staphylococcus aureus, the sensitivity of all definitions was milk sample) isolated (definition A). With the exception of "any organism" and coagulase-negative staphylococci, all Sp estimates were over 94% in the

  14. Evaluation of wastewater contaminant transport in surface waters using verified Lagrangian sampling

    Science.gov (United States)

    Antweiler, Ronald C.; Writer, Jeffrey H.; Murphy, Sheila F.

    2014-01-01

    Contaminants released from wastewater treatment plants can persist in surface waters for substantial distances. Much research has gone into evaluating the fate and transport of these contaminants, but this work has often assumed constant flow from wastewater treatment plants. However, effluent discharge commonly varies widely over a 24-hour period, and this variation controls contaminant loading and can profoundly influence interpretations of environmental data. We show that methodologies relying on the normalization of downstream data to conservative elements can give spurious results, and should not be used unless it can be verified that the same parcel of water was sampled. Lagrangian sampling, which in theory samples the same water parcel as it moves downstream (the Lagrangian parcel), links hydrologic and chemical transformation processes so that the in-stream fate of wastewater contaminants can be quantitatively evaluated. However, precise Lagrangian sampling is difficult, and small deviations – such as missing the Lagrangian parcel by less than 1 h – can cause large differences in measured concentrations of all dissolved compounds at downstream sites, leading to erroneous conclusions regarding in-stream processes controlling the fate and transport of wastewater contaminants. Therefore, we have developed a method termed “verified Lagrangian” sampling, which can be used to determine if the Lagrangian parcel was actually sampled, and if it was not, a means for correcting the data to reflect the concentrations which would have been obtained had the Lagrangian parcel been sampled. To apply the method, it is necessary to have concentration data for a number of conservative constituents from the upstream, effluent, and downstream sites, along with upstream and effluent concentrations that are constant over the short-term (typically 2–4 h). These corrections can subsequently be applied to all data, including non-conservative constituents. Finally, we

  15. Microbiological evaluation of milk samples positive to California Mastitis Test in dairy buffalo cows (Buballus bubalis

    Directory of Open Access Journals (Sweden)

    D.J. Sturion

    2010-02-01

    Full Text Available In order to observe the microbiological status of CMT positive samples, 734 apparently health mammary quarters from buffalo cows were submitted to physical evaluation, strip cup test and CMT. After milk samples inoculation in 10% ovine blood agar base media and in MacConkey agar and incubation under aerobic condition for 72 hours at 37oC, identification was proceeded. According to CMT, 227 quarters (30,93% were positive, among them 73 (32,16% presented 1+ reaction, 53 (23,35% were 2+ and 101 (44,49% were 3+. Microbiological exams of such samples were positive in 147 (64,76% out of 227 CMT positive samples and among the remaining 72 (31,72% were negative and 8 (3,52 were contaminated. In the 147 microbiological positive samples 204 bacteria were found in pure or associated growth and the most frequent agents were: Corynebacterium sp (59,25%; Staphylococcus sp (17,65% among which 86,11% were coagulase negative and 13,89% were coagulase positive; and Micrococcus sp (6,37%. The results revealed that, excluding the eight contaminated samples, 147 (67,12% quarters out of 219 CMT positive could be considered as bacteria-carrier and that even in a smaller percentage false-positive results can cause problems in a sanitary program for mastitis control in dairy buffalo cows.

  16. Analysis and evaluation of compounds from Cichorium intybus aromatic water trade market samples

    Directory of Open Access Journals (Sweden)

    A. Hosseini*

    2017-11-01

    Full Text Available Background and objectives: Cichorium intybus products are one of the best sellers in market Because of their effect on treatment of infection, poisoning, diabetes and allergy. This is the first study about Cichorium intybus market samplephytochemical compounds and the aim of this study was to define a method to recognize the original products. Methods: The sample compounds were extracted by liquid-liquid method and evaluated by GC-MS and compared with the references like Adams 2007. The obtained phytochemical data were analyzed with SPSS and classified by dendrogram method and was compared with the data earned from the standard sample. Results: Forty one compounds were detected. Carvacrol was available in all samples from 1.14 to 39.34%. Also, thymol was present in most of samples from 1.24 to 69.32%. Moreover, we understood that some compounds like pulegone, carvone, carvacrol and piperitenone could be detected in all samples mostly with different percentages. Some linear hydrocarbon was detected in this method along with some other unexpected compounds like cinnamaldehyde. Conclusion: Existence of some impure compounds like: pulegone, carvone, piperitenone and cinnamaldehyde in trade samples showed cleaning of container might not have been proper. Carvacrol and thymol are common compounds to define acceptable standard for Cichorium intybus aromatic water.

  17. Savoir-faire des populations locales des taxons du Jardin Botanique ...

    African Journals Online (AJOL)

    Objectif : En vu de connaître l'usage des espèces végétales du Jardin Botanique de Bingerville par les populations locales, diverses activités de recherche ont été réalisées. Méthodologies et résultats : Le recensement de la flore a été effectué et a permis d'enregistrer 419 taxons. A l'issue d'une enquête ethnobotanique ...

  18. Rediscovery of Jasminum parkeri Dunn, an endemic and endangered taxon from the western Himalaya, India

    Directory of Open Access Journals (Sweden)

    Lal Brij

    2014-06-01

    Full Text Available The present article deals with the rediscovery of Jasminum parkeri Dunn (Oleaceae collected from its type locality after a lapse of about 100 years. J. parkeri is a highly endangered and narrowly endemic taxon restricted to a small pocket in the remote mountain area of Chamba district, Himachal Pradesh in the western Himalaya, India. In order to facilitate identification of this species, the plant description along with a brief history of its discovery, affinity with the other taxa of Jasminum, ecological notes, and pictures are provided. Subsequently, possibility of cultivation of this species in ex-situ conditions is also discussed.

  19. The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees

    DEFF Research Database (Denmark)

    Sand, Andreas; Steel, Mike

    2013-01-01

    Evolutionary events such as incomplete lineage sorting and lateral gene transfers constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species tree. One particularly simple and efficient way to infer...... species trees from gene trees under such conditions is to combine three-taxon analyses for several genes using a majority vote approach. For incomplete lineage sorting this method is known to be statistically consistent; however, for lateral gene transfers it was recently shown that a zone...

  20. Primeros registros para Colombia de cuatro taxones de la familia Tyrannidae (Aves: Passeriformes)

    OpenAIRE

    Rojas R. Rosario; Piragua A. William; Stiles Hurd Frank Galfierd; McNish Thomas

    1997-01-01

    En esta comunicación presentamos datos sobre cuatro taxones de la familia Tyrannidae que representan registros nuevos para el territorio colombiano, todos respaldados con especímenes en la colección del Instituto de Ciencias Naturales (ICN). La mayoría de los registros son del campo petrolero de Caño Limón, a unos 55 km al occidente de la ciudad de Arauca, en la parte septentrional del Departamento de Arauca. Las características de este sitio y datos generales de su avifauna fueron presentado...

  1. Contemporary Models of Pediatric Obsessive Compulsive Disorder: An Evaluation with a Large Clinical Sample

    OpenAIRE

    De Nadai, Alessandro; Nagpal, Prianka S.; Piacentini, John; Peris, Tara S.; Geffken, Gary R.; Geller, Daniel A; Murphy, Tanya K.; Storch, Eric A.; Lewin, Adam B.

    2015-01-01

    We evaluated the construct validity of the Child Yale-Brown Obsessive Compulsive Scale (CYBOCS) in a large clinical sample (N=730) using confirmatory factor analysis. Results found inadequate fit for a priori models, though a model accounting for overlapping item content displayed good fit. Parallel obsessions/compulsions items may provide largely redundant information on the CYBOCS. Findings suggest modifying the CYBOCS to reduce burden on researchers, patients, and clinicians, and to more a...

  2. Evaluation of a PCR assay on overgrown environmental samples cultured for Mycobacterium avium subsp. paratuberculosis.

    Science.gov (United States)

    Arango-Sabogal, Juan C; Labrecque, Olivia; Paré, Julie; Fairbrother, Julie-Hélène; Roy, Jean-Philippe; Wellemans, Vincent; Fecteau, Gilles

    2016-11-01

    Culture of Mycobacterium avium subsp. paratuberculosis (MAP) is the definitive antemortem test method for paratuberculosis. Microbial overgrowth is a challenge for MAP culture, as it complicates, delays, and increases the cost of the process. Additionally, herd status determination is impeded when noninterpretable (NI) results are obtained. The performance of PCR is comparable to fecal culture, thus it may be a complementary detection tool to classify NI samples. Our study aimed to determine if MAP DNA can be identified by PCR performed on NI environmental samples and to evaluate the performance of PCR before and after the culture of these samples in liquid media. A total of 154 environmental samples (62 NI, 62 negative, and 30 positive) were analyzed by PCR before being incubated in an automated system. Growth was confirmed by acid-fast bacilli stain and then the same PCR method was again applied on incubated samples, regardless of culture and stain results. Change in MAP DNA after incubation was assessed by converting the PCR quantification cycle (Cq) values into fold change using the 2-ΔCq method (ΔCq = Cq after culture - Cq before culture). A total of 1.6% (standard error [SE] = 1.6) of the NI environmental samples had detectable MAP DNA. The PCR had a significantly better performance when applied after culture than before culture (p = 0.004). After culture, a 66-fold change (SE = 17.1) in MAP DNA was observed on average. Performing a PCR on NI samples improves MAP culturing. The PCR method used in our study is a reliable and consistent method to classify NI environmental samples. © 2016 The Author(s).

  3. [Design of standard voice sample text for subjective auditory perceptual evaluation of voice disorders].

    Science.gov (United States)

    Li, Jin-rang; Sun, Yan-yan; Xu, Wen

    2010-09-01

    To design a speech voice sample text with all phonemes in Mandarin for subjective auditory perceptual evaluation of voice disorders. The principles for design of a speech voice sample text are: The short text should include the 21 initials and 39 finals, this may cover all the phonemes in Mandarin. Also, the short text should have some meanings. A short text was made out. It had 155 Chinese words, and included 21 initials and 38 finals (the final, ê, was not included because it was rarely used in Mandarin). Also, the text covered 17 light tones and one "Erhua". The constituent ratios of the initials and finals presented in this short text were statistically similar as those in Mandarin according to the method of similarity of the sample and population (r = 0.742, P text were statistically not similar as those in Mandarin (r = 0.731, P > 0.05). A speech voice sample text with all phonemes in Mandarin was made out. The constituent ratios of the initials and finals presented in this short text are similar as those in Mandarin. Its value for subjective auditory perceptual evaluation of voice disorders need further study.

  4. Females' sampling strategy to comparatively evaluate prospective mates in the peacock blenny Salaria pavo

    Science.gov (United States)

    Locatello, Lisa; Rasotto, Maria B.

    2017-08-01

    Emerging evidence suggests the occurrence of comparative decision-making processes in mate choice, questioning the traditional idea of female choice based on rules of absolute preference. In such a scenario, females are expected to use a typical best-of- n sampling strategy, being able to recall previous sampled males based on memory of their quality and location. Accordingly, the quality of preferred mate is expected to be unrelated to both the number and the sequence of female visits. We found support for these predictions in the peacock blenny, Salaria pavo, a fish where females have the opportunity to evaluate the attractiveness of many males in a short time period and in a restricted spatial range. Indeed, even considering the variability in preference among females, most of them returned to previous sampled males for further evaluations; thus, the preferred male did not represent the last one in the sequence of visited males. Moreover, there was no relationship between the attractiveness of the preferred male and the number of further visits assigned to the other males. Our results suggest the occurrence of a best-of- n mate sampling strategy in the peacock blenny.

  5. Evaluation of Rectoanal Mucosal Swab Sampling for Molecular Detection of Enterohemorrhagic Escherichia coli in Beef Cattle.

    Science.gov (United States)

    Agga, Getahun E; Arthur, Terrance M; Hinkley, Susanne; Bosilevac, Joseph M

    2017-04-01

    Cattle are a primary reservoir of enterohemorrhagic Escherichia coli (EHEC), and contaminated beef products are a source of human infections. The U.S. Department of Agriculture Food Safety and Inspection Service declared seven EHEC serogroups (O26, O45, O103, O111, O121, O145, and O157) as adulterants in raw ground beef. Sampling a large number of animals for EHEC surveillance or evaluations of EHEC-focused preharvest interventions requires a convenient and robust sampling method. We evaluated the diagnostic performance of rectoanal mucosal swab (RAMS) for the detection of the top seven EHEC serogroups. Paired fecal grab (FG) and RAMS samples were collected from 176 beef cattle and tested using the NeoSEEK Shiga toxin-producing E. coli (STEC) confirmation method. The prevalence of virulence-associated genes (stx 1 , stx 2 , stx 2c , eae, and nleB) was higher in RAMS than in FG samples. The results of the two methods had poor agreement, as indicated by kappa statistics, for the detection of the seven serogroups. When FG and RAMS results were combined for comparison, RAMS was more sensitive than FG for the detection of serogroups O103 (82% versus 39%), O157 (75% versus 67%), and O45 (79% versus 73%) with similar sensitivity for the detection of serogroup O145 (67%). Serogroups O111 and O121 were detected from one and two samples, respectively, by FG and were not detected by RAMS. Serogroup O26 was not detected with either method. RAMS appears to be equivalent or superior to FG sampling for detection of the top seven EHEC serogroups in the feces of beef cattle with the NeoSEEK STEC confirmation test.

  6. Spatial scale and cross-taxon congruence of terrestrial vertebrate and vascular plant species richness in China.

    Science.gov (United States)

    Qian, Hong; Kissling, W Daniel

    2010-04-01

    In ecology and biogeography it is often recognized that the species richness of different groups of organisms is spatially congruent (and thus positively correlated). However, ecological phenomena are often scale dependent and can change with spatial scale (i.e., grain size and extent). Because species richness gradients are also correlated with environmental gradients and plant species richness is thought to influence animal species richness, the relative roles of environment and plant richness in influencing cross-taxon congruence of animal richness at different spatial scales remain poorly explored. In this study, we examine the spatial concordance in species richness among terrestrial vertebrates and vascular plants at two spatial grain sizes (local and regional) across China. We hypothesize that (H1) cross-taxon richness relationships are weaker at the local scale; (H2) climatic predictors of species richness are stronger at the regional scale; (H3) effects of habitat heterogeneity on species richness are stronger at the local scale; (H4) plant richness positively affects vertebrate richness after accounting for environmental effects; and (H5) the plant-vertebrate richness relationship is weaker at the regional scale. We found significant and positive correlations between species richness of the groups, with correlations being stronger at the regional scale than at the local scale (supporting H1). Climate has weaker effects on species richness at the regional scale than at the local scale (rejecting H2), and for vertebrates (but not for plants) effects of habitat heterogeneity are stronger at the local scale (supporting hypothesis H3). Plant richness positively affects vertebrate richness after accounting for environmental effects (supporting H4), but the effect is stronger for the two endothermic groups (mammals and birds) than for the two ectothermic groups (reptiles and amphibians). In contrast to hypothesis H5, the effect of plant richness on species

  7. [The first stage of toxicology evaluation and analysis of 1502 pesticide samples].

    Science.gov (United States)

    Zheng, Yanyan; Li, Xianjun; Xie, Jing; Ling, Jianan; Shi, Nian

    2014-07-01

    To analyze the results of the first-stage toxicological evaluation of 1 502 pesticide samples. The classification of the 1 502 pesticide samples was analyzed, and the experimental results of the samples in different years were compared. Most of the 1 502 pesticide samples were insecticides, accounting for 52.5% of all, followed by bactericides and herbicides. In the 5 years, the proportion of biogenic insecticides showed a significant rising trend (χ² = 11.426, P pesticides was 65.8%; mixed pesticides accounted for 32.7%; original pesticides accounted for only 1.5%. From 2008 to 2012, most pesticides had low toxicity, regardless of the exposure route (via the mouth, skin, or respiratory tract). Acute oral and dermal toxicity tests showed that pesticides with moderate toxicity declined year by year (oral exposure χ² = 18.036, P pesticides with high toxicity. We did not detect any pesticide with extreme toxicity. Acute skin irritation and eye irritation test showed an upward trend in proportion of non-irritating pesticides (χ² = 77.110, P pesticides decreased significantly (χ² = 18.941, P pesticides was insecticide. Most samples were single pesticides, and there was a certain proportion of mixed pesticides. Novel pesticides such as bio-pesticides are the development tendency. The tested pesticides were mainly low-toxicity pesticides, with a certain proportion of medium- and high-toxicity pesticides. Personal protection should be strengthened during production and use of pesticides.

  8. Characterisation, classification, and evaluation of some ground water samples in upper Egypt.

    Science.gov (United States)

    Soltan, M E

    1998-08-01

    Study of the ground water quality at upper Egypt is an essential ingredient for a healthy population, irrigation, and industrial purposes at this developed region. Thus, the measurements of water quality parameters (pH, conductivity, HCO3-, Cl-, NO3-, PO4(3-), SO4(2-), Ca, Mg, TH, Co, Cr, Cu, Fe, K, Mn, Na, Ni, Pb, Zn, and DS) were carried out on ground water samples at different localities in Aswan governorate, Egypt. Differentation of ground water samples according to Cl-, SO4(2-), HCO3- + CO3(2-)' base exchange, and hydrochemical parameters were calculated. Evaluation of the samples for different uses (drinking and domestic uses, irrigation and industrial purposes) were obtained according to WHO standards, sodium adsorption ratio (SAR), and saturation index. Results of this study show that the most ground water samples characterize by good quality for different uses. Statistical analysis of data exhibits positive, good, and interesting correlation values lead to interpretation the results of analyses and suggestion the forms of ions in the water samples.

  9. Evaluation of denuder sampling for a mixture of three common gaseous diisocyanates

    Energy Technology Data Exchange (ETDEWEB)

    Nordqvist, Y.; Nilsson, U.; Colmsjoe, A. [Department of Analytical Chemistry, Stockholm University, 106 91, Stockholm (Sweden)

    2003-03-01

    A denuder sampler has been evaluated for a mixture of three gaseous diisocyanates, i.e. toluene diisocyanate (TDI), hexamethylene diisocyanate (HDI) and isophorone diisocyanate (IPDI). Sampling was performed at a total concentration of diisocyanates close to the Swedish occupational exposure limit (OEL), which is 10 ppbv (69-92 {mu}g m{sup -3}), for a 5-min period. The denuder tube was coated with a chemosorptive stationary phase consisting of SE-30 (polydimethylsiloxane) and the derivatising reagent dibutylamine (DBA). It was shown that the denuder has a collection efficiency for HDI and IPDI comparable to that of an impinger method, while sampling of TDI resulted in an 8% lower concentration. Both short-term (15 min) and long-term (8 h) sampling periods were shown to yield reproducible results. For 8-h measurements, a sampling flow rate of 5 mL min{sup -1} was shown to be suitable for the investigated concentration range, i.e. 10-100 ppbv (69-921 {mu}g m{sup -3}). A flow rate of 25 mL min{sup -1} or higher resulted in breakthrough after 8 h due to chromatography of the compounds in the adsorbent. The limit of detection (LOD) for the air sampling method is nearly 500 times lower than the OEL. The denuder tubes can be prepared at least 10 days prior to sampling without degradation of performance. Furthermore, they can be stored up to 6 days in a freezer after sampling without significant loss of analytes. (orig.)

  10. Evaluation of a New Environmental Sampling Protocol for Detection of Human Norovirus on Inanimate Surfaces

    Science.gov (United States)

    Lee, David; Treffiletti, Aimee; Hrsak, Mario; Shugart, Jill; Vinjé, Jan

    2015-01-01

    Inanimate surfaces are regarded as key vehicles for the spread of human norovirus during outbreaks. ISO method 15216 involves the use of cotton swabs for environmental sampling from food surfaces and fomites for the detection of norovirus genogroup I (GI) and GII. We evaluated the effects of the virus drying time (1, 8, 24, or 48 h), swab material (cotton, polyester, rayon, macrofoam, or an antistatic wipe), surface (stainless steel or a toilet seat), and area of the swabbed surface (25.8 cm2 to 645.0 cm2) on the recovery of human norovirus. Macrofoam swabs produced the highest rate of recovery of norovirus from surfaces as large as 645 cm2. The rates of recovery ranged from 2.2 to 36.0% for virus seeded on stainless-steel coupons (645.0 cm2) to 1.2 to 33.6% for toilet seat surfaces (700 cm2), with detection limits of 3.5 log10 and 4.0 log10 RNA copies. We used macrofoam swabs to collect environmental samples from several case cabins and common areas of a cruise ship where passengers had reported viral gastroenteritis symptoms. Seventeen (18.5%) of 92 samples tested positive for norovirus GII, and 4 samples could be sequenced and had identical GII.1 sequences. The viral loads of the swab samples from the cabins of the sick passengers ranged from 80 to 31,217 RNA copies, compared with 16 to 113 RNA copies for swab samples from public spaces. In conclusion, our swab protocol for norovirus may be a useful tool for outbreak investigations when no clinical samples are available to confirm the etiology. PMID:26116675

  11. Delineating species with DNA barcodes: a case of taxon dependent method performance in moths.

    Directory of Open Access Journals (Sweden)

    Mari Kekkonen

    Full Text Available The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs, few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65% OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90% in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.

  12. Rediscovery and reclassification of the dipteran taxon Nothomicrodon Wheeler, an exclusive endoparasitoid of gyne ant larvae

    Science.gov (United States)

    Pérez-Lachaud, Gabriela; Jahyny, Benoit J. B.; Ståhls, Gunilla; Rotheray, Graham; Delabie, Jacques H. C.; Lachaud, Jean-Paul

    2017-01-01

    The myrmecophile larva of the dipteran taxon Nothomicrodon Wheeler is rediscovered, almost a century after its original description and unique report. The systematic position of this dipteran has remained enigmatic due to the absence of reared imagos to confirm indentity. We also failed to rear imagos, but we scrutinized entire nests of the Brazilian arboreal dolichoderine ant Azteca chartifex which, combined with morphological and molecular studies, enabled us to establish beyond doubt that Nothomicrodon belongs to the Phoridae (Insecta: Diptera), not the Syrphidae where it was first placed, and that the species we studied is an endoparasitoid of the larvae of A. chartifex, exclusively attacking sexual female (gyne) larvae. Northomicrodon parasitism can exert high fitness costs to a host colony. Our discovery adds one more case to the growing number of phorid taxa known to parasitize ant larvae and suggests that many others remain to be discovered. Our findings and literature review confirm that the Phoridae is the only taxon known that parasitizes both adults and the immature stages of different castes of ants, thus threatening ants on all fronts. PMID:28361946

  13. A higher-taxon approach to rodent conservation priorities for the 21st century

    Directory of Open Access Journals (Sweden)

    Amori, G.

    2003-12-01

    Full Text Available Although rodents are not considered among the most threatened mammals, there is ample historical evidence concerning the vulnerability to extinction of several rodent phylogenetic lineages. Owing to the high number of species, poor taxonomy and the lack of detailed information on population status, the assessment of threat status according to IUCN criteria has still to be considered arbitrary in some cases. Public appreciation is scarce and tends to overlook the ecological role and conservation problems of an order representing about 41 percent of mammalian species. We provide an overview of the most relevant information concerning the conservation status of rodents at the genus, subfamily, and family level. For species¿poor taxa, the importance of distinct populations is highlighted and a splitter approach in taxonomy is adopted. Considering present constraints, strategies for the conservation of rodent diversity must rely mainly on higher taxon and hot-spot approaches. A clear understanding of phyletic relationships among difficult groups -such as Rattus, for instance- is an urgent goal. Even if rodent taxonomy is still unstable, high taxon approach is amply justified from a conservation standpoint as it offers a more subtle overview of the world terrestrial biodiversity than that offered by large mammals. Of the circa 451 living rodent genera, 126 (27,9 %, representing 168 living species, deserve conservation attention according to the present study. About 76 % of genera at risk are monotypic, confirming the danger of losing a considerable amount of phylogenetic distinctiveness.

  14. Implementation of Objective PASC-Derived Taxon Demarcation Criteria for Official Classification of Filoviruses

    Directory of Open Access Journals (Sweden)

    Yīmíng Bào

    2017-05-01

    Full Text Available The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC tool of the US National Center for Biotechnology Information (Bethesda, MD, USA. Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55–58% sequence diversity threshold range for genera and at the 23–36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type sequences.

  15. A multi-taxon approach reveals the effect of management intensity on biodiversity in Alpine larch grasslands.

    Science.gov (United States)

    Nascimbene, Juri; Fontana, Veronika; Spitale, Daniel

    2014-07-15

    In the Alps, larch grasslands form one of the most pleasing aspects of the landscape. However, their effectiveness in contributing to biodiversity conservation may depend on the intensity of their management. We used a multi-taxon approach to evaluate the effects of the intensification of management practices and those of abandonment on the biodiversity of the main autotrophic organisms hosted in this habitat, including vascular plants, bryophytes, and lichens. The study was carried out in the eastern part of South Tyrol, in the Italian Alps, where the diversity patterns of these three organismal groups were compared among intensively managed, extensively managed, and abandoned stands. The management intensity was found to strongly influence the biodiversity of the organisms, with a general pattern indicating the best conditions in extensively managed stands. Both abandonment and management intensification were detrimental to biodiversity through different mechanisms that led to species loss or to major shifts in species composition. However, the most negative effects were related to management intensification, mainly due to the high nitrogen supply, providing evidence for the increasing impact of eutrophication on Alpine environments. Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Quantitative evaluation method of arc sound spectrum based on sample entropy

    Science.gov (United States)

    Yao, Ping; Zhou, Kang; Zhu, Qiang

    2017-08-01

    Arc sound analysis is an effective way to evaluate the stability of the arc welding process. Current methods cannot effectively quantify the disorder of the process. By studying the characteristics of the arc sound signal, we found that low frequency random mutation of arc sound power resulted from unstable factors, such as splashes or short circuits, increased the complexity and randomness of the arc sound signals. Then the arc sound signals were visualized on time-frequency interface by means of spectrogram, and it was found that the max power spectral density (PSD) distribution of spectrogram was closely related to the stability of arc welding process. Moreover, a method based on sample entropy was proposed to further quantify the relation. Finally, considering the factors such as averages of max PSD and the standard deviations of sample entropy, a compound quantitative evaluation indicator, arc sound sample entropy (ASSE), which can avoid the influence of different parameters on the quantitative results, was proposed, so that the stability of arc welding process can be quantitatively presented. Testing results showed that the accuracy rate of the method was more than 90 percent.

  17. Evaluation of PCR Approaches for Detection of Bartonella bacilliformis in Blood Samples.

    Directory of Open Access Journals (Sweden)

    Cláudia Gomes

    2016-03-01

    Full Text Available The lack of an effective diagnostic tool for Carrion's disease leads to misdiagnosis, wrong treatments and perpetuation of asymptomatic carriers living in endemic areas. Conventional PCR approaches have been reported as a diagnostic technique. However, the detection limit of these techniques is not clear as well as if its usefulness in low bacteriemia cases. The aim of this study was to evaluate the detection limit of 3 PCR approaches.We determined the detection limit of 3 different PCR approaches: Bartonella-specific 16S rRNA, fla and its genes. We also evaluated the viability of dry blood spots to be used as a sample transport system. Our results show that 16S rRNA PCR is the approach with a lowest detection limit, 5 CFU/μL, and thus, the best diagnostic PCR tool studied. Dry blood spots diminish the sensitivity of the assay.From the tested PCRs, the 16S rRNA PCR-approach is the best to be used in the direct blood detection of acute cases of Carrion's disease. However its use in samples from dry blood spots results in easier management of transport samples in rural areas, a slight decrease in the sensitivity was observed. The usefulness to detect by PCR the presence of low-bacteriemic or asymptomatic carriers is doubtful, showing the need to search for new more sensible techniques.

  18. Evaluation of an automated protocol for efficient and reliable DNA extraction of dietary samples.

    Science.gov (United States)

    Wallinger, Corinna; Staudacher, Karin; Sint, Daniela; Thalinger, Bettina; Oehm, Johannes; Juen, Anita; Traugott, Michael

    2017-08-01

    Molecular techniques have become an important tool to empirically assess feeding interactions. The increased usage of next-generation sequencing approaches has stressed the need of fast DNA extraction that does not compromise DNA quality. Dietary samples here pose a particular challenge, as these demand high-quality DNA extraction procedures for obtaining the minute quantities of short-fragmented food DNA. Automatic high-throughput procedures significantly decrease time and costs and allow for standardization of extracting total DNA. However, these approaches have not yet been evaluated for dietary samples. We tested the efficiency of an automatic DNA extraction platform and a traditional CTAB protocol, employing a variety of dietary samples including invertebrate whole-body extracts as well as invertebrate and vertebrate gut content samples and feces. Extraction efficacy was quantified using the proportions of successful PCR amplifications of both total and prey DNA, and cost was estimated in terms of time and material expense. For extraction of total DNA, the automated platform performed better for both invertebrate and vertebrate samples. This was also true for prey detection in vertebrate samples. For the dietary analysis in invertebrates, there is still room for improvement when using the high-throughput system for optimal DNA yields. Overall, the automated DNA extraction system turned out as a promising alternative to labor-intensive, low-throughput manual extraction methods such as CTAB. It is opening up the opportunity for an extensive use of this cost-efficient and innovative methodology at low contamination risk also in trophic ecology.

  19. Petrophysical studies of north American carbonate rock samples and evaluation of pore-volume compressibility models

    Science.gov (United States)

    da Silva, Gilberto Peixoto; Franco, Daniel R.; Stael, Giovanni C.; da Costa de Oliveira Lima, Maira; Sant'Anna Martins, Ricardo; de Moraes França, Olívia; Azeredo, Rodrigo B. V.

    2015-12-01

    In this work, we evaluate two pore volume compressibility models that are currently discussed in the literature (Horne, 1990; Jalalh, 2006b). Five groups of carbonate rock samples from the three following sedimentary basins in North America that are known for their association with hydrocarbon deposits were selected for this study: (i) the Guelph Formation of the Michigan Basin (Middle Silurian); (ii) the Edwards Formation of the Central Texas Platform (Middle Cretaceous); and (iii) the Burlington-Keokuk Formation of the Mississippian System (Lower Mississippian). In addition to the evaluation of the compressibility model, a petrophysical evaluation of these rock samples was conducted. Additional characterizations, such as grain density, the effective porosity, absolute grain permeability, thin section petrography, MICP and NMR, were performed to complement constant pore-pressure compressibility tests. Although both models presented an overall good representation of the compressibility behavior of the studied carbonate rocks, even when considering their broad porosity range (~ 2-38%), the model proposed by Jalalh (2006b) performed better with a confidence level of 95% and a prediction interval of 68%.

  20. Evaluation of Sample Handling Effects on Serum Vitamin E and Cholesterol Concentrations in Alpacas

    Directory of Open Access Journals (Sweden)

    Andrea S. Lear

    2014-01-01

    Full Text Available Clinical cases of vitamin E deficiencies have been diagnosed in camelids and may indicate that these species are more sensitive to inadequate vitamin E in hay-based diets compared to other ruminant and equine species. In bovine, cholesterol has been reported to affect vitamin E concentrations. In order to evaluate vitamin E deficiencies in camelids, the effects of collection and storage of the blood samples prior to processing were necessary. Reports vary as to factors affecting vitamin E and cholesterol in blood samples, and diagnostic laboratories vary in instructions regarding sample handling. Blood was collected from healthy alpacas and processed under conditions including exposure to fluorescent light, serum and red blood cell contact, tube stopper contact, temperature, and hemolysis. Serum vitamin E and cholesterol concentrations were then measured. Statistical analyses found that the vitamin E concentrations decreased with prolonged contact with the tube stopper and with increasing hemolysis. Vitamin E concentration variations were seen with other factors but were not significant. Time prior to serum separation and individual animal variation was found to alter cholesterol concentrations within the sample, yet this finding was clinically unremarkable. No correlation was seen between vitamin E and cholesterol concentration, possibly due to lack of variation of cholesterol.

  1. SPINning factors: factor analytic evaluation of the Social Phobia Inventory in clinical and nonclinical undergraduate samples.

    Science.gov (United States)

    Carleton, R Nicholas; Collimore, Kelsey C; Asmundson, Gordon J G; McCabe, Randi E; Rowa, Karen; Antony, Martin M

    2010-01-01

    The Social Phobia Inventory (SPIN) was designed to assess three dimensions of social anxiety (i.e., fear, avoidance, and physiological arousal) as posited by the scale authors (Connor et al., 2000). Despite expectations of a 3-factor solution, analyses of the SPIN to date have provided support for 3- and 5-factor solutions (Radomsky et al., 2006). Moreover, a 3-item version, the Mini-SPIN (Connor et al., 2001), has good sensitivity and specificity for generalized social anxiety disorder (SAD), implying some item redundancy. Another recent psychometric analysis of the SPIN was performed in a diagnostically diverse clinical sample (Antony et al., 2006); however, the study did not include a comprehensive evaluation of the factor structure. The current study was designed to comprehensively assess the SPIN factor structure using exploratory (EFA) and confirmatory (CFA) factor analyses in undergraduate (N=227) and clinical samples (N=355) using current recommendations for factor analyses (Osborne et al., 2008). Results suggest a 10-item 3-factor solution may be an ideal fit for clinical samples; however, using the undergraduate sample, the same solution was significantly better than precedent solutions but nonetheless not ideal. Implications and recommendations for future research are discussed.

  2. An inexpensive and portable microvolumeter for rapid evaluation of biological samples.

    Science.gov (United States)

    Douglass, John K; Wcislo, William T

    2010-08-01

    We describe an improved microvolumeter (MVM) for rapidly measuring volumes of small biological samples, including live zooplankton, embryos, and small animals and organs. Portability and low cost make this instrument suitable for widespread use, including at remote field sites. Beginning with Archimedes' principle, which states that immersing an arbitrarily shaped sample in a fluid-filled container displaces an equivalent volume, we identified procedures that maximize measurement accuracy and repeatability across a broad range of absolute volumes. Crucial steps include matching the overall configuration to the size of the sample, using reflected light to monitor fluid levels precisely, and accounting for evaporation during measurements. The resulting precision is at least 100 times higher than in previous displacement-based methods. Volumes are obtained much faster than by traditional histological or confocal methods and without shrinkage artifacts due to fixation or dehydration. Calibrations using volume standards confirmed accurate measurements of volumes as small as 0.06 microL. We validated the feasibility of evaluating soft-tissue samples by comparing volumes of freshly dissected ant brains measured with the MVM and by confocal reconstruction.

  3. Bioequivalence evaluation of two formulations of pidotimod using a limited sampling strategy.

    Science.gov (United States)

    Huang, Ji-Han; Huang, Xiao-Hui; Wang, Kun; Li, Jian-Chun; Xie, Xue-Feng; Shen, Chen-Lin; Li, Lu-Jin; Zheng, Qing-Shan

    2013-07-01

    The aim of this study was to develop a limited sampling strategy (LSS) to assess the bioequivalence of two formulations of pidotimod. A randomized, two-way, cross-over study was conducted in healthy Chinese volunteers to compare two formulations of pidotimod. A limited sampling model was established using regression models to estimate the pharmacokinetic parameters and assess the bioequivalence of pidotimod. The model was internally validated by the Jack-knife method and graphical methods. The traditional non-compartmental method was also used to analyze the data and compared with LSS method. The results indicate that following oral administration of a single 800 mg dose, the plasma AUC(0-12 h) and C(max) of pidotimod can be predicted accurately using only two to four plasma samples. The bioequivalence assessment based on the LSS models provided results very similar to that obtained using all the observed concentration-time data points and indicate that the two pidotimod formulations were bioequivalent. A LSS method for assessing the bioequivalence of pidotimod formulations was established and proved to be applicable and accurate. This LSS method could be considered appropriate for a pidotimod bioequivalence study, providing an inexpensive cost of sampling acquisition and analysis. And the methodology presented here may also be applicable to bioequivalence evaluation of other medications. Crown Copyright © 2013. Published by Elsevier Masson SAS. All rights reserved.

  4. Evaluation of sample preparation methods and optimization of nickel determination in vegetable tissues

    Directory of Open Access Journals (Sweden)

    Rodrigo Fernando dos Santos Salazar

    2011-02-01

    Full Text Available Nickel, although essential to plants, may be toxic to plants and animals. It is mainly assimilated by food ingestion. However, information about the average levels of elements (including Ni in edible vegetables from different regions is still scarce in Brazil. The objectives of this study were to: (a evaluate and optimize a method for preparation of vegetable tissue samples for Ni determination; (b optimize the analytical procedures for determination by Flame Atomic Absorption Spectrometry (FAAS and by Electrothermal Atomic Absorption (ETAAS in vegetable samples and (c determine the Ni concentration in vegetables consumed in the cities of Lorena and Taubaté in the Vale do Paraíba, State of São Paulo, Brazil. By means of the analytical technique for determination by ETAAS or FAAS, the results were validated by the test of analyte addition and recovery. The most viable method tested for quantification of this element was HClO4-HNO3 wet digestion. All samples but carrot tissue collected in Lorena contained Ni levels above the permitted by the Brazilian Ministry of Health. The most disturbing results, requiring more detailed studies, were the Ni concentrations measured in carrot samples from Taubaté, where levels were five times higher than permitted by Brazilian regulations.

  5. Multi-scale sampling to evaluate assemblage dynamics in an oceanic marine reserve.

    Science.gov (United States)

    Thompson, Andrew R; Watson, William; McClatchie, Sam; Weber, Edward D

    2012-01-01

    To resolve the capacity of Marine Protected Areas (MPA) to enhance fish productivity it is first necessary to understand how environmental conditions affect the distribution and abundance of fishes independent of potential reserve effects. Baseline fish production was examined from 2002-2004 through ichthyoplankton sampling in a large (10,878 km(2)) Southern Californian oceanic marine reserve, the Cowcod Conservation Area (CCA) that was established in 2001, and the Southern California Bight as a whole (238,000 km(2) CalCOFI sampling domain). The CCA assemblage changed through time as the importance of oceanic-pelagic species decreased between 2002 (La Niña) and 2003 (El Niño) and then increased in 2004 (El Niño), while oceanic species and rockfishes displayed the opposite pattern. By contrast, the CalCOFI assemblage was relatively stable through time. Depth, temperature, and zooplankton explained more of the variability in assemblage structure at the CalCOFI scale than they did at the CCA scale. CalCOFI sampling revealed that oceanic species impinged upon the CCA between 2002 and 2003 in association with warmer offshore waters, thus explaining the increased influence of these species in the CCA during the El Nino years. Multi-scale, spatially explicit sampling and analysis was necessary to interpret assemblage dynamics in the CCA and likely will be needed to evaluate other focal oceanic marine reserves throughout the world.

  6. High-risk human papillomavirus in Galicia, Spain: prevalence and evaluation of the sample representativeness.

    Science.gov (United States)

    Trigo-Daporta, Matilde; García-Campello, Marta; Pérez-Ríos, Monica; Santiago-Pérez, Maria Isolina; Fernandez-Rodriguez, Eva; Guinarte, Genoveva; Troncoso, Ana; Pardavila, Raquel; Malvar, Alberto

    2014-11-01

    The prevalence of high-risk genotypes of the human papillomavirus (HR-HPV) in Galicia remained unknown before the introduction of the HPV vaccine. The objective of this study was to estimate this prevalence in non-vaccinated women when vaccination against HR-HPV started. Sample representativeness was also evaluated. Female volunteers aged 16-64 years, residents in Galicia, Spain, completed a questionnaire and provided biological samples for a virological study and for cytology. The sample was weighted; prevalence rates were estimated and are shown with 95% confidence intervals. Virological results were available for 1703 women. HR-HPV prevalence was 10.1%, decreasing notably at ages above 30 years. HPV-16 was the most frequent genotype and 3.6% of women were infected by more than one genotype. No adjustment was necessary to generalize the results of the study. In Galicia in 2009 there would be 96 400 women aged 16-64 years infected with HR-HPV. It is possible to estimate HR-HPV prevalence in a population starting from a volunteer sample.

  7. Evaluation of three sampling methods for the microbiological analysis of broiler carcasses after immersion chilling.

    Science.gov (United States)

    Giombelli, Audecir; Cavani, Ricardo; Gloria, Maria Beatriz Abreu

    2013-08-01

    Countries have different official programs and implement different sampling methods for the detection of Salmonella on poultry carcasses. In Brazil, a 25-g sample of skin and muscle excision (SME) from the wings, neck, and pericloacal parts is used; in the European Union (EU), a 25-g sample of neck skin (NSE) is used; and, in the United States, the whole carcass is rinsed with 400 ml of diluent (WCR). In the present study, these methods were evaluated to compare Salmonella occurrence and counts of hygiene indicator microorganisms (Escherichia coli, Enterobacteriaceae, and total viable count of aerobic mesophilic bacteria) using different carcasses from the same flock and also using different analytical units taken from the same carcass. Eighty flocks, with four broiler carcasses from each, were included in this study; three broilers were sampled according to protocols from Brazil, the EU, and the United States, and the last one by all three methods. SME, NSE, and WCR provided equivalent results (P > 0.05) for Salmonella detection on broiler carcasses when using different carcasses from the same flock and when using the same carcass. The predominant serovar was Salmonella Enteritidis. For the enumeration of hygiene indicator microorganisms, WRC provided higher counts than SME or NSE (P < 0.05), when using both the same or different carcasses. Therefore, it is possible to directly compare Salmonella results in poultry carcasses when using the methods recommended by the legislative bodies of Brazil, the United States, and the EU. However, WCR provides the best results for hygiene indicator microorganisms.

  8. Evaluation of the readsorption of plutonium and americium in dynamic fractionations of environmental solid samples.

    Science.gov (United States)

    Petersen, Roongrat; Hou, Xiaolin; Hansen, Elo Harald

    2008-07-01

    A dynamic extraction system exploiting sequential injection (SI) for sequential extractions incorporating a specially designed extraction column is developed to fractionate radionuclides in environmental solid samples such as soils and sediments. The extraction column can contain up to 5 g of a soil sample, and under optimal operational conditions it does not give rise to creation of back pressure. Attention has been placed on studies of the readsorption problems during sequential extraction using a modified Standards, Measurements and Testing (SM&T) scheme with four-step sequential extractions. The degree of readsorption in dynamic and conventional batch extraction systems is compared and evaluated by using a double-spiking technique. A high degree of readsorption of plutonium and americium (>75%) was observed in both systems, and they also exhibited similar distribution patterns of the two radionuclides. However, the dynamic system is fully automated, eliminates manual separations, significantly reduces the operational time required, and offers detailed kinetic information.

  9. A sampling method for estimating the accuracy of predicted breeding values in genetic evaluation

    Directory of Open Access Journals (Sweden)

    Laloë Denis

    2001-09-01

    Full Text Available Abstract A sampling-based method for estimating the accuracy of estimated breeding values using an animal model is presented. Empirical variances of true and estimated breeding values were estimated from a simulated n-sample. The method was validated using a small data set from the Parthenaise breed with the estimated coefficient of determination converging to the true values. It was applied to the French Salers data file used for the 2000 on-farm evaluation (IBOVAL of muscle development score. A drawback of the method is its computational demand. Consequently, convergence can not be achieved in a reasonable time for very large data files. Two advantages of the method are that a it is applicable to any model (animal, sire, multivariate, maternal effects... and b it supplies off-diagonal coefficients of the inverse of the mixed model equations and can therefore be the basis of connectedness studies.

  10. The phylogenetic relationships among non-diplomystid catfishes as inferred from mitochondrial cytochrome b sequences; the search for the ictalurid sister taxon (Otophysi: Siluriformes).

    Science.gov (United States)

    Hardman, Michael

    2005-12-01

    The relationships among families of catfishes are poorly understood and have yet to be the subject of a comprehensive investigation with molecular data. Existing phylogenetic hypotheses are based on morphological data and incompletely resolved. This study analyzed complete sequences of mitochondrial gene cytochrome b for 170 species from 29 of 33 extant families, and focused on the relationships of Ictaluridae to other catfishes. In addition to previous phylogenetic studies, the fossil record, paleogeography, biogeography, and distribution of extant catfish families collectively suggest the location (if extant) of the ictalurid sister taxon to be Northern or Eastern Asia. Of the extant catfishes currently native to this area and included in this analysis, parsimony and Bayesian likelihood analyses recovered Cranoglanis bouderius as the most proximal sister taxon of Ictaluridae. Seemingly, ictalurids and cranoglanidids represent another biogeographic component linking freshwater fishes of North America and eastern Asia, e.g., catostomids and paddlefishes. The results coupled with present-day catfish distributions and inferences from the fossil record collectively suggest the ancestor of Ictaluridae to have invaded freshwaters of North America at the close of the Cretaceous through northeastern Asia and northwestern North America. Other superfamilial nodes supported the results of previous phylogenetic studies of narrower taxonomic scope. Several novel relationships were recovered (including a clade composed of Pimelodidae, Pseudopimelodidae, and Heptapteridae) and these along with sources of systematic error are discussed. A broad sampling of Bagridae permitted an examination of intergeneric relationships within this family and in light of recent morphological and molecular studies.

  11. Contemporary models of pediatric obsessive-compulsive disorder: An evaluation with a large clinical sample.

    Science.gov (United States)

    De Nadai, Alessandro; Nagpal, Prianka S; Piacentini, John; Peris, Tara S; Geffken, Gary R; Geller, Daniel A; Murphy, Tanya K; Storch, Eric A; Lewin, Adam B

    2015-09-30

    We evaluated the construct validity of the Child Yale-Brofwn Obsessive-Compulsive Scale (CYBOCS) in a large clinical sample (N=730) using confirmatory factor analysis. Results found inadequate fit for a priori models, though a model accounting for overlapping item content displayed good fit. Parallel obsessions/compulsions items may provide largely redundant information on the CYBOCS. Findings suggest modifying the CYBOCS to reduce burden on researchers, patients, and clinicians, and to more accurately measure pediatric obsessive-compulsive disorder (OCD). Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Evaluation of Botanical Reference Materials for the Determination of Vanadium in Biological Samples

    DEFF Research Database (Denmark)

    Heydorn, Kaj; Damsgaard, Else

    1982-01-01

    Three botanical reference materials prepared by the National Bureau of Standards have been studied by neutron activation analysis to evaluate their suitability with respect to the determination of vanadium in biological samples. Various decomposition methods were applied in connection with chemic....... A reference value of 1.15 mg/kg of this material is recommended, based on results from 3 different methods. All three materials are preferable to SRM 1571 Orchard Leaves, while Bowen's Kale remains the material of choice because of its lower concentration....

  13. An evaluation of sampling methodology for assessing settlement of temperate fish in seagrass meadows

    Directory of Open Access Journals (Sweden)

    I. A. CATALAN

    2014-03-01

    Full Text Available All demersal fish with planktonic larvae settle at some point early in life, generally around the transformation from larvae to juveniles or soon after. Sampling pre-settlement or very young, settled fish is challenging due to spatial concretions within the habitat and the pulsed, rapid nature of the settlement process. There is a lack of robust methods that enable this sampling, but information on the settlement, that represents a mortality bottleneck, is crucial for the follow-up of populations for fisheries and conservation purposes. An empirical evaluation of sampling methods has not been conducted in temperate habitats. Here, we compare six different sampling methods to collect pre- and post-settlement stages of fish to determine the best combination of techniques to utilise in Posidonia oceanica, an endemic Mediterranean seagrass that provides a key nursery habitat for coastal fish. We considered three types of pelagic nets (bongo net, neuston net and ring net, two types of light-traps (Quatrefoil and Ecocean CARE® to sample pre-settled stages and a low-impact epibenthic trawl for recent settlers. Our results show a significantly different size-spectrum for each method, with a continuous range of sizes from 2 mm to 200 mm. The smallest sizes were collected by the bongo net, followed by the ring net, the neuston net, the Quatrefoil, the Ecocean and finally the epibenthic trawl. Our results suggest that an appropriate strategy for collecting and estimating the abundance of key littoral fish species around settlement size is the combination of the Ecocean light trap and the epibenthic trawl.

  14. EVALUATION OF ARG-1 SAMPLES PREPARED BY CESIUM CARBONATE DISSOLUTION DURING THE ISOLOK SME ACCEPTABILITY TESTING

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, T.; Hera, K.; Coleman, C.

    2011-12-05

    Evaluation of Defense Waste Processing Facility (DWPF) Chemical Process Cell (CPC) cycle time identified several opportunities to improve the CPC processing time. The Mechanical Systems & Custom Equipment Development (MS&CED) Section of the Savannah River National Laboratory (SRNL) recently completed the evaluation of one of these opportunities - the possibility of using an Isolok sampling valve as an alternative to the Hydragard valve for taking DWPF process samples at the Slurry Mix Evaporator (SME). The use of an Isolok for SME sampling has the potential to improve operability, reduce maintenance time, and decrease CPC cycle time. The SME acceptability testing for the Isolok was requested in Task Technical Request (TTR) HLW-DWPF-TTR-2010-0036 and was conducted as outlined in Task Technical and Quality Assurance Plan (TTQAP) SRNLRP-2011-00145. RW-0333P QA requirements applied to the task, and the results from the investigation were documented in SRNL-STI-2011-00693. Measurement of the chemical composition of study samples was a critical component of the SME acceptability testing of the Isolok. A sampling and analytical plan supported the investigation with the analytical plan directing that the study samples be prepared by a cesium carbonate (Cs{sub 2}CO{sub 3}) fusion dissolution method and analyzed by Inductively Coupled Plasma - Optical Emission Spectroscopy (ICP-OES). The use of the cesium carbonate preparation method for the Isolok testing provided an opportunity for an additional assessment of this dissolution method, which is being investigated as a potential replacement for the two methods (i.e., sodium peroxide fusion and mixed acid dissolution) that have been used at the DWPF for the analysis of SME samples. Earlier testing of the Cs{sub 2}CO{sub 3} method yielded promising results which led to a TTR from Savannah River Remediation, LLC (SRR) to SRNL for additional support and an associated TTQAP to direct the SRNL efforts. A technical report resulting

  15. Evaluation of neon focused ion beam milling for TEM sample preparation.

    Science.gov (United States)

    Pekin, T C; Allen, F I; Minor, A M

    2016-10-01

    Gallium-based focused ion beams generated from liquid-metal sources are widely used in micromachining and sample preparation for transmission electron microscopy, with well-known drawbacks such as sample damage and contamination. In this work, an alternative (neon) focused ion beam generated by a gas field-ionization source is evaluated for the preparation of electron-transparent specimens. To do so, electron-transparent sections of Si and an Al alloy are prepared with both Ga and Ne ion beams for direct comparison. Diffraction-contrast imaging and energy dispersive x-ray spectroscopy are used to evaluate the relative damage induced by the two beams, and cross-sections of milled trenches are examined to compare the implantation depth with theoretical predictions from Monte Carlo simulations. Our results show that for the beam voltages and materials systems investigated, Ne ion beam milling does not significantly reduce the focused ion beam induced artefacts. However, the Ne ion beam does enable more precise milling and may be of interest in cases where Ga contamination cannot be tolerated. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.

  16. Radiochemistry methods in DOE methods for evaluating environmental and waste management samples

    Energy Technology Data Exchange (ETDEWEB)

    Fadeff, S.K.; Goheen, S.C.

    1994-08-01

    Current standard sources of radiochemistry methods are often inappropriate for use in evaluating US Department of Energy environmental and waste management (DOE/EW) samples. Examples of current sources include EPA, ASTM, Standard Methods for the Examination of Water and Wastewater and HASL-300. Applicability of these methods is limited to specific matrices (usually water), radiation levels (usually environmental levels), and analytes (limited number). Radiochemistry methods in DOE Methods for Evaluating Environmental and Waste Management Samples (DOE Methods) attempt to fill the applicability gap that exists between standard methods and those needed for DOE/EM activities. The Radiochemistry chapter in DOE Methods includes an ``analysis and reporting`` guidance section as well as radiochemistry methods. A basis for identifying the DOE/EM radiochemistry needs is discussed. Within this needs framework, the applicability of standard methods and targeted new methods is identified. Sources of new methods (consolidated methods from DOE laboratories and submissions from individuals) and the methods review process will be discussed. The processes involved in generating consolidated methods add editing individually submitted methods will be compared. DOE Methods is a living document and continues to expand by adding various kinds of methods. Radiochemistry methods are highlighted in this paper. DOE Methods is intended to be a resource for methods applicable to DOE/EM problems. Although it is intended to support DOE, the guidance and methods are not necessarily exclusive to DOE. The document is available at no cost through the Laboratory Management Division of DOE, Office of Technology Development.

  17. A psychometric evaluation of the Pain Response Preference Questionnaire in a chronic pain patient sample.

    Science.gov (United States)

    McWilliams, Lachlan A; Dick, Bruce D; Bailey, Kristen; Verrier, Michelle J; Kowal, John

    2012-05-01

    The Pain Response Preference Questionnaire (PRPQ) assesses preferences regarding pain-related social support. The initial factor analytic study of the PRPQ conducted with a nonclinical sample identified scales labeled Solicitude, Management, Suppression, and Encouragement. The first aim of the current study was to evaluate whether these scales would be appropriate for use with chronic pain patients. The construct validity of the emerging scales and their relations to pain-related disability were also investigated. A large sample of chronic pain patients (N = 300) completed the PRPQ along with self-reports of personality constructs, coping styles, pain severity, and disability. Factor analysis supported a three-factor solution. Two factors were similar to those obtained in its initial evaluation, and were given the identical labels of Solicitude and Suppression. The remaining factor was labeled Activity Direction and was comprised primarily of items that were part of the earlier Management and Encouragement scales. Internally consistent PRPQ scales based on these factors were created. Correlation analyses involving the personality and coping measures provided support for the construct validity of these PRPQ scales. Supportive of their clinical utility, multiple regression analyses indicated that, after adjusting for pain severity, the PRPQ scales accounted for significant variance in disability ratings. Additional factor analytic research aimed at identifying the most appropriate set of PRPQ scales is warranted. The present findings indicate that the PRPQ scales used in the current study have strong psychometric properties and hold promise as research and clinical tools.

  18. Evaluation applications of instrument calibration research findings in psychology for very small samples

    Science.gov (United States)

    Fisher, W. P., Jr.; Petry, P.

    2016-11-01

    Many published research studies document item calibration invariance across samples using Rasch's probabilistic models for measurement. A new approach to outcomes evaluation for very small samples was employed for two workshop series focused on stress reduction and joyful living conducted for health system employees and caregivers since 2012. Rasch-calibrated self-report instruments measuring depression, anxiety and stress, and the joyful living effects of mindfulness behaviors were identified in peer-reviewed journal articles. Items from one instrument were modified for use with a US population, other items were simplified, and some new items were written. Participants provided ratings of their depression, anxiety and stress, and the effects of their mindfulness behaviors before and after each workshop series. The numbers of participants providing both pre- and post-workshop data were low (16 and 14). Analysis of these small data sets produce results showing that, with some exceptions, the item hierarchies defining the constructs retained the same invariant profiles they had exhibited in the published research (correlations (not disattenuated) range from 0.85 to 0.96). In addition, comparisons of the pre- and post-workshop measures for the three constructs showed substantively and statistically significant changes. Implications for program evaluation comparisons, quality improvement efforts, and the organization of communications concerning outcomes in clinical fields are explored.

  19. An environmental bacterial taxon with a large and distinct metabolic repertoire.

    Science.gov (United States)

    Wilson, Micheal C; Mori, Tetsushi; Rückert, Christian; Uria, Agustinus R; Helf, Maximilian J; Takada, Kentaro; Gernert, Christine; Steffens, Ursula A E; Heycke, Nina; Schmitt, Susanne; Rinke, Christian; Helfrich, Eric J N; Brachmann, Alexander O; Gurgui, Cristian; Wakimoto, Toshiyuki; Kracht, Matthias; Crüsemann, Max; Hentschel, Ute; Abe, Ikuro; Matsunaga, Shigeki; Kalinowski, Jörn; Takeyama, Haruko; Piel, Jörn

    2014-02-06

    Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, such 'talented' producers represent only a minute fraction of the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived as a large, untapped resource of new drug candidates, but so far it is unknown whether taxa containing talented bacteria indeed exist. Here we report the single-cell- and metagenomics-based discovery of such producers. Two phylotypes of the candidate genus 'Entotheonella' with genomes of greater than 9 megabases and multiple, distinct biosynthetic gene clusters co-inhabit the chemically and microbially rich marine sponge Theonella swinhoei. Almost all bioactive polyketides and peptides known from this animal were attributed to a single phylotype. 'Entotheonella' spp. are widely distributed in sponges and belong to an environmental taxon proposed here as candidate phylum 'Tectomicrobia'. The pronounced bioactivities and chemical uniqueness of 'Entotheonella' compounds provide significant opportunities for ecological studies and drug discovery.

  20. Primeros registros para Colombia de cuatro taxones de la familia Tyrannidae (Aves: Passeriformes

    Directory of Open Access Journals (Sweden)

    Rojas R. Rosario

    1997-11-01

    Full Text Available En esta comunicación presentamos datos sobre cuatro taxones de la familia Tyrannidae que representan registros nuevos para el territorio colombiano, todos respaldados con especímenes en la colección del Instituto de Ciencias Naturales (ICN. La mayoría de los registros son del campo petrolero de Caño Limón, a unos 55 km al occidente de la ciudad de Arauca, en la parte septentrional del Departamento de Arauca. Las características de este sitio y datos generales de su avifauna fueron presentados por McN ish & Stiles (1992, Yun análisis detallado de la ecología y afinidades biogeográficas de esta avifauna fue realizado por Rojas & Piragua (1992.

  1. 'Candidatus Phytoplasma hispanicum', a novel taxon associated with Mexican periwinkle virescence disease of Catharanthus roseus.

    Science.gov (United States)

    Davis, Robert E; Harrison, Nigel A; Zhao, Yan; Wei, Wei; Dally, Ellen L

    2016-09-01

    Mexican periwinkle virescence (MPV) phytoplasma was originally discovered in diseased plants of Madagascar periwinkle (Catharanthus roseus) in Yucatán, Mexico. On the basis of results from RFLP analysis of PCR-amplified 16S rRNA gene sequences, strain MPV was previously classified as the first known member of phytoplasma group 16SrXIII, and a new subgroup (16SrXIII-A) was established to accommodate MPV phytoplasma. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MPV represents a lineage distinct from previously described 'CandidatusPhytoplasma' species. Nucleotide sequence alignments revealed that strain MPV shared less than 97.5 % 16S rRNA gene sequence similarity with all previously described 'Ca.Phytoplasma' species. Based on unique properties of the DNA, we propose recognition of Mexican periwinkle virescence phytoplasma strain MPV as representative of a novel taxon, 'CandidatusPhytoplasma hispanicum'.

  2. Critical evaluation of distillation procedure for the determination of methylmercury in soil samples.

    Science.gov (United States)

    Perez, Pablo A; Hintelman, Holger; Quiroz, Waldo; Bravo, Manuel A

    2017-11-01

    In the present work, the efficiency of distillation process for extracting monomethylmercury (MMHg) from soil samples was studied and optimized using an experimental design methodology. The influence of soil composition on MMHg extraction was evaluated by testing of four soil samples with different geochemical characteristics. Optimization suggested that the acid concentration and the duration of the distillation process were most significant and the most favorable conditions, established as a compromise for the studied soils, were determined to be a 70 min distillation using an 0.2 M acid. Corresponding limits of detection (LOD) and quantification (LOQ) were 0.21 and 0.7 pg absolute, respectively. The optimized methodology was applied with satisfactory results to soil samples and was compared to a reference methodology based on isotopic dilution analysis followed by gas chromatography-inductively coupled plasma mass spectrometry (IDA-GC-ICP-MS). Using the optimized conditions, recoveries ranged from 82 to 98%, which is an increase of 9-34% relative to the previously used standard operating procedure. Finally, the validated methodology was applied to quantify MMHg in soils collected from different sites impacted by coal fired power plants in the north-central zone of Chile, measuring MMHg concentrations ranging from 0.091 to 2.8 ng g-1. These data are to the best of our knowledge the first MMHg measurements reported for Chile. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Evaluation of surface sampling techniques for collection of Bacillus spores on common drinking water pipe materials.

    Science.gov (United States)

    Packard, Benjamin H; Kupferle, Margaret J

    2010-01-01

    Drinking water utilities may face biological contamination of the distribution system from a natural incident or deliberate contamination. Determining the extent of contamination or the efficacy of decontamination is a challenge, because it may require sampling of the wetted surfaces of distribution infrastructure. This study evaluated two sampling techniques that utilities might use to sample exhumed pipe sections. Polyvinyl chloride (PVC), cement-lined ductile iron, and ductile iron pipe coupons (3 cm x 14 cm) cut from new water main piping were conditioned for three months in dechlorinated Cincinnati, Ohio tap water. Coupons were spiked with Bacillus atrophaeus subsp. globigii, a surrogate for Bacillus anthracis. Brushing and scraping were used to recover the inoculated spores from the coupons. Mean recoveries for all materials ranged from 37 +/- 30% to 43 +/- 20% for brushing vs. 24 +/- 10% to 51 +/- 29% for scraping. On cement-lined pipe, brushing yielded a significantly different recovery than scraping. No differences were seen between brushing and scraping the PVC and iron pipe coupons. Mean brushing and scraping recoveries from PVC coupons were more variable than mean recoveries from cement-lined and iron coupons. Spore retention differed between pipe materials and the presence of established biofilms also had an impact. Conditioned PVC coupons (with established biofilms) had significantly lower spore retention (31 +/- 11%) than conditioned cement-lined coupons (61 +/- 14%) and conditioned iron coupons (71 +/- 8%).

  4. Ecotoxicological evaluation of industrial port of Venice (Italy) sediment samples after a decontamination treatment

    Energy Technology Data Exchange (ETDEWEB)

    Libralato, Giovanni [Environmental Sciences Department, Venice University Ca Foscari, Campo della Celestia 2737/b, I-30122 Venice (Italy)], E-mail: giovanni.libralato@unive.it; Losso, Chiara; Arizzi Novelli, Alessandra [Environmental Sciences Department, Venice University Ca Foscari, Campo della Celestia 2737/b, I-30122 Venice (Italy); Citron, Marta; Della Sala, Stefano; Zanotto, Emanuele [Environmental Department, Venice Port Authority, Zattere 1401, I-30123, Venice (Italy); Cepak, Franka [Institute of Public Health, Vojkovo nabrezje 4a, 6000 Koper (Slovenia); Volpi Ghirardini, Annamaria [Environmental Sciences Department, Venice University Ca Foscari, Campo della Celestia 2737/b, I-30122 Venice (Italy)

    2008-12-15

    This work assesses the ecotoxicological effects of polluted sediment after a decontamination treatment process using a new sediment washing technique. Sediment samples were collected from four sites in Marghera Port industrial channels (Venice, Italy). Ecotoxicological evaluations were performed with Vibrio fischeri and Crassostrea gigas bioassays. Whole sediment and elutriate were deemed as the most suitable environmental matrices for this study. Toxicity scores developed in the Lagoon of Venice for V. fischeri on whole sediment and for C. gigas on elutriate were considered for the final ranking of samples. Ecotoxicological results showed that the treated sediment samples presented both acute and sub-chronic toxicities, which were mainly attributed to the presence of some remaining chemicals such as metals and polyaromatic hydrocarbons. The acute toxicity ranged from low to medium, while the sub-chronic one from absent to very high, suggesting that treated sediments could not be reused in direct contact with seawater. - A sediment washing technique was assessed for port contaminated sediment remediation and reuse, indicating its reduced efficiency and the need for further improvements.

  5. Sample size calculations for evaluating treatment policies in multi-stage designs.

    Science.gov (United States)

    Dawson, Ree; Lavori, Philip W

    2010-12-01

    Sequential multiple assignment randomized (SMAR) designs are used to evaluate treatment policies, also known as adaptive treatment strategies (ATS). The determination of SMAR sample sizes is challenging because of the sequential and adaptive nature of ATS, and the multi-stage randomized assignment used to evaluate them. We derive sample size formulae appropriate for the nested structure of successive SMAR randomizations. This nesting gives rise to ATS that have overlapping data, and hence between-strategy covariance. We focus on the case when covariance is substantial enough to reduce sample size through improved inferential efficiency. Our design calculations draw upon two distinct methodologies for SMAR trials, using the equality of the optimal semi-parametric and Bayesian predictive estimators of standard error. This 'hybrid' approach produces a generalization of the t-test power calculation that is carried out in terms of effect size and regression quantities familiar to the trialist. Simulation studies support the reasonableness of underlying assumptions as well as the adequacy of the approximation to between-strategy covariance when it is substantial. Investigation of the sensitivity of formulae to misspecification shows that the greatest influence is due to changes in effect size, which is an a priori clinical judgment on the part of the trialist. We have restricted simulation investigation to SMAR studies of two and three stages, although the methods are fully general in that they apply to 'K-stage' trials. Practical guidance is needed to allow the trialist to size a SMAR design using the derived methods. To this end, we define ATS to be 'distinct' when they differ by at least the (minimal) size of effect deemed to be clinically relevant. Simulation results suggest that the number of subjects needed to distinguish distinct strategies will be significantly reduced by adjustment for covariance only when small effects are of interest.

  6. Psychometric evaluation of the arabic brief pain inventory in a sample of Lebanese cancer patients.

    Science.gov (United States)

    Ballout, Suha; Noureddine, Samar; Huijer, Huda Abu-Saad; Kanazi, Ghassan

    2011-07-01

    Pain is a common complaint in oncology patients, and success in its treatment requires accurate assessment. Thus, assessment tools that are practical, culturally sensitive, and psychometrically sound are needed. The purpose of this study was to evaluate the psychometric properties and cultural sensitivity of the Arabic Brief Pain Inventory (BPI) in a Lebanese sample of cancer patients. The BPI measures the location and severity of pain; pain relief from treatment; and the pain's interference with life. The BPI was translated into Arabic. Its cultural sensitivity was evaluated by a panel of experts. This instrument and a visual analogue scale for pain were administered to a convenience sample of 75 adult oncology patients receiving pain treatment. The experts' ratings indicated that the tool was culturally sensitive. The majority of the patient sample (88%) was married, male (78.7%), older than 46 years (56%), and with at least a secondary education (84%). The mean pain intensity rating was 5.3 ± 1.7, with interference ratings of 5.3 ± 2.0 to 7.0 ± 2.5. Most patients (78.4%) reported more than 50% pain relief with treatment. Cronbach alpha coefficients were 0.82 and 0.92 for the severity and interference items, respectively. Factor analysis yielded two factors, replicating the severity and interference dimensions. Correlations between the severity and interference items ranged between 0.25 and 0.57 (P < 0.05). The findings support the validity, reliability, and cultural sensitivity of the Arabic BPI in Lebanese oncology patients. This tool can be used to assess pain and improve its management in this population. Copyright © 2011 U.S. Cancer Pain Relief Committee. Published by Elsevier Inc. All rights reserved.

  7. Assessment of family functioning: evaluation of the General Functioning Scale in a Swedish Bariatric Sample.

    Science.gov (United States)

    Bylund, Ami; Årestedt, Kristofer; Benzein, Eva; Thorell, Anders; Persson, Carina

    2016-09-01

    The General Functioning Scale (GFS) was developed to assess self-perceived overall family functioning. The scale has satisfactory psychometric properties, is internationally recognised and has been used in different contexts. However, no validated Swedish version is available. Healthy family functioning can support patients and help them adhere to treatment regimens. Moreover, it maintains the physical and emotional health and that of the family as a unit. Yet, there is limited information regarding family functioning postgastric bypass surgery. Thus, it is important to use validated instruments to understand family functioning in bariatric contexts. To evaluate aspects of reliability and validity in GFS in a Swedish bariatric sample, focusing on factor structure. The Swedish version of the GFS (S-GFS) was administered on two occasions to 163 participants who had undergone gastric bypass surgery 6-8 weeks prior to testing. Internal consistency, temporal stability and construct validity were assessed. Data were positively skewed. The S-GFS showed good internal consistency (ordinal α = 0.92) with a sufficient overall mean interitem correlation (0.500) and adequate temporal stability (intraclass correlation coefficient = 0.833). After modifying response alternatives, confirmatory factor analysis indicated acceptable fit for a one-factor model. The scale is a promising tool for assessing family functioning in bariatric settings. The S-GFS showed satisfactory reliability - consistent with prior research - and acceptable validity in the study sample. This study contributes to the limited research on the scale's validity. However, the S-GFS needs to be evaluated in different cultural and clinical contexts, focusing on various aspects of validity and responsiveness (sensitivity to detect significant change over time) in different samples. © 2015 Nordic College of Caring Science.

  8. Evaluation of Protamine Level in Human Sperm Samples Using Chromomycin A3 and Aniline Blue Staining

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    Durdi Qujeq

    2016-02-01

    Full Text Available Background: Current microscopic experimental methods cannot diagnose DNA damages present in spermatozoa .Therefore, some methods are needed to address the abnormality of the genetic material status on the sperm samples. As reported by many investigators aniline blue staining technique has been used for identifying sperm chromatin condensation. Also, chromomycin A3 is used for evaluation of the degree of protamination of spermatozoa. This study aimed at evaluating these two different staining techniques on human sperm protamine status. Materials and Methods: Sperm samples were collected from 72 males [including 37 infertile men: (seven asetenotratospermic, two trato-espermic, and one azo-spermic and 35 healthy fertile men]   attending the research and clinical center for infertility affiliated with Babol University of Medical Sciences. Measurement of sperm motility, volume and density of semen samples were carried out in andrology laboratory. In estimation with light microscopy aniline blue tool, in each slide, blue stained were assumed as normal spermatozoa, but dark blue stained were regarded as abnormal spermatozoa. Bright yellow stained chromomycin-reacted spermatozoa (CMA3+ were observed under fluorescent microscope with 460 nm filter considered as normal and yellowish green were assumed as abnormal. Statistical analysis results were expressed as mean ± SD. Results: The rate of reacted spermatozoa to aniline blue in the infertile group was higher than that of the healthy control group 42.8% ±8.7 vs. 17.9% ±6.4. Also, the rate of reacted spermatozoa to CMA3 in infertile and normal group was [53.6 ± 8.7 and 24.7% ±5.1], respectively. Conclusion: Infertility status could be assessed by staining the spermatozoa via aniline blue and CMA3 techniques. Combination of these two staining methods had the best predictive values for semen analysis compared to using just one method. Our results showed that both CMA3 and AB staining methods were

  9. Los taxones como tipos: Buffon, Cuvier y Lamarck Taxa as types: Buffon, Cuvier and Lamarck

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    Gustavo Caponi

    2011-03-01

    Full Text Available Darwinianamente, los grupos taxonómicos son entendidos como entidades históricas que surgen en un momento de la evolución y que siempre pueden desaparecer. Pero esos grupos también fueron entendidos por muchos naturalistas como clases naturales; es decir, como tipos permanentes, a-históricos. Es mi interés señalar algunas de las formas que ese pensamiento tipológico de hecho ha tomado, subrayando que la adopción de esa perspectiva tipológica, además de no responder a compromisos teológicos, tampoco tiene porqué obedecer a la adopción de una ontología que pueda estar en conflicto con la ciencia natural. Analizaré así el modo en el que Buffon entendió las especies y el modo en los que Cuvier y Lamarck entendieron los órdenes taxonómicos superiores.From a Darwinian point of view, taxonomic groups are understood as historical entities that arise at an evolutionary moment and that can always disappear. But these groups were also understood by many naturalists as natural kinds; in other words, as permanent, ahistorical types. I will explore some of the forms that this typological thought took, showing that this typological perspective neither depends on theological beliefs, nor obeys the adoption of an ontology that might contradict natural science. Thus I shall analyze Buffon's understanding of species and the ways in which Cuvier and Lamarck understood the higher taxonomic orders.

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

    Directory of Open Access Journals (Sweden)

    Fabíola Feres

    2006-07-01

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

  11. Taxon-restricted genes at the origin of a novel trait allowing access to a new environment.

    Science.gov (United States)

    Santos, M Emília; Le Bouquin, Augustin; Crumière, Antonin J J; Khila, Abderrahman

    2017-10-20

    Taxon-restricted genes make up a considerable proportion of genomes, yet their contribution to phenotypic evolution is poorly understood. We combined gene expression with functional and behavioral assays to study the origin and adaptive value of an evolutionary innovation exclusive to the water strider genus Rhagovelia: the propelling fan. We discovered that two taxon-restricted genes, which we named geisha and mother-of-geisha, specifically control fan development. geisha originated through a duplication event at the base of the Rhagovelia lineage, and both duplicates acquired a novel expression in a specific cell population prefiguring fan development. These gene duplicates played a central role in Rhagovelia's adaptation to a new physical environment, demonstrating that the evolution of taxon-restricted genes can contribute directly to evolutionary novelties that allow access to unexploited ecological niches. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  12. Evaluation of dengue NS1 antigen rapid tests and ELISA kits using clinical samples.

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    Subhamoy Pal

    Full Text Available Early diagnosis of dengue virus (DENV infection can improve clinical outcomes by ensuring close follow-up, initiating appropriate supportive therapies and raising awareness to the potential of hemorrhage or shock. Non-structural glycoprotein-1 (NS1 has proven to be a useful biomarker for early diagnosis of dengue. A number of rapid diagnostic tests (RDTs and enzyme-linked immunosorbent assays (ELISAs targeting NS1 antigen (Ag are now commercially available. Here we evaluated these tests using a well-characterized panel of clinical samples to determine their effectiveness for early diagnosis.Retrospective samples from South America were used to evaluate the following tests: (i "Dengue NS1 Ag STRIP" and (ii "Platelia Dengue NS1 Ag ELISA" (Bio-Rad, France, (iii "Dengue NS1 Detect Rapid Test (1st Generation" and (iv "DENV Detect NS1 ELISA" (InBios International, United States, (v "Panbio Dengue Early Rapid (1st generation" (vi "Panbio Dengue Early ELISA (2nd generation" and (vii "SD Bioline Dengue NS1 Ag Rapid Test" (Alere, United States. Overall, the sensitivity of the RDTs ranged from 71.9%-79.1% while the sensitivity of the ELISAs varied between 85.6-95.9%, using virus isolation as the reference method. Most tests had lower sensitivity for DENV-4 relative to the other three serotypes, were less sensitive in detecting secondary infections, and appeared to be most sensitive on Day 3-4 post symptom onset. The specificity of all evaluated tests ranged from 95%-100%.ELISAs had greater overall sensitivity than RDTs. In conjunction with other parameters, the performance data can help determine which dengue diagnostics should be used during the first few days of illness, when the patients are most likely to present to a clinic seeking care.

  13. Evaluation of physiologic complexity in time series using generalized sample entropy and surrogate data analysis

    Science.gov (United States)

    Eduardo Virgilio Silva, Luiz; Otavio Murta, Luiz

    2012-12-01

    Complexity in time series is an intriguing feature of living dynamical systems, with potential use for identification of system state. Although various methods have been proposed for measuring physiologic complexity, uncorrelated time series are often assigned high values of complexity, errouneously classifying them as a complex physiological signals. Here, we propose and discuss a method for complex system analysis based on generalized statistical formalism and surrogate time series. Sample entropy (SampEn) was rewritten inspired in Tsallis generalized entropy, as function of q parameter (qSampEn). qSDiff curves were calculated, which consist of differences between original and surrogate series qSampEn. We evaluated qSDiff for 125 real heart rate variability (HRV) dynamics, divided into groups of 70 healthy, 44 congestive heart failure (CHF), and 11 atrial fibrillation (AF) subjects, and for simulated series of stochastic and chaotic process. The evaluations showed that, for nonperiodic signals, qSDiff curves have a maximum point (qSDiffmax) for q ≠1. Values of q where the maximum point occurs and where qSDiff is zero were also evaluated. Only qSDiffmax values were capable of distinguish HRV groups (p-values 5.10×10-3, 1.11×10-7, and 5.50×10-7 for healthy vs. CHF, healthy vs. AF, and CHF vs. AF, respectively), consistently with the concept of physiologic complexity, and suggests a potential use for chaotic system analysis.

  14. Problems with the claim of ecotype and taxon status of the wolf in the Great Lakes region

    Science.gov (United States)

    Cronin, Matthew A.; Mech, L. David

    2009-01-01

    Koblmuller et al. (2009) analysed molecular genetic data of the wolf in the Great Lakes (GL) region of the USA and concluded that the animal was a unique ecotype of grey wolf and that genetic data supported the population as a discrete wolf taxon. However, some of the literature that the researchers used to support their position actually did not, and additional confusion arises from indefinite use of terminology. Herein, we discuss the problems with designation of a wolf population as a taxon or ecotype without proper definition and assessment of criteria.

  15. Cast Stone Oxidation Front Evaluation: Preliminary Results For Samples Exposed To Moist Air

    Energy Technology Data Exchange (ETDEWEB)

    Langton, C. A.; Almond, P. M.

    2013-11-26

    chromium and technetium (i.e., effective Cr and Tc oxidation fronts). Residual reduction capacity in the oxidized region of the test samples indicates that the remaining reduction capacity is not effective in re-reducing Cr(VI) or Tc(VII) in the presence of oxygen. Depth discrete sampling and leaching is a useful for evaluating Cast Stone and other chemically reducing waste forms containing ground granulated blast furnace slag (GGBFS) or other reduction / sequestration reagents to control redox sensitive contaminant chemistry and leachability in the near surface disposal environment. Based on results presented in this report, reduction capacity measured by the Angus-Glasser Ce(IV) method is not an appropriate or meaningful parameter for determining or predicting Tc and Cr oxidation / retentions, speciation, or solubilities in cementitious materials such as Cast Stone. A model for predicting Tc(IV) oxidation to soluble Tc(VII) should consider the waste form porosity (pathway for oxygen ingress), oxygen source, and the contaminant specific oxidation rates and oxidation fronts. Depth discrete sampling of materials exposed to realistic conditions in combination with short term leaching of crushed samples has potential for advancing the understanding of factors influencing performance. This information can be used to support conceptual model development.

  16. Molecular phylogeny and divergence times of Malagasy tenrecs: influence of data partitioning and taxon sampling on dating analyses

    NARCIS (Netherlands)

    Poux, C.; Madsen, O.; Glos, J.; Jong, de W.W.; Vences, M.

    2008-01-01

    Background Malagasy tenrecs belong to the Afrotherian clade of placental mammals and comprise three subfamilies divided in eight genera (Tenrecinae: Tenrec, Echinops, Setifer and Hemicentetes; Oryzorictinae: Oryzorictes, Limnogale and Microgale; Geogalinae:Geogale). The diversity of their morphology

  17. Evaluation of sampling systems in iron ore concentrating and pelletizing processes - quantification of total sampling error (TSE) vs. apparent process variation

    DEFF Research Database (Denmark)

    Engström, Karin; Esbensen, Kim Harry

    2018-01-01

    Process sampling is involved in grade control in all parts of the production value chain in mineral processing. Reliable sampling and assaying is essential to ensure final product quality, but the need for representative sampling is not always taken into account. By continuous control...... analyses will form a basis for suggestions of possible improvements. The results show that variographic analysis is a powerful tool to evaluate both process variations and the variability of the sampling systems employed. The extensive access to time series data allow variographic characterization (quality...... control) of all critical measurement systems and locations. At the same time, periodicity and small changes in process variation can be detected and counteracted early, minimizing the risk for producing products out of specification....

  18. Psychometric Evaluation of the MMPI-2/MMPI-2-RF Restructured Clinical Scales in an Israeli Sample.

    Science.gov (United States)

    Shkalim, Eleanor

    2015-10-01

    The current study cross-culturally evaluated the psychometric properties of the Minnesota Multiphasic Personality Inventory-2 (MMPI-2)/MMPI-2-Restructured Form Restructured Clinical (RC) Scales in psychiatric settings in Israel with a sample of 100 men and 133 women. Participants were administered the MMPI-2 and were rated by their therapists on a 188-item Patient Description Form. Results indicated that in most instances the RC Scales demonstrated equivalent or better internal consistencies and improved intercorrelation patterns relative to their clinical counterparts. Furthermore, external analyses revealed comparable or improved convergent validity (with the exceptions of Antisocial Behavior [RC4] and Ideas of Persecution [RC6] among men), and mostly greater discriminant validity. Overall, the findings indicate that consistent with previous findings, the RC Scales generally exhibit comparable to improved psychometric properties over the Clinical Scales. Implications of the results, limitations, and recommendations for future research are discussed. © The Author(s) 2014.

  19. MICROBIOLOGICAL EVALUATION OF BOVINE FROZEN SEMEN SAMPLES IN WEST BENGAL, INDIA

    Directory of Open Access Journals (Sweden)

    Joyjit Mitra

    2016-12-01

    Full Text Available A total number of 860 French mini straws (0.25 ml of frozen semen from 215 bulls from three different farms namely frozen semen bull station (FSBS, Harighata Farm (98, FSBS, Salboni (93 and Sperm Station, Beldanga (24 were evaluated for bacterial load by standard plate count (SPC technique using soyabean casein digest agar and 1% plain agar media. Following incubation at 37°C for 72 hrs average colony forming unit (CFU was estimated and bacteria were identified. Different micro-organisms identified in frozen semen samples were Staphylococcus spp., Micrococcus spp., Escherichia coli, Pseudomonas spp., Corynebacterium spp., Proteus spp., Klebsiella spp., Bacillus spp. other than Bacillus anthracis and Streptococcus spp. Several of these bacteria have been identified in association with breeding failure in cattle and warrants precautionary and preventive measures for successful breeding program.

  20. Evaluation of the Mythic 18 hematology analyzer for use with canine, feline, and equine samples.

    Science.gov (United States)

    Wassmuth, Andrea K; Riond, Barbara; Hofmann-Lehmann, Regina; Lutz, Hans

    2011-05-01

    The Mythic 18 is a fully automated hematology bench-top analyzer using impedance technology for a complete blood cell count (CBC) and a 3-part white blood cell count (WBC) differential. The purpose of the current study was to evaluate the Mythic for assessment of agreement, precision, linearity, carry-over, stability, and usability under practice conditions. Ethylenediamine tetra-acetic acid-blood samples from 122 dogs, 140 cats, and 123 horses were analyzed with the Mythic and reference methods (Sysmex XT-2000iV, manual hematocrit, and microscopic WBC differentiation). Pearson's coefficient of correlation, Passing-Bablok regression analysis, and Bland-Altman difference plots were performed to determine agreement. For precision, standard deviation and coefficients of variation were calculated. Linearity was determined according to Emancipator-Kroll. Red blood cell parameters showed excellent correlation and small biases, except for red cell distribution width and mean corpuscular hemoglobin concentration. Total WBC correlated excellently in canine and equine and very well in feline samples. In 23 feline specimens with platelet aggregates, the Mythic overestimated WBC. In all 3 species, absolute granulocyte counts correlated excellently. Equine lymphocyte counts showed good correlation whereas canine and feline lymphocyte counts correlated poorly. Feline platelets showed good correlation with a negative bias. The instrument showed good to excellent precision. The whole 3-part differential was found to be accurate in horses. In dogs and cats, absolute granulocyte counts were reliable. As with all impedance-based hematological instruments, evaluation of a blood smear is absolutely indicated to check for the presence of platelet aggregates, to verify WBC differentiation, and to identify possible abnormalities. © 2011 The Author(s)

  1. Evaluation of sampling and analytical methods for the determination of chlorodifluoromethane in air.

    Science.gov (United States)

    Seymour, M J; Lucas, M F

    1993-05-01

    In January 1989, the Occupational Safety and Health Administration (OSHA) published revised permissible exposure limits (PELs) for 212 compounds and established PELs for 164 additional compounds. In cases where regulated compounds did not have specific sampling and analytical methods, methods were suggested by OSHA. The National Institute for Occupational Safety and Health (NIOSH) Manual of Analytical Methods (NMAM) Method 1020, which was developed for 1,1,2-trichloro-1,2,2-trifluoroethane, was suggested by OSHA for the determination of chlorodifluoromethane in workplace air. Because this method was developed for a liquid and chlorodifluoromethane is a gas, the ability of NMAM Method 1020 to adequately sample and quantitate chlorodifluoromethane was questioned and tested by researchers at NIOSH. The evaluation of NMAM Method 1020 for chlorodifluoromethane showed that the capacity of the 100/50-mg charcoal sorbent bed was limited, the standard preparation procedure was incorrect for a gas analyte, and the analyte had low solubility in carbon disulfide. NMAM Method 1018 for dichlorodifluoromethane uses two coconut-shell charcoal tubes in series, a 400/200-mg tube followed by a 100/50-mg tube, which are desorbed with methylene chloride. This method was evaluated for chlorodifluoromethane. Test atmospheres, with chlorodifluoromethane concentrations from 0.5-2 times the PEL were generated. Modifications of NMAM Method 1018 included changes in the standard preparation procedure, and the gas chromatograph was equipped with a capillary column. These revisions to NMAM 1018 resulted in a 96.5% recovery and a total precision for the method of 7.1% for chlorodifluoromethane. No significant bias in the method was found. Results indicate that the revised NMAM Method 1018 is suitable for the determination of chlorodifluoromethane in workplace air.

  2. The Evaluation of a Low-Cost Colorimeter for Glucose Detection in Salivary Samples

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    Rocio B. Dominguez

    2017-11-01

    Full Text Available Given the limited access to healthcare resources, low-income settings require the development of affordable technology. Here we present the design and evaluation of a low-cost colorimeter applied to the non-invasive monitoring of Diabetes Mellitus through the detection of glucose in salival fluid. Samples were processed by the glucose oxidase-peroxidase enzymatic system and analyzed with the development equipment. A light emission diode of 532.5 nm was used as an excitation source and a RGB module was used as a receptor. A calibration curve to quantify the concentration of salivary glucose (0 to 18 mg/dL was carried out by relating the RGB components registered with glucose concentrations, achieving a limit of detection of 0.17 mg/dL with a CV of 5% (n = 3. Salivary samples of diabetic and healthy volunteers were processed with the equipment showing an average concentration of 1.5519 ± 0.4511 mg/dL for the first and 4.0479 ± 1.6103 mg/dL for the last, allowing a discrimination between both groups. Results were validated against a UV-Vis-NIR spectrophotometer with a correspondence of R2 of 0.98194 between both instruments. Results suggest the potential application of the developed device to the sensitive detection of relevant analytes with a low-cost, user-friendly, low-power and portable instrumentation.

  3. Comparative evaluation of different thermally modified wood samples finishing with UV-curable and waterborne coatings

    Science.gov (United States)

    Herrera, René; Muszyńska, Monika; Krystofiak, Tomasz; Labidi, Jalel

    2015-12-01

    Thermally modified wood has been developed as an industrial method to improve durability and dimensional stability of wood and thus extends the range of uses and service life of wood-based products. Despite the improvements gained by treatment, surface finishing using coatings prevents esthetical changes such as color degradation or occasional growth of mold adding protection in outdoor use and extending the service life of products. The wood finishing process was carried out with commercially available waterborne and UV-curable coatings on industrially modified at 192, 200, 212 °C and unmodified European ash (Fraxinus excelsior L.) wood, using an industrial rollers system and a laboratory brushing system. Changes caused by thermal treatment which could affect the surface finish were measured and compared with control samples, such as water uptake, wettability and acidity. Following the wood finishing, surface properties and esthetic changes were evaluated; as well as the coatings performance. Thermally modified wood presented improved adherence compared with unmodified wood with a significant improvement in samples modified at 212 °C, which also present the highest hardness when UV-cured. Finishes with UV-curing maintain the hydrophobic effect of thermally modified wood, whereas waterborne finishes increase the surface wettability. Thermal modification did not negatively influence on the elastic properties of the coated substrate and thus allows this material to be finished with different coating systems in the same conditions as unmodified wood.

  4. Evaluation of Cholesterol as a Biomarker for Suicidality in a Veteran Sample.

    Science.gov (United States)

    Reuter, Chuck; Caldwell, Barbara; Basehore, Heather

    2017-08-01

    A reduction in total cholesterol may alter the microviscosity of the brain-cell-membrane, reducing serotonin receptor exposure. The resulting imbalance between serotonin and dopamine may lead to an increased risk for suicidality. The objective of this research was to evaluate total cholesterol as a biological marker for suicidality in a sample of US military veterans. The study population consisted of veterans who received care at the Coatesville Veterans Affairs Medical Center (VAMC) and were included in the Suicide Prevention Coordinator's database for having suicidal ideation with evidence of escalating intent, a documented suicide attempt, or committed suicide between 2009 and 2015. The veterans' medical data were obtained from the facility's computerized patient record system. The final sample was 188 observations from 128 unique veterans. Veterans with total cholesterol levels below 168 mg/dl appeared to have a higher suicide risk than those with higher levels. The cholesterol levels of veterans reporting suicidal ideation or attempt were significantly lower than the group reporting neither [F(2, 185) = 30.19, p cholesterol levels from an earlier visit in which they did not report suicidality. A latent class analysis revealed that among other differences, suicidal veterans were younger, leaner, and had more anxiety, sleep problems, and higher education than those being seen for an issue unrelated to suicidality. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  5. Performance evaluation of continuous blood sampling system for PET study. Comparison of three detector-systems

    CERN Document Server

    Matsumoto, K; Sakamoto, S; Senda, M; Yamamoto, S; Tarutani, K; Minato, K

    2002-01-01

    To measure cerebral blood flow with sup 1 sup 5 O PET, it is necessary to measure the time course of arterial blood radioactivity. We examined the performance of three different types of continuous blood sampling system. Three kinds of continuous blood sampling system were used: a plastic scintillator-based beta detector (conventional beta detector (BETA)), a bismuth germinate (BGO)-based coincidence gamma detector (Pico-count flow-through detector (COINC)) and a Phoswich detector (PD) composed by a combination of plastic scintillator and BGO scintillator. Performance of these systems was evaluated for absolute sensitivity, count rate characteristic, sensitivity to background gamnra photons, and reproducibility for nylon tube geometry. The absolute sensitivity of the PD was 0.21 cps/Bq for sup 6 sup 8 Ga positrons at the center of the detector. This was approximately three times higher than BETA, two times higher than COINC. The value measured with BETA was stable, even when background radioactivity was incre...

  6. Evaluation of lung flute in sputum samples for molecular analysis of lung cancer.

    Science.gov (United States)

    Anjuman, Nigar; Li, Ning; Guarnera, Maria; Stass, Sanford A; Jiang, Feng

    2013-09-22

    Molecular analysis of sputum provides a promising approach for lung cancer diagnosis, yet is limited by the difficulty in collecting the specimens from individuals who can't spontaneously expectorate sputum. Lung Flute is a small self-powered audio device that can induce sputum by generating sound waves and vibrating in the airways of the lungs. Here we propose to evaluate the usefulness of Lung Flute for sputum sampling to assist diagnosis of lung cancer. Forty-three stage I lung cancer patients and 47 cancer-free individuals who couldn't spontaneously cough sputum were instructed to use Lung Flute for sputum sampling. Expressions of two microRNAs, miRs-31 and 210, were determined in the specimens by qRT-PCR. The results were compared with sputum cytology. Sputum was easily collected from 39 of 43 (90.7%) lung cancer patients and 42 of 47 (89.4%) controls with volume ranges from 1 to 5 ml (median, 2.6 ml). The specimens had less than 4% oral squamous cells, indicating that sputum was obtained from low respiratory tract. Expressions of miRs-31 and 210 in sputum were considerably higher in cancer patients than cancer-free individuals (8.990 vs. 4.514; 0.6847 vs. 0.3317; all P Flute could potentially be useful in convenient and efficient collection of sputum for molecular diagnosis of lung cancer.

  7. Development, optimization, and single laboratory validation of an event-specific real-time PCR method for the detection and quantification of Golden Rice 2 using a novel taxon-specific assay.

    Science.gov (United States)

    Jacchia, Sara; Nardini, Elena; Savini, Christian; Petrillo, Mauro; Angers-Loustau, Alexandre; Shim, Jung-Hyun; Trijatmiko, Kurniawan; Kreysa, Joachim; Mazzara, Marco

    2015-02-18

    In this study, we developed, optimized, and in-house validated a real-time PCR method for the event-specific detection and quantification of Golden Rice 2, a genetically modified rice with provitamin A in the grain. We optimized and evaluated the performance of the taxon (targeting rice Phospholipase D α2 gene)- and event (targeting the 3' insert-to-plant DNA junction)-specific assays that compose the method as independent modules, using haploid genome equivalents as unit of measurement. We verified the specificity of the two real-time PCR assays and determined their dynamic range, limit of quantification, limit of detection, and robustness. We also confirmed that the taxon-specific DNA sequence is present in single copy in the rice genome and verified its stability of amplification across 132 rice varieties. A relative quantification experiment evidenced the correct performance of the two assays when used in combination.

  8. Evaluation of bacterial diversity recovered from petroleum samples using different physical matrices

    Directory of Open Access Journals (Sweden)

    Bruna Martins Dellagnezze

    Full Text Available ABSTRACT Unraveling the microbial diversity and its complexity in petroleum reservoir environments has been a challenge throughout the years. Despite the techniques developed in order to improve methodologies involving DNA extraction from crude oil, microbial enrichments using different culture conditions can be applied as a way to increase the recovery of DNA from environments with low cellular density for further microbiological analyses. This work aimed at the evaluation of different matrices (arenite, shale and polyurethane foam as support materials for microbial growth and biofilm formation in enrichments using a biodegraded petroleum sample as inoculum in sulfate reducing condition. Subsequent microbial diversity characterization was carried out using Scanning Electronic Microscopy (SEM, Denaturing Gradient Gel Electrophoresis (DGGE and 16S rRNA gene libraries in order to compare the microbial biomass yield, DNA recovery efficiency and diversity among the enrichments. The DNA from microbial communities in petroleum enrichments was purified according to a protocol established in this work and used for 16S rRNA amplification with bacterial generic primers. The PCR products were cloned, and positive clones were screened by Amplified Ribosomal DNA Restriction Analysis (ARDRA. Sequencing and phylogenetic analyses revealed that the bacterial community was mostly represented by members of the genera Petrotoga, Bacillus, Pseudomonas, Geobacillus and Rahnella. The use of different support materials in the enrichments yielded an increase in microbial biomass and biofilm formation, indicating that these materials may be employed for efficient biomass recovery from petroleum reservoir samples. Nonetheless, the most diverse microbiota were recovered from the biodegraded petroleum sample using polyurethane foam cubes as support material.

  9. Monitoreo de la ictiofauna usando grupos taxonómicos superiores en el Parque Nacional Cabo Pulmo, México

    Directory of Open Access Journals (Sweden)

    Romeo Saldívar-Lucio

    2011-06-01

    Full Text Available El uso de indicadores biológicos es una herramienta útil para la descripción de las comunidades y permite ahorrar recursos en programas de monitoreo. Con el fin de evaluar el potencial bioindicador de grupos taxonómicos superiores en el Parque Nacional Cabo Pulmo, México, se construyeron modelos de regresión múltiple por pasos con valores de abundancia agrupados a nivel género y familia como predictores, mediante el uso de variables dependientes, los índices ecológicos de diversidad (H’, equidad (J’ y distintividad taxonómica (Δ*. Posteriormente se compararon los resultados de los modelos contra los valores de los índices ecológicos observados en un muestreo independiente. Los resultados mostraron que todos los modelos fueron altamente significativos; los valores más altos del coeficiente de determinación se obtuvieron en las regresiones aplicadas a H’, mientras que las usadas por Δ* fueron las menos precisas. Los resultados sugieren que los modelos predictivos aquí generados son susceptibles de ser aplicados en un programa de monitoreo. Este estudio sugiere la implementación de un programa de monitoreo a largo plazo basado en bioindicadores de la estructura comunitaria de peces en el Parque Nacional Cabo Pulmo, el cual combine la precisión con la facilidad de obtención de datos.Ichthyofauna monitoring using higher taxa in Cabo Pulmo National Park, México. The uses of biological indicators allow to save time, resources and staff efforts when monitoring programs are conducted. The reef fishes are among the species with biggest potential as indicators since they are conspicuous, easy to identify in the field and have ecological and economical importance. The objective of this study was to evaluate the usefulness of higher taxa to predict fish ecological indices in Cabo Pulmo reef. We generated multiple stepwise regression equations with species abundance data grouped at genera and family levels as factors, and using

  10. Application of petroleum geophysical well logging and sampling techniques for evaluating aquifer characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Temples, T.J.; Waddell, M.G. [Univ. of South Carolina, Columbia, SC (United States). Earth Science and Resource Inst.

    1996-05-01

    The Hilton Head Island Test Well {number_sign}1 was drilled to a depth of 3,833 feet to evaluate the upper Cretaceous section as a potential ground-water source for Hilton Head Island, South Carolina. The initial plan was to analyze continuous conventional cores. The interval to be analyzed extended from the top of the Eocene to the base of the Cretaceous (approximately 3,500 feet). However, due to the high cost ($400,000), the decision was made to evaluate aquifer potential using advanced geophysical logs with sidewall cores for calibration. The logging suite consisted of a dual induction resistivity, spontaneous potential, compensated neutron, density log, gamma ray, spectral gamma, multipole array acoustic log, caliper, high resolution dipmeter, and a circumferential borehole imaging log. In addition to the wireline logs, 239 sidewall cores and 12 Formation Multi-Test samples were obtained. The log, sidewall core, and FMT information were integrated into an interpretive package using computer generated logs and simple spreadsheets to calculate aquifer properties. Porosity, hydraulic conductivity, transmissivity, and lithologic data derived from this integrated analysis were then used to select screen zones. Water quality in relation to drinking water standards exceeded expectations. The information obtained from the integrated program allowed estimates to be made about the well`s productivity without the expense of conventional coring, flow testing, and completion of the well.

  11. Development of a novel flow cytometric approach to evaluate fish sperm chromatin using fixed samples

    Science.gov (United States)

    Jenkins, Jill A.

    2013-01-01

    The integrity of the paternal DNA is essential for the accurate transmission of genetic information, yet fertilization is not inhibited by chromatin breakage. Some methods are available for the sensitive detection of DNA damage and can be applied in studies of environmental toxicology, carcinogenesis, aging, and assisted reproduction techniques in both clinical and experimental settings. Because semen samples obtained from remote locations undergo chromatin damage prior to laboratory assessment, the present study was undertaken to evaluate treatments for effective chromatin staining in the development of a DNA fragmentation assay using fixed milt from yellow perch (Perca flavescens). Similar to the sperm chromatin structure assay (SCSA), susceptibility of nuclear DNA to acid-induced denaturation was measured by flow cytometry (FCM). Use of 10% buffered formalin for milt fixation allowed easier peak discrimination than 4% paraformaldehyde. The effects of time and temperature of incubation in 0.08 N HCl were evaluated in order to determine the ideal conditions for promoting DNA decondensation and making strand breaks more available for staining and detection by FCM. The best results were obtained with incubation at 37°C for 1 minute, followed by cold propidium iodide staining for 30 minutes.

  12. Evaluation of exposure-specific risks from two independent samples: a simulation study.

    Science.gov (United States)

    Reichmann, William M; Gagnon, David; Horsburgh, C Robert; Losina, Elena

    2011-01-05

    Previous studies have proposed a simple product-based estimator for calculating exposure-specific risks (ESR), but the methodology has not been rigorously evaluated. The goal of our study was to evaluate the existing methodology for calculating the ESR, propose an improved point estimator, and propose variance estimates that will allow the calculation of confidence intervals (CIs). We conducted a simulation study to test the performance of two estimators and their associated confidence intervals: 1) current (simple product-based estimator) and 2) proposed revision (revised product-based estimator). The first method for ESR estimation was based on multiplying a relative risk (RR) of disease given a certain exposure by an overall risk of disease. The second method, which is proposed in this paper, was based on estimates of the risk of disease in the unexposed. We then multiply the updated risk by the RR to get the revised product-based estimator. A log-based variance was calculated for both estimators. Also, a binomial-based variance was calculated for the revised product-based estimator. 95% CIs were calculated based on these variance estimates. Accuracy of point estimators was evaluated by comparing observed relative bias (percent deviation from the true estimate). Interval estimators were evaluated by coverage probabilities and expected length of the 95% CI, given coverage. We evaluated these estimators across a wide range of exposure probabilities, disease probabilities, relative risks, and sample sizes. We observed more bias and lower coverage probability when using the existing methodology. The revised product-based point estimator exhibited little observed relative bias (max: 4.0%) compared to the simple product-based estimator (max: 93.9%). Because the simple product-based estimator was biased, 95% CIs around this estimate exhibited small coverage probabilities. The 95% CI around the revised product-based estimator from the log-based variance provided better

  13. Evaluation of exposure-specific risks from two independent samples: A simulation study

    Directory of Open Access Journals (Sweden)

    Gagnon David

    2011-01-01

    Full Text Available Abstract Background Previous studies have proposed a simple product-based estimator for calculating exposure-specific risks (ESR, but the methodology has not been rigorously evaluated. The goal of our study was to evaluate the existing methodology for calculating the ESR, propose an improved point estimator, and propose variance estimates that will allow the calculation of confidence intervals (CIs. Methods We conducted a simulation study to test the performance of two estimators and their associated confidence intervals: 1 current (simple product-based estimator and 2 proposed revision (revised product-based estimator. The first method for ESR estimation was based on multiplying a relative risk (RR of disease given a certain exposure by an overall risk of disease. The second method, which is proposed in this paper, was based on estimates of the risk of disease in the unexposed. We then multiply the updated risk by the RR to get the revised product-based estimator. A log-based variance was calculated for both estimators. Also, a binomial-based variance was calculated for the revised product-based estimator. 95% CIs were calculated based on these variance estimates. Accuracy of point estimators was evaluated by comparing observed relative bias (percent deviation from the true estimate. Interval estimators were evaluated by coverage probabilities and expected length of the 95% CI, given coverage. We evaluated these estimators across a wide range of exposure probabilities, disease probabilities, relative risks, and sample sizes. Results We observed more bias and lower coverage probability when using the existing methodology. The revised product-based point estimator exhibited little observed relative bias (max: 4.0% compared to the simple product-based estimator (max: 93.9%. Because the simple product-based estimator was biased, 95% CIs around this estimate exhibited small coverage probabilities. The 95% CI around the revised product

  14. Extended evaluation of polymeric and lipophilic sorbents for passive sampling of marine toxins.

    Science.gov (United States)

    Zendong, Zita; Herrenknecht, Christine; Abadie, Eric; Brissard, Charline; Tixier, Céline; Mondeguer, Florence; Séchet, Véronique; Amzil, Zouher; Hess, Philipp

    2014-12-01

    Marine biotoxins are algal metabolites that can accumulate in fish or shellfish and render these foodstuffs unfit for human consumption. These toxins, released into seawater during algal occurrences, can be monitored through passive sampling. Acetone, methanol and isopropanol were evaluated for their efficiency in extracting toxins from algal biomass. Isopropanol was chosen for further experiments thanks to a slightly higher recovery and no artifact formation. Comparison of Oasis HLB, Strata-X, BondElut C18 and HP-20 sorbent materials in SPE-mode led to the choice of Oasis HLB, HP-20 and Strata-X. These three sorbents were separately exposed as passive samplers for 24 h to seawater spiked with algal extracts containing known amounts of okadaic acid (OA), azaspiracids (AZAs), pinnatoxin-G (PnTX-G), 13-desmethyl spirolide-C (SPX1) and palytoxins (PlTXs). Low density polyethylene (LDPE) and silicone rubber (PDMS) strips were tested in parallel on similar mixtures of spiked natural seawater for 24 h. These strips gave significantly lower recoveries than the polymeric sorbents. Irrespective of the toxin group, the adsorption rate of toxins on HP-20 was slower than on Oasis HLB and Strata-X. However, HP-20 and Strata-X gave somewhat higher recoveries after 24 h exposure. Irrespective of the sorbent tested, recoveries were generally highest for cyclic imines and OA group toxins, slightly lower for AZAs, and the lowest for palytoxins. Trials in re-circulated closed tanks with mussels exposed to Vulcanodinium rugosum or Prorocentrum lima allowed for further evaluation of passive samplers. In these experiments with different sorbent materials competing for toxins in the same container, Strata-X accumulated toxins faster than Oasis HLB, and HP-20, and to higher levels. The deployment of these three sorbents at Ingril French Mediterranean lagoon to detect PnTX-G in the water column showed accumulation of higher levels on HP-20 and Oasis HLB compared to Strata-X. This study

  15. Revisión taxonómica de la Familia Iridaceae para Colombia Revisión taxonómica de la Familia Iridaceae para Colombia

    Directory of Open Access Journals (Sweden)

    Betancur Betancur Julio César

    2000-06-01

    Full Text Available RESUMENSe presenta la revisión taxonómica de la familia Iridaceaepara Colombia que incluye descripcionesmorfológicas de la familia, los géneros y las especies. Se presentan claves dicotómicas paraidentificar los géneros y las especies y un análisis de la distribución geográfica y altitudinal de lasmismas. En Sisyrinchiumse incluye, asi mismo, una clave sinóptica. Se encontraron 24 especies,distribuidas en 10 géneros, de las cuales dos son naturalizadas (Crocosmia x crocosmiifloray Tigridiapavonia, 4 son nuevos registros para el país (Eleutherine bulbosa, Orthrosanthus acorifolius, O. monadelphusy Sisyrinchium mandonii, 4 tienen distribución restringida o endémica (Cipura sp. nov.?, Cypella sp.nov.?, Hesperoxiphium huilensey Libertia colombiana y dos son posibles especies nuevas para la ciencia(Cipura sp. nov.?, Cypella sp. nov.?. Las especies se distribuyen con preferencia por la región Andina(ca. 80% y Caribe (ca. 42%, mientras que la región Pacífica es la más pobremente representada(ca. 4 %. Las subregiones del país con más especies son el Altiplano Cundiboyacense, el MacizoAntioqueño, la Montaña Santandereana, las vertientes Oriental Andina y Caucana y la SierraNevada de Santa Marta. Por otra parte, las especies de Iridaceaecrecen desde el nivel del mar hasta4.500 m de altitud, pero la mayor concentración se encuentra entre 2.400 y 3.600 m, lo que co-rresponde a la abundacia de especies de los géneros Orthrosanthusy Sisyrinchium, siendo éste últimoel género que presenta la mayor amplitud de distribución altitudinal. Colombia no es un país espe-cialmente rico al compararlo con otros vecinos y regiones cercanas. Sin embargo, los páramos deColombia tienen mayor diversidad en Iridaceaeque todo el conjunto de los páramos americanos.This taxonomic revision for Colombian Iridaceaeincludes the family, genera and speciesmorphological descriptions. A geographic distribution and elevational range analysis for thespecies, a

  16. Giant Galápagos tortoises; molecular genetic analyses identify a trans-island hybrid in a repatriation program of an endangered taxon

    Directory of Open Access Journals (Sweden)

    Caccone Adalgisa

    2007-02-01

    Full Text Available Abstract Background Giant Galápagos tortoises on the island of Española have been the focus of an intensive captive breeding-repatriation programme for over 35 years that saved the taxon from extinction. However, analysis of 118 samples from released individuals indicated that the bias sex ratio and large variance in reproductive success among the 15 breeders has severely reduced the effective population size (Ne. Results We report here that an analysis of an additional 473 captive-bred tortoises released back to the island reveals an individual (E1465 that exhibits nuclear microsatellite alleles not found in any of the 15 breeders. Statistical analyses incorporating genotypes of 304 field-sampled individuals from all populations on the major islands indicate that E1465 is most probably a hybrid between an Española female tortoise and a male from the island of Pinzón, likely present on Española due to human transport. Conclusion Removal of E1465 as well as its father and possible (half-siblings is warranted to prevent further contamination within this taxon of particular conservation significance. Despite this detected single contamination, it is highly noteworthy to emphasize the success of this repatriation program conducted over nearly 40 years and involving release of over 2000 captive-bred tortoises that now reproduce in situ. The incorporation of molecular genetic analysis of the program is providing guidance that will aid in monitoring the genetic integrity of this ambitious effort to restore a unique linage of a spectacular animal.

  17. Sampling design and required sample size for evaluating contamination levels of 137Cs in Japanese fir needles in a mixed deciduous forest stand in Fukushima, Japan.

    Science.gov (United States)

    Oba, Yurika; Yamada, Toshihiro

    2017-05-01

    We estimated the sample size (the number of samples) required to evaluate the concentration of radiocesium (137Cs) in Japanese fir (Abies firma Sieb. & Zucc.), 5 years after the outbreak of the Fukushima Daiichi Nuclear Power Plant accident. We investigated the spatial structure of the contamination levels in this species growing in a mixed deciduous broadleaf and evergreen coniferous forest stand. We sampled 40 saplings with a tree height of 150 cm-250 cm in a Fukushima forest community. The results showed that: (1) there was no correlation between the 137Cs concentration in needles and soil, and (2) the difference in the spatial distribution pattern of 137Cs concentration between needles and soil suggest that the contribution of root uptake to 137Cs in new needles of this species may be minor in the 5 years after the radionuclides were released into the atmosphere. The concentration of 137Cs in needles showed a strong positive spatial autocorrelation in the distance class from 0 to 2.5 m, suggesting that the statistical analysis of data should consider spatial autocorrelation in the case of an assessment of the radioactive contamination of forest trees. According to our sample size analysis, a sample size of seven trees was required to determine the mean contamination level within an error in the means of no more than 10%. This required sample size may be feasible for most sites. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Development of a Whole Slide Imaging System on Smartphones and Evaluation With Frozen Section Samples.

    Science.gov (United States)

    Yu, Hong; Gao, Feng; Jiang, Liren; Ma, Shuoxin

    2017-09-15

    public. The image quality is reliable and throughput is approximately 1 FoV per second, yielding a 15-by-15 mm slide under 20X object lens in approximately 30-35 minutes, with little training required for the operator. The expected cost for setup is approximately US $100 and scanning each slide costs between US $1 and $10, making sWSI highly cost-effective for infrequent or low-throughput usage. In the clinical evaluation of sample-wise diagnostic reliability, average accuracy scores achieved by sWSI-scan-based diagnoses were as follows: 0.78 for breast, 0.88 for uterine corpus, 0.68 for thyroid, and 0.50 for lung samples. The respective low-sensitivity rates were 0.05, 0.05, 0.13, and 0.25 while the respective low-specificity rates were 0.18, 0.08, 0.20, and 0.25. The participating pathologists agreed that the overall quality of sWSI was generally on par with that produced by high-end scanners, and did not affect diagnosis in most cases. Pathologists confirmed that sWSI is reliable enough for standard diagnoses of most tissue categories, while it can be used for quick screening of difficult cases. As an ultra-low-cost alternative to whole slide scanners, diagnosis-ready VS quality and robustness for commercial usage is achieved in the sWSI solution. Operated on main-stream smartphones installed on normal optical microscopes, sWSI readily offers affordable and reliable WSI to resource-limited or infrequent clinical users.

  19. Development of a Whole Slide Imaging System on Smartphones and Evaluation With Frozen Section Samples

    Science.gov (United States)

    Jiang, Liren

    2017-01-01

    is currently being offered to the public. The image quality is reliable and throughput is approximately 1 FoV per second, yielding a 15-by-15 mm slide under 20X object lens in approximately 30-35 minutes, with little training required for the operator. The expected cost for setup is approximately US $100 and scanning each slide costs between US $1 and $10, making sWSI highly cost-effective for infrequent or low-throughput usage. In the clinical evaluation of sample-wise diagnostic reliability, average accuracy scores achieved by sWSI-scan-based diagnoses were as follows: 0.78 for breast, 0.88 for uterine corpus, 0.68 for thyroid, and 0.50 for lung samples. The respective low-sensitivity rates were 0.05, 0.05, 0.13, and 0.25 while the respective low-specificity rates were 0.18, 0.08, 0.20, and 0.25. The participating pathologists agreed that the overall quality of sWSI was generally on par with that produced by high-end scanners, and did not affect diagnosis in most cases. Pathologists confirmed that sWSI is reliable enough for standard diagnoses of most tissue categories, while it can be used for quick screening of difficult cases. Conclusions As an ultra-low-cost alternative to whole slide scanners, diagnosis-ready VS quality and robustness for commercial usage is achieved in the sWSI solution. Operated on main-stream smartphones installed on normal optical microscopes, sWSI readily offers affordable and reliable WSI to resource-limited or infrequent clinical users. PMID:28916508

  20. Evaluation of storage and filtration protocols for alpine/subalpine lake water quality samples

    Science.gov (United States)

    John L. Korfmacher; Robert C. Musselman

    2007-01-01

    Many government agencies and other organizations sample natural alpine and subalpine surface waters using varying protocols for sample storage and filtration. Simplification of protocols would be beneficial if it could be shown that sample quality is unaffected. In this study, samples collected from low ionic strength waters in alpine and subalpine lake inlets...

  1. Evaluation and Proposed Refinement of the Sampling Design for the Long Term Resource Monitoring Program's Fish Component

    National Research Council Canada - National Science Library

    Ickes, Brian

    2002-01-01

    ... if the sampling design adequately addresses program goals and objectives. Periodic evaluations also permit assessment of a program's ability to provide adequate and useful information for changing management and science needs...

  2. A Case control study to evaluate oxidative stress in plasma samples of oral malignancy

    Directory of Open Access Journals (Sweden)

    Kumar Chandan Srivastava

    2012-01-01

    Full Text Available Background: Imbalances between the oxidant -antioxidant status have been implicated in the pathogenesis of several diseases, including cancer. Aim: The aim of this study was to evaluate the extent of lipid peroxidation and antioxidants in the venous blood samples of oral squamous cell carcinoma patients of different Clinicopathologic stages in comparison with the healthy controls. Setting and Design: A Case control study was designed in a hospital (Rajah Muthiah Dental College and Hospital, Annamalai University based setting. Materials and Methods: Twenty new histopathologically proven oral carcinoma patients, and equal number of age, sex and habit matched healthy subjects were recruited for this study. Their blood samples were subjected to evaluation of Thiobarbituric Acid Reactive Substances (TBARS and antioxidant enzymes, namely, superoxide dismutase (SOD, Catalase (CAT reduced glutathione (GSH and glutathione peroxidase (GPx using spectrophotometric methods. Statistical Analysis: The data are expressed as mean±SD. The statistical comparisons were performed by independent Student′s t-test and One Way ANOVA. P value <0.05 was considered statistically significant. Karl Pearson correlation was performed for the biochemical parameters within the group and between the groups. For statistically significant correlations, linear regression was performed. Results: Significant enhanced lipid peroxidation (P<0.001 with decrease in antioxidants (P<0.001 was observed in the venous blood of oral squamous cell carcinoma patients as compared with the healthy controls. Accordingly, significant (P<0.001 pattern of progression in TBARS levels was observed at various clinical stages of patients. (GSH showed significant (P<0.01 negative correlation with TBARS and positive correlation (P<0.001 with SOD. On linear regression analysis, GSH showed significance for SOD (P<0.001, GPx, CAT and TBARS (P<0.01. It was also found that, 70% of variance in SOD can be

  3. Evaluation of Chromosomal Disorders in Tissue and Blood Samples in Patients with Oral Squamous Cell Carcinoma

    Directory of Open Access Journals (Sweden)

    A. Parvaneroo

    2004-12-01

    Full Text Available Statement of Problem: Many studies have indicated that genetic disturbances are common findings in patients with Oral Squamous Cell Carcinoma (OSCC. Identification of these changes can be helpful in diagnostic procedures of these tumors.Purpose: The aim of this study was to appraise the chromosomal disorders in blood and tissue patients with OSCC.Methods and Materials: In this descriptive study, the study group consisted of all OSCC patients who were referred to the Faculty of Dentistry, Tehran University of Medical Sciences, Maxillofacial Surgery Clinic of Shariati Hospital, and Amir Aalam Hospital fromSeptember 2000 to November 2002. In order to study chromosomal disorders in the peripheral blood lymphocytes, 5 mL of blood was obtained from each patient In patients with the large lesion, a piece of involved tissue were obtained and cultured for 24 hours.This led to 29 blood samples and 16 tissue specimens and any relation between OSCC and age, sex, smoking and alcohol use were evaluated.Results: In this study, OSCC was more common in males than in females (3 to 5. 31% of our patients were smokers, and one had a history of alcoholic consumption. There was an increase in incidence of OSCC with age. In this study, all patients had numerical(aneuploidy, polyploidy and structural chromosomal disorders (double minute, fragment,breakage and dicentric. There was significant difference between blood and tissue chromosomal disorders (aneuploidy, polyploidy,breakage in OSCC patients.Conclusion: It can be concluded that chromosomes in patients with OSCC might show some genetic aberration and evaluation of involved tissue might be better way for determining this disorders.

  4. Trade-off between taxon diversity and functional diversity in European lake ecosystems.

    Science.gov (United States)

    Grossmann, Lars; Beisser, Daniela; Bock, Christina; Chatzinotas, Antonis; Jensen, Manfred; Preisfeld, Angelika; Psenner, Roland; Rahmann, Sven; Wodniok, Sabina; Boenigk, Jens

    2016-12-01

    Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater data set which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a.s.l) to 3110 m a.s.l. The dominant taxa were Chlorophyta and streptophytic algae, Ciliophora, Bacillariophyta and Chrysophyta. Metatranscriptomics provided insights into differences in community composition and into functional diversity via the relative share of taxa to the overall read abundance of distinct functional genes on the ecosystem level. The dominant metabolic pathways in terms of the fraction of expressed sequences in the cDNA libraries were affiliated with primary metabolism, specifically oxidative phosphorylation, photosynthesis and the TCA cycle. Our analyses indicate that community composition is a good first proxy for the analysis of ecosystem functions. However, differential gene regulation modifies the relative importance of taxa in distinct pathways. Whereas taxon composition varies considerably between lakes, the relative importance of distinct metabolic pathways is much more stable, indicating that ecosystem functioning is buffered against shifts in community composition through a functional redundancy of taxa. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  5. 'Candidatus Phytoplasma brasiliense', a new phytoplasma taxon associated with hibiscus witches' broom disease.

    Science.gov (United States)

    Montano, H G; Davis, R E; Dally, E L; Hogenhout, S; Pimentel, J P; Brioso, P S

    2001-05-01

    Hibiscus rosa-sinensis is a valuable ornamental species widely planted in Brazil. Many plants are affected by witches' broom disease, which is characterized by excessive axillary branching, abnormally small leaves, and deformed flowers, symptoms that are characteristic of diseases attributed to phytoplasmas. A phytoplasma was detected in diseased Hibiscus by amplification of rRNA operon sequences by PCRs, and was characterized by RFLP and nucleotide sequence analyses of 16S rDNA. The collective RFLP patterns of amplified 16S rDNA differed from the patterns described previously for other phytoplasmas. On the basis of the RFLP patterns, the hibiscus witches' broom phytoplasma was classified in a new 16S rRNA RFLP group, designated group 16SrXV. A phylogenetic analysis of 16S rDNA sequences from this and other phytoplasmas identified the hibiscus witches' broom phytoplasma as a member of a distinct subclade (designated subclade xiv) of the class Mollicutes. A phylogenetic tree constructed on the basis of 16S rRNA gene sequences was consistent with the hypothesis that there was divergent evolution of hibiscus witches' broom phytoplasma and its closest relatives (members of 16S rRNA RFLP group 16SrII) from a common ancestor. On the basis of unique properties of the DNA from hibiscus witches' broom phytoplasma, it is proposed that it represents a new taxon, namely 'Candidatus Phytoplasma brasiliense'.

  6. 'Candidatus Phytoplasma luffae', a novel taxon associated with witches' broom disease of loofah, Luffa aegyptica Mill.

    Science.gov (United States)

    Davis, Robert E; Zhao, Yan; Wei, Wei; Dally, Ellen L; Lee, Ing-Ming

    2017-08-01

    The phytoplasma associated with witches' broom disease of loofah [Luffa aegyptica Mill., syn. Luffa cylindrica (L.) M.J. Roem.] in Taiwan was classified in group 16SrVIII, subgroup A (16SrVIII-A), based on results from actual and in silico RFLP analysis of 16S rRNA gene sequences. Nucleotide sequencing of PCR-amplified, cloned DNA segments revealed rrn interoperon sequence heterogeneity in the loofah witches' broom (LfWB) phytoplasma. Whereas the 16S-23S rRNA spacer region of rrnA contained a complete tRNA-Ile gene, the spacer of rrnB contained a nonfunctional remnant of a tRNA gene. Phylogenetic analysis of the rrnA and rrnB 16S rRNA genes revealed that the LfWB phytoplasma represented a distinct lineage within the phytoplasma clade, and the LfWB phytoplasma shared less than 97.5 % nucleotide sequence similarity of 16S rRNA genes with previously described 'CandidatusPhytoplasma' taxa. Based on unique properties of DNA, we propose recognition of loofah witches' broom phytoplasma strain LfWBR as representative of a novel taxon, 'CandidatusPhytoplasma luffae'.

  7. A New Taxon of Basal Ceratopsian from China and the Early Evolution of Ceratopsia.

    Science.gov (United States)

    Han, Fenglu; Forster, Catherine A; Clark, James M; Xu, Xing

    2015-01-01

    Ceratopsia is one of the best studied herbivorous ornithischian clades, but the early evolution of Ceratopsia, including the placement of Psittacosaurus, is still controversial and unclear. Here, we report a second basal ceratopsian, Hualianceratops wucaiwanensis gen. et sp. nov., from the Upper Jurassic (Oxfordian) Shishugou Formation of the Junggar Basin, northwestern China. This new taxon is characterized by a prominent caudodorsal process on the subtemporal ramus of the jugal, a robust quadrate with an expansive quadratojugal facet, a prominent notch near the ventral region of the quadrate, a deep and short dentary, and strongly rugose texturing on the lateral surface of the dentary. Hualianceratops shares several derived characters with both Psittacosaurus and the basal ceratopsians Yinlong, Chaoyangsaurus, and Xuanhuaceratops. A new comprehensive phylogeny of ceratopsians weakly supports both Yinlong and Hualianceratops as chaoyangsaurids (along with Chaoyangsaurus and Xuanhuaceratops), as well as the monophyly of Chaoyangosauridae + Psittacosaurus. This analysis also weakly supports the novel hypothesis that Chaoyangsauridae + Psittacosaurus is the sister group to the rest of Neoceratopsia, suggesting a basal split between these clades before the Late Jurassic. This phylogeny and the earliest Late Jurassic age of Yinlong and Hualianceratops imply that at least five ceratopsian lineages (Yinlong, Hualianceratops, Chaoyangsaurus + Xuanhuaceratops, Psittacosaurus, Neoceratopsia) were present at the beginning of the Late Jurassic.

  8. A New Taxon of Basal Ceratopsian from China and the Early Evolution of Ceratopsia.

    Directory of Open Access Journals (Sweden)

    Fenglu Han

    Full Text Available Ceratopsia is one of the best studied herbivorous ornithischian clades, but the early evolution of Ceratopsia, including the placement of Psittacosaurus, is still controversial and unclear. Here, we report a second basal ceratopsian, Hualianceratops wucaiwanensis gen. et sp. nov., from the Upper Jurassic (Oxfordian Shishugou Formation of the Junggar Basin, northwestern China. This new taxon is characterized by a prominent caudodorsal process on the subtemporal ramus of the jugal, a robust quadrate with an expansive quadratojugal facet, a prominent notch near the ventral region of the quadrate, a deep and short dentary, and strongly rugose texturing on the lateral surface of the dentary. Hualianceratops shares several derived characters with both Psittacosaurus and the basal ceratopsians Yinlong, Chaoyangsaurus, and Xuanhuaceratops. A new comprehensive phylogeny of ceratopsians weakly supports both Yinlong and Hualianceratops as chaoyangsaurids (along with Chaoyangsaurus and Xuanhuaceratops, as well as the monophyly of Chaoyangosauridae + Psittacosaurus. This analysis also weakly supports the novel hypothesis that Chaoyangsauridae + Psittacosaurus is the sister group to the rest of Neoceratopsia, suggesting a basal split between these clades before the Late Jurassic. This phylogeny and the earliest Late Jurassic age of Yinlong and Hualianceratops imply that at least five ceratopsian lineages (Yinlong, Hualianceratops, Chaoyangsaurus + Xuanhuaceratops, Psittacosaurus, Neoceratopsia were present at the beginning of the Late Jurassic.

  9. Estudo taxonômico de Cylindrotermes Holmgren (Isoptera, Termitidae Termitinae

    Directory of Open Access Journals (Sweden)

    Mauricio Martins da Rocha

    2007-01-01

    Full Text Available O trabalho é um estudo taxonômico de Cylindrotermes Holmgren (Isoptera, Termitidae, Termitinae, incluindo a redescrição do gênero, a descrição de três espécies novas C. caata, C. capixaba e C. sapiranga, além da redescrição de quatro, das cinco espécies anteriormente conhecidas: C. parvignathus, C. brevipilosus, C. macrognathus e C. flangiatus. Os alados de C. brevipilosus e C. macrognathus são descritos pela primeira vez. Há ilustrações de todos os soldados e alados das espécies estudadas, bem como uma chave dicotômica de identificação baseada nos soldados.A taxonomic study of Cylindrotermes Holmgren (Isoptera, Termitidae, Termitinae is presented, with a redescription of the genus, a description of three new species C. caata, C. capixaba and C. sapiranga, and a redescription of four out of the five previously known species: C. parvignathus, C. brevipilosus, C. macrognathus and C. flangiatus. The imagos of C. brevipilosus and C. macrognathus are described for the first time. Illustrations of all soldiers and imagos are provided, as well as an identificaton key based on soldiers.

  10. Sampling and Analysis Instruction for Evaluation of Residual Chromium Contamination in the Subsurface Soil at 100-C-7

    Energy Technology Data Exchange (ETDEWEB)

    W. S. Thompson

    2007-02-15

    This sampling and analysis instruction (SAI) provides the requirements for sample collection and laboratory analysis to evaluate the extent of hexavalent chromium contamination present in the soil below the 100-C-7 and 100-C-7:1 remedial action waste site excavations.

  11. Evaluation of Methods to Compute Complex Sample Standard Errors in Latent Regression Models. Research Report. ETS RR-09-49

    Science.gov (United States)

    Oranje, Andreas; Li, Deping; Kandathil, Mathew

    2009-01-01

    Several complex sample standard error estimators based on linearization and resampling for the latent regression model of the National Assessment of Educational Progress (NAEP) are studied with respect to design choices such as number of items, number of regressors, and the efficiency of the sample. This paper provides an evaluation of the extent…

  12. Evaluation of a modified sampling method for molecular analysis of air microflora.

    Science.gov (United States)

    Lech, T; Ziembinska-Buczynska, A

    2015-04-10

    A serious issue concerning the durability of economically important materials for humans related to cultural heritage is the process of biodeterioration. As a result of this phenomenon, priceless works of art, documents, and old prints have undergone a process of decomposition caused by microorganisms. Therefore, it is important to constantly monitor the presence and diversity of microorganisms in exposition rooms and storage areas of historical objects. In addition, the use of molecular biology tools for conservation studies will enable detailed research as well as reduce the time needed to perform the analyses compared with using conventional methods related to microbiology and conservation. The aim of this study was to adapt the sampling indoor air method for direct DNA extraction from microorganisms, including evaluating the extracted DNA quality and concentration. The obtained DNA was used to study the diversity of mold fungi in indoor air using polymerase chain reaction-denaturing gradient gel electrophoresis in specific archives and museum environments. The research was conducted in 2 storage rooms of the National Archives in Krakow and in 1 exposition room of the Archaeological Museum in Krakow (Poland).

  13. Precuneus proportions and cortical folding: A morphometric evaluation on a racially diverse human sample.

    Science.gov (United States)

    Bruner, Emiliano; Pereira-Pedro, Ana Sofia; Chen, Xu; Rilling, James K

    2017-05-01

    Recent analyses have suggested that the size and proportions of the precuneus are remarkably variable among adult humans, representing a major source of geometrical difference in midsagittal brain morphology. The same area also represents the main midsagittal brain difference between humans and chimpanzees, being more expanded in our species. Enlargement of the upper parietal surface is a specific feature of Homo sapiens, when compared with other fossil hominids, suggesting the involvement of these cortical areas in recent modern human evolution. Here, we provide a survey on midsagittal brain morphology by investigating whether precuneus size represents the largest component of variance within a larger and racially diverse sample of 265 adult humans. Additionally, we investigate the relationship between precuneus shape variation and folding patterns. Precuneus proportions are confirmed to be a major source of human brain variation even when racial variability is considered. Larger precuneus size is associated with additional precuneal gyri, generally in its anterior district. Spatial variation is most pronounced in the dorsal areas, with no apparent differences between hemispheres, between sexes, or among different racial groups. These dorsal areas integrate somatic and visual information together with the lateral elements of the parietal cortex, representing a crucial node for self-centered mental imagery. The histological basis and functional significance of this intra-specific variation in the upper precuneus remains to be evaluated. Copyright © 2017 Elsevier GmbH. All rights reserved.

  14. Using co-occurrence to evaluate belief coherence in a large non clinical sample.

    Directory of Open Access Journals (Sweden)

    Rachel Pechey

    Full Text Available Much of the recent neuropsychological literature on false beliefs (delusions has tended to focus on individual or single beliefs, with few studies actually investigating the relationship or co-occurrence between different types of co-existing beliefs. Quine and Ullian proposed the hypothesis that our beliefs form an interconnected web in which the beliefs that make up that system must somehow "cohere" with one another and avoid cognitive dissonance. As such beliefs are unlikely to be encapsulated (i.e., exist in isolation from other beliefs. The aim of this preliminary study was to empirically evaluate the probability of belief co-occurrence as one indicator of coherence in a large sample of subjects involving three different thematic sets of beliefs (delusion-like, paranormal & religious, and societal/cultural. Results showed that the degree of belief co-endorsement between beliefs within thematic groupings was greater than random occurrence, lending support to Quine and Ullian's coherentist account. Some associations, however, were relatively weak, providing for well-established examples of cognitive dissonance.

  15. Epidemiologic evaluation of Vancomycin Resistant genes in Enterococcus spp. isolated from clinical samples

    Directory of Open Access Journals (Sweden)

    Omid Teymournejad

    2011-09-01

    Full Text Available Background & Objectives: Isolation of vancomycin resistant Enterococcus from clinical samples is very important. The aim of this study was evaluation of phenotype and genotype of van genes in vancomycine resistant Enterococcus. Materials and Methods: 411 Enterococcus isolates were collected from selected Tehran’s hospitals between March 2004 and December 2007. The enterococcal isolates were identified by biochemical confirmation tests. Resistance of each isolate to vancomycin determined by disk diffusion and agar dilution test. The presence of the vanA, B, C, D, E resistance gene was assessed by PCR. Results: 185(45% and 23(5.6% with disc-diffusion method and agar-dilution method were resistant to vancomucin (VRE and all of VREs were Enterococcus faecium. 12 (52.2%, 7(30.4% of the VRE isolates had vanA, vanB and 3(13% had both of vanA and vanB gene. Conclusion: Most important mechanism for high level resistance to vancomycin is presence of van genes and these genes can transfer between Enterococci. Significance of investigation in molecular level of resistance to vancomycin was due to relation between phenotypic resistant and presence of van genes.

  16. Analytical performance evaluation of Anyplex II HPV28 and Euroarray HPV for genotyping of cervical samples.

    Science.gov (United States)

    Latsuzbaia, Ardashel; Tapp, Jessica; Nguyen, Trung; Fischer, Marc; Arbyn, Marc; Weyers, Steven; Mossong, Joël

    2016-07-01

    Analytically accurate human papillomavirus (HPV) genotyping methods are required to assess the impact of HPV vaccination. The aim of this study was to evaluate the analytical performance of Anyplex II HPV28 (Seegene, Korea) and Euroarray HPV (Euroimmun, Germany) genotyping kits, for conducting a future HPV vaccine efficacy monitoring study in Luxembourg. A total number of 150 cervical swabs were collected from women with mean age 31.4 years. Agreements for detecting any HPV between Aptima/Anyplex (88.0%) and Aptima/Euroarray (90.7%) were similar. Agreement of Anyplex/EuroArray with Aptima was higher for Genotypes 16, 18 or 45 than for the other 11 HPVs. The average number of HPV genotypes detected per sample was similar with 2.6 and 2.5, for Anyplex and EuroArray, respectively. In conclusion, Anyplex and Euroarray showed high agreement in general and in particular for detecting genotypes contained in HPV vaccines. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Evaluating sample allocation and effort in detecting population differentiation for discrete and continuously distributed individuals

    Science.gov (United States)

    Erin L. Landguth; Michael K. Schwartz

    2014-01-01

    One of the most pressing issues in spatial genetics concerns sampling. Traditionally, substructure and gene flow are estimated for individuals sampled within discrete populations. Because many species may be continuously distributed across a landscape without discrete boundaries, understanding sampling issues becomes paramount. Given large-scale, geographically broad...

  18. Evaluation of Two Surface Sampling Methods for Microbiological and Chemical Analyses To Assess the Presence of Biofilms in Food Companies.

    Science.gov (United States)

    Maes, Sharon; Huu, Son Nguyen; Heyndrickx, Marc; Weyenberg, Stephanie van; Steenackers, Hans; Verplaetse, Alex; Vackier, Thijs; Sampers, Imca; Raes, Katleen; Reu, Koen De

    2017-12-01

    Biofilms are an important source of contamination in food companies, yet the composition of biofilms in practice is still mostly unknown. The chemical and microbiological characterization of surface samples taken after cleaning and disinfection is very important to distinguish free-living bacteria from the attached bacteria in biofilms. In this study, sampling methods that are potentially useful for both chemical and microbiological analyses of surface samples were evaluated. In the manufacturing facilities of eight Belgian food companies, surfaces were sampled after cleaning and disinfection using two sampling methods: the scraper-flocked swab method and the sponge stick method. Microbiological and chemical analyses were performed on these samples to evaluate the suitability of the sampling methods for the quantification of extracellular polymeric substance components and microorganisms originating from biofilms in these facilities. The scraper-flocked swab method was most suitable for chemical analyses of the samples because the material in these swabs did not interfere with determination of the chemical components. For microbiological enumerations, the sponge stick method was slightly but not significantly more effective than the scraper-flocked swab method. In all but one of the facilities, at least 20% of the sampled surfaces had more than 102 CFU/100 cm2. Proteins were found in 20% of the chemically analyzed surface samples, and carbohydrates and uronic acids were found in 15 and 8% of the samples, respectively. When chemical and microbiological results were combined, 17% of the sampled surfaces were contaminated with both microorganisms and at least one of the analyzed chemical components; thus, these surfaces were characterized as carrying biofilm. Overall, microbiological contamination in the food industry is highly variable by food sector and even within a facility at various sampling points and sampling times.

  19. Thermophilic Campylobacter spp. in turkey samples: evaluation of two automated enzyme immunoassays and conventional microbiological techniques

    DEFF Research Database (Denmark)

    Borck, Birgitte; Stryhn, H.; Ersboll, A.K.

    2002-01-01

    , neckskin and environmental samples) were collected over a period of 4 months at a turkey slaughterhouse and meat-cutting plant in Denmark. Faecal and environmental samples were tested by the conventional culture method and by the two EIAs, whereas meat and neckskin samples were tested by the two EIAs only......Aims: To determine the sensitivity and specificity of two automated enzyme immunoassays (EIA), EiaFoss and Minividas, and a conventional microbiological culture technique for detecting thermophilic Campylobacter spp. in turkey samples. Methods and Results: A total of 286 samples (faecal, meat...

  20. A multistep approach in the cytologic evaluation of liver biopsy samples of dogs with hepatic diseases.

    Science.gov (United States)

    Stockhaus, C; Van Den Ingh, T; Rothuizen, J; Teske, E

    2004-09-01

    Cytologic criteria were evaluated for their diagnostic value in liver disease in dogs. Therefore, histopathologic and cytologic examination was performed on liver biopsy samples of 73 dogs with liver diseases and 28 healthy dogs. Logistic regression analysis was used to select the measured parameters to be included in a multistep approach. With the logistic regression method, different characteristic cytologic parameters could be defined for each histopathologic diagnosis. In malignant lymphoma of the liver, the presence of large numbers of lymphoblasts with a minimum of 5% of all cells was found. Clusters of epithelial cells with several cytologic characteristics of malignancy intermixed with normal hepatocytes were indicative of metastatic carcinoma or cholangiocellular carcinoma. Liver cells in hepatocellular carcinoma were characterized by a high nucleus/cytoplasm ratio, large cell diameters, increased numbers of nucleoli per nuclei, small numbers of cytoplasmic vacuoles, and frequently, small numbers of lymphocytes. Extrahepatic cholestasis was characterized by excessive extracellular bile pigment in the form of biliary casts, an increased number of nucleoli within hepatocytes, decreased hepatic cell size, and low numbers of lymphocytes. In destructive cholangiolitis, increased numbers of neutrophils and a small mean nuclear size within hepatocytes were seen. Acute and nonspecific reactive hepatitis are diagnosed based on the presence of moderate reactive nuclear patterns, including more pronounced chromatin, prominent nucleoli, increased numbers of inflammatory cells, excluding lymphocytes, and the absence of increased numbers of bile duct cell clusters. Increased number of mast cells also was indicative of nonspecific reactive hepatitis. Important cytologic criteria for the diagnosis of liver cirrhosis, in addition to chronic hepatitis, are intracellular bile accumulation and increased numbers of bile duct cell clusters. In summary, the stepwise approach

  1. [Evaluation of usefulness of different methods for detection of Cryptosporidium in human and animal stool samples].

    Science.gov (United States)

    Werner, Anna; Sulima, Paweł; Majewska, Anna C

    2004-01-01

    There are many methods for detection of Cryptosporidium oocysts. Most of them (more than 20) enable the microscopic detection of Cryptosporidium oocysts in faecal smears. Such a great variability of diagnostic methods may lead to confusion as far as the choice of an appropriate technique by a given laboratory is concerned. This study evaluated the diagnostic usefulness of Cryptosporidium oocysts and coproantigen detection methods in the diagnosis of cryptosporidiosis in human (266 stool specimen) and animals (205 from cattle, 160 from sheep, 30 from horses, 80 from cats, 227 from dogs and 11 from wild animals). The total number of human and animal stool specimens processed was 266 and 713, respectively. In this study the usefulness of several diagnostic methods was compared. The following techniques were taken into account: wet mounts, hematoxylin staining, four different specific methods (modified Zeihl-Neelsen, Kinyoun's, safranin-methylene blue, as well as carbol-methyl violet and tartrazyne) and commercially available kit based on enzyme-linked immunoassay (ProspecT(r) Cryptosporidium Microplate Assay). The final number of positive specimens was 123. Out of them 77 were positive in all specific methods. The oocysts found in stool specimens were measured. Humans were infected with C. parvum and animals with C. parvum, C. andersoni or C. felis. The statistical analysis has shown that EIA test was a better than microscopy method for identification of Cryptosporidium in faecal samples in human and wild animal. Sensitivity and specificity are important factors for the choice of a proper diagnostic method for Cryptosporidium detection, however other factors such as cost, simplicity and ease of interpretation of results are also important considerations.

  2. Evaluation of the DSM-5 severity indicator for binge eating disorder in a community sample.

    Science.gov (United States)

    Grilo, Carlos M; Ivezaj, Valentina; White, Marney A

    2015-03-01

    Research has examined various aspects of the diagnostic criteria for binge-eating disorder (BED) but has yet to evaluate the DSM-5 severity criterion. This study examined the DSM-5 severity criterion for BED based on binge-eating frequency and tested an alternative severity specifier based on overvaluation of shape/weight. 338 community volunteers categorized with DSM-5 BED completed a battery of self-report instruments. Participants were categorized first using DSM-5 severity levels and second by shape/weight overvaluation and were compared on clinical variables. 264 (78.1%) participants were categorized as mild, 67 (19.8%) as moderate, 6 (1.8%) as severe, and 1 (0.3%) as extreme. Analyses comparing mild and moderate severity groups revealed no significant differences in demographic variables or BMI; the moderate severity group had greater eating-disorder psychopathology (small effect-sizes) but not depression than the mild group. Participants with overvaluation (N = 196; 60.1%) versus without (N = 130; 39.9%) did not differ significantly in age, sex, BMI, or binge-eating frequency. The overvaluation group had significantly greater eating-disorder psychopathology and depression than the non-overvaluation group. The greater eating-disorder and depression levels (medium-to-large effect-sizes) persisted after adjusting for ethnicity/race and binge-eating severity/frequency, without attenuation of effect-sizes. Findings from this non-clinical community sample provide support for overvaluation of shape/weight as a specifier for BED as it provides stronger information about severity than the DSM-5 rating based on binge-eating. Future research should include treatment-seeking patients with BED to test the utility of DSM-5 severity specifiers and include broader clinical validators. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Comparison of sampling procedures and microbiological and non-microbiological parameters to evaluate cleaning and disinfection in broiler houses.

    Science.gov (United States)

    Luyckx, K; Dewulf, J; Van Weyenberg, S; Herman, L; Zoons, J; Vervaet, E; Heyndrickx, M; De Reu, K

    2015-04-01

    Cleaning and disinfection of the broiler stable environment is an essential part of farm hygiene management. Adequate cleaning and disinfection is essential for prevention and control of animal diseases and zoonoses. The goal of this study was to shed light on the dynamics of microbiological and non-microbiological parameters during the successive steps of cleaning and disinfection and to select the most suitable sampling methods and parameters to evaluate cleaning and disinfection in broiler houses. The effectiveness of cleaning and disinfection protocols was measured in six broiler houses on two farms through visual inspection, adenosine triphosphate hygiene monitoring and microbiological analyses. Samples were taken at three time points: 1) before cleaning, 2) after cleaning, and 3) after disinfection. Before cleaning and after disinfection, air samples were taken in addition to agar contact plates and swab samples taken from various sampling points for enumeration of total aerobic flora, Enterococcus spp., and Escherichia coli and the detection of E. coli and Salmonella. After cleaning, air samples, swab samples, and adenosine triphosphate swabs were taken and a visual score was also assigned for each sampling point. The mean total aerobic flora determined by swab samples decreased from 7.7±1.4 to 5.7±1.2 log CFU/625 cm2 after cleaning and to 4.2±1.6 log CFU/625 cm2 after disinfection. Agar contact plates were used as the standard for evaluating cleaning and disinfection, but in this study they were found to be less suitable than swabs for enumeration. In addition to measuring total aerobic flora, Enterococcus spp. seemed to be a better hygiene indicator to evaluate cleaning and disinfection protocols than E. coli. All stables were Salmonella negative, but the detection of its indicator organism E. coli provided additional information for evaluating cleaning and disinfection protocols. Adenosine triphosphate analyses gave additional information about the

  4. Critical applications of SW 846 US EPA methods to evaluation of marine samples quality

    Directory of Open Access Journals (Sweden)

    Patrícia Ferreira Silvério

    2010-06-01

    Full Text Available Technical evaluation of analytical data is of extreme relevance considering it can be used for comparisons with environmental quality standards and decision-making as related to the management of disposal of dredged sediments and the evaluation of salt and brackish water quality in accordance with CONAMA 357/05 Resolution. It is, therefore, essential that the project manager discusses the environmental agency's technical requirements with the laboratory contracted for the follow-up of the analysis underway and even with a view to possible re-analysis when anomalous data are identified. The main technical requirements are: (1 method quantitation limits (QLs should fall below environmental standards; (2 analyses should be carried out in laboratories whose analytical scope is accredited by the National Institute of Metrology (INMETRO or qualified or accepted by a licensing agency; (3 chain of custody should be provided in order to ensure sample traceability; (4 control charts should be provided to prove method performance; (5 certified reference material analysis or, if that is not available, matrix spike analysis, should be undertaken and (6 chromatograms should be included in the analytical report. Within this context and with a view to helping environmental managers in analytical report evaluation, this work has as objectives the discussion of the limitations of the application of SW 846 US EPA methods to marine samples, the consequences of having data based on method detection limits (MDL and not sample quantitation limits (SQL, and present possible modifications of the principal method applied by laboratories in order to comply with environmental quality standards.Avaliação técnica do resultado analítico é de extrema relevância, pois o mesmo será utilizado para comparação com legislações e tomadas de decisão, tais como, disposição adequada de sedimento dragado e avaliação da qualidade de água superficial salobra e salina

  5. Marine Biodiversity in Temperate Western Australia: Multi-Taxon Surveys of Minden and Roe Reefs

    Directory of Open Access Journals (Sweden)

    Zoe Richards

    2016-03-01

    Full Text Available A growing body of evidence indicates that temperate marine ecosystems are being tropicalised due to the poleward extension of tropical species. Such climate mediated changes in species distribution patterns have the potential to profoundly alter temperate communities, as this advance can serve to push temperate taxa, many of which are southern Australian endemics, southward. These changes can lead to cascading effects for the biodiversity and function of coastal ecosystems, including contraction of ranges/habitats of sensitive cool water species. Hence there is growing concern for the future of Australia’s temperate marine biodiversity. Here we examine the diversity and abundance of marine flora and fauna at two reefs near Perth’s metropolitan area—Minden Reef and Roe Reef. We report the presence of 427 species of marine flora and fauna from eight taxon groups occurring in the Perth metropolitan area; at least three species of which appear to be new to science. Our data also extends the known range of 15 species, and in numerous instances, thousands of kilometres south from the Kimberley or Pilbara and verifies that tropicalisation of reef communities in the Perth metropolitan area is occurring. We report the presence of 24 species endemic to south-west Australia that may be at risk of range contractions with continued ocean warming. The results of these surveys add to our knowledge of local nearshore marine environments in the Perth metropolitan area and support the growing body of evidence that indicates a diverse and regionally significant marine fauna occurs in temperate Western Australia. Regular, repeated survey work across seasons is important in order to thoroughly document the status of marine biodiversity in this significant transition zone.

  6. Revisión taxonómica del grupo Haplothrips-Karnyothrips (Thysanoptera: Phlaeothripidae

    Directory of Open Access Journals (Sweden)

    Axel P Retana-Salazar

    2007-06-01

    Full Text Available Se revisa el estado taxonómico del grupo Haplothrips y al mismo tiempo del grupo Karnyothrips, separándose este en varios nuevos géneros por considerarse parafilético; se describen los nuevos géneros Vargasia, Willeia y Aguilaria separados del antiguo Karnyothrips. Se describe un nuevo género de Thysanoptera-Phlaeothripidae procedente del Pacífico Central de Costa Rica. Este género se distingue por los estiletes maxilares muy apartados entre sí, carece de puente maxilar, la forma de la pelta y la seta B1 que es 2/3 la longitud del tubo. Se presenta el análisis crítico de este género y los posibles táxones emparentados, estableciendo un nuevo grupo a partir de las condiciones presentadas por Jironiella gen. n.Taxonomic revision of the Haplothrips-Karnyothrips group (Thysanoptera: Phlaeothripidae. The generic group ("ensemble" Haplothrips-Karnyothrips is reviewed, following the most recently published criteria for distinguishing generic characters. We establish a new diagnosis for each genus. A review of a Central American collection is included and a new genus of Phlaeothripidae is described from the Central Pacific of Costa Rica from specimens collected on Cyperaceae flowers during the dry season. The genus can be distinguished by widely separated maxillary stylets, absent maxillary bridge, pelta shape and the setae B1, which measures two thirds of the tube length. We include a key based on characters of phylogenetic importance. Rev. Biol. Trop. 55 (2: 627-635. Epub 2007 Jun 29.

  7. Utilization of industrial enzymes in the evaluation of neutral detergent insoluble fiber content in high-starch samples

    Directory of Open Access Journals (Sweden)

    Daiany Íris Gomes

    2014-09-01

    Full Text Available It were performed two experiments to evaluate the utilization of industrial enzymes in the evaluation of NDF contents in high-starch materials. In the first experiment, it was verified the accuracy of estimates of neutral detergent fiber (NDF obtained with the utilization of three industrial enzymes (Termamyl 2X, Liquozyme Supra 2.2.X, and Amylase AG 300L at different volumes (50, 100, 250 or 500 mL/ sample. Samples were simulated to contain starch at 0, 100, 300, 500 and 1000 g/kg using purified cellulose and starch (n = 240. In the second experiment, samples of corn grain and sorghum grain were evaluated considering the same enzyme types and volumes used in the first experiment adding aliquots without using enzyme (n = 104. There was no significant bias of NDF recovery for simulated samples containing starch up to 300 g/kg. Considering those samples, none difference among enzymes was observed. It was observed a more intense decrease in NDF content according to each enzyme unit added on corn when compared to sorghum. Considering NDF evaluation in samples with mass of 0.7 to 1.0 g, it can be recommended the utilization of 250 mL the ?-amylases Termamyl and 2X Liquozyme 2.2X with activities of 240 and 300 KNU/g, respectively.

  8. An evaluation of sampling and full enumeration strategies for Fisher Jenks classification in big data settings

    Science.gov (United States)

    Rey, Sergio J.; Stephens, Philip A.; Laura, Jason R.

    2017-01-01

    Large data contexts present a number of challenges to optimal choropleth map classifiers. Application of optimal classifiers to a sample of the attribute space is one proposed solution. The properties of alternative sampling-based classification methods are examined through a series of Monte Carlo simulations. The impacts of spatial autocorrelation, number of desired classes, and form of sampling are shown to have significant impacts on the accuracy of map classifications. Tradeoffs between improved speed of the sampling approaches and loss of accuracy are also considered. The results suggest the possibility of guiding the choice of classification scheme as a function of the properties of large data sets.

  9. Evaluation of sampling methods for the detection of Salmonella in broiler flocks

    DEFF Research Database (Denmark)

    Skov, Marianne N.; Carstensen, B.; Tornoe, N.

    1999-01-01

    The present study compares four different sampling methods potentially applicable to detection of Salmonella in broiler flocks, based on collection of faecal samples (i) by hand, 300 fresh faecal samples (ii) absorbed on five sheets of paper (iii) absorbed on five pairs of socks (elastic cotton...... horizontal or vertical) were found in the investigation. The results showed that the sock method (five pairs of socks) had a sensitivity comparable with the hand collection method (60 pools of five faecal samples); the paper collection method was inferior, as was the use of only one pair of socks, Estimation...

  10. Using and Evaluating ISEE, a New Computer Program for Teaching Sampling and Statistical Inference.

    Science.gov (United States)

    Dimitrova, Ganka; And Others

    1993-01-01

    Describes the background, development, and testing of a computer software program designed to teach principles of statistical sampling in social science courses. Compares results of a field test of the program, Introduction to Sampling Error Experiments (ISEE), with traditional instruction. (CFR)

  11. Evaluating Quality of Aged Archival Formalin-Fixed Paraffin-Embedded Samples for RNA-Sequencing

    Science.gov (United States)

    Archival formalin-fixed paraffin-embedded (FFPE) samples offer a vast, untapped source of genomic data for biomarker discovery. However, the quality of FFPE samples is often highly variable, and conventional methods to assess RNA quality for RNA-sequencing (RNA-seq) are not infor...

  12. Method Evaluation And Field Sample Measurements For The Rate Of Movement Of The Oxidation Front In Saltstone

    Energy Technology Data Exchange (ETDEWEB)

    Almond, P. M. [Savannah River Site (SRS), Aiken, SC (United States); Kaplan, D. I. [Savannah River Site (SRS), Aiken, SC (United States); Langton, C. A. [Savannah River Site (SRS), Aiken, SC (United States); Stefanko, D. B. [Savannah River Site (SRS), Aiken, SC (United States); Spencer, W. A. [Savannah River Site (SRS), Aiken, SC (United States); Hatfield, A. [Clemson University, Clemson, SC (United States); Arai, Y. [Clemson University, Clemson, SC (United States)

    2012-08-23

    The objective of this work was to develop and evaluate a series of methods and validate their capability to measure differences in oxidized versus reduced saltstone. Validated methods were then applied to samples cured under field conditions to simulate Performance Assessment (PA) needs for the Saltstone Disposal Facility (SDF). Four analytical approaches were evaluated using laboratory-cured saltstone samples. These methods were X-ray absorption spectroscopy (XAS), diffuse reflectance spectroscopy (DRS), chemical redox indicators, and thin-section leaching methods. XAS and thin-section leaching methods were validated as viable methods for studying oxidation movement in saltstone. Each method used samples that were spiked with chromium (Cr) as a tracer for oxidation of the saltstone. The two methods were subsequently applied to field-cured samples containing chromium to characterize the oxidation state of chromium as a function of distance from the exposed air/cementitious material surface.

  13. Towards steady-state direct solid sample analysis by inductively coupled plasma atomic emission spectrometry: qualitative evaluation of an intraplasmic powdered sample digester

    Science.gov (United States)

    Hamier, Jan; Salin, Eric D.

    1998-08-01

    A new type of reactor designed for continuous halogen-assisted digestion and analysis of powdered samples was evaluated. Two different halogenating gas introduction methods were tested, as well as the use of an internal baffle to increase the residence time of the solids inside the reactor. Studies were carried out on Al 2O 3 and CuO as model compounds for optimization of the reactor's parameters, such as the carrier gas flow, the fraction of halogenating gas and the feed rate, using Freon-12 as the halogenating gas. A qualitative study of a pseudo fluidized bed reactor (PFBR) was also performed on a soil sample certified reference material (SO-4). The internal gas flow rate had to be kept to an absolute minimum in order to minimize cooling of the PFBR's inner walls. Pre-mixing of the halogenating reagent into the solid aerosol carrier resulted in a much more efficient reaction than separate flow introduction. The use of a baffle drastically improved the digestion efficiency by virtue of an increased solid residence time. The argon plasma did not have a sufficiently high heat transfer capability to ensure proper operation of the PFBR under continuous sample loading. The porosity of the graphite used for the PFBR construction caused some tailing and memory effects due to analyte seepage into the reactor's walls.

  14. Evaluation of Freshness of Soft Tissue Samples with Optical Coherence Tomography Assisted by Low Frequency Electric Field

    OpenAIRE

    A. Pena; A. Sadovoy; A. Doronin; A. Bykov; I. Meglinski

    2015-01-01

    We present an optical coherence tomography based methodology to determine freshness of soft tissue samples by evaluation of their interaction with low frequency electric field. Various biological tissues samples of different stages of freshness were exposed by low frequency electric current. The influence of the low frequency electric field on tissues was observed and quantified by the double correlation optical coherence tomography (dcOCT) approach developed in house. The quantitative evalua...

  15. Estudio taxonómico preliminar de los Grylloidea de España (Insecta, Orthoptera

    Directory of Open Access Journals (Sweden)

    Gorochov, A. V.

    2001-12-01

    >Modicogryllus (M. algirius (Saussure, 1877 is also recorded for the first time for France. On the other hand, we recognise Eugryllodes panteli (Cazurro, 1888 as a good species. An identification key with figures for the species of the genus Petaloptila is presented. The male genitalia of several species is also studied for the first time. The type series of Gryllodes macropterus Fuente, 1894 and Gryllotalpa septemdecimchromosomica Ortiz, 1958 and two paratypes of Gryllomorpha adspersa merobricensis Fernandes, 1959, stat. n. are localized. Lectotypes and paralectotypes of 17 taxons are designated. The distribution of all species is revised.

    En el presente trabajo se realiza un estudio taxonómico y faunístico de la superfamilia Grylloidea de España, incluyendo las islas Baleares y Canarias. Se examinan las 60 especies y subespecies que se han encontrado hasta ahora en este país, siendo seis de ellas nuevas para la ciencia: Petaloptila (P. fermini, P. (P. isabelae, P. (Zapetaloptila venosa, P. (Z. barrancoi, Paramogoplistes dentatus sp. n. y Grylloderes orlovskajae adventicius subsp. n.; asimismo se crean dos nuevos subgéneros Italoptila y Zapetaloptila. Se establece una sinonimia correcta del género Grylloderes Bolívar, 1894 (=Platygryllus Chopard, 1961, syn. dist., así como siete sinonimias específicas: Gryllomorpha (G. dalmatina (Ocskay, 1832 (=Gryllomorpha dalmatina strumae Andreeva, 1982, syn. n., Petaloptila (P. aliena (Brunner-Wattenwyl, 1882 (=Discoptila eitschbergeri Harz, 1976, syn. n., Acheta hispanicus Rambur, 1839 (=Gryllus erythrospilus Walker, 1869, syn. n., Gryllus hispanicus var. fusculus Bolívar, 1927, syn. n., Eumodicogryllus bordigalensis (Latreille, 1802 (=Gryllodes ferdinandi Bolívar, 1899, syn. n., Gryllus chinensis var. intermedia Bolívar, 1927, syn. n., Eugryllodes pipiens

  16. Shorlist Masterplan Wind. Evaluation of the sampling grid of the year-round ichthyoplankton survey

    NARCIS (Netherlands)

    Bolle, L.J.; Beek, van J.K.L.

    2011-01-01

    Within the research programme 'Shortlist Masterplan Wind' a year-round ichthyoplankton survey is being carried out. The sampling area is based on known spawning concentrations and prevailing currents.

  17. A QUANTITATIVE EVALUATION OF THE WATER DISTRIBUTION IN A SOIL SAMPLE USING NEUTRON IMAGING

    Directory of Open Access Journals (Sweden)

    Jan Šácha

    2016-10-01

    Full Text Available This paper presents an empirical method by Kang et al. recently proposed for correcting two-dimensional neutron radiography for water quantification in soil. The method was tested on data from neutron imaging of the water infiltration in a soil sample. The raw data were affected by neutron scattering and by beam hardening artefacts. Two strategies for identifying the correction parameters are proposed in this paper. The method has been further developed for the case of three-dimensional neutron tomography. In a related experiment, neutron imaging is used to record ponded-infiltration experiments in two artificial soil samples. Radiograms, i.e., two-dimensional projections of the sample, were acquired during infiltration. A calculation was made of the amount of water and its distribution within the radiograms, in the form of two-dimensional water thickness maps. Tomograms were reconstructed from the corrected and uncorrected water thickness maps to obtain the 3D spatial distribution of the water content within the sample. Without the correction, the beam hardening and the scattering effects overestimated the water content values close to the perimeter of the sample, and at the same time underestimated the values close to the centre of the sample. The total water content of the entire sample was the same in both cases. The empirical correction method presented in this study is a relatively accurate, rapid and simple way to obtain the quantitatively determined water content from two-dimensional and three-dimensional neutron images. However, an independent method for measuring the total water volume in the sample is needed in order to identify the correction parameters.

  18. Evaluation of different sized blood sampling tubes for thromboelastometry, platelet function, and platelet count

    DEFF Research Database (Denmark)

    Andreasen, Jo Bønding; Pistor-Riebold, Thea Unger; Knudsen, Ingrid Hell

    2014-01-01

    Background: To minimise the volume of blood used for diagnostic procedures, especially in children, we investigated whether the size of sample tubes affected whole blood coagulation analyses. Methods: We included 20 healthy individuals for rotational thromboelastometry (RoTEM®) analyses and compa......Background: To minimise the volume of blood used for diagnostic procedures, especially in children, we investigated whether the size of sample tubes affected whole blood coagulation analyses. Methods: We included 20 healthy individuals for rotational thromboelastometry (RoTEM®) analyses...

  19. Evaluation of fungal contamination in operating rooms using a dusting cloth pad: comparison among different sampling methods.

    Science.gov (United States)

    D'Alessandro, Daniela; Cerquetani, Franco; Deriu, Maria Grazia; Montagna, Maria Teresa; Mura, Ida; Napoli, Christian; Vescia, Nicoletta

    2013-07-01

    To evaluate microbial contamination in hospitals environments, several methods are available, each one having its limitations. Therefore, the choice of system to use is open. This study compares the ability of a dusting cloth pad (DC pad) with 2 other methods (Rodac contact plate and air sampling) to detect contamination because of filamentous fungi in operating rooms, performing 110 sampling campaigns in hospitals of 3 Italian cities. Overall, 96% of the DC pad samples were positive compared with 51% of Rodac plates (P contamination of filamentous fungi. Copyright © 2013 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

  20. An evaluation of sampling methods for the detection of Escherichia coli and Salmonella on Turkey carcasses.

    Science.gov (United States)

    McEvoy, J M; Nde, C W; Sherwood, J S; Logue, C M

    2005-01-01

    The efficacy of rinse, excision, and swab methods for the microbiological analysis of prechill turkey carcasses was investigated. Aerobic plate counts from a 50-cm2 area of the breast sampled by excision and by swabbing were compared. Escherichia coli and Salmonella recoveries were determined from turkeys sampled by a carcass rinse (CR), a modified rinse with the carcass supported in a swing (MCR), a two-site swab of 50 cm2 at the back and thigh (2S), a one-site swab of 50 cm2 beneath the wing (1S), a whole-carcass swab of the inner and outer carcass surface (WS), and excision of 25 g of neck skin tissue (NE). The effect of diluent volume (25, 50, and 100 ml) on E. coli counts from swab samples was also assessed. The aerobic plate count from breast tissue sampled by excision was greater than that by swabbing (P diluent (P diluent, E. coli recoveries by the MCR, 2S, 1S, and WS methods were similar. For swabs stomached in 50 ml of diluent, Salmonella recoveries by the WS and MCR methods were higher than those by the 2S and 1S methods. Excision was more effective than swabbing for obtaining total bacterial counts from reduced turkey carcass areas. Whole-carcass sampling by rinsing or swabbing is necessary for optimum Salmonella recovery. Sampling a reduced area of the carcass is sufficient for E. coli analysis.

  1. Evaluation of micro-colorimetric lipid determination method with samples prepared using sonication and accelerated solvent extraction methods.

    Science.gov (United States)

    Billa, Nanditha; Hubin-Barrows, Dylan; Lahren, Tylor; Burkhard, Lawrence P

    2014-02-01

    Two common laboratory extraction techniques were evaluated for routine use with the micro-colorimetric lipid determination method developed by Van Handel (1985) [2] and recently validated for small samples by Inouye and Lotufo (2006) [1]. With the accelerated solvent extraction method using chloroform:methanol solvent and the colorimetric lipid determination method, 28 of 30 samples had significant proportional bias (α=1%, determined using standard additions) and 1 of 30 samples had significant constant bias (α=1%, determined using Youden Blank measurements). With sonic extraction, 0 of 6 samples had significant proportional bias (α=1%) and 1 of 6 samples had significant constant bias (α=1%). These demonstrate that the accelerated solvent extraction method with chloroform:methanol solvent system creates an interference with the colorimetric assay method, and without accounting for the bias in the analysis, inaccurate measurements would be obtained. Published by Elsevier B.V.

  2. Evaluating the performance of sampling plans to detect hypoglycin A in ackee fruit shipments imported into the United States.

    Science.gov (United States)

    Whitaker, Thomas B; Saltsman, Joyce J; Ware, George M; Slate, Andrew B

    2007-01-01

    Hypoglycin A (HGA) is a toxic amino acid that is naturally produced in unripe ackee fruit. In 1973, the U.S. Food and Drug Administration (FDA) placed a worldwide import alert on ackee fruit, which banned the product from entering the United States. The FDA has considered establishing a regulatory limit for HGA and lifting the ban, which will require development of a monitoring program. The establishment of a regulatory limit for HGA requires the development of a scientifically based sampling plan to detect HGA in ackee fruit imported into the United States. Thirty-three lots of ackee fruit were sampled according to an experimental protocol in which 10 samples, i.e., ten 19 oz cans, were randomly taken from each lot and analyzed for HGA by using liquid chromatography. The total variance was partitioned into sampling and analytical variance components, which were found to be a function of the HGA concentration. Regression equations were developed to predict the total, sampling, and analytical variances as a function of HGA concentration. The observed HGA distribution among the test results for the 10 HGA samples was compared with the normal and lognormal distributions. A computer model based on the lognormal distribution was developed to predict the performance of sampling plan designs to detect HGA in ackee fruit shipments. The performance of several sampling plan designs was evaluated to demonstrate how to manipulate sample size and accept/reject limits to reduce misclassification of ackee fruit lots.

  3. Evaluation of microbial contamination of feces and soil on a laying-hen farm depending on sampling site and season

    Directory of Open Access Journals (Sweden)

    Beata Trawińska

    2016-04-01

    Full Text Available ABSTRACT The objective of the present study was to evaluate soil collected from a laying-hen farm and bird manure according to the season of the year and sampling site. Soil samples were taken at the poultry facility wall and at the distances of 15 m and 45 m from the building. Bird feces samples were collected inside the poultry house at the entrance and at 1/4 and 1/2 length of the building. Soil and bird feces samples were evaluated by bacteriological qualitative and quantitative analyses. The largest bacterial load was determined in the samples taken at the poultry facility wall in December/January. Soil microbial contamination degree was low. The highest bacterial count in bird manure was found in the samples collected at 1/2 length of the hen house at the end of December/January. The qualitative study of bird feces showed the presence of E. coli bacteria all through the research period and Enterobacter spp. in the samples taken from July until September. Microbial contamination of soil environment and bird feces is most likely to be affected by winter period as at that time the highest microbial population can be determined. This fact may be linked to the prevailing climatic and microclimatic conditions.

  4. Evaluation of the COMSOL software electro-polishing of samples; Evaluation du logiciel COMSOL electropolissage d'echantillons

    Energy Technology Data Exchange (ETDEWEB)

    Bruchon, M

    2007-07-01

    The niobium electro-polishing is efficient if a viscous layer exists at the surface. In order to define parameters of samples electro-polishing, opened with difficulty to the experiments, the simulation is essential. This report presents works realized with the COMSOL software. The Nernst Planck equations have been associated to the Navier Stockes ones for an incompressible fluid. The study of the potential behaviour on the viscous layer and the mobility value have been detailed. (A.L.B.)

  5. Signature Evaluation Tool (SET: a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures

    Directory of Open Access Journals (Sweden)

    Lin Chi-Hung

    2008-01-01

    Full Text Available Abstract Background The identification of specific gene expression signature for distinguishing sample groups is a dominant field in cancer research. Although a number of tools have been developed to identify optimal gene expression signatures, the number of signature genes obtained is often overly large to be applied clinically. Furthermore, experimental verification is sometimes limited by the availability of wet-lab materials such as antibodies and reagents. A tool to evaluate the discrimination power of candidate genes is therefore in high demand by clinical researchers. Results Signature Evaluation Tool (SET is a Java-based tool adopting the Golub's weighted voting algorithm as well as incorporating the visual presentation of prediction strength for each array sample. SET provides a flexible and easy-to-follow platform to evaluate the discrimination power of a gene signature. Here, we demonstrated the application of SET for several purposes: (1 for signatures consisting of a large number of genes, SET offers the ability to rapidly narrow down the number of genes; (2 for a given signature (from third party analyses or user-defined, SET can re-evaluate and re-adjust its discrimination power by selecting/de-selecting genes repeatedly; (3 for multiple microarray datasets, SET can evaluate the classification capability of a signature among datasets; and (4 by providing a module to visualize the prediction strength for each sample, SET allows users to re-evaluate the discrimination power on mis-grouped or less-certain samples. Information obtained from the above applications could be useful in prognostic analyses or clinical management decisions. Conclusion Here we present SET to evaluate and visualize the sample-discrimination ability of a given gene expression signature. This tool provides a filtration function for signature identification and lies between clinical analyses and class prediction (or feature selection tools. The simplicity

  6. The taxonomic status of the Mexican oak Quercus undata (Fagaceae, Quercus, Section Quercus El estatus taxonómico del encino mexicano Quercus undata (Fagaceae, Quercus, Sección Quercus

    Directory of Open Access Journals (Sweden)

    Jeffrey R. Bacon

    2011-12-01

    Full Text Available Quercus undata Trel. (Fagaceae, Quercus, Section Quercus has a complex taxonomic and nomenclatural history. Intensive sampling of oaks at the type locality of Q. undata Trel. in Durango, Mexico and evaluation of herbarium specimens and plants in the field indicate that Q. undata represents variation in Quercus chihuahuensis Trel. in white oak communities where introgressive hybridization among Q. chihuahuensis, Q. grisea Liebm., and a third white oak, Q. arizonica Sarg. made species identification difficult. Endlich's type specimen of Q. undata, as designated by Trelease, was apparently destroyed in bombing raids on Berlin during World War II, and we propose herein as lectotype the Trelease illustration of the type. An epitype is also designated in support of the lectotype, given that some features cannot be critically observed on the illustration. The long peduncles of the specimen illustrated by Trelease indicate a close relation to Q. chihuahuensis.Quercus undata Trel. (Fagaceae, Quercus, Section Quercus tiene una compleja historia taxonómica y de nomenclatura. Un muestreo intensivo de los encinos en la localidad tipo de Q. undata en Durango, México y análisis de ejemplares en herbario y en el campo indican que Q. undata representa variación en Q. chihuahuensis Trel. en los sitios donde la hibridación introgresiva entre Q. chihuahuensis, Q. grisea Liebm., y un tercer encino blanco, Q. arizonica Sarg., dificultan la identificación de especies. El ejemplar tipo designado por Trelease aparentemente fue destruido en el bombardeo de Berlín durante la Segunda Guerra Mundial, por lo que se propone como lectotipo a la ilustración del tipo en la obra de Trelease. Se designa también un epitipo dado que algunos rasgos no pueden ser críticamente observados en la ilustración. Los largos pedúnculos del espécimen ilustrado por Trelease indican la relación cercana a Q. chihuahuensis.

  7. El género Marielliottia (Hifomicetes, Ascomycota: Nuevo taxón asociado a la Micoflora del Grano de Trigo en Argentina The genus Marielliottia (Hyphomycetes, Ascomycota: a new taxon associated with wheat grain mycoflora in Argentina

    Directory of Open Access Journals (Sweden)

    Marina Sisterna

    2006-12-01

    Full Text Available Se registra por primera vez al género Marielliottia asociado a la micoflora del grano de trigo pan en Argentina. Marielliottia biseptata fue aislada de muestras de semillas provenientes de ensayos conducidos en la Estación Experimental Julio Hirschhorn (Los Hornos, Buenos Aires. Las semillas fueron sembradas en agar papa glucosado (APG e incubadas a 21± 1°C ; HR 80% bajo 12 h luz + UV; 12 h de oscuridad. La evaluación para el relevamiento de los hongos se realizó a los 5 y 8 días mediante una lupa estereoscópica. Para la identificación taxonómica, se examinaron las características micromorfológicas y de cultivo. Se realizaron inoculaciones sobre semillas con suspensión de esporas. Se presenta una descripción, ilustraciones, antecedentes e importancia del hongo aquí tratado.For the first time, the genus Marielliottia is registered on wheat grains in Argentina. This fungus was isolated from seed samples from trials conducted at the Estación Experimental Julio Hirschhorn (Los Hornos, Buenos Aires. The seeds were plated on potato dextrose agar (PDA and incubated at 21±1°C; HR 80% under fluorescent lamps supplemented with UV light during 12 h photoperiod. Evaluation was performed for the presence of fungi at 5 and 8 days with the aid of a stereoscopic microscope. For taxonomic identification, the micromorphology and cultures features were examined. As a result of this study, Marielliottia biseptata was determined and inoculations with spore suspension on seeds were carried out. A description, illustrations, antecedents and importance of the treated fungus are presented.

  8. Evaluation of ELISA screening test for detecting aflatoxin in biogenic dust samples

    Energy Technology Data Exchange (ETDEWEB)

    Durant, J.T.

    1996-05-01

    Aflatoxin is a carcinogenic chemical that is sometimes produced when agricultural commodities are infested by the fungi Aspergillus flavus and A. Parasiticus. Aflatoxin has been found to be present in air samples taken around persons handling materials likely to be contaminated. The purpose of this investigation was to demonstrate the feasibility of using an Enzyme Linked Immunosorbent Assay (ELISA) test kit that was developed to screen for aflatoxin in bulk agricultural commodities, to an air sample. Samples were taken from two environments likely to be contaminated with aflatoxin, a dairy farm feed mixing operation and a peanut bagging operation. The dust collected from these environments was considered to be biogenic, in that it originated primarily from biological materials.

  9. Standard sampling method of Longkong leaf for evaluation of plant nutrient status

    Directory of Open Access Journals (Sweden)

    Sae-lim, M.

    2005-05-01

    Full Text Available Leaf analysis is a tool for effective fertilizer recommendations in fruit trees. To achieve this goal, suitable leaf sampling method is a very important step. This study aimed to investigate leaf age, leaflet from different compound leaf positions and number of trees to be sampled as a representative sample for plant nutrient status of Longkong (Aglaia dookkoo Griff. tree. The middle pair of leaflets from the 1st, 2nd, 3rd, and 4th compound leaves from growing twigs at the lower canopy of Longkong trees were separately sampled and the following nutrients were determined: nitrogen (N, phosphorus (P, potassium (K, calcium (Ca and magnesium (Mg. The effect of soil fertility management and leaf age collected from twigs flushed at flowering and post harvest stages on nutrient concentration was investigated. Results showed that concentrations of plant nutrients in leaflets collected from different compound leaf positions were not significantly different. The leaf nutrient concentration depended on soil fertility management, higher fertilizer input resulting in higher leaf nutrient concentration. As leaf age increased, concentrations of N, P and K tended to decrease. In contrast, concentrations of Ca and Mg increased with leaf age. However, concentrations of most nutrients showed minimum variation with leaf aged 3-6 months. It is, thus, suggested that the middle pair leaflet of the 2nd compound leaf position aged 3-6 months of the lower twig should be sampled at post harvest stage from 25-35 trees to be used as a composite sample for plant nutrient analysis.

  10. Evaluation of a new commercial assay for the detection of Rotavirus in stool samples

    Directory of Open Access Journals (Sweden)

    Maria Cristina Arcangeletti

    2010-06-01

    Full Text Available Rotaviruses belonging to the Reoviridae family, are the most common causative agents of severe diarrhoea in infants and young children. Rotaviruses are easily spread by hand-to-mouth contact with stool from an infected person.Although most children with rotavirus diarrhoea recover on their own, in same cases they become very ill with severe vomiting, diarrhoea and life-threatening loss of fluids that requires hospitalization. In this context, the availability of effective laboratory diagnostic methods is important to assure a correct and rapid identification of these agents and to control viral spread. In this study 58 stool samples were analyzed by traditional virological methods used in diagnostic routine, such as electron microscopy (ME, a commercial assay based on latex agglutination for rotavirus proteins and the analysis of the electropherotype of rotavirus RNA segments (used only for those samples with a negative agglutination test. An additional method, the immunochromatographic assay RIDA ®QUICK Rotavirus (R-Biopharm for the research of virus-specific proteins, was applied retrospectively on the same samples stored at -80°C. Among the 58 stool samples included in this study, 46/58 (79.3% were identified as reovirus-like by ME; 41/58 (70.6% of them resulted positive for rotavirus by the latex agglutination test.The 5 samples negative by the latter method were tested for the electropherotype analysis, that demonstrated the positivity for rotavirus genome segments.The immunochromatographic assay RIDA ®QUICK Rotavirus identified as positive all the 46 samples (yet found as reovirus-like by EM, including those positive by the agglutination method, as well as those resulted positive with the electropherotype analysis. Taken together, these data support the effectiveness of the immunochromatographic test RIDA ®QUICK Rotavirus, that is not only a cheap and simple-to-use method, allowing an easy interpretation of results, but also showed a

  11. Evaluation of the Validity of Groundwater Samples Obtained Using the Purge Water Management System at SRS

    Energy Technology Data Exchange (ETDEWEB)

    Beardsley, C.C.

    1999-04-27

    As part of the demonstration testing of the Purge Water Management System (PWMS) technology at the Savannah River Site (SRS), four wells were equipped with PWMS units in 1997 and a series of sampling events were conducted at each during 1997-1998. Three of the wells were located in A/M Area while the fourth was located at the Old Radioactive Waste Burial Ground in the General Separations Area.The PWMS is a ''closed-loop'', non-contact, system used to collect and return purge water to the originating aquifer after a sampling event without having significantly altered the water quality. One of the primary concerns as to its applicability at SRS, and elsewhere, is whether the PWMS might resample groundwater that is returned to the aquifer during the previous sampling event. The purpose of the present investigation was to compare groundwater chemical analysis data collected at the four test wells using the PWMS vs. historical data collected using the standard monitoring program methodology to determine if the PWMS provides representative monitoring samples.The analysis of the groundwater chemical concentrations indicates that the PWMS sampling methodology acquired representative groundwater samples at monitoring wells ABP-1A, ABP-4, ARP-3 and BGO-33C. Representative groundwater samples are achieved if the PWMS does not resample groundwater that has been purged and returned during a previous sampling event. Initial screening calculations, conducted prior to the selection of these four wells, indicated that groundwater velocities were high enough under the ambient hydraulic gradients to preclude resampling from occurring at the time intervals that were used at each well. Corroborating evidence included a tracer test that was conducted at BGO-33C, the high degree of similarity between analyte concentrations derived from the PWMS samples and those obtained from historical protocol sampling, as well as the fact that PWMS data extend all previously

  12. Evaluation of toxicity of sediment samples collected from the Santa Ana National Wildlife Refuge, Texas

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The objective of this study was to evaluate the toxicity of sediments collected from the Santa Ana National Wildlife Refuge, Hidalgo Co in southern Texas, USA. A...

  13. Evaluation of some toxic metals in blood samples of smokers in ...

    African Journals Online (AJOL)

    Purpose: To determine some toxic elements in the blood of cigarette and tobacco pipe smokers in Riyadh, Saudi Arabia. Methods: The study setting was Riyadh, the capital city of Saudi Arabia, Riyadh City. Male volunteers, aged 20 - 58 year, whose blood samples were collected, were classified into three groups of ...

  14. EVALUATION OF ZEBU NELLORE CATTLE BLOOD SAMPLES USING THE CELL-DYN 3500 HEMATOLOGY ANALYZER

    Directory of Open Access Journals (Sweden)

    Alexandre Secorun Borges

    2014-12-01

    Full Text Available The Cell-dyn 3500 is a multiparameter flow cytometer, which may analyze samples from several species performing several simultaneous analyses. It is able to perform white blood cells, red blood cells and platelet counts, besides differential leukocyte counts, packed cell volume and hemoglobin determination. Cell-Dyn 3500 performs total leukocyte count both optically and by impedance. The equipment may choose one or other method, based on the reliability of the results. Erythrocyte and platelet counts are determined by impedance. Leukocyte differentiation is based on an optical principle, using separation in multiangular polarized light. The objective of this study was to compare the results of complete blood count of Zebu Nellore heifers from Celldyn 3500, with those obtained from a semi-automated cell counter (Celm CC 510 and the manual technique. Blood samples were collected from the jugular vein in 5 mL EDTA vacuum tubes from 58 Nellore heifers, at 24 months of age. Samples were processed in parallel in the three different techniques. Results were analyzed using paired t test, Pearson’s correlation and the Bland-Altmann method. There was a strong correlation for all parameters analyzed by Cell-Dyn 3500, manual method and semiautomated cell counter, except for basophils and monocytes counts. These results confirm that this analyzer is reliable for blood samples analysis of zebu cattle.

  15. Evaluation of surface sampling method performance for Bacillus Spores on clean and dirty outdoor surfaces.

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Mollye C.; Einfeld, Wayne; Boucher, Raymond M.; Brown, Gary Stephen; Tezak, Matthew Stephen

    2011-06-01

    Recovery of Bacillus atrophaeous spores from grime-treated and clean surfaces was measured in a controlled chamber study to assess sampling method performance. Outdoor surfaces investigated by wipe and vacuum sampling methods included stainless steel, glass, marble and concrete. Bacillus atrophaeous spores were used as a surrogate for Bacillus anthracis spores in this study designed to assess whether grime-coated surfaces significantly affected surface sampling method performance when compared to clean surfaces. A series of chamber tests were carried out in which known amounts of spores were allowed to gravitationally settle onto both clean and dirty surfaces. Reference coupons were co-located with test coupons in all chamber experiments to provide a quantitative measure of initial surface concentrations of spores on all surfaces, thereby allowing sampling recovery calculations. Results from these tests, carried out under both low and high humidity conditions, show that spore recovery from grime-coated surfaces is the same as or better than spore recovery from clean surfaces. Statistically significant differences between method performance for grime-coated and clean surfaces were observed in only about half of the chamber tests conducted.

  16. Water-quality sampling plan for evaluating the distribution of bigheaded carps in the Illinois Waterway

    Science.gov (United States)

    Duncker, James J.; Terrio, Paul J.

    2017-02-27

    The two nonnative invasive bigheaded carp species (bighead carp Hypophthalmichthys nobilis and silver carp H. molitrix) that were accidentally released in the 1970s have spread widely into the rivers and waterways of the Mississippi River Basin. First detected in the lower reaches of the Illinois Waterway (IWW, the combined Illinois River-Des Plaines River-Chicago Area Waterway System) in the 1990s, bighead and silver carps moved quickly upstream, approaching the Chicago Area Waterway System. The potential of substantial negative ecological and economic impact to the Great Lakes from the presence of these species is a concern. However, since 2006, the population front of bigheaded carps has remained in the vicinity of Joliet, Illinois, near river mile 278. This reach of the IWW is characterized by stark changes in habitat, water quality, and food resources as the waterway transitions from a primarily agricultural landscape to a metropolitan and industrial canal system. This report describes a 2015 plan for sampling the IWW to establish water-quality conditions that might be contributing to the apparent stalling of the population front of bigheaded carps in this reach. A detailed description of the study plan, Lagrangian-style sampling approach, selected analytes, sampling methods and protocols are provided. Hydrographs from streamflow-gaging stations show IWW conditions during the 2015 sampling runs.

  17. Measurement of nasal nitric oxide : evaluation of six different sampling methods

    NARCIS (Netherlands)

    de Winter-de Groot, K. M.; van der Ent, C. K.

    Specific guidelines are developed for the measurement of bronchial FE(NO), however, nasal nitric oxide (nNO) measurement is not standardised yet, resulting in divergent nNO values. This study compares six different sampling methods for nNO as described in the literature, to analyse their outcome and

  18. Evaluation of a gas chromatography method for azelaic acid determination in selected biological samples

    Science.gov (United States)

    Garelnabi, Mahdi; Litvinov, Dmitry; Parthasarathy, Sampath

    2010-01-01

    Background: Azelaic acid (AzA) is the best known dicarboxilic acid to have pharmaceutical benefits and clinical applications and also to be associated with some diseases pathophysiology. Materials and Methods: We extracted and methylesterified AzA and determined its concentration in human plasma obtained from healthy individuals and also in mice fed AzA containing diet for three months. Results: AzA was detected in Gas Chromatography (GC) and confirmed by Liquid chromatography mass spectrometry (LCMS), and gas chromatography mass spectrometry (GCMC). Our results have shown that AzA can be determined efficiently in selected biological samples by GC method with 1nM limit of detection (LoD) and the limit of quantification (LoQ); was established at 50nM. Analytical Sensitivity as assayed by hexane demonstrated an analytical sensitivity at 0.050nM. The method has demonstrated 8-10% CV batch repeatability across the sample types and 13-18.9% CV for the Within-Lab Precision analysis. The method has shown that AzA can efficiently be recovered from various sample preparation including liver tissue homogenate (95%) and human plasma (97%). Conclusions: Because of its simplicity and lower limit of quantification, the present method provides a useful tool for determining AzA in various biological sample preparations. PMID:22558586

  19. Development and evaluation of a lightweight sensor system for emission sampling from open area sources

    Science.gov (United States)

    A new sensor system for mobile and aerial emission sampling was developed for open area sources, such as open burning. The sensor system, termed “Kolibri”, consists of multiple low-cost air quality sensors measuring CO2, CO, and black carbon, samplers for particulate matter with ...

  20. Development and evaluation of a lightweight sensor system for aerial emission sampling from open area sources

    Science.gov (United States)

    A new sensor system for mobile and aerial emission sampling was developed for open area pollutant sources, such as prescribed forest burns. The sensor system, termed “Kolibri”, consists of multiple low-cost air quality sensors measuring CO2, CO, samplers for particulate matter wi...

  1. Evaluation of a new commercial assay for the detection of norovirus in stool samples

    Directory of Open Access Journals (Sweden)

    Maria Cristina Arcangeletti

    2010-03-01

    Full Text Available Noroviruses are important human pathogens causing acute gastroenteritis; they can hardly be propagated in any cell culture system and are often difficult to visualize by using electron microscopy (ME. These aspects, as well as the need of an accurate diagnosis justify the development of a number of rapid diagnostic methods aimed at improving the identification of noroviruses and based on the research of viral genomic sequences or, alternatively, of norovirus specific proteins. In this study 60 stool samples were analyzed by traditional techniques, such as cell culture (MT, and by rapid methods like ME and nested reverse transcriptase-polimerase chain reaction (nRT-PCR.A third rapid test, the immunochromatographic assay RIDA ®QUICK Norovirus (R-Biopharm for the research of norovirus proteins (belonging to genogroups I and II, was used retrospectively on the same samples stored at -80°C. The results obtained by using nRT-PCR (i.e. the most sensitive method and the immunochromatographic assay were compared, showing that 39 samples were positive and 21 negative in nRT-PCR, while only 28 (71.8% were positive with the immunochromatographic assay; among the negative samples, one resulted positive with RIDA ®QUICK Norovirus. The latter test proved to be appreciably sensitive, even if nRT-PCR still remains the gold standard method for the laboratory diagnosis of norovirus. Nevertheless, the easy-to-use and cheaper immunochromatographic assay can be usefully applied as a screening test.

  2. EVALUATING PROBABILITY SAMPLING STRATEGIES FOR ESTIMATING REDD COUNTS: AN EXAMPLE WITH CHINOOK SALMON (Oncorhynchus tshawytscha)

    Science.gov (United States)

    Precise, unbiased estimates of population size are an essential tool for fisheries management. For a wide variety of salmonid fishes, redd counts from a sample of reaches are commonly used to monitor annual trends in abundance. Using a 9-year time series of georeferenced censuses...

  3. The negative affect repair questionnaire: factor analysis and psychometric evaluation in three samples

    Directory of Open Access Journals (Sweden)

    Scherer Anne

    2013-01-01

    Full Text Available Abstract Background Negative affect and difficulties in its regulation have been connected to several adverse psychological consequences. While several questionnaires exist, it would be important to have a theory-based measure that includes clinically relevant items and shows good psychometric properties in healthy and patient samples. This study aims at developing such a questionnaire, combining the two Gross [1] scales Reappraisal and Suppression with an additional response-focused scale called Externalizing Behavioral Strategies covering clinically relevant items. Methods The samples consisted of 684 students (mean age = 23.3, SD = 3.5; 53.6% female and 369 persons with mixed mental disorders (mean age = 36.0 SD = 14.6; 71.2% female. Items for the questionnaire were derived from existing questionnaires and additional items were formulated based on suggestions by clinical experts. All items start with “When I don’t feel well, in order to feel better…”. Participants rated how frequently they used each strategy on a 5-point Likert scale. Confirmatory Factor Analyses were conducted to verify the factor structure in two separate student samples and a clinical sample. Group comparisons and correlations with other questionnaires were calculated to ensure validity. Results After modification, the CFA showed good model fit in all three samples. Reliability scores (Cronbach’s α for the three NARQ scales ranged between .71 and .80. Comparisons between students and persons with mental disorders showed the postulated relationships, as did comparisons between male and female students and persons with or without Borderline Personality Disorder. Correlations with other questionnaires suggest the NARQ’s construct validity. Conclusions The results indicate that the NARQ is a psychometrically sound and reliable measure with practical use for therapy planning and tracking of treatment outcome across time. We advocate the integration

  4. Revisión Taxonómica de las Especies Monoicas de Amaranthus (Amaranthaceae): Amaranthus subg. Amaranthus y Amaranthus subg. Albersia1

    National Research Council Canada - National Science Library

    Néstor D. Bayón

    2015-01-01

    ... revisión taxonómica de las especies monoicas del género Amaranthus, esto es las que conforman Amaranthus subg. Amaranthus (13 especies) y Amaranthus subg. Albersia (Kunth) Gren. & Godr. (52 especies...

  5. Comparative Evaluation of Drug Deposition in Hair Samples Collected from Different Anatomical Body Sites.

    Science.gov (United States)

    Tzatzarakis, Manolis N; Alegakis, Athanasios K; Kavvalakis, Matthaios P; Vakonaki, Elena; Stivaktakis, Polychronis D; Kanaki, Katerina; Vardavas, Alexander I; Barbounis, Emmanouil G; Tsatsakis, Aristidis M

    2017-04-01

    In this study, we focused on the validation of a method for the simultaneous detection and quantification of cannabinoids, cocaine and opiates in hair as well as on the distribution of the drugs deposition in hair collected from different anatomical body sites. The proposed analytical procedure was validated for various parameters such as selectivity, linearity, limit of quantification, precision, accuracy, matrix effect and recovery. Four hundred and eighty-one samples were collected during 2010-2015 from 231 drug abusers. A 6-h ultrasonic-assisted methanolic extraction was applied for the isolation of the drugs. The analysis was performed in an liquid chromatography-mass spectrometry system for the opiates and cocaine and in a gas chromatography-mass spectrometry system for the cannabinoids. Cocaine was the most frequent detected drug (68.8-80.5%) followed by cannabinoids (47.6-63.3%) and opiates (34.7-46.7%) depending on the body site that the samples were collected. The mean concentrations of Δ9-tetrahydrocannabinol (THC) were 0.63 ± 2.11 for head, 0.54 ± 1.03 for pubic, 0.34 ± 0.51 for axillary and 0.18 ± 0.18 ng/mg for chest hair samples. The values of cocaine were 6.52 ± 15.98, 4.64 ± 10.77, 6.96 ± 38.21 and 3.94 ± 6.35 ng/mg, while the values of 6-monoacetylmorphine (MAM) were 3.33 ± 5.89, 3.06 ± 9.33, 1.37 ± 1.37 and 16.4 ± 1.77 ng/mg for head, pubic, axillary and chest samples, respectively. Differences between the detected concentrations of cocaine and opiates between the hair samples of different anatomical sites, as well as the ratio of drug metabolites to the parent compounds were observed in some cases. Statistically significant differences in the mean detected levels were noticed for morphine and heroin between head and pubic hair and also for cocaine and benzoylecgonine, between head and axillary hair samples. Moreover, the ratio of MAM to morphine and THC to cannabinol seems to correlate statistically with the total opiate or

  6. Psychometric Evaluation of Somatic and Psychological Health Report: A Sample from Chinese Adolescents.

    Science.gov (United States)

    Shi, Ling; Wu, Fuxiang; Ye, Lin; Zhu, Gu; Lu, Zuhong; Liu, Yangyang

    2017-04-01

    The purpose of the present study was to do a psychometric evaluation of the somatic and psychological health report (SPHERE) among Chinese adolescents. Our participants were 116 twins (50 females). Psychometric evaluation indicated that the reliability and validity of this scale were good. The internal consistencies and split-half reliabilities of all subscales were above 0.80. Furthermore, the item-total correlations were acceptable for all the subscales (all the values were higher than 0.20). The present findings suggest that the SPHERE can be well used to measure Chinese adolescents' somatic and psychological health.

  7. Impact of spatially constrained sampling of temporal contact networks on the evaluation of the epidemic risk

    CERN Document Server

    Vestergaard, Christian L; Génois, Mathieu; Poletto, Chiara; Colizza, Vittoria; Barrat, Alain

    2016-01-01

    The ability to directly record human face-to-face interactions increasingly enables the development of detailed data-driven models for the spread of directly transmitted infectious diseases at the scale of individuals. Complete coverage of the contacts occurring in a population is however generally unattainable, due for instance to limited participation rates or experimental constraints in spatial coverage. Here, we study the impact of spatially constrained sampling on our ability to estimate the epidemic risk in a population using such detailed data-driven models. The epidemic risk is quantified by the epidemic threshold of the susceptible-infectious-recovered-susceptible model for the propagation of communicable diseases, i.e. the critical value of disease transmissibility above which the disease turns endemic. We verify for both synthetic and empirical data of human interactions that the use of incomplete data sets due to spatial sampling leads to the underestimation of the epidemic risk. The bias is howev...

  8. Evaluating the performance of species richness estimators: sensitivity to sample grain size

    DEFF Research Database (Denmark)

    Hortal, Joaquín; Borges, Paulo A. V.; Gaspar, Clara

    2006-01-01

    scores in a number of estimators (the above-mentioned plus ICE, Chao2, Michaelis-Menten, Negative Exponential and Clench). The estimations from those four sample sizes were also highly correlated. 4.  Contrary to other studies, we conclude that most species richness estimators may be useful......Fifteen species richness estimators (three asymptotic based on species accumulation curves, 11 nonparametric, and one based in the species-area relationship) were compared by examining their performance in estimating the total species richness of epigean arthropods in the Azorean Laurisilva forests...... different sampling units on species richness estimations. 2.  Estimated species richness scores depended both on the estimator considered and on the grain size used to aggregate data. However, several estimators (ACE, Chao1, Jackknife1 and 2 and Bootstrap) were precise in spite of grain variations. Weibull...

  9. Municipal solid waste composition: Sampling methodology, statistical analyses, and case study evaluation

    DEFF Research Database (Denmark)

    Edjabou, Vincent Maklawe Essonanawe; Jensen, Morten Bang; Götze, Ramona

    2015-01-01

    stratification parameter. Separating food leftovers from food packaging during manual sorting of the sampled waste did not have significant influence on the proportions of food waste and packaging materials, indicating that this step may not be required. (C) 2014 Elsevier Ltd. All rights reserved.......Sound waste management and optimisation of resource recovery require reliable data on solid waste generation and composition. In the absence of standardised and commonly accepted waste characterisation methodologies, various approaches have been reported in literature. This limits both...... comparability and applicability of the results. In this study, a waste sampling and sorting methodology for efficient and statistically robust characterisation of solid waste was introduced. The methodology was applied to residual waste collected from 1442 households distributed among 10 individual sub...

  10. Experimental Evaluation of the Surface Alteration of Gasket Samples under Operative Conditions

    Directory of Open Access Journals (Sweden)

    M.C. Bignozzi

    2015-12-01

    Full Text Available This paper investigates the surface alteration of gasket samples commercialized by two alternative producers. These gaskets, in polymeric materials, are installed in process plants used for cleaning tires molds by a pioneering ultrasonic process. They are exposed to a combination of ultrasonic waves, temperature, humidity and acid attack causing several erosion phenomena. Their surface degradation under ordinary operative conditions was investigated using mechanical and tribological tests. The experimental characterization was performed by optical microscopy, scanning electron microscopy, thermograms, differential scanning calorimetry curves and infrared spectra aiming at defining the specific mechanics of wearing. As a conclusion, it was possible to state that even if samples exhibit similar chemical structures, their thermal and mechanical properties as well as their geometric dimensions are different. Such differences in the materials might cause various unexpected wear behaviors when gaskets are employed in the same working conditions.


  11. Evaluation of the HB&L system for the culture of prosthetic and osteoarticular origin samples

    Directory of Open Access Journals (Sweden)

    Agostina Ronca

    2010-06-01

    Full Text Available Prosthetic and osteoarticular infections represent a complex condition to diagnose and resolve. In both cases, the eradication of microorganisms is difficult because of anatomical and physiological characteristics of the site of infection (bone.The best strategy for an effective pharmacological treatment is based on an early diagnosis confirmed by microbiological testing of bone, periprosthetic tissue or removed prostheses, to support clinicians to undertake prolonged targeted therapy. The purpose of this paper is to assess the clinical correlation between the results of the cultures performed with automated HB&L (ALIFAX system compared to the result of traditional methods. HB&L is a system to perform bacterial cultures, susceptibility and direct P.A.R. tests on biological materials based on detection of bacteria and fungi by laser light-scattering kinetics in liquid culture medium at 37°C. Samples get to laboratory are inoculated in rich broth and placed in the incubator. The next day are processed accordin to the following protocol: 500 ml of the broth are transferred in the vial of the instrument and 200 ml of supplement DEB for fastidious organisms are added.The cultures are incubated for 360 minutes in the same time PAR test (antimicrobial residual power is determined. In the first half of 2009 418 samples collected from prostheses and osteoarticular infections from 118 patients were analyzed.The tests showed 304 negative and 114 positive samples (27.30% from which were isolated Gram negative (17.5% and Gram positive (82.5% bacteria. Gram positive included 38.3% S. aureus, 33% coagulase negative Staphylococci and 26.6% Enterococci. Preliminary data obtained by the HB&L system for the culture of tissue sample, as well as the improvement of surgical techniques have led to a significant increase in correlation with the clinical data compared to traditional microbiological analysis.

  12. Pharmacognostical Evaluation of Arctii Fructus (2) : Adulteration on the Chinese Commercial Samples

    OpenAIRE

    TING-GUO, KANGO; TOMOKO, KAWAMURA; YUKIO, NORO; TOSHIIHRO, TANAKA; Department of Chinese Material Medica, Liaoning College of Traditional Chinese Medicine; Faculty of Pharmacy, Meijo University

    1999-01-01

    Samples of Arctii Fructus, fruits of Arctium lappa, commercially obtained in various provinces of China were found to be adulterated with fruits of five species, Arctium tomentosum, Silybum marianum, Amorpha fruticosa, Onopordum acanthium and Aucklandia lappa. HPLC revealed that the chemical compositions of the fruits of Ar. tomentosum was very similar composition to that of Arctium lappa, the origin plant of Arctii Fructus. The fruits of O. acanthium and Au. lappa containedarctiin, but, thei...

  13. Evaluation of limited sampling methods for estimation of tacrolimus exposure in adult kidney transplant recipients

    Science.gov (United States)

    Barraclough, Katherine A; Isbel, Nicole M; Kirkpatrick, Carl M; Lee, Katie J; Taylor, Paul J; Johnson, David W; Campbell, Scott B; Leary, Diana R; Staatz, Christine E

    2011-01-01

    AIMS To examine the predictive performance of limited sampling methods for estimation of tacrolimus exposure in adult kidney transplant recipients. METHODS Twenty full tacrolimus area under the concentration–time curve from 0 to 12 h post-dose (AUC0–12) profiles (AUCf) were collected from 20 subjects. Predicted tacrolimus AUC0–12 (AUCp) was calculated using the following: (i) 42 multiple regression-derived limited sampling strategies (LSSs); (ii) five population pharmacokinetic (PK) models in the Bayesian forecasting program TCIWorks; and (iii) a Web-based consultancy service. Correlations (r2) between C0 and AUCf and between AUCp and AUCf were examined. Median percentage prediction error (MPPE) and median absolute percentage prediction error (MAPE) were calculated. RESULTS Correlation between C0 and AUCf was 0.53. Using the 42 LSS equations, correlation between AUCp and AUCf ranged from 0.54 to 0.99. The MPPE and MAPE were tacrolimus exposure compared with C0 measurement. Several LSSs based on sampling taken 2 h or less post-dose predicted exposure with acceptable bias and imprecision. Generally, Bayesian forecasting methods required inclusion of a concentration measurement from <2 h post-dose to adequately predict exposure. PMID:21219401

  14. Evaluation of metal ions in rice samples: extraction and direct determination by ICP OES

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Andrea; Cadore, Solange, E-mail: cadore@iqm.unicamp.br [Instituto de Quimica, Universidade Estadual de Campinas, Campinas-SP (Brazil); Baccan, Nivaldo [Faculdade de Paulinia, Paulinia-SP (Brazil)

    2012-05-15

    A method for extraction of metal ions present in rice samples using ammoniacal EDTA solution, pH = 10, as extractor agent is proposed under the following optimized conditions: 0.20 g of rice sample and 5.00 mL of ammoniacal EDTA (ethylenediaminetetraacetic acid) solution, with 5 min of ultrasound exposure time. Using robust ICP OES (inductively coupled plasma atomic emission spectrometry) conditions, direct analysis of the extraction solution was allowed, and the recovery values obtained were above 90% for most of the studied elements (P, K, Mg, Ca, Zn, Mn, Cu and Mo) with RSD < 5%. The results were in good agreement with those obtained by microwave assisted extraction and for the reference material of rice flour (NIST SRM 1568a). The limits of detection of method were in the range of 0.007 mg kg{sup -1} (Mn) - 48.68 mg kg{sup -1} (K), showing adequate detectability for the determination of the analytes. The analysis of different samples indicated that Brazilian 'integral' rice contains higher contents of the constituents studied, followed by 'parboiled' rice, and the 'agulhinha' rice a long and thin grain type. (author)

  15. Developmental evaluation of atypical auditory sampling in dyslexia: Functional and structural evidence.

    Science.gov (United States)

    Lizarazu, Mikel; Lallier, Marie; Molinaro, Nicola; Bourguignon, Mathieu; Paz-Alonso, Pedro M; Lerma-Usabiaga, Garikoitz; Carreiras, Manuel

    2015-12-01

    Whether phonological deficits in developmental dyslexia are associated with impaired neural sampling of auditory information at either syllabic- or phonemic-rates is still under debate. In addition, whereas neuroanatomical alterations in auditory regions have been documented in dyslexic readers, whether and how these structural anomalies are linked to auditory sampling and reading deficits remains poorly understood. In this study, we measured auditory neural synchronization at different frequencies corresponding to relevant phonological spectral components of speech in children and adults with and without dyslexia, using magnetoencephalography. Furthermore, structural MRI was used to estimate cortical thickness of the auditory cortex of participants. Dyslexics showed atypical brain synchronization at both syllabic (slow) and phonemic (fast) rates. Interestingly, while a left hemispheric asymmetry in cortical thickness was functionally related to a stronger left hemispheric lateralization of neural synchronization to stimuli presented at the phonemic rate in skilled readers, the same anatomical index in dyslexics was related to a stronger right hemispheric dominance for neural synchronization to syllabic-rate auditory stimuli. These data suggest that the acoustic sampling deficit in development dyslexia might be linked to an atypical specialization of the auditory cortex to both low and high frequency amplitude modulations. © 2015 Wiley Periodicals, Inc.

  16. Evaluation of the Cardiac Depression Visual Analogue Scale in a medical and non-medical sample.

    Science.gov (United States)

    Di Benedetto, Mirella; Sheehan, Matthew

    2014-01-01

    Comorbid depression and medical illness is associated with a number of adverse health outcomes such as lower medication adherence and higher rates of subsequent mortality. Reliable and valid psychological measures capable of detecting a range of depressive symptoms found in medical settings are needed. The Cardiac Depression Visual Analogue Scale (CDVAS) is a recently developed, brief six-item measure originally designed to assess the range and severity of depressive symptoms within a cardiac population. The current study aimed to further investigate the psychometric properties of the CDVAS in a general and medical sample. The sample consisted of 117 participants, whose mean age was 40.0 years (SD = 19.0, range 18-84). Participants completed the CDVAS, the Cardiac Depression Scale (CDS), the Depression Anxiety Stress Scales (DASS) and a demographic and health questionnaire. The CDVAS was found to have adequate internal reliability (α = .76), strong concurrent validity with the CDS (r = .89) and the depression sub-scale of the DASS (r = .70), strong discriminant validity and strong predictive validity. The principal components analysis revealed that the CDVAS measured only one component, providing further support for the construct validity of the scale. Results of the current study indicate that the CDVAS is a short, simple, valid and reliable measure of depressive symptoms suitable for use in a general and medical sample.

  17. Performance evaluation of an importance sampling technique in a Jackson network

    Science.gov (United States)

    brahim Mahdipour, E.; Masoud Rahmani, Amir; Setayeshi, Saeed

    2014-03-01

    Importance sampling is a technique that is commonly used to speed up Monte Carlo simulation of rare events. However, little is known regarding the design of efficient importance sampling algorithms in the context of queueing networks. The standard approach, which simulates the system using an a priori fixed change of measure suggested by large deviation analysis, has been shown to fail in even the simplest network settings. Estimating probabilities associated with rare events has been a topic of great importance in queueing theory, and in applied probability at large. In this article, we analyse the performance of an importance sampling estimator for a rare event probability in a Jackson network. This article carries out strict deadlines to a two-node Jackson network with feedback whose arrival and service rates are modulated by an exogenous finite state Markov process. We have estimated the probability of network blocking for various sets of parameters, and also the probability of missing the deadline of customers for different loads and deadlines. We have finally shown that the probability of total population overflow may be affected by various deadline values, service rates and arrival rates.

  18. An Evaluation of Plotless Sampling Using Vegetation Simulations and Field Data from a Mangrove Forest.

    Directory of Open Access Journals (Sweden)

    Renske Hijbeek

    Full Text Available In vegetation science and forest management, tree density is often used as a variable. To determine the value of this variable, reliable field methods are necessary. When vegetation is sparse or not easily accessible, the use of sample plots is not feasible in the field. Therefore, plotless methods, like the Point Centred Quarter Method, are often used as an alternative. In this study we investigate the accuracy of different plotless sampling methods. To this end, tree densities of a mangrove forest were determined and compared with estimates provided by several plotless methods. None of these methods proved accurate across all field sites with mean underestimations up to 97% and mean overestimations up to 53% in the field. Applying the methods to different vegetation patterns shows that when random spatial distributions were used the true density was included within the 95% confidence limits of all the plotless methods tested. It was also found that, besides aggregation and regularity, density trends often found in mangroves contribute to the unreliability. This outcome raises questions about the use of plotless sampling in forest monitoring and management, as well as for estimates of density-based carbon sequestration. We give recommendations to minimize errors in vegetation surveys and recommendations for further in-depth research.

  19. Evaluation of pesticide residues in human blood samples from Punjab (India

    Directory of Open Access Journals (Sweden)

    Jasbir Singh Bedi

    2015-01-01

    Full Text Available Aim: The present study was undertaken to estimate the current status of residues of organochlorine pesticides (OCPs, organophosphates (OPs and synthetic pyrethroids (SPs pesticides in human blood. Materials and Methods: Human blood samples were analyzed by gas chromatography and confirmed by gas chromatographymass spectrometry in selective ion monitoring mode. Results: The gas chromatographic analysis of human blood samples collected from Punjab revealed the presence of p,p’-dichlorodiphenyl dichloroethylene (DDE, p,p’ dichlorodiphenyl dichloroethane (DDD, o,p’ DDE and β-endosulfan at mean levels of 15.26, 2.71, 5.62 and 4.02 ng/ml respectively. p,p’ DDE residue was observed in 18.0% blood samples, and it contributes 55% of the total pesticide burden in human blood. The difference of total dichlorordiphenyl trichloroethane (DDT between different age groups of humans was found to be statistically significant (p<0.05. The difference of DDT and endosulfan between dietary habits, gender and spraying of pesticides was found statistically non-significant, however endosulfan residues were observed only in pesticide sprayer’s population. Conclusion: Occurrence of p,p’ DDE, p,p’ DDD, o,p’ DDE in human blood indicated restricted use of DDT. However, presence of endosulfan residues in occupationally exposed population is a matter of public health concern.

  20. Stratified sampling design and loss to follow-up in survival models: evaluation of efficiency and bias.

    Science.gov (United States)

    César, Cibele C; Carvalho, Marilia S

    2011-06-26

    Longitudinal studies often employ complex sample designs to optimize sample size, over-representing population groups of interest. The effect of sample design on parameter estimates is quite often ignored, particularly when fitting survival models. Another major problem in long-term cohort studies is the potential bias due to loss to follow-up. In this paper we simulated a dataset with approximately 50,000 individuals as the target population and 15,000 participants to be followed up for 40 years, both based on real cohort studies of cardiovascular diseases. Two sample strategies--simple random (our golden standard) and Stratified by professional group, with non-proportional allocation--and two loss to follow-up scenarios--non-informative censoring and losses related to the professional group--were analyzed. Two modeling approaches were evaluated: weighted and non-weighted fit. Our results indicate that under the correctly specified model, ignoring the sample weights does not affect the results. However, the model ignoring the interaction of sample strata with the variable of interest and the crude estimates were highly biased. In epidemiological studies misspecification should always be considered, as different sources of variability, related to the individuals and not captured by the covariates, are always present. Therefore, allowance must be made for the possibility of unknown confounders and interactions with the main variable of interest in our data. It is strongly recommended always to correct by sample weights.

  1. Multi-block data analysis using ComDim for the evaluation of complex samples: Characterization of edible oils.

    Science.gov (United States)

    Rosa, Larissa Naida; de Figueiredo, Luana Caroline; Bonafé, Elton Guntendorfer; Coqueiro, Aline; Visentainer, Jesuí Vergílio; Março, Paulo Henrique; Rutledge, Douglas N; Valderrama, Patrícia

    2017-04-08

    The ComDim chemometrics method for multi-block analysis was employed to evaluate thirty-two vegetable oil samples analyzed by near infrared (NIR) and ultraviolet-visible (UV-Vis) spectroscopy, and by Gas Chromatography with flame ionization detection (GC-FID) for their fatty acids composition. This unsupervised pattern recognition method was able to extract information from the tables of results that could be presented in informative graphs showing the relationship between the samples through the scores, the predominance of information in particular tables through the saliences and the contribution of the variables in each table which were responsible for the similarities observed in the samples, through the loadings plots. It was possible to infer similarities and differences among the samples studied according to the specific absorption in the UV-Vis and NIR region, as well as their fatty acids composition. The proposed methodology demonstrates the applicability of ComDim for the characterization of samples when different variables (different techniques) describe the same samples. In this particular study, the ComDim chemometrics method was able to discriminate samples by their characteristics and compositions. Published by Elsevier B.V.

  2. Techniques for the detection of pathogenic Cryptococcus species in wood decay substrata and the evaluation of viability in stored samples

    Directory of Open Access Journals (Sweden)

    Christian Alvarez

    2013-02-01

    Full Text Available In this study, we evaluated several techniques for the detection of the yeast form of Cryptococcus in decaying wood and measured the viability of these fungi in environmental samples stored in the laboratory. Samples were collected from a tree known to be positive for Cryptococcus and were each inoculated on 10 Niger seed agar (NSA plates. The conventional technique (CT yielded a greater number of positive samples and indicated a higher fungal density [in colony forming units per gram of wood (CFU.g-1] compared to the humid swab technique (ST. However, the difference in positive and false negative results between the CT-ST was not significant. The threshold of detection for the CT was 0.05.10³ CFU.g-1, while the threshold for the ST was greater than 0.1.10³ CFU-1. No colonies were recovered using the dry swab technique. We also determined the viability of Cryptococcus in wood samples stored for 45 days at 25ºC using the CT and ST and found that samples not only continued to yield a positive response, but also exhibited an increase in CFU.g-1, suggesting that Cryptococcus is able to grow in stored environmental samples. The ST.1, in which samples collected with swabs were immediately plated on NSA medium, was more efficient and less laborious than either the CT or ST and required approximately 10 min to perform; however, additional studies are needed to validate this technique.

  3. Evaluation of the readsorption of plutonium and americium in dynamic fractionations of environmental solid samples

    DEFF Research Database (Denmark)

    Petersen, Roongrat; Hou, Xiaolin; Hansen, Elo Harald

    2008-01-01

    extractions. The degree of readsorption in dynamic and conventional batch extraction systems are compared and evaluated by using a double-spiking technique. A high degree of readsorption of plutonium and americium (>75%) was observed in both systems, and they also exhibited similar distribution patterns...

  4. Evaluation of temperature increase with different amounts of magnetite in liver tissue samples.

    Science.gov (United States)

    Hilger, I; Andrä, W; Bähring, R; Daum, A; Hergt, R; Kaiser, W A

    1997-11-01

    The biologic effects of magnetically induced heating effects using iron oxide, magnetite, were examined in vitro in liver tissue samples as a first step toward potential applications in cancer therapy. For the determination of the temperature profile around an iron oxide sample, a cylinder containing 170 mg of magnetite was constructed and placed into pureed liver tissue from pig, together with thermocouples of copper and constantan wires positioned at defined distances from it. Temperature measurements were performed during the exposure to an alternating magnetic field (frequency: 400 kHz; amplitude: approximately 6.5 kA/m) generated by a circular coil (90 mm of diameter). Moreover, variable amounts of magnetite (dissolved in approximately 0.2 mL physiologic saline) were injected directly into carrageenan gels. During the exposure to a magnetic field for 4 minutes the temperature increase was determined in the area of iron oxide deposition using a thermocouple. Additionally, variable amounts of magnetite were injected directly into isolated liver tissue samples (diameter: 20 mm; height: 30 mm) and exposed to a magnetic field for 2 minutes. The extent of the induced macroscopically visible tissue alterations (light brown colorations caused by heating) was examined by means of volume estimations. The degrees of cellular necrosis were investigated by histopathologic studies. The temperature profile around a magnetite cylinder revealed a significant decrease of temperature difference between the beginning and the end of heating, depending on increasing distance from the sample center. The extent of the temperature difference correlated with increasing heating time. No significant variations of temperature were observed at a distance of approximately 12 mm from the sample center. A good correlation (r = 0.98) between the injected amounts (31 to 200 mg) and the temperature increase since the start of heating (6.8-33.7 degrees C) in the area of iron oxide deposits was

  5. Genotoxic and mutagenic evaluation of water samples from a river under the influence of different anthropogenic activities.

    Science.gov (United States)

    Batista, Nelson Jorge Carvalho; de Carvalho Melo Cavalcante, Ana Amélia; de Oliveira, Maria Geci; Medeiros, Eugênia Cristina Nascimento; Machado, Joseane Lustosa; Evangelista, Sebastiana Ribeiro; Dias, Johnny F; Dos Santos, Carla E I; Duarte, Anaí; da Silva, Fernanda R; da Silva, Juliana

    2016-12-01

    Pollution of aquatic ecosystems is associated with the discharge of mostly industrial and urban effluents, which may cause loss of biodiversity and damage to public health. This study aims to evaluate the toxicity and mutagenicity of water samples collected in the Corrente River, a major waterway in the river basin district of Pedro II, Piauí (Brazil). This river is exposed to intense anthropogenic influence from urban, automotive mechanical and family farm waste, and it is used as the main source of water supply by the population. Water samples were collected during the rainy and dry seasons, at four sites in the Corrente River, and evaluated by physicochemical, microbiological and inorganic elements analyses. The samples were evaluated for mutagenicity using the Allium cepa test (toxicity, chromosomal aberration and micronucleus tests) and fish (Tilapia rendalli and Hoplias malabaricus). The physicochemical, microbiological and inorganic results show a large contribution to the pollution loads at collection points in the town of Pedro II, demonstrating the influence of urban pollution. The Al, Si, Ti, Cr, Ni and Cu contents were determined by PIXE. These same Corrente River water samples demonstrated mutagenic effect for A. cepa and fish, as well as toxicity in the A. cepa test. The observations of mutagenic effect may suggest that the complex mixture of agents is comprised of both clastogenic and aneugenic agents. This study also showed the need for constant monitoring in places with environmental degradation caused by urban sewage discharges. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Utility of manual liquid-based cytology and conventional smears in the evaluation of various fine-needle aspiration samples

    Directory of Open Access Journals (Sweden)

    P Arul

    2016-01-01

    Full Text Available Background: Liquid-based cytology (LBC preparation is a way to improve and refine the fine-needle aspiration (FNA samples. There are a few studies comparing LBC with conventional smear (CS. Aim: The present study was undertaken to evaluate the utility of manual LBC (MLBC and CS preparations in various FNA samples. Materials and Methods: In this cross-sectional study, a total of 100 FNA samples from various anatomical sites were evaluated using MLBC and CS preparations. Cellularity, blood, informative background, monolayers, cell architecture, cytoplasmic, and nuclear preservation were compared with MLBC and CS preparations by Wilcoxon signed rank test. P < 0.05 is considered statistically significant. Results: MLBC preparations were superior to CS preparations in view of absence of blood and debris (P = 0.001, presence of monolayers (P < 0.001, and preservation of cytoplasmic (P = 0.001 and nuclear details (P = 0.001. However, no statistically significant differences were found between MLBC and CS preparations with regard to cellularity (P = 0.157, informative background (P = 0.083, and architecture (P = 0.739. Conclusion: MLBC preparations in FNAC are a safe, easy, and less time-consuming procedure, and it may have promising diagnostic value in the evaluation of FNA samples from various anatomical sites. However, the use of both MLBC and CS preparations is recommended to achieve optimal diagnostic yield.

  7. [Evaluating the applicability of medical examinations constituting "the protocol of obtaining a blood sample" in measuring the degree of intoxication].

    Science.gov (United States)

    Engelgardt, Piotr; Grzech, Weronika; Drzewiecki, Jarosław; Sliwka, Karol

    2010-01-01

    Breathalysing and blood analysis is the basic instrument of measuring the level of intoxication. Prior to collecting a blood sample, an individual suspected of being under the influence of alcohol is examined by a physician, who fills out the "protocol of obtaining a blood sample". This work aims at evaluating the applicability of the described examination in measuring the level of intoxication. In order to do so, our team analyzed 352 "protocols of obtaining blood sample" referred to the Forensic Laboratory KWP in Bydgoszcz, Poland, and compared them with the results of blood analysis. The results of the above analysis point to the fact that the elements of medical examination constituting "the protocol of obtaining a blood sample" are of a minor usefulness in determining the degree of intoxication with ethyl alcohol. The smell from the mouth and the conclusions formulated the examining physician prove to be the most useful. The summary usage of deviations from the norm does not seem to increase the usefulness of methods used within "the protocol of obtaining a blood sample" in evaluating the degree of intoxication.

  8. Disentangling effects of abiotic factors and biotic interactions on cross-taxon congruence in species turnover patterns of plants, moths and beetles

    Science.gov (United States)

    Duan, Meichun; Liu, Yunhui; Yu, Zhenrong; Baudry, Jacques; Li, Liangtao; Wang, Changliu; Axmacher, Jan C.

    2016-04-01

    High cross-taxon congruence in species diversity patterns is essential for the use of surrogate taxa in biodiversity conservation, but presence and strength of congruence in species turnover patterns, and the relative contributions of abiotic environmental factors and biotic interaction towards this congruence, remain poorly understood. In our study, we used variation partitioning in multiple regressions to quantify cross-taxon congruence in community dissimilarities of vascular plants, geometrid and arciinid moths and carabid beetles, subsequently investigating their respective underpinning by abiotic factors and biotic interactions. Significant cross-taxon congruence observed across all taxon pairs was linked to their similar responses towards elevation change. Changes in the vegetation composition were closely linked to carabid turnover, with vegetation structure and associated microclimatic conditions proposed causes of this link. In contrast, moth assemblages appeared to be dominated by generalist species whose turnover was weakly associated with vegetation changes. Overall, abiotic factors exerted a stronger influence on cross-taxon congruence across our study sites than biotic interactions. The weak congruence in turnover observed particularly between plants and moths highlights the importance of multi-taxon approaches based on groupings of taxa with similar turnovers, rather than the use of single surrogate taxa or environmental proxies, in biodiversity assessments.

  9. Evaluation of septum-capped vials for storage of gas samples during air transport.

    Science.gov (United States)

    Glatzel, Stephan; Well, Reinhard

    2008-01-01

    In order to provide information on the suitability of commonly used gas storage vials for air transport, we tested two vial types on their ability to preserve defined nitrous oxide concentrations and excess pressure when exposed to low pressure, low temperature and puncture by needles. Unlike in Crimp Cap vials, in Exetainers no nitrous oxide loss following low pressure storage was detectable. Tightness of Exetainers following multiple puncture was best using a small needle diameter. Pressure loss following 5, 10, or 25 punctures was lowest in the Exetainers. We conclude that Exetainers are suitable for storing gas samples for an extended period of time during aircraft transport.

  10. Non-destructive high-resolution thermal imaging techniques to evaluate wildlife and delicate biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Lavers, C; Franklin, P; Franklin, P; Plowman, A; Sayers, G; Bol, J; Shepard, D; Fields, D, E-mail: brnc-radarcomms1@nrta.mod.u [Sensors Team, Plymouth University at Britannia Royal Naval College, Dartmouth, Devon (United Kingdom) and Paignton Zoological Park, Paignton, Devon (United Kingdom); Thermal Wave Imaging, Inc., 845 Livernoise St, Ferndale, MI (United States); Buckfast Butterfly and Otter Sanctuary, Buckfast, Devon (United Kingdom)

    2009-07-01

    Thermal imaging cameras now allows routine monitoring of dangerous yet endangered wildlife in captivity. This study looks at the potential applications of radiometrically calibrated thermal data to wildlife, as well as providing parameters for future materials applications. We present a non-destructive active testing technique suitable for enhancing imagery contrast of thin or delicate biological specimens yielding improved thermal contrast at room temperature, for analysis of sample thermal properties. A broad spectrum of animals is studied with different textured surfaces, reflective and emissive properties in the infra red part of the electromagnetic spectrum. Some surface features offer biomimetic materials design opportunities.

  11. MDMS: Molecular dynamics meta-simulator for evaluating exchange type sampling methods

    Science.gov (United States)

    Smith, Daniel B.; Okur, Asim; Brooks, Bernard R.

    2012-08-01

    Replica exchange methods have become popular tools to explore conformational space for small proteins. For larger biological systems, even with enhanced sampling methods, exploring the free energy landscape remains computationally challenging. This problem has led to the development of many improved replica exchange methods. Unfortunately, testing these methods remains expensive. We propose a molecular dynamics meta-simulator (MDMS) based on transition state theory to simulate a replica exchange simulation, eliminating the need to run explicit dynamics between exchange attempts. MDMS simulations allow for rapid testing of new replica exchange based methods, greatly reducing the amount of time needed for new method development.

  12. Pilot evaluation of the Computer-Based Assessment for Sampling Personal Characteristics test.

    Science.gov (United States)

    Shipper, Edward S; Mazer, Laura M; Merrell, Sylvia Bereknyei; Lin, Dana T; Lau, James N; Melcher, Marc L

    2017-07-01

    High attrition rates hint at deficiencies in the resident selection process. The evaluation of personal characteristics representative of success is difficult. Here, we evaluate a novel tool for assessing personal characteristics. To evaluate feasibility, we used an anonymous voluntary survey questionnaire offered to study participants before and after contact with the CASPer test. To evaluate the CASPer test as a predictor of success, we compared CASPer test assessments of personal characteristics versus traditional faculty assessment of personal characteristics with applicant rank list position. All applicants (n = 77) attending an in-person interview for general surgery residency, and all faculty interviewers (n = 34) who reviewed these applications were invited to participate. Among applicants, 84.4% of respondents (65 of 77) reported that a requirement to complete the CASPer test would have no bearing or would make them more likely to apply to the program (mean = 3.30, standard deviation = 0.96). Among the faculty, 62.5% respondents (10 of 16) reported that the same condition would have no bearing or would make applicants more likely to apply to the program (mean = 3.19, standard deviation = 1.33). The Spearman's rank-order correlation coefficients for the relationships between traditional faculty assessment of personal characteristics and applicant rank list position, and novel CASPer assessment of personal characteristics and applicant rank list position, were -0.45 (P = 0.033) and -0.41 (P = 0.055), respectively. The CASPer test may be feasibly implemented as component of the resident selection process, with the potential to predict applicant rank list position and improve the general surgery resident selection process. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Evaluation of the DSM-5 Severity Indicator for Binge Eating Disorder in a Community Sample

    OpenAIRE

    Grilo, Carlos. M.; Ivezaj, Valentina; White, Marney A.

    2015-01-01

    Research has examined various aspects of the diagnostic criteria for binge-eating disorder (BED) but has yet to evaluate the DSM-5 severity criterion. This study examined the DSM-5 severity criterion for BED based on binge-eating frequency and tested an alternative severity specifier based on overvaluation of shape/weight. 338 community volunteers categorized with DSM-5 BED completed a battery of self-report instruments. Participants were categorized first using DSM-5 severity levels and seco...

  14. Contribución a la resolución de un viejo problema taxonómico: Cladonia subrangiformis

    OpenAIRE

    Pino Bodas, Raquel; Burgaz, A. R.; Durán, F.; Martín, María P.; Lumbsch, T.

    2011-01-01

    Objetivos: Cladonia subrangiformis Sandst.es una especie que se desarrolla sobre sustratos básicos o neutros, con distribución mediterránea (Ahti & Shorabi, 2006) y, desde el punto de vista morfológico, está estrechamente relacionada con Cladonia furcata (Huds.) Schrad. que presenta distribución cosmopolita. El rango taxonómico de estas dos especies, así como su independencia ha sido muy discutido. De acuerdo con Sandstede (1922), su principal diferencia es la presencia de atra...

  15. Evaluation of DNA extraction kits for molecular diagnosis of human Blastocystis subtypes from fecal samples.

    Science.gov (United States)

    Yoshikawa, Hisao; Dogruman-Al, Funda; Dogruman-Ai, Funda; Turk, Songul; Kustimur, Semra; Balaban, Neriman; Sultan, Nedim

    2011-10-01

    Blastocystis sp. is now recognized as one of the most common intestinal parasite in human fecal examinations. Recently, PCR-based diagnostic methods of Blastocystis infection using direct DNA extraction from fresh fecal samples with commercially available kits are reported. Several kits have been developed, but little has been done in comparing the detective sensitivity between PCR methods using the commercial kits. In this study, we compared the detective sensitivity among five commercially available kits (MagNA Pure LC DNA Isolation Kit I, Roche; QuickGene SP Kit DNA, FujiFilm; NucleoSpin Plant II, Macherey-Nagel; QIAamp DNA Stool Mini Kit, Qiagen; ZR Fecal DNA Kit, Zymo Research) and fecal culture method. In a preliminary test, the DNA isolated with two kits (FujiFilm and Macherey-Nagel) showed negative PCR, while the other three kits showed positive PCR. Then, DNA from 50 clinical samples that was Blastocystis-positive in the examination of fecal culture method were isolated with the three kits and 1.1 kbp SSU rRNA gene was detected with PCR. The positive rates of the three kits (Roche, Qiagen, and Zymo Research) were 10, 48 and 94%, respectively. The present study indicated that there is different detective sensitivity among the commercial kits, and fecal culture method is superior in detection rate and cost performance than DNA-elution kits for diagnosis of Blastocystis sp. subtypes.

  16. Sampling plan for using a motorized penetrometer in soil compaction evaluation

    Directory of Open Access Journals (Sweden)

    Lindolfo Storck

    2016-03-01

    Full Text Available ABSTRACT This study aimed to estimate the size of blocks of observations of resistance to penetration, obtained by a motorized digital penetrometer, and the number of blocks with semi-amplitude of the confidence interval between 5 and 20% of the mean penetration resistance, for different soil depth ranges and cone diameters. Data were collected in two contrasting plots of a crop-livestock integration experiment, located in Abelardo Luz, SC, Brazil. Ten blocks were delimited and the resistance to penetration was determined in 20 points spaced by 20 cm, using a motorized digital soil penetrometer. To estimate the mean of resistance to penetration, 12 blocks of four points per experimental plot should be used for a semi-amplitude of the confidence interval equal to 10% of the mean (1 - p = 0.95. Twenty random points may be sampled to estimate mean of penetration resistance for a semiamplitude confidence interval of 10% of the man (1 - p = 0.95. The sample size for the layer of 0-10 cm is larger than in the deeper layers (0-20, 0-30 and 0-40 cm and smaller for cones with larger diameter.

  17. EVALUATION OF THE CONTENT OF SELECTED HEAVY METALS IN SAMPLES OF POLISH HONEYS

    Directory of Open Access Journals (Sweden)

    Elżbieta Sitarz-Palczak

    2015-06-01

    Full Text Available This paper presents the result of the determination of the total content of Cu, Pb and Zn by the method of atomic absorption spectrometry with atomization in an air-acetylene flame in Polish honeys samples. The research material was a honeydew, monofloral honey and buckwheat honey. For the mineralization of samples, the following solutions were applied: 1 HNO3(conc, 2 HNO3(conc and H2O2(conc in the volume ratio equal to 4:1 and 3:1. On the basis of the results and recommended food standards the percentage of the recommended dietary allowances (RDA in connection with the consumption of 100 g of product were estimated. To verify the results validation of analytical method used was carried out. It was included defining the following validation parameters values: the limit of detection and quantification; linearity and measurement range; repeatability and accuracy of the results. The contamination of the analyzed honeys by Pb is higher than the acceptable level of contamination of this element. The highest contents of Cu and Zn were characterized by monofloral honeys.

  18. Accelerated Evaluation of Automated Vehicles Safety in Lane-Change Scenarios Based on Importance Sampling Techniques.

    Science.gov (United States)

    Zhao, Ding; Lam, Henry; Peng, Huei; Bao, Shan; LeBlanc, David J; Nobukawa, Kazutoshi; Pan, Christopher S

    2017-03-01

    Automated vehicles (AVs) must be thoroughly evaluated before their release and deployment. A widely used evaluation approach is the Naturalistic-Field Operational Test (N-FOT), which tests prototype vehicles directly on the public roads. Due to the low exposure to safety-critical scenarios, N-FOTs are time consuming and expensive to conduct. In this paper, we propose an accelerated evaluation approach for AVs. The results can be used to generate motions of the other primary vehicles to accelerate the verification of AVs in simulations and controlled experiments. Frontal collision due to unsafe cut-ins is the target crash type of this paper. Human-controlled vehicles making unsafe lane changes are modeled as the primary disturbance to AVs based on data collected by the University of Michigan Safety Pilot Model Deployment Program. The cut-in scenarios are generated based on skewed statistics of collected human driver behaviors, which generate risky testing scenarios while preserving the statistical information so that the safety benefits of AVs in nonaccelerated cases can be accurately estimated. The cross-entropy method is used to recursively search for the optimal skewing parameters. The frequencies of the occurrences of conflicts, crashes, and injuries are estimated for a modeled AV, and the achieved accelerated rate is around 2000 to 20 000. In other words, in the accelerated simulations, driving for 1000 miles will expose the AV with challenging scenarios that will take about 2 to 20 million miles of real-world driving to encounter. This technique thus has the potential to greatly reduce the development and validation time for AVs.

  19. Development of Natural Flaw Samples for Evaluating Nondestructive Testing Methods for Foam Thermal Protection Systems

    Science.gov (United States)

    Workman, Gary L.; Davis, Jason; Farrington, Seth; Walker, James

    2007-01-01

    Low density polyurethane foam has been an important insulation material for space launch vehicles for several decades. The potential for damage from foam breaking away from the NASA External Tank was not realized until the foam impacts on the Columbia Orbiter vehicle caused damage to its Leading Edge thermal protection systems (TPS). Development of improved inspection techniques on the foam TPS is necessary to prevent similar occurrences in the future. Foamed panels with drilled holes for volumetric flaws and Teflon inserts to simulate debonded conditions have been used to evaluate and calibrate nondestructive testing (NDT) methods. Unfortunately the symmetric edges and dissimilar materials used in the preparation of these simulated flaws provide an artificially large signal while very little signal is generated from the actual defects themselves. In other words, the same signal are not generated from the artificial defects in the foam test panels as produced when inspecting natural defect in the ET foam TPS. A project to create more realistic voids similar to what actually occurs during manufacturing operations was began in order to improve detection of critical voids during inspections. This presentation describes approaches taken to create more natural voids in foam TPS in order to provide a more realistic evaluation of what the NDT methods can detect. These flaw creation techniques were developed with both sprayed foam and poured foam used for insulation on the External Tank. Test panels with simulated defects have been used to evaluate NDT methods for the inspection of the External Tank. A comparison of images between natural flaws and machined flaws generated from backscatter x-ray radiography, x-ray laminography, terahertz imaging and millimeter wave imaging show significant differences in identifying defect regions.

  20. An Inset CT Specimen for Evaluating Fracture in Small Samples of Material

    OpenAIRE

    Yahyazadehfar, M.; Nazari, A.; Kruzic, J. J.; Quinn, G. D.; Arola, D.

    2013-01-01

    In evaluations on the fracture behavior of hard tissues and many biomaterials, the volume of material available to study is not always sufficient to apply a standard method of practice. In the present study an inset Compact Tension (inset CT) specimen is described, which uses a small cube of material (approximately 2×2×2 mm3) that is molded within a secondary material to form the compact tension geometry. A generalized equation describing the Mode I stress intensity was developed for the spec...

  1. Comparative Evaluation of Inoculation of Urine Samples with the Copan WASP® and BD Kiestra™ InoqulA™ Instruments

    DEFF Research Database (Denmark)

    Iversen, Jesper; Stendal, Gitta; Gerdes, Cecilie Marie

    2016-01-01

    This study evaluated quantitative results as well as the quality of the inoculation patterns on urine specimens produced by two automated instruments, the Copan WASP® and the BD InoqulA™. 526 urine samples submitted in 10 ml canisters containing boric acid were processed within 30 minutes...... on an InoqulA, plating 10 ul of specimen, and two WASP instruments, one plating 1 ul of specimen (WASP-1) and the second WASP 10 ul (WASP-10). All samples were incubated, analysed, and digitally imaged using the BD Kiestra™ Total Lab Automation system. Results were evaluated using a quantitative protocol...... as well as for presence or absence of ≥5 distinct colonies. Separate studies were conducted using QC organisms to determine the relative accuracy of WASP-1, WASP-10 and InoqulA compared to results obtained with a calibrated pipet. Results with QC organisms were calculated as ratios of the counts...

  2. BLOOD SMEAR EVALUATION OF BALI DUCKS SAMPLED FROM TRADITIONAL FARMING SYSTEMS IN BALI

    Directory of Open Access Journals (Sweden)

    Iwan Haryono Utama

    2008-12-01

    Full Text Available Research to confirm the abnormalities of blood corpuscles in Bali ducks based on blood smear examination has been conducted. The research samples consisted of 105 ducks from various regencies in Bali. The blood smear examination was conducted by the method described in this literature and the data was collected and tabulated by means of the descriptive method. Erythrocyte abnormalities were: polychromasia (61.9%, anisocytosis (17.1%, poikilocytosis (21.0%. Abnormalities associated with leukocyte composition were: Lymphopenic (46.7%; Heterophylic (44.8%; Heteropenic (3.8%, also Thrombocyto penia (2.9% was present in 105 ducks. In conclusion 61,9% ducks examined deal with regenerative anaemia. They also have some blood abnormalities such as basophylia, eosinophylia, heterophylia, heteropenia, lymphopenia, and monocytosis.

  3. Evaluation Of Gas Diffusion Through Plastic Materials Used In Experimental And Sampling Equipment

    DEFF Research Database (Denmark)

    Kjeldsen, Peter

    1993-01-01

    Plastic materials are often used in experimental and sampling equipment. Plastics are not gas tight, since gases are able to diffuse through the walls of tubing and containers made of plastic. Methods for calculating the significance of gas diffusion through the walls of containers and the walls...... of tubings for both turbulent and laminar flow conditions is presented. A more complex model for diffusion under laminar flow conditions is developed. A comprehensive review on gas diffusion coefficients for the main gases (O2, N2, CO2, CH4 etc.) and for a long range of plastic materials is also presented....... Calculations show that diffusion of oxygen through plastic tubing and reactors into anoxic water can be a serious problem for a series of plastic materials. Comparison of the method for turbulent and laminar flow in tubings shows that the difference is insignificant for most cases. Calculations show also...

  4. Comprehensive neuropsychological evaluation of children and adolescents with sickle cell anemia: a hospital-based sample

    Directory of Open Access Journals (Sweden)

    Samantha Nunes

    Full Text Available Abstract Background: Individuals with sickle cell anemia may suffer symptomatic or silent cerebral infarcts leading to neurocognitive complications. This study investigated the cognitive and intellectual performance of children and adolescents with sickle cell anemia. Methods: The socioeconomic status, clinical aspects and behavioral profile of 15 young individuals with sickle cell anemia were evaluated. The Wechsler Intelligence Scale for Children, the Developmental Neuropsychological Assessment Test, and the Child Behavior Checklist were applied. Results: Participants with a history of stroke had lower intelligence quotient (IQ scores. Alterations were found in attention and executive functioning, language, verbal and visual memory, visuospatial processing and sensorimotor skills. These alterations were found both in the children and adolescents who had had a cerebral infarction and in those who apparently had not. In the majority of cases, there were learning difficulties, a history of repeating school years and a need for specialist educational support. The most common additional diagnoses in accordance with the Diagnostic and Statistical Manual of Mental Disorders IV were depressive disorder, anxiety disorder and somatic disorder, as well as conditions associated with physical and psychosocial repercussions of sickle cell anemia. Conclusion: As sickle cell anemia is considered a progressive cerebral vasculopathy, it is a potential risk factor for neurocognitive and psychosocial development. Therefore, periodic neuropsychological and behavioral evaluations of children and adolescents with sickle cell anemia may represent a useful measure to reduce long-term biopsychosocial repercussions.

  5. Comprehensive neuropsychological evaluation of children and adolescents with sickle cell anemia: a hospital-based sample.

    Science.gov (United States)

    Nunes, Samantha; Argollo, Nayara; Mota, Marivania; Vieira, Camilo; Sena, Eduardo Pondé de

    Individuals with sickle cell anemia may suffer symptomatic or silent cerebral infarcts leading to neurocognitive complications. This study investigated the cognitive and intellectual performance of children and adolescents with sickle cell anemia. The socioeconomic status, clinical aspects and behavioral profile of 15 young individuals with sickle cell anemia were evaluated. The Wechsler Intelligence Scale for Children, the Developmental Neuropsychological Assessment Test, and the Child Behavior Checklist were applied. Participants with a history of stroke had lower intelligence quotient (IQ) scores. Alterations were found in attention and executive functioning, language, verbal and visual memory, visuospatial processing and sensorimotor skills. These alterations were found both in the children and adolescents who had had a cerebral infarction and in those who apparently had not. In the majority of cases, there were learning difficulties, a history of repeating school years and a need for specialist educational support. The most common additional diagnoses in accordance with the Diagnostic and Statistical Manual of Mental Disorders IV were depressive disorder, anxiety disorder and somatic disorder, as well as conditions associated with physical and psychosocial repercussions of sickle cell anemia. As sickle cell anemia is considered a progressive cerebral vasculopathy, it is a potential risk factor for neurocognitive and psychosocial development. Therefore, periodic neuropsychological and behavioral evaluations of children and adolescents with sickle cell anemia may represent a useful measure to reduce long-term biopsychosocial repercussions. Copyright © 2016 Associação Brasileira de Hematologia, Hemoterapia e Terapia Celular. Published by Elsevier Editora Ltda. All rights reserved.

  6. Toxicity evaluation of vinasse and biosolid samples in diplopod midgut: heat shock protein in situ localization.

    Science.gov (United States)

    Coelho, Maria Paula Mancini; Moreira-de-Sousa, Cristina; de Souza, Raphael Bastão; Ansoar-Rodríguez, Yadira; Silva-Zacarin, Elaine Cristina Mathias; Fontanetti, Carmem Silvia

    2017-09-01

    Large amounts of residues generated by agricultural, urban and industrial activities are dumped daily on the soil. This practice deserves special attention because it causes serious environmental problems. This study evaluated the toxic potential of the sugarcane vinasse, a by-product of the sugar-alcohol industry, and the biosolid, a residue produced by wastewater treatment plants, both widely used as fertilizers. The evaluation was performed through bioassays using a typical soil bioindicator, the diplopod Rhinocricus padbergi. The specimens were exposed to soils containing these residues in concentrations that are compatible with the Brazilian regulation for agricultural use. Semi-quantitative immunolabelling analyses of the stress protein HSP70 were performed on the midgut of the studied diplopods. There was a significant increase in the immunolabelling of HSP70 proteins as a response to xenobiotics from both residues, particularly in regions where the function of the cells is the detoxification of the organ (e.g. the hepatic cell layer and specific regions of the epithelium). Higher immunolabelling was observed in the specimens exposed to vinasse in comparison with the biosolid exposure. This demonstrates that the substances in the tested residues had proteotoxic action in the exposed animals and induced a cytoprotective response, which led to higher stress protein immunolabelling. Therefore, caution is needed for the use of such residues in agriculture.

  7. Further evaluation of an updated PCR assay for the detection of Schistosoma mansoni DNA in human stool samples.

    Science.gov (United States)

    Gomes, Luciana I; Marques, Letícia H S; Enk, Martin J; Coelho, Paulo Marcos Z; Rabello, Ana

    2009-12-01

    A previously reported sensitive PCR assay for the detection of Schistosoma mansoni DNA was updated and evaluated. Changes in the DNA extraction method, including the use of a worldwide available commercial kit and the inclusion of additional quality control measures, increased the robustness of the test, as confirmed by the analysis of 67 faecal samples from an endemic area in Brazil. The PCR assay is at hand as a proven, reliable diagnostic test for the control of schistosomiasis in specific settings.

  8. Clinical characteristics of patients with tinnitus evaluated with the Tinnitus Sample Case History Questionnaire in Japan: A case series.

    Directory of Open Access Journals (Sweden)

    Takashi Kojima

    Full Text Available The Tinnitus Sample Case History Questionnaire was determined as a standardized questionnaire for obtaining patient case histories and for characterizing patients into subgroups at the Tinnitus Research Initiative in 2006. In this study, we developed a Japanese version of this questionnaire for evaluating the clinical characteristics of patients with tinnitus. The Japanese version of the questionnaire will be available for evaluating treatments for tinnitus and for comparing data on tinnitus in research centers.To evaluate the clinical characteristics of patients with tinnitus in Japan using a newly developed Japanese version of Tinnitus Sample Case History Questionnaire.This was a prospective study based on patient records.University hospitals, general hospitals, and clinics.We collected patient data using a Japanese translated version of the Tinnitus Sample Case History Questionnaire. In total, 584 patients who visited our institutions in Japan between August 2012 and March 2014 were included (280 males and 304 females; age 13-92 years; mean age, 60.8. We examined patients after dividing them into two groups according to the presence or absence of hyperacusis. The collected results were compared with those from the Tinnitus Research Initiative database.Compared with the TRI database, there were significantly more elderly female patients and fewer patients with trauma-associated tinnitus. There was a statistically lower ratio of patients with hyperacusis. We found that patients with tinnitus in addition to hyperacusis had greater tinnitus severity and exhibited higher rates of various complications.The Japanese version of the Tinnitus Sample Case History Questionnaire developed in this study can be a useful tool for evaluating patients with tinnitus in Japan. The results of this multicenter study reflect the characteristics of patients with tinnitus who require medical care in Japan. Our data provides a preliminary basis for an international

  9. An approach based on HPLC-fingerprint and chemometrics to quality consistency evaluation of Matricaria chamomilla L. commercial samples

    Directory of Open Access Journals (Sweden)

    Agnieszka Viapiana

    2016-10-01

    Full Text Available Chamomile has been used as an herbal medication since ancient times and is still popular because it contains various bioactive phytochemicals that could provide therapeutic effects. In this study, a simple and reliable HPLC method was developed to evaluate the quality consistency of nineteen chamomile samples through establishing a chromatographic fingerprint, quantification of phenolic compounds and determination of antioxidant activity. For fingerprint analysis, 12 peaks were selected as the common peaks to evaluate the similarities of commercial samples of chamomile obtained from different manufacturers. A similarity analysis was performed to assess the similarity/dissimilarity of chamomile samples where values varied from 0.868 to 0.990 what indicating that samples from different manufacturers were consistent. Additionally, simultaneous quantification of five phenolic acids (gallic, caffeic, syringic, p-coumaric, ferulic and four flavonoids (rutin, myricetin, quercetin and keampferol was performed to interpret the quality consistency. In quantitative analysis, the nine individual phenolic compounds showed good regression (r > 0.9975. Inter- and intra-day precisions for all analysed compounds expressed as relative standard deviation (CV ranged from 0.05% to 3.12%. Since flavonoids and other polyphenols are commonly recognised as natural antioxidants, the antioxidant activity of chamomile samples was evaluated using 1,1-diphenyl-2-picrylhydrazyl (DPPH radical scavenging activity and ferric reducing/antioxidant power (FRAP assay. Correlation analysis was used to assess the relationship between antioxidant activity and phenolic composition, and multivariate analysis (PCA and HCA were applied to distinguish chamomile samples. Results shown in the study indicate high similarity of chamomile samples among them, widely spread in the market and commonly used by people as infusions or teas, as well as that there were no statistically significant

  10. Piloting a Non-Invasive Genetic Sampling Method for Evaluating Population-Level Benefits of Wildlife Crossing Structures

    Directory of Open Access Journals (Sweden)

    Anthony P. Clevenger

    2010-03-01

    Full Text Available Intuitively, wildlife crossing structures should enhance the viability of wildlife populations. Previous research has demonstrated that a broad range of species will use crossing structures, however, questions remain as to whether these measures actually provide benefits to populations. To assess this, studies will need to determine the number of individuals using crossings, their sex, and their genetic relationships. Obtaining empirical data demonstrating population-level benefits for some species can be problematic and challenging at best. Molecular techniques now make it possible to identify species, individuals, their sex, and their genetic relatedness from hair samples collected through non-invasive genetic sampling (NGS. We describe efforts to pilot a method to assess potential population-level benefits of wildlife crossing structures. We tested the feasibility of a prototype NGS system designed to sample hair from black bears (Ursus americanus and grizzly bears (U. arctos at two wildlife underpasses. The piloted hair-sampling method did not deter animal use of the trial underpasses and was effective at sampling hair from more than 90% of the bear crossing events at the underpasses. Hair samples were also obtained from non-target carnivore species, including three out of five (60% cougar (Puma concolor crossing events. Individual identification analysis revealed that three female and two male grizzly bears used one wildlife underpass, whereas two female and three male black bears were identified as using the other underpass. Of the 36 hair samples from bears analyzed, five failed, resulting in an 87% extraction success rate, and six more were only identified to species. Overall, 70% of the hair samples from bears collected in the field had sufficient DNA for extraction purposes. Preliminary data from our NGS suggest the technique can be a reliable method to assess the population-level benefits of Banff wildlife crossings. Furthermore, NGS

  11. Validation and Clinical Evaluation of a Novel Method To Measure Miltefosine in Leishmaniasis Patients Using Dried Blood Spot Sample Collection.

    Science.gov (United States)

    Kip, A E; Rosing, H; Hillebrand, M J X; Blesson, S; Mengesha, B; Diro, E; Hailu, A; Schellens, J H M; Beijnen, J H; Dorlo, T P C

    2016-04-01

    To facilitate future pharmacokinetic studies of combination treatments against leishmaniasis in remote regions in which the disease is endemic, a simple cheap sampling method is required for miltefosine quantification. The aims of this study were to validate a liquid chromatography-tandem mass spectrometry method to quantify miltefosine in dried blood spot (DBS) samples and to validate its use with Ethiopian patients with visceral leishmaniasis (VL). Since hematocrit (Ht) levels are typically severely decreased in VL patients, returning to normal during treatment, the method was evaluated over a range of clinically relevant Ht values. Miltefosine was extracted from DBS samples using a simple method of pretreatment with methanol, resulting in >97% recovery. The method was validated over a calibration range of 10 to 2,000 ng/ml, and accuracy and precision were within ±11.2% and ≤7.0% (≤19.1% at the lower limit of quantification), respectively. The method was accurate and precise for blood spot volumes between 10 and 30 μl and for Ht levels of 20 to 35%, although a linear effect of Ht levels on miltefosine quantification was observed in the bioanalytical validation. DBS samples were stable for at least 162 days at 37°C. Clinical validation of the method using paired DBS and plasma samples from 16 VL patients showed a median observed DBS/plasma miltefosine concentration ratio of 0.99, with good correlation (Pearson'sr= 0.946). Correcting for patient-specific Ht levels did not further improve the concordance between the sampling methods. This successfully validated method to quantify miltefosine in DBS samples was demonstrated to be a valid and practical alternative to venous blood sampling that can be applied in future miltefosine pharmacokinetic studies with leishmaniasis patients, without Ht correction. Copyright © 2016 Kip et al.

  12. Total reflection x-ray fluorescence spectroscopy as a tool for evaluation of iron concentration in ferrofluids and yeast samples

    Energy Technology Data Exchange (ETDEWEB)

    Kulesh, N.A., E-mail: nikita.kulesh@urfu.ru [Ural Federal University, Mira 19, 620002 Ekaterinburg (Russian Federation); Novoselova, I.P. [Ural Federal University, Mira 19, 620002 Ekaterinburg (Russian Federation); Immanuel Kant Baltic Federal University, 236041 Kaliningrad (Russian Federation); Safronov, A.P. [Ural Federal University, Mira 19, 620002 Ekaterinburg (Russian Federation); Institute of Electrophysics UD RAS, Amundsen 106, 620016 Ekaterinburg (Russian Federation); Beketov, I.V.; Samatov, O.M. [Institute of Electrophysics UD RAS, Amundsen 106, 620016 Ekaterinburg (Russian Federation); Kurlyandskaya, G.V. [Ural Federal University, Mira 19, 620002 Ekaterinburg (Russian Federation); University of the Basque Country UPV-EHU, 48940 Leioa (Spain); Morozova, M. [Ural Federal University, Mira 19, 620002 Ekaterinburg (Russian Federation); Denisova, T.P. [Irkutsk State University, Karl Marks 1, 664003 Irkutsk (Russian Federation)

    2016-10-01

    In this study, total reflection x-ray fluorescent (TXRF) spectrometry was applied for the evaluation of iron concentration in ferrofluids and biological samples containing iron oxide magnetic nanoparticles obtained by the laser target evaporation technique. Suspensions of maghemite nanoparticles of different concentrations were used to estimate the limitation of the method for the evaluation of nanoparticle concentration in the range of 1–5000 ppm in absence of organic matrix. Samples of single-cell yeasts grown in the nutrient media containing maghemite nanoparticles were used to study the nanoparticle absorption mechanism. The obtained results were analyzed in terms of applicability of TXRF for quantitative analysis in a wide range of iron oxide nanoparticle concentrations for biological samples and ferrofluids with a simple established protocol of specimen preparation. - Highlights: • Ferrofluids and yeasts samples were analysed by TXRF spectroscopy. • Simple protocol for iron quantification by means of TXRF was proposed. • Results were combined with magnetic, structural, and morphological characterization. • Preliminary conclusion on nanoparticles uptake mechanism was made.

  13. Evaluation and subsequent minimization of matrix effects caused by phospholipids in LC-MS analysis of biological samples.

    Science.gov (United States)

    Janusch, Franziska; Kalthoff, Lena; Hamscher, Gerd; Mohring, Siegrun Ai

    2013-09-01

    The influence of matrix effects in LC-MS/MS analysis of biological samples can be enormous and has to be evaluated during method development. Phospholipids, which are present in considerable quantities in biological fluids, are supposed to cause matrix effects when co-eluting with analytes. Therefore, the reduction of phospholipids should lead to the minimization of matrix effects. METHODOLOGY & RESULTS: Here, a polymeric reversed-phase (PRP) SPE cartridge was compared with a combination of mixed-mode-anion-exchange (MAX) and mixed-mode-cation-exchange (MCX) SPE cartridges regarding elimination of matrix effects during sample clean-up. For evaluation of matrix effects post-column infusion experiments were performed. Phospholipid amount in the sample extract and matrix effects are enhanced using PRP in contrast to the combination of MAX/MCX. For an efficient elimination of phospholipids during sample preparation and to improve method accuracy and precision it is advisable to use a combination of MAX/MCX SPE cartridges.

  14. Temporal stability in the genetic structure of Sarcoptes scabiei under the host-taxon law: empirical evidences from wildlife-derived Sarcoptes mite in Asturias, Spain

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    Rossi Luca

    2011-07-01

    Full Text Available Abstract Background Implicitly, parasite molecular studies assume temporal genetic stability. In this study we tested, for the first time to our knowledge, the extent of changes in genetic diversity and structure of Sarcoptes mite populations from Pyrenean chamois (Rupicapra pyrenaica in Asturias (Spain, using one multiplex of 9 microsatellite markers and Sarcoptes samples from sympatric Pyrenean chamois, red deer (Cervus elaphus, roe deer (Capreolus capreolus and red fox (Vulpes vulpes. Results The analysis of an 11-years interval period found little change in the genetic diversity (allelic diversity, and observed and expected heterozygosity. The temporal stability in the genetic diversity was confirmed by population structure analysis, which was not significantly variable over time. Population structure analysis revealed temporal stability in the genetic diversity of Sarcoptes mite under the host-taxon law (herbivore derived- and carnivore derived-Sarcoptes mite among the sympatric wild animals from Asturias. Conclusions The confirmation of parasite temporal genetic stability is of vital interest to allow generalizations to be made, which have further implications regarding the genetic structure, epidemiology and monitoring protocols of the ubiquitous Sarcoptes mite. This could eventually be applied to other parasite species.

  15. Municipal solid waste composition: Sampling methodology, statistical analyses, and case study evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Edjabou, Maklawe Essonanawe, E-mail: vine@env.dtu.dk [Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby (Denmark); Jensen, Morten Bang; Götze, Ramona; Pivnenko, Kostyantyn [Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby (Denmark); Petersen, Claus [Econet AS, Omøgade 8, 2.sal, 2100 Copenhagen (Denmark); Scheutz, Charlotte; Astrup, Thomas Fruergaard [Department of Environmental Engineering, Technical University of Denmark, 2800 Kgs. Lyngby (Denmark)

    2015-02-15

    Highlights: • Tiered approach to waste sorting ensures flexibility and facilitates comparison of solid waste composition data. • Food and miscellaneous wastes are the main fractions contributing to the residual household waste. • Separation of food packaging from food leftovers during sorting is not critical for determination of the solid waste composition. - Abstract: Sound waste management and optimisation of resource recovery require reliable data on solid waste generation and composition. In the absence of standardised and commonly accepted waste characterisation methodologies, various approaches have been reported in literature. This limits both comparability and applicability of the results. In this study, a waste sampling and sorting methodology for efficient and statistically robust characterisation of solid waste was introduced. The methodology was applied to residual waste collected from 1442 households distributed among 10 individual sub-areas in three Danish municipalities (both single and multi-family house areas). In total 17 tonnes of waste were sorted into 10–50 waste fractions, organised according to a three-level (tiered approach) facilitating comparison of the waste data between individual sub-areas with different fractionation (waste from one municipality was sorted at “Level III”, e.g. detailed, while the two others were sorted only at “Level I”). The results showed that residual household waste mainly contained food waste (42 ± 5%, mass per wet basis) and miscellaneous combustibles (18 ± 3%, mass per wet basis). The residual household waste generation rate in the study areas was 3–4 kg per person per week. Statistical analyses revealed that the waste composition was independent of variations in the waste generation rate. Both, waste composition and waste generation rates were statistically similar for each of the three municipalities. While the waste generation rates were similar for each of the two housing types (single

  16. Sampling times and genotyping concerns in bioequivalence evaluation of branded and generic formulations

    Directory of Open Access Journals (Sweden)

    Zhao XY

    2013-11-01

    Full Text Available Xiao-Ying Zhao,1 Hui-Min Xu,2 Quan Zhou2 1The Medical Ethics Committee, 2Department of Pharmacy, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People's Republic of ChinaWe read with great interest the study by Del Tacca et al,1 who performed a comparative pharmacokinetic (PK and pharmacodynamic (PD evaluation of branded and generic formulations of meloxicam in healthy male subjects, and concluded that the two products can be used interchangeably in clinical practice. We especially appreciate their exploratory study on the PD/PK relationship which provides an important reference for bioequivalence studies of analgesics. However, we found two points worthy of discussion and we would like to share our perspectives in the following paragraphs.View original paper by Del Tacca and colleagues.

  17. An inset CT specimen for evaluating fracture in small samples of material.

    Science.gov (United States)

    Yahyazadehfar, M; Nazari, A; Kruzic, J J; Quinn, G D; Arola, D

    2014-02-01

    In evaluations on the fracture behavior of hard tissues and many biomaterials, the volume of material available to study is not always sufficient to apply a standard method of practice. In the present study an inset Compact Tension (inset CT) specimen is described, which uses a small cube of material (approximately 2×2×2mm(3)) that is molded within a secondary material to form the compact tension geometry. A generalized equation describing the Mode I stress intensity was developed for the specimen using the solutions from a finite element model that was defined over permissible crack lengths, variations in specimen geometry, and a range in elastic properties of the inset and mold materials. A validation of the generalized equation was performed using estimates for the fracture toughness of a commercial dental composite via the "inset CT" specimen and the standard geometry defined by ASTM E399 (2006). Results showed that the average fracture toughness obtained from the new specimen (1.23±0.02MPam(0.5)) was within 2% of that from the standard. Applications of the inset CT specimen are presented for experimental evaluations on the crack growth resistance of dental enamel and root dentin, including their fracture resistance curves. Potential errors in adopting this specimen are then discussed, including the effects of debonding between the inset and molding material on the estimated stress intensity distribution. Results of the investigation show that the inset CT specimen offers a viable approach for studying the fracture behavior of small volumes of structural materials. © 2013 Elsevier Ltd. All rights reserved.

  18. Unraveling the sequence information in COI barcode to achieve higher taxon assignment based on Indian freshwater fishes.

    Science.gov (United States)

    Chakraborty, Mohua; Ghosh, Sankar Kumar

    2015-04-01

    Efficacy of cytochrome c oxidase subunit I (COI) DNA barcode in higher taxon assignment is still under debate in spite of several attempts, using the conventional DNA barcoding methods, to assign higher taxa. Here we try to understand whether nucleotide and amino acid sequence in COI gene carry sufficient information to assign species to their higher taxonomic rank, using 160 species of Indian freshwater fishes. Our results reveal that with increase in the taxonomic rank, sequence conservation decreases for both nucleotides and amino acids. Order level exhibits lowest conservation with 50% of the nucleotides and amino acids being conserved. Among the variable sites, 30-50% were found to carry high information content within an order, while it was 70-80% within a family and 80-99% within a genus. High information content shows sites with almost conserved sequence but varying at one or two locations, which can be due to variations at species or population level. Thus, the potential of COI gene in higher taxon assignment is revealed with validation of ample inherent signals latent in the gene.

  19. Novedades taxonómicas y sinopsis del género Digitaria (Poaceae: Panicoideae: Paniceae en Bolivia

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    Andrea S. Vega

    2002-01-01

    Full Text Available El género Digitaria está representado en Bolivia por 27 taxones: 22 especies y 5 variedades. Se describe e ilustra a Digitaria argillacea var. nulliseta A. S. Vega & Rúgolo var. nov. Digitaria catamarcensis, D. ternata, D. setigera y D. aequiglumis var. laetevirens constituyen nuevas citas para este país y D. laxa representa una cita dudosa para Bolivia. Se confirma la identidad y la presencia de D. gerdesii var. boliviensis y D. similis en Bolivia. Digitaria neesiana, D. sanguinalis, D. violascens y D. corynotricha son excluídas de este tratamiento. Digitaria lanuginosa y D. setigera se ilustran con detalles y Digitaria fragilis es ilustrada por primera vez. El trabajo incluye la sinonimia, iconografía, distribución geográfica y ecología, usos, nombres vernáculos, exsiccata y observaciones. Se provee también una clave para la identificación de los taxones

  20. Monitoreo de la ictiofauna usando grupos taxonómicos superiores en el Parque Nacional Cabo Pulmo, México

    Directory of Open Access Journals (Sweden)

    Romeo Saldívar-Lucio

    2011-06-01

    Full Text Available El uso de indicadores biológicos es una herramienta útil para la descripción de las comunidades y permite ahorrar recursos en programas de monitoreo. Con el fin de evaluar el potencial bioindicador de grupos taxonómicos superiores en el Parque Nacional Cabo Pulmo, México, se construyeron modelos de regresión múltiple por pasos con valores de abundancia agrupados a nivel género y familia como predictores, mediante el uso de variables dependientes, los índices ecológicos de diversidad (H’, equidad (J’ y distintividad taxonómica (Δ*. Posteriormente se compararon los resultados de los modelos contra los valores de los índices ecológicos observados en un muestreo independiente. Los resultados mostraron que todos los modelos fueron altamente significativos; los valores más altos del coeficiente de determinación se obtuvieron en las regresiones aplicadas a H’, mientras que las usadas por Δ* fueron las menos precisas. Los resultados sugieren que los modelos predictivos aquí generados son susceptibles de ser aplicados en un programa de monitoreo. Este estudio sugiere la implementación de un programa de monitoreo a largo plazo basado en bioindicadores de la estructura comunitaria de peces en el Parque Nacional Cabo Pulmo, el cual combine la precisión con la facilidad de obtención de datos.

  1. Evaluation of Inflammatory Markers in a Large Sample of Obstructive Sleep Apnea Patients without Comorbidities

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    Izolde Bouloukaki

    2017-01-01

    Full Text Available Systemic inflammation is important in obstructive sleep apnea (OSA pathophysiology and its comorbidity. We aimed to assess the levels of inflammatory biomarkers in a large sample of OSA patients and to investigate any correlation between these biomarkers with clinical and polysomnographic (PSG parameters. This was a cross-sectional study in which 2983 patients who had undergone a polysomnography for OSA diagnosis were recruited. Patients with known comorbidities were excluded. Included patients (n=1053 were grouped according to apnea-hypopnea index (AHI as mild, moderate, and severe. Patients with AHI < 5 served as controls. Demographics, PSG data, and levels of high-sensitivity C-reactive protein (hs-CRP, fibrinogen, erythrocyte sedimentation rate (ESR, and uric acid (UA were measured and compared between groups. A significant difference was found between groups in hs-CRP, fibrinogen, and UA. All biomarkers were independently associated with OSA severity and gender (p<0.05. Females had increased levels of hs-CRP, fibrinogen, and ESR (p<0.001 compared to men. In contrast, UA levels were higher in men (p<0.001. Our results suggest that inflammatory markers significantly increase in patients with OSA without known comorbidities and correlate with OSA severity. These findings may have important implications regarding OSA diagnosis, monitoring, treatment, and prognosis. This trial is registered with ClinicalTrials.gov number NCT03070769.

  2. Evaluation of knowledge of the term "nephrology" in a population sample.

    Science.gov (United States)

    Di Luca, Daniel Garbin; de Oliveira, Diogo Costa Leandro; Guimarães, Luis Eduardo Reis; Tamiasso, Gabriel Cruz; Goulart, Lis Bastos Zampier; Rosa, Maria Luiza Garcia; Lugon, Jocemir Ronaldo

    2013-01-01

    The consolidation of nephrology as a medical specialty is relatively new and its denomination does not intuitively reflects its true scope. To assess the degree of knowledge from a population sample regarding the term "nephrology". We carried out a cross-sectional study in Niterói, RJ, with adult passerby individuals answering to the question "Do you know what nephrology is?". The variables recorded included: gender, age, skin-color, residence, income, educational level and kidney-disease history in the family. p values 30 years. The mean age among participants was 39 (22-56) years, 49% were males and 56% caucasians. Twenty-eight percent of the interviewees knew the term "nephrology". Their knowledge came from school (39%) and family (30%). Those who knew about the term "nephrology" were older (42 ± 17 vs. 39 ± 17 years, p nephrology", illustrating the specialty's low penetration. We must strive to popularize this field of medicine aiming at better educating the population concerning the prevention and care of kidney diseases.

  3. Evaluation of coral pathogen growth rates after exposure to atmospheric African dust samples

    Science.gov (United States)

    Lisle, John T.; Garrison, Virginia H.; Gray, Michael A.

    2014-01-01

    Laboratory experiments were conducted to assess if exposure to atmospheric African dust stimulates or inhibits the growth of four putative bacterial coral pathogens. Atmospheric dust was collected from a dust-source region (Mali, West Africa) and from Saharan Air Layer masses over downwind sites in the Caribbean [Trinidad and Tobago and St. Croix, U.S. Virgin Islands (USVI)]. Extracts of dust samples were used to dose laboratory-grown cultures of four putative coral pathogens: Aurantimonas coralicida (white plague type II), Serratia marcescens (white pox), Vibrio coralliilyticus, and V. shiloi (bacteria-induced bleaching). Growth of A. coralicida and V. shiloi was slightly stimulated by dust extracts from Mali and USVI, respectively, but unaffected by extracts from the other dust sources. Lag time to the start of log-growth phase was significantly shortened for A. coralicida when dosed with dust extracts from Mali and USVI. Growth of S. marcescens and V. coralliilyticus was neither stimulated nor inhibited by any of the dust extracts. This study demonstrates that constituents from atmospheric dust can alter growth of recognized coral disease pathogens under laboratory conditions.

  4. Concept formation based on value relations evaluated with a matching-to-sample procedure.

    Science.gov (United States)

    Pérez-González, Luis Antonio

    2008-01-01

    To study concept formation based on relations, adults were taught and tested on complex discriminations involving figures that varied in colors, forms, and orientations. In Experiment 1, participants learned to select figures with values A1 and B1 or values B1 and C1; thereafter, they consistently selected figures with values A1 and C1. Selections were based on the relations among the values, rather than on perceptual properties. Experiments 2 and 3 studied generalization with a matching-to-sample procedure: participants learned to select "yes" in the presence of the positive figures, such as A1B1, and "no" in the presence of the negative figures. Thereafter, all figures that resulted from combining three values of the three relevant dimensions were probed. Participants typically selected "yes" in the presence of the novel figures that had two or three values related to one another and selected "no" in the presence of the other figures. Finally, two participants learned a simple discrimination. They did not generalize responding to other figures with the same values; instead, their performance in the generalization test remained almost unaltered. Thus, the concept based on relations was not affected by the simple discrimination. These results showed some unique properties of the concept based on relations and challenge previous theories on concept formation.

  5. Quality evaluation of commercially sold table water samples in Michael Okpara University of Agriculture, Umudike, Nigeria and surrounding environments

    Directory of Open Access Journals (Sweden)

    D.O. Okorie

    2015-01-01

    Full Text Available In Michael Okpara University of Agriculture, Umudike, Nigeria (MOUAU and surrounding environments, table water of different brands is commercially hawked by vendors. To the best of our knowledge, there is no scientific documentation on the quality of these water samples. Hence this study which evaluated the quality of different brands of water samples commercially sold in MOUAU and surrounding environments. The physicochemical properties (pH, total dissolved solids (TDS, biochemical oxygen demand (BOD, total hardness, dissolved oxygen, Cl, NO3, ammonium nitrogen (NH3N, turbidity, total suspended solids (TSS, Ca, Mg, Na and K of the water samples as indices of their quality were carried out using standard techniques. Results obtained from this study indicated that most of the chemical constituents of these table water samples commercially sold in Umudike environment conformed to the standards given by the Nigerian Industrial Standard (NIS, World Health Organization (WHO and American Public Health Association (APHA, respectively, while values obtained for ammonium nitrogen in these water samples calls for serious checks on methods of their production and delivery to the end users.

  6. Evaluation in pre-diagnosis samples discounts ICAM-1 and TIMP-1 as biomarkers for earlier diagnosis of pancreatic cancer.

    Science.gov (United States)

    Jenkinson, C; Elliott, V; Menon, U; Apostolidou, S; Fourkala, O E; Gentry-Maharaj, A; Pereira, S P; Jacobs, I; Cox, T F; Greenhalf, W; Timms, J F; Sutton, R; Neoptolemos, J P; Costello, E

    2015-01-15

    Circulating intercellular adhesion molecule-1 (ICAM-1) and tissue inhibitor of metalloproteinases-1 (TIMP-1) have been widely proposed as potential diagnostic biomarkers for pancreatic ductal adenocarcinoma (PDAC). We report on serum protein levels prior to clinical presentation of pancreatic cancer. Serum ICAM-1 and TIMP-1 were measured by ELISA in two case–control sets: 1) samples from patients diagnosed with pancreatic cancer (n = 40), chronic pancreatitis (n = 20), benign jaundice due to gall stones (n = 20) and healthy subjects (n = 20); 2) a preclinical set from the UK Collaborative Trial of Ovarian Cancer Screening biobank of samples collected from 27 post-menopausal women 0–12 months prior to diagnosis of pancreatic cancer and controls matched for date of donation and centre. Levels of ICAM-1 and TIMP-1 were significantly elevated in set 1 in PDAC patients with jaundice compared to PDAC patients without jaundice and both proteins were elevated in patients with jaundice due to gall stones. Neither protein was elevated in samples taken 0–12 months prior to PDAC diagnosis compared to non-cancer control samples. In conclusion, evaluation in pre-diagnosis samples discounts ICAM-1 and TIMP-1 as biomarkers for earlier diagnosis of pancreatic cancer. Failure to account for obstructive jaundice may have contributed to the previous promise of these candidate biomarkers. Pancreatic cancer is usually diagnosed when at an advanced stage which greatly limits therapeutic options. Biomarkers that could facilitate earlier diagnosis are urgently sought.

  7. Evaluation of a susceptibility gene for schizophrenia: genotype based meta-analysis of RGS4 polymorphisms from thirteen independent samples.

    Science.gov (United States)

    Talkowski, Michael E; Seltman, Howard; Bassett, Anne S; Brzustowicz, Linda M; Chen, Xiangning; Chowdari, Kodavali V; Collier, David A; Cordeiro, Quirino; Corvin, Aiden P; Deshpande, Smita N; Egan, Michael F; Gill, Michael; Kendler, Kenneth S; Kirov, George; Heston, Leonard L; Levitt, Pat; Lewis, David A; Li, Tao; Mirnics, Karoly; Morris, Derek W; Norton, Nadine; O'Donovan, Michael C; Owen, Michael J; Richard, Christian; Semwal, Prachi; Sobell, Janet L; St Clair, David; Straub, Richard E; Thelma, B K; Vallada, Homero; Weinberger, Daniel R; Williams, Nigel M; Wood, Joel; Zhang, Feng; Devlin, Bernie; Nimgaonkar, Vishwajit L

    2006-07-15

    Associations between schizophrenia (SCZ) and polymorphisms at the regulator of G-protein signaling 4 (RGS4) gene have been reported (single nucleotide polymorphisms [SNPs] 1, 4, 7, and 18). Yet, similar to other SCZ candidate genes, studies have been inconsistent with respect to the associated alleles. In an effort to resolve the role for RGS4 in SCZ susceptibility, we undertook a genotype-based meta-analysis using both published and unpublished family-based and case-control samples (total n = 13,807). The family-based dataset consisted of 10 samples (2160 families). Significant associations with individual SNPs/haplotypes were not observed. In contrast, global analysis revealed significant transmission distortion (p = .0009). Specifically, analyses suggested overtransmission of two common haplotypes that account for the vast majority of all haplotypes. Separate analyses of 3486 cases and 3755 control samples (eight samples) detected a significant association with SNP 4 (p = .01). Individual haplotype analyses were not significant, but evaluation of test statistics from individual samples suggested significant associations. Our collaborative meta-analysis represents one of the largest SCZ association studies to date. No individual risk factor arose from our analyses, but interpretation of these results is not straightforward. Our analyses suggest risk due to at least two common haplotypes in the presence of heterogeneity. Similar analysis for other putative susceptibility genes is warranted.

  8. Evaluating Complex Mixtures in the Zebrafish Embryo by Reconstituting Field Water Samples: A Metal Pollution Case Study

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    Ellen D. G. Michiels

    2017-03-01

    Full Text Available Accurately assessing the toxicity of complex, environmentally relevant mixtures remains an important challenge in ecotoxicology. The goal was to identify biological effects after exposure to environmental water samples and to determine whether the observed effects could be explained by the waterborne metal mixture found in the samples. Zebrafish embryos were exposed to water samples of five different sites originating from two Flemish (Mol and Olen, Belgium metal contaminated streams: “Scheppelijke Nete” (SN and “Kneutersloop” (K, and a ditch (D, which is the contamination source of SN. Trace metal concentrations, and Na, K, Mg and Ca concentrations were measured using ICP-MS and were used to reconstitute site-specific water samples. We assessed whether the effects that were observed after exposure to environmental samples could be explained by metal mixture toxicity under standardized laboratory conditions. Exposure to “D” or “reconstituted D” water caused 100% mortality. SN and reconstituted SN water caused similar effects on hatching, swim bladder inflation, growth and swimming activity. A canonical discriminant analysis confirmed a high similarity between both exposure scenarios, indicating that the observed toxicity was indeed primarily caused by metals. The applied workflow could be a valuable approach to evaluate mixture toxicity that limits time and costs while maintaining biological relevance.

  9. Evaluating Complex Mixtures in the Zebrafish Embryo by Reconstituting Field Water Samples: A Metal Pollution Case Study.

    Science.gov (United States)

    Michiels, Ellen D G; Vergauwen, Lucia; Hagenaars, An; Fransen, Erik; Dongen, Stefan Van; Van Cruchten, Steven J; Bervoets, Lieven; Knapen, Dries

    2017-03-02

    Accurately assessing the toxicity of complex, environmentally relevant mixtures remains an important challenge in ecotoxicology. The goal was to identify biological effects after exposure to environmental water samples and to determine whether the observed effects could be explained by the waterborne metal mixture found in the samples. Zebrafish embryos were exposed to water samples of five different sites originating from two Flemish (Mol and Olen, Belgium) metal contaminated streams: "Scheppelijke Nete" (SN) and "Kneutersloop" (K), and a ditch (D), which is the contamination source of SN. Trace metal concentrations, and Na, K, Mg and Ca concentrations were measured using ICP-MS and were used to reconstitute site-specific water samples. We assessed whether the effects that were observed after exposure to environmental samples could be explained by metal mixture toxicity under standardized laboratory conditions. Exposure to "D" or "reconstituted D" water caused 100% mortality. SN and reconstituted SN water caused similar effects on hatching, swim bladder inflation, growth and swimming activity. A canonical discriminant analysis confirmed a high similarity between both exposure scenarios, indicating that the observed toxicity was indeed primarily caused by metals. The applied workflow could be a valuable approach to evaluate mixture toxicity that limits time and costs while maintaining biological relevance.

  10. Evaluation of a New Technique for iFOBT Utilising a New Sample Collection Device with Increased Buffer Stability.

    Science.gov (United States)

    Bruns-Toepler, Markus; Hardt, Philip

    2017-07-01

    The aims of the present study were: (i) Evaluate specificity and sensitivity of Hb Smart enzyme-linked immunosorbent assay (ELISA) (ScheBo Biotech) compared to colonoscopy results and (ii) assess stability of a new sample collection device containing a newly formulated buffer to extract haemoglobin using buffer and stool samples spiked with defined concentrations of haemoglobin. Stool samples were quantified with the ELISA method. The stability of haemoglobin in the extraction buffer and in native stool samples, respectively, was determined daily by ELISA during storage for 5 days at 4°C and at room temperature after addition of haemoglobin. Haemoglobin ELISA had a sensitivity of 78.4% for detection of CRC with a specificity of 98%. Haemoglobin extracted in corresponding extraction buffer demonstrated stability throughout storage for 5 days at 4°C and at room temperature. Hb Smart represents a very promising tool for large-scale screening of CRC with regard to sample handling, stability and analysis of haemoglobin in faeces. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  11. A combined photometric and kinematic recipe for evaluating the nature of bulges using the CALIFA sample

    Science.gov (United States)

    Neumann, J.; Wisotzki, L.; Choudhury, O. S.; Gadotti, D. A.; Walcher, C. J.; Bland-Hawthorn, J.; García-Benito, R.; González Delgado, R. M.; Husemann, B.; Marino, R. A.; Márquez, I.; Sánchez, S. F.; Ziegler, B.; Califa Collaboration

    2017-07-01

    Understanding the nature of bulges in disc galaxies can provide important insights into the formation and evolution of galaxies. For instance, the presence of a classical bulge suggests a relatively violent history. In contrast, the presence of an inner disc instead (also referred to as a "pseudobulge") indicates the occurrence of secular evolution processes in the main disc. However, we still lack criteria to effectively categorise bulges, limiting our ability to study their impact on the evolution of the host galaxies. Here we present a recipe to separate inner discs from classical bulges by combining four different parameters from photometric and kinematic analyses: the bulge Sérsic index nb, the concentration index C20,50, the Kormendy (1977, ApJ, 217, 406) relation and the inner slope of the radial velocity dispersion profile ∇σ. With that recipe we provide a detailed bulge classification for a sample of 45 galaxies from the integral-field spectroscopic survey CALIFA. To aid in categorising bulges within these galaxies, we perform 2D image decomposition to determine bulge Sérsic index, bulge-to-total light ratio, surface brightness and effective radius of the bulge and use growth curve analysis to derive a new concentration index, C20,50. We further extract the stellar kinematics from CALIFA data cubes and analyse the radial velocity dispersion profile. The results of the different approaches are in good agreement and allow a safe classification for approximately 95% of the galaxies. In particular, we show that our new "inner" concentration index performs considerably better than the traditionally used C50,90 when yielding the nature of bulges. We also found that a combined use of this index and the Kormendy relation gives a very robust indication of the physical nature of the bulge.

  12. Evaluation of the DSM-5 severity indicator for binge eating disorder in a clinical sample

    Science.gov (United States)

    Grilo, Carlos M.; Ivezaj, Valentina; White, Marney A.

    2015-01-01

    Objective This study tested the new DSM-5 severity criterion for binge eating disorder (BED) based on frequency of binge-eating in a clinical sample. This study also tested overvaluation of shape/weight as an alternative severity specifier. Method Participants were 834 treatment-seeking adults diagnosed with DSM-5 BED using semistructured diagnostic and eating-disorder interviews. Participants sub-grouped based on DSM-5 severity levels and on overvaluation of shape/weight were compared on demographic and clinical variables. Results Based on DSM-5 severity definitions, 331 (39.7%) participants were categorized as mild, 395 (47.5%) as moderate, 83 (10.0%) as severe, and 25 (3.0%) as extreme. Analyses comparing three (mild, moderate, and severe/extreme) severity groups revealed no significant differences in demographic variables or body mass index (BMI). Analyses revealed significantly higher eating-disorder psychopathology in the severe/extreme than moderate and mild groups and higher depression in moderate and severe/extreme groups than the mild group; effect sizes were small. Participants characterized with overvaluation (N = 449; 54%) versus without overvaluation (N = 384; 46%) did not differ significantly in age, sex, BMI, or binge-eating frequency, but had significantly greater eating-disorder psychopathology and depression. The robustly greater eating-disorder psychopathology and depression levels (medium-to-large effect sizes) in the overvaluation group was observed without attenuation of effect sizes after adjusting for ethnicity/race and binge-eating severity/frequency. Conclusions Our findings provide support for overvaluation of shape/weight as a severity specifier for BED as it provides stronger information about the severity of homogeneous groupings of patients than the DSM-5 rating based on binge-eating. PMID:26114779

  13. Evaluation of the DSM-5 severity indicator for binge eating disorder in a clinical sample.

    Science.gov (United States)

    Grilo, Carlos M; Ivezaj, Valentina; White, Marney A

    2015-08-01

    This study tested the new DSM-5 severity criterion for binge eating disorder (BED) based on frequency of binge-eating in a clinical sample. This study also tested overvaluation of shape/weight as an alternative severity specifier. Participants were 834 treatment-seeking adults diagnosed with DSM-5 BED using semi-structured diagnostic and eating-disorder interviews. Participants sub-grouped based on DSM-5 severity levels and on overvaluation of shape/weight were compared on demographic and clinical variables. Based on DSM-5 severity definitions, 331 (39.7%) participants were categorized as mild, 395 (47.5%) as moderate, 83 (10.0%) as severe, and 25 (3.0%) as extreme. Analyses comparing three (mild, moderate, and severe/extreme) severity groups revealed no significant differences in demographic variables or body mass index (BMI). Analyses revealed significantly higher eating-disorder psychopathology in the severe/extreme than moderate and mild groups and higher depression in moderate and severe/extreme groups than the mild group; effect sizes were small. Participants characterized with overvaluation (N = 449; 54%) versus without overvaluation (N = 384; 46%) did not differ significantly in age, sex, BMI, or binge-eating frequency, but had significantly greater eating-disorder psychopathology and depression. The robustly greater eating-disorder psychopathology and depression levels (medium-to-large effect sizes) in the overvaluation group was observed without attenuation of effect sizes after adjusting for ethnicity/race and binge-eating severity/frequency. Our findings provide support for overvaluation of shape/weight as a severity specifier for BED as it provides stronger information about the severity of homogeneous groupings of patients than the DSM-5 rating based on binge-eating. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. SLUDGE BATCH 6 ACCEPTANCE EVALUATION: RADIONUCLIDE CONCENTRATIONS IN TANK 51 SB6 QUALIFICATION SAMPLE PREPARED AT SRNL

    Energy Technology Data Exchange (ETDEWEB)

    Bannochie, C.; Bibler, N.; Diprete, D.

    2010-05-21

    Presented in this report are radionuclide concentrations required as part of the program of qualifying Sludge Batch Six (SB6) for processing in the Defense Waste Processing Facility (DWPF). The SB6 material is currently in Tank 51 being washed and prepared for transfer to Tank 40. The acceptance evaluation needs to be completed prior to the transfer of the material in Tank 51 to Tank 40. The sludge slurry in Tank 40 has already been qualified for DWPF and is currently being processed as SB5. The radionuclide concentrations were measured or estimated in the Tank 51 SB6 Qualification Sample prepared at Savannah River National Laboratory (SRNL). This sample was prepared from the three liter sample of Tank 51 sludge slurry (HTF-51-09-110) taken on October 8, 2009. The sample was delivered to SRNL where it was initially characterized in the Shielded Cells. Under the direction of the Liquid Waste Organization it was then modified by eight washes, nine decants, an addition of Pu from Canyon Tank 16.3, and an addition of NaNO{sub 2}. This final slurry now has a composition expected to be similar to that of the slurry in Tank 51 after final preparations have been made for transfer of that slurry to Tank 40. Determining the radionuclide concentrations in this Tank 51 SB6 Qualification Sample is part of the work requested in Technical Task Request (TTR) No. HLW-DWPF-TTR-2009-0014. The work with this qualification sample is covered by a Task Technical and Quality Assurance Plan and an Analytical Study Plan. The radionuclides included in this report are needed for the DWPF Radiological Program Evaluation, the DWPF Waste Acceptance Criteria (TSR/WAC) Evaluation, and the DWPF Solid Waste Characterization Program (TTR Task I.2). Radionuclides required to meet the Waste Acceptance Product Specifications (TTR Task II.2.) will be measured at a later date after the slurry from Tank 51 has been transferred to Tank 40. Then a sample of the as-processed SB6 will be taken and transferred

  15. Judges' views of child sexual abuse: evaluating beliefs against research findings in a Finnish sample.

    Science.gov (United States)

    Korkman, Julia; Svanbäck, Jatta; Finnilä, Katarina; Santtila, Pekka

    2014-10-01

    Beliefs impact our decision-making and different professionals have been shown to have beliefs about child sexual abuse (CSA) that do not coincide with scientific findings. In the present study, judges' beliefs regarding CSA were explored. Finnish judges (N = 104) answered a questionnaire about CSA related issues as well as questions regarding their professional experience of CSA cases. The judges held both correct and incorrect beliefs; while their CSA prevalence estimates were rather well in line with research findings, half of the participants estimated that no professionals use suggestive methods when interviewing children and more than 40% thought suggestive methods can be useful when trying to get a child to tell about real events. Judges correctly assumed symptoms cannot be used to assess a CSA case, however, the majority thought play observations were appropriate means for evaluating such suspicions. Experience seemed to lead to more confidence in their own expertise but not in an actual increase in knowledge, namely, judges thought themselves more expert when more experienced although their expertise as measured by the questionnaire did not improve. Overall, the judges had both correct and erroneous beliefs but while experience did not improve the situation, gaining information about CSA did. More research about the beliefs of judges and how such beliefs impact legal decision-making is needed. © 2014 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

  16. Psychometric evaluation of the muscle appearance satisfaction scale in a Mexican male sample.

    Science.gov (United States)

    Escoto Ponce de León, María Del Consuelo; Bosques-Brugada, Lilián Elizabeth; Camacho Ruiz, Esteban Jaime; Alvarez-Rayón, Georgina; Franco Paredes, Karina; Rodríguez Hernández, Gabriela

    2017-03-02

    The purpose of this study was to determine whether the muscle appearance satisfaction scale (MASS) shows acceptable psychometric properties in Mexican bodybuilders. A total of 258 Mexican male bodybuilders were recruited. Two self-report questionnaires, including the MASS and drive for muscularity scale (DMS), were administered. Six models of the latent structure of the MASS were evaluated, using confirmatory factor analysis with maximum likelihood, considering robust Satorra-Bentler correction to estimate the fit of the models to the data. Similar to the original MASS, the series of CFA confirmed that the Mexican version was well represented with the 17-item five-factor structure, which showed a good model fit [Satorra-Bentler Chi-square (109, n = 258) = 189.18, p muscle checking scale (0.77). Test-retest reliability analysis showed stability of the MASS total as well as of the subscale scores over a 2-week period (intraclass correlation coefficients = 0.75-0.91). Construct validity was demonstrated by a significant positive correlation between MASS and DMS results (r = 0.75; p = 0.0001). These results were similar to those of previous studies, which demonstrate the scale's usefulness. Our results support the suitability of the MASS and its subscales to measure muscle dysmorphia symptoms in Mexican male bodybuilders.

  17. Las Calamitáceas españolas. Índice taxonómico y clave analítica

    Directory of Open Access Journals (Sweden)

    Diéguez, M. C.

    1986-02-01

    Full Text Available The present work consists of the check-list of the Calamitae para-espcies collected in Spain with the synonims used. These have been compiled in a1phabetical order for case of reference. and is followed by an evaluation of them, considering some elected characters for its rapid identification, with whose we have made one key the para-species, which, helps its determination from the collecting place.

    En el presente trabajo se realiza un índice taxonómico de para-especies de Calamitáceas recogidas en España, con sus principales sinonimias. disponiéndose en orden alfabético para facilitar su utilización. Este índice es seguido por una evaluación de dichas para-especies. en atención a caracteres que faciliten su identificación y a partir de los cuales proponemos una clave analítica, que permita su determinación en el lugar de recogida.

  18. Evaluation of PET quantification accuracy in vivo. Comparison of measured FDG concentration in the bladder with urine samples.

    Science.gov (United States)

    Maus, J; Hofheinz, F; Schramm, G; Oehme, L; Beuthien-Baumann, B; Lukas, M; Buchert, R; Steinbach, J; Kotzerke, J; van den Hoff, J

    2014-01-01

    Quantitative positron emission tomography (PET) requires accurate scanner calibration, which is commonly performed using phantoms. It is not clear to what extent this procedure ensures quantitatively correct results in vivo, since certain conditions differ between phantom and patient scans. We, therefore, have evaluated the actual quantification accuracy in vivo of PET under clinical routine conditions. We determined the activity concentration in the bladder in patients undergoing routine [18F]FDG whole body investigations with three different PET scanners (Siemens ECAT EXACT HR+ PET: n = 21; Siemens Biograph 16 PET/CT: n = 16; Philips Gemini-TF PET/CT: n = 19). Urine samples were collected immediately after scan. Activity concentration in the samples was determined in well counters cross-calibrated against the respective scanner. The PET (bladder) to well counter (urine sample) activity concentration ratio was determined. Activity concentration in the bladder (PET) was systematically lower than in the urine samples (well counter). The patient-averaged PET to well counter ratios for the investigated scanners are (mean ± SEM): 0.881 ± 0.015 (ECAT HR+), 0.898 ± 0.024 (Biograph 16), 0.932 ± 0.024 (Gemini-TF). These values correspond to underestimates by PET of 11.9%, 10.2%, and 6.8%, respectively. The investigated PET systems consistently underestimate activity concentration in the bladder. The comparison of urine samples with PET scans of the bladder is a straightforward means for in vivo evaluation of the expectable quantification accuracy. The method might be interesting for multi-center trials, for additional quality assurance in PET and for investigation of PET/MR systems for which clear proof of sufficient quantitative accuracy in vivo is still missing.

  19. Evaluation of protein spectra cluster analysis for Streptococcus spp. identification from various swine clinical samples.

    Science.gov (United States)

    Matajira, Carlos E C; Moreno, Luisa Z; Gomes, Vasco T M; Silva, Ana Paula S; Mesquita, Renan E; Doto, Daniela S; Calderaro, Franco F; de Souza, Fernando N; Christ, Ana Paula G; Sato, Maria Inês Z; Moreno, Andrea M

    2017-03-01

    Traditional microbiological methods enable genus-level identification of Streptococcus spp. isolates. However, as the species of this genus show broad phenotypic variation, species-level identification or even differentiation within the genus is difficult. Herein we report the evaluation of protein spectra cluster analysis for the identification of Streptococcus species associated with disease in swine by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A total of 250 S. suis-like isolates obtained from pigs with clinical signs of encephalitis, arthritis, pneumonia, metritis, and urinary or septicemic infection were studied. The isolates came from pigs in different Brazilian states from 2001 to 2014. The MALDI-TOF MS analysis identified 86% (215 of 250) as S. suis and 14% (35 of 250) as S. alactolyticus, S. dysgalactiae, S. gallinaceus, S. gallolyticus, S. gordonii, S. henryi, S. hyointestinalis, S. hyovaginalis, S. mitis, S. oralis, S. pluranimalium, and S. sanguinis. The MALDI-TOF MS identification was confirmed in 99.2% of the isolates by 16S rDNA sequencing, with MALDI-TOF MS misidentifying 2 S. pluranimalium as S. hyovaginalis. Isolates were also tested by a biochemical automated system that correctly identified all isolates of 8 of the 10 species in the database. Neither the isolates of the 3 species not in the database ( S. gallinaceus, S. henryi, and S. hyovaginalis) nor the isolates of 2 species that were in the database ( S. oralis and S. pluranimalium) could be identified. The topology of the protein spectra cluster analysis appears to sustain the species phylogenetic similarities, further supporting identification by MALDI-TOF MS examination as a rapid and accurate alternative to 16S rDNA sequencing.

  20. Evaluation of Multiple-Sampling Function used with a Microtek flatbed scanner for Radiation Dosimetry Calibration of EBT2 Film

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Liyun [Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung 82445, Taiwan (China); Ho, Sheng-Yow [Department of Nursing, Chang Jung Christian University, Tainan 71101, Taiwan (China); Department of Radiation Oncology, Chi Mei Medical Center, Liouying, Tainan 73657, Taiwan (China); Ding, Hueisch-Jy [Department of Medical Imaging and Radiological Sciences, I-Shou University, Kaohsiung 82445, Taiwan (China); Hwang, Ing-Ming [Department of Medical Imaging and Radiology, Shu Zen College of Medicine and Management, Kaohsiung 82144, Taiwan (China); Chen, Pang-Yu, E-mail: pangyuchen@yahoo.com.tw [Department of Radiation Oncology, Sinlau Christian Hospital, Tainan 70142, Taiwan (China); Lee, Tsair-Fwu, E-mail: tflee@kuas.edu.tw [Medical Physics and Informatics Laboratory, Department of Electronics Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan (China)

    2016-10-01

    The radiochromic EBT2 film is a widely used quality assurance device for radiation therapy. This study evaluated the film calibration performance of the multiple-sampling function, a function of the ScanWizard Pro scanning software provided by the manufacturer, when used with Microtek 9800XL plus (9800XL{sup +}) flatbed scanner. By using the PDD method, each one of the eight EBT2 films, four delivered by 290 monitor unit (MU) and four by 88 MU via 6-MV photon beams, was tightly sandwiched in a 30{sup 3}-cm{sup 3} water equivalent polystyrene phantom prior to irradiation. Before and after irradiation, all films were scanned using the Microtek 9800XL{sup +} scanner with five different modes of the multiple-sampling function, which could generate the image with the averaged result of multiple-sampling. The net optical densities (netOD) on the beam central axis of film were assigned to corresponding depth doses for calibration. For each sampling mode with either delivered MU, the depth-dose uncertainty of a single film from repeated scans and that of a single scan of the four films were analyzed. Finally, the calibration error and the combined calibration uncertainty between film determined depth-doses and delivered depth-doses were calculated and evaluated for each sampling mode. All standard deviations and the calibration error were demonstrated to be unrelated to the number of sampling lines. The calibration error of the 2-line and 16-line mode was within 3 cGy and better than that of the other modes. The combined uncertainty of the 2-line mode was the lowest, which was generally less than 6 cGy except for the delivered dose around 100 cGy. The evaluation described herein revealed that the EBT2 film calibrated with the 2-line mode has relatively lower error, scanning time and combined uncertianty. Therefore, it is recommended for routine EBT2 film calibration and verification of treatment plans.

  1. Evaluation of endocrine disruptor levels in Kafue Lechwe (Kobus leche kafuensis) samples from the Blue Lagoon National Park of Zambia.

    Science.gov (United States)

    Sichilongo, Kwenga; Torto, Nelson

    2009-12-01

    The concentrations of endocrine disruptors were determined in 36 liver tissue, serum and whole blood sample extracts drawn from 15 Blue Lagoon National Park Kafue lechwe. Out of 10 analytes evaluated, 89% of the sample extracts showed very high dieldrin concentrations of between 0.08–100 μg/mL in serum, 0.08–24.8 μg/mL in whole blood and 0.08–4.6 μg/g wet weight in liver tissue extracts. pp-DDE was detected in 83% of the sample extracts at 0.006–5.1 μg/mL in serum, 0.006–8.5 μg/mL in whole blood and 0.006–0.12 μg/g wet weight in liver tissue extracts. There was strong correlation between pp-DDE and dieldrin in all the three matrices. Deltamethrin and endosulfan detected at 50% frequency each. Percent recoveries in spiked laboratory blanks ranged between 60–100% while calculated detection limits ranged from 0.004 to 0.21 μg/mL for all the endocrine disruptors evaluated.

  2. Psychometric evaluation of the mini-social phobia inventory (Mini-SPIN) in a treatment-seeking sample.

    Science.gov (United States)

    Weeks, Justin W; Spokas, Megan E; Heimberg, Richard G

    2007-01-01

    The Mini-Social Phobia Inventory (Mini-SPIN) is a 3-item, self-rated screening instrument to assess social anxiety disorder, but its psychometric properties have not yet been examined in a sample seeking treatment for psychiatric disorders. We analyzed responses from 291 adults who telephoned the Adult Anxiety Clinic of Temple (AACT) seeking treatment for social anxiety or generalized anxiety and worry. The Mini-SPIN demonstrated strong internal consistency. Support for the convergent validity of the Mini-SPIN was provided by moderate correlations with several self-report measures and a clinician-administered measure of social anxiety completed by the subsample of callers who later came to the AACT for evaluation. Furthermore, the Mini-SPIN correlated significantly with two of three measures of functional disability, but not with a measure of life satisfaction. Correlations with measures of other constructs were nonsignificant, providing support for the discriminant validity of the Mini-SPIN. In addition, a cutoff score of 6 on the Mini-SPIN yielded strong sensitivity and diagnostic efficiency in the subsample of treatment seekers that later completed pretreatment evaluation, although the specificity of this cutoff score was not optimal in this sample. Overall, the Mini-SPIN demonstrated sound psychometric properties in this treatment-seeking sample. (c) 2006 Wiley-Liss, Inc.

  3. Preliminary Evaluation of the Field and Laboratory Emission Cell (FLEC) for Sampling Attribution Signatures from Building Materials

    Energy Technology Data Exchange (ETDEWEB)

    Harvey, Scott D.; He, Lijian; Wahl, Jon H.

    2012-08-30

    This study provides a preliminary evaluation of the Field and Laboratory Emission Cell (FLEC) for its suitability for sampling building materials for toxic compounds and their associated impurities and residues that might remain after a terrorist chemical attack. Chemical warfare (CW) agents and toxic industrial chemicals were represented by a range of test probes that included CW surrogates. The test probes encompassed the acid-base properties, volatilities, and polarities of the expected chemical agents and residual compounds. Results indicated that dissipation of the test probes depended heavily on the underlying material. Near complete dissipation of almost all test probes occurred from galvanized stainless steel within 3.0 hrs, whereas far stronger retention with concomitant slower release was observed for vinyl composition floor tiles. The test probes displayed immediated permanence on Teflon. FLEC sampling was further evaluated by profiling residues remaining after the evaporation of 2-chloroethyl ethyl sulfide, a sulfur mustard simulant. This study lays the groundwork for the eventual goal of applying this sampling approach for collection of forensic attribution signatures that remain after a terrorist chemical attack.

  4. Air sampling procedures to evaluate microbial contamination: a comparison between active and passive methods in operating theatres

    Directory of Open Access Journals (Sweden)

    Napoli Christian

    2012-08-01

    Full Text Available Abstract Background Since air can play a central role as a reservoir for microorganisms, in controlled environments such as operating theatres regular microbial monitoring is useful to measure air quality and identify critical situations. The aim of this study is to assess microbial contamination levels in operating theatres using both an active and a passive sampling method and then to assess if there is a correlation between the results of the two different sampling methods. Methods The study was performed in 32 turbulent air flow operating theatres of a University Hospital in Southern Italy. Active sampling was carried out using the Surface Air System and passive sampling with settle plates, in accordance with ISO 14698. The Total Viable Count (TVC was evaluated at rest (in the morning before the beginning of surgical activity and in operational (during surgery. Results The mean TVC at rest was 12.4 CFU/m3 and 722.5 CFU/m2/h for active and passive samplings respectively. The mean in operational TVC was 93.8 CFU/m3 (SD = 52.69; range = 22-256 and 10496.5 CFU/m2/h (SD = 7460.5; range = 1415.5-25479.7 for active and passive samplings respectively. Statistical analysis confirmed that the two methods correlate in a comparable way with the quality of air. Conclusion It is possible to conclude that both methods can be used for general monitoring of air contamination, such as routine surveillance programs. However, the choice must be made between one or the other to obtain specific information.

  5. Preliminary evaluation of a lateral flow immunoassay device for screening urine samples for the presence of sulphamethazine.

    Science.gov (United States)

    O'Keeffe, M; Crabbe, P; Salden, M; Wichers, J; Van Peteghem, C; Kohen, F; Pieraccini, G; Moneti, G

    2003-07-01

    A lateral flow immunoassay (LFIA) device was developed and applied to testing urine samples for residues of the antimicrobial sulphamethazine (SMZ). This report describes the preparation of a rat monoclonal antibody to SMZ and its characterisation in an ELISA format. Apart from SMZ, the antibody showed high (> or =50%) cross-reactivity to N4-acetyl-sulphamethazine (55%), sulphamerazine (59%) and sulphisoxazole (50%) and lower cross-reactivity of 18% to sulphachlorpyridazine and sulphadiazine. The LFIA device consisted of a nitrocellulose membrane spotted with SMZ-ovalbumin and goat anti-mouse antibody as capture line and control line, respectively. Mouse anti-rat IgG F(ab')2 fragment specific antibody, adsorbed to colloidal carbon, was used as the detection ligand in the LFIA. The LFIA device had a cut-off value of 6.3 ng/ml in diluted (1/10) urine. Urine samples from SMZ-treated pigs, and bovine and porcine urine samples fortified with SMZ were used for a blind, four-laboratory evaluation of the performance of the LFIA device. Concentrations of SMZ in the test samples (n=29), as determined by LC-MS/MS, ranged from 0 (LFIA device showed an overall sensitivity of 100%, a specificity of 71%, and positive and negative prediction values of 73% and 100%, respectively. The LFIA device has been fabricated as a test kit for determining SMZ residues in animals produced for slaughter.

  6. Detection and Evaluate the Frequency of Cytomegalovirus and Epstein-Barr Virus in Bladder Tumor Samples in Hamedan Province, 1392

    Directory of Open Access Journals (Sweden)

    Zohreh Alinezhad

    2015-04-01

    Full Text Available Background and Aim: Some unknown reasons as the cytomegalovirus (CMV and Epstein-Barr virus (EBV in the incidence of bladder cancer has been much discussed in recent years. The purpose of this study was to identify and Evaluate the frequency CMV and EBV in bladder tumors. Materials and Methods: Fourty samlps of TCC bladder carcinoma collected from the pathology department of the dr Gharazi hospital in hamedan during summer 2012. samples deparaffinized and DNA extracted  by tissue kit (Qiagen. The human beta-globin gene amplified to ensure the accuracy and integrity of the extracted DNA. To perform the PCR, primers amplified BRLF1 gene for EPV and UL123 for CMV.  Therefore amplified fragments were observed on 1.5% agarose gel. Finaly  the chi-square test were used to assess the relationship between viruses and their relationship to the incidence of bladder cancer. Results: From 40 carcinoma samples studied 4 (10% were infected with the CMV virus and 29 samples (72.5% were infected with EBV. Four samples were simultaneously infected with both viruses. The relationship between age, tumor stage, CMV and EBV virus wasn’t observed (P <0.05.. Conclusions: CMV and EBV can be detected by optimized PCR protocol from bladder cancer. No significant association was observed. The high prevalence of EBV develops this theory that EBV was a factor in bladder cancer.

  7. Sludge batch 9 (SB9) accepance evaluation: Radionuclide concentrations in tank 51 SB9 qualification sample prepared at SRNL

    Energy Technology Data Exchange (ETDEWEB)

    Bannochie, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Diprete, D. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Pareizs, J. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-03-01

    Presented in this report are radionuclide concentrations required as part of the program of qualifying Sludge Batch 9 (SB9) for processing in the Defense Waste Processing Facility (DWPF). The SB9 material is currently in Tank 51 and has been washed and prepared for transfer to Tank 40. The acceptance evaluation needs to be completed prior to the transfer of the material in Tank 51 to Tank 40. The sludge slurry in Tank 40 has already been qualified for DWPF processing and is currently being processed as Sludge Batch 8 (SB8). The radionuclide concentrations were measured or estimated in the Tank 51 SB9 Washed Qualification Sample prepared at Savannah River National Laboratory (SRNL). This sample was prepared from a three liter sample of Tank 51 sludge slurry (HTF-51-15-81) taken on July 23, 2015. The sample was delivered to SRNL where it was initially characterized in the Shielded Cells. Under the direction of Savannah River Remediation (SRR) it was then adjusted per the Tank Farm washing strategy as of October 20, 2015. This final slurry now has a compositioniv expected to be similar to that of the slurry in Tank 51 after final preparations have been made for transfer of that slurry to Tank 40.

  8. Sludge batch 9 (SB9) acceptance evaluation. Radionuclide concentrations in tank 51 SB9 qualification sample prepared at SRNL

    Energy Technology Data Exchange (ETDEWEB)

    Bannochie, C. J. [Savannah River Site (SRS), Aiken, SC (United States); Diprete, D. P. [Savannah River Site (SRS), Aiken, SC (United States); Pareizs, J. M. [Savannah River Site (SRS), Aiken, SC (United States)

    2016-02-10

    Presented in this report are radionuclide concentrations required as part of the program of qualifying Sludge Batch 9 (SB9) for processing in the Defense Waste Processing Facility (DWPF). The SB9 material is currently in Tank 51 and has been washed and prepared for transfer to Tank 40. The acceptance evaluation needs to be completed prior to the transfer of the material in Tank 51 to Tank 40. The sludge slurry in Tank 40 has already been qualified for DWPF processing and is currently being processed as Sludge Batch 8 (SB8). The radionuclide concentrations were measured or estimated in the Tank 51 SB9 Washed Qualification Sample prepared at Savannah River National Laboratory (SRNL). This sample was prepared from a three liter sample of Tank 51 sludge slurry (HTF-51-15-81) taken on July 23, 2015. The sample was delivered to SRNL where it was initially characterized in the Shielded Cells. Under the direction of Savannah River Remediation (SRR) it was then adjusted per the Tank Farm washing strategy as of October 20, 2015. This final slurry now has a composition expected to be similar to that of the slurry in Tank 51 after final preparations have been made for transfer of that slurry to Tank 40.

  9. Further evaluation of an updated PCR assay for the detection of Schistosoma mansoni DNA in human stool samples

    Directory of Open Access Journals (Sweden)

    Luciana I Gomes

    2009-12-01

    Full Text Available A previously reported sensitive PCR assay for the detection of Schistosoma mansoni DNA was updated and evaluated. Changes in the DNA extraction method, including the use of a worldwide available commercial kit and the inclusion of additional quality control measures, increased the robustness of the test, as confirmed by the analysis of 67 faecal samples from an endemic area in Brazil. The PCR assay is at hand as a proven, reliable diagnostic test for the control of schistosomiasis in specific settings.

  10. Evaluation of Streck tissue fixative, a nonformalin fixative for preservation of stool samples and subsequent parasitologic examination.

    Science.gov (United States)

    Nace, E K; Steurer, F J; Eberhard, M L

    1999-12-01

    We undertook a study to evaluate Streck tissue fixative (STF) as a substitute for formalin and polyvinyl alcohol (PVA) in fecal preservation. A comparison of formalin, PVA, (mercuric chloride based), and STF was done by aliquoting fecal samples into each fixative. Stool specimens were collected in Haiti, and parasites included Cyclospora cayetanensis, Giardia intestinalis, Entamoeba coli, Iodamoeba butschlii, Endolimax nana, Ascaris lumbricoides, Trichuris trichiura, Strongyloides stercoralis, and Necator americanus. Preserved stools were examined at various predetermined times (1 week, 1 month, and 3 months) to establish the quality of the initial preservation as well as the suitability of the fixative for long-term storage. At each time point, stool samples in fixatives were examined microscopically as follows: (i) in wet mounts (with bright-field and epifluorescence microscopy), (ii) in modified acid-fast-, trichrome-, and safranin-stained smears, and (iii) with two commercial test kits. At the time points examined, morphologic features remained comparable for samples fixed with 10% formalin and STF. For comparisons of STF- and 10% formalin-fixed samples, specific findings showed that Cyclospora oocysts retained full fluorescence, modified acid-fast- and safranin-stained smears of Cryptosporidium and Cyclospora oocysts were equal in staining quality, and results were comparable in the immunofluorescence assay and enzyme immunoassay commercial kits. Stool fixed in STF and stained with trichrome showed less-than-acceptable staining quality compared with stool fixed in PVA. STF provides an excellent substitute for formalin as a fixative in routine examination of stool samples for parasites. However, modifications to the trichrome staining procedures will be necessary to improve the staining quality for protozoal cysts fixed in STF to a level comparable to that with PVA.

  11. Spatio-temporal variability of solid, total dissolved and labile metal: passive vs. discrete sampling evaluation in river metal monitoring.

    Science.gov (United States)

    Priadi, Cindy; Bourgeault, Adeline; Ayrault, Sophie; Gourlay-Francé, Catherine; Tusseau-Vuillemin, Marie-Hélène; Bonté, Philippe; Mouchel, Jean-Marie

    2011-05-01

    In order to obtain representative dissolved and solid samples from the aquatic environment, a spectrum of sampling methods are available, each one with different advantages and drawbacks. This article evaluates the use of discrete sampling and time-integrated sampling in illustrating medium-term spatial and temporal variation. Discrete concentration index (CI) calculated as the ratio between dissolved and solid metal concentrations in grab samples are compared with time-integrated concentration index (CI) calculated from suspended particulate matter (SPM) collected in sediment traps and labile metals measured by the diffusive gel in thin films (DGT) method, collected once a month during one year at the Seine River, upstream and downstream of the Greater Paris Region. Discrete CI at Bougival was found to be significantly higher than at Triel for Co, Cu, Mn, Ni and Zn, while discrete metal partitioning at Marnay was found to be similar to Bougival and Triel. However, when using time-integrated CI, not only was Bougival CI significantly higher than Triel CI, CI at Marnay was also found to be significantly higher than CI at Triel which was not observed for discrete CI values. Since values are time-averaged, dramatic fluctuations were smoothed out and significant medium-term trends were enhanced. As a result, time-integrated concentration index (CI) was able to better illustrate urbanization impact between sites when compared to discrete CI. The impact of significant seasonal phenomenon such as winter flood, low flow and redox cycles was also, to a certain extent, visible in time-integrated CI values at the upstream site. The use of time-integrated concentration index may be useful for medium- to long-term metal studies in the aquatic environment.

  12. Evaluation of bilirubin concentration in hemolysed samples, is it really impossible? The altitude-curve cartography approach to interfered assays.

    Science.gov (United States)

    Brunori, Paola; Masi, Piergiorgio; Faggiani, Luigi; Villani, Luciano; Tronchin, Michele; Galli, Claudio; Laube, Clarissa; Leoni, Antonella; Demi, Maila; La Gioia, Antonio

    2011-04-11

    Neonatal jaundice might lead to severe clinical consequences. Measurement of bilirubin in samples is interfered by hemolysis. Over a method-depending cut-off value of measured hemolysis, bilirubin value is not accepted and a new sample is required for evaluation although this is not always possible, especially with newborns and cachectic oncological patients. When usage of different methods, less prone to interferences, is not feasible an alternative recovery method for analytical significance of rejected data might help clinicians to take appropriate decisions. We studied the effects of hemolysis over total bilirubin measurement, comparing hemolysis-interfered bilirubin measurement with the non-interfered value. Interference curves were extrapolated over a wide range of bilirubin (0-30 mg/mL) and hemolysis (H Index 0-1100). Interference "altitude" curves were calculated and plotted. A bimodal acceptance table was calculated. Non-interfered bilirubin of given samples was calculated, by linear interpolation between the nearest lower and upper interference curves. Rejection of interference-sensitive data from hemolysed samples for every method should be based not upon the interferent concentration but upon a more complex algorithm based upon the concentration-dependent bimodal interaction between the interfered analyte and the measured interferent. The altitude-curve cartography approach to interfered assays may help laboratories to build up their own method-dependent algorithm and to improve the trueness of their data by choosing a cut-off value different from the one (-10% interference) proposed by manufacturers. When re-sampling or an alternative method is not available the altitude-curve cartography approach might also represent an alternative recovery method for analytical significance of rejected data. Copyright © 2011 Elsevier B.V. All rights reserved.

  13. Evaluation of PCR, DNA hybridization and immunomagnetic separation - PCR for detection of Burkholderia mallei in artificially inoculated environmental samples.

    Science.gov (United States)

    Merwyn, S; Kumar, S; Agarwal, G S; Rai, G P

    2010-06-01

    Glanders is highly contagious disease of equines, caused by Burkholderia mallei. The disease though rare, can be transmitted to humans. Here, we report a strategy for rapid detection of B. mallei from environmental samples. Different bacteriological media were evaluated and brain heart infusion broth medium with selective supplements (BHIB-SS) of penicillin (200 U/ml) and crystal violet (1:10,00000) was found to support the maximum growth of B. mallei even in the presence of other bacteria like Escherichia coli and Staphylococcus aureus. A polymerase chain reaction (PCR) and a DNA hybridization method was standardized for 823 bp specific dNA sequence of B. mallei. To enable the quicker and direct enrichment of B. mallei bacteria from environmental samples, an immunomagnetic separation (IMS) method was also standardized. Water, husk, grass and gram samples were artificially contaminated by B. mallei bacteria and after enrichment of B. mallei in BHIB-SS, detection was carried out by PCR and DNA hybridization. PCR was found to be a better method of the two with a detection limit of 10(4)-10(6) CFU/ml (6 h enrichment in BHIB-SS) in water and other particulate matrices. Detection by PCR in the above samples without enrichment in BHIBSS was carried out following IMS where the detection limit was about 1-2 log higher than PCR following enrichment in BHIB-SS. We recommend PCR for 823 bp for detection of B. mallei from environmental samples either following enrichment in BHIB-SS or IMS. IMS-PCR method may be preferred in situations where numbers of B. mallei bacteria are expected to be high and results are required in short time.

  14. Lerneca inalata beripocone subsp. nov. (Orthoptera: Phalangopsidae; Luzarinae): a new taxon for the northern Pantanal of Brazil.

    Science.gov (United States)

    Lima, Raysa Martins; Martins, Luciano De Pinho; Pereira, Marcelo Ribeiro; Ganchev, Todor D; Jahn, Olaf; Lhano, Marcos Gonçalves; Marques, Marinêz Isaac; Schuchmann, Karl-L

    2016-10-17

    The first record of the Orthoptera species Lerneca inalata for Brazil is presented here. The taxon is represented by a new subspecies Lerneca inalata beripocone subsp. nov. (Phalangopsidae, Luzarinae), collected in the Pantanal of Poconé, Mato Grosso, Brazil. This work includes morphological and morphometric data as well as descriptions of female genitalia and calling song. The new subspecies has as diagnostic features the male genitalia with six ventral spines on the B sclerite, the first spine having a subtle bifurcation; the mid-region of the strongly sclerotized pseudepiphallus; inclination of C sclerite with slightly concave curvature; tegmina-length ratio and the speculum (syn. mirror) width approximately three times the length of the apical area. The description of the female genitalia and the calling song is presented for the first time for the species Lerneca inalata. A distribution map covers the local occurrence of its subspecies.

  15. Sampling characteristics and calibration of snorkel counts to estimate stream fish populations

    Science.gov (United States)

    Weaver, D.; Kwak, Thomas J.; Pollock, Kenneth

    2014-01-01

    Snorkeling is a versatile technique for estimating lotic fish population characteristics; however, few investigators have evaluated its accuracy at population or assemblage levels. We evaluated the accuracy of snorkeling using prepositioned areal electrofishing (PAE) for estimating fish populations in a medium-sized Appalachian Mountain river during fall 2008 and summer 2009. Strip-transect snorkel counts were calibrated with PAE counts in identical locations among macrohabitats, fish species or taxa, and seasons. Mean snorkeling efficiency (i.e., the proportion of individuals counted from the true population) among all taxa and seasons was 14.7% (SE, 2.5%), and the highest efficiencies were for River Chub Nocomis micropogon at 21.1% (SE, 5.9%), Central Stoneroller Campostoma anomalum at 20.3% (SE, 9.6%), and darters (Percidae) at 17.1% (SE, 3.7%), whereas efficiencies were lower for shiners (Notropis spp., Cyprinella spp., Luxilus spp.) at 8.2% (SE, 2.2%) and suckers (Catostomidae) at 6.6% (SE, 3.2%). Macrohabitat type, fish taxon, or sampling season did not significantly explain variance in snorkeling efficiency. Mean snorkeling detection probability (i.e., probability of detecting at least one individual of a taxon) among fish taxa and seasons was 58.4% (SE, 6.1%). We applied the efficiencies from our calibration study to adjust snorkel counts from an intensive snorkeling survey conducted in a nearby reach. Total fish density estimates from strip-transect counts adjusted for snorkeling efficiency were 7,288 fish/ha (SE, 1,564) during summer and 15,805 fish/ha (SE, 4,947) during fall. Precision of fish density estimates is influenced by variation in snorkeling efficiency and sample size and may be increased with additional sampling effort. These results demonstrate the sampling properties and utility of snorkeling to characterize lotic fish assemblages with acceptable efficiency and detection probability, less effort, and no mortality, compared with traditional

  16. Evaluation of sample holders designed for long-lasting X-ray micro-tomographic scans of ex-vivo soft tissue samples

    Science.gov (United States)

    Dudak, J.; Zemlicka, J.; Krejci, F.; Karch, J.; Patzelt, M.; Zach, P.; Sykora, V.; Mrzilkova, J.

    2016-03-01

    X-ray microradiography and microtomography are imaging techniques with increasing applicability in the field of biomedical and preclinical research. Application of hybrid pixel detector Timepix enables to obtain very high contrast of low attenuating materials such as soft biological tissue. However X-ray imaging of ex-vivo soft tissue samples is a difficult task due to its structural instability. Ex-vivo biological tissue is prone to fast drying-out which is connected with undesired changes of sample size and shape producing later on artefacts within the tomographic reconstruction. In this work we present the optimization of our Timepix equipped micro-CT system aiming to maintain soft tissue sample in stable condition. Thanks to the suggested approach higher contrast of tomographic reconstructions can be achieved while also large samples that require detector scanning can be easily measured.

  17. Sommerxylon spiralosus from Upper Triassic in southernmost Paraná Basin (Brazil: a new taxon with taxacean affinity

    Directory of Open Access Journals (Sweden)

    Etiene F. Pires

    2004-09-01

    Full Text Available The anatoical description of silici?ed Gymnospermae woods from Upper Triassic sequences of southernmost Paraná Basin (Brazil has allowed the identi?cation of a new taxon: Sommerxylon spiralosus n.gen. et n.sp. Diagnostic parameters, such as heterocellular medulla composed of parenchymatous and sclerenchymatous cells, primary xylem endarch, secondary xylem with dominant uniseriate bordered pits, spiral thickenings in the radial walls of tracheids, medullar rays homocellular, absence of resiniferous canals and axial parenchyma, indicate its relationship with the family Taxaceae, reporting on the first recognition of this group in the Triassic on Southern Pangea. This evidence supports the hypothesis that the Taxaceae at the Mesozoic were not con?ned to the Northern Hemisphere.A descrição anatômica de lenhos silicificados de Gymnospermae em seqüência do Triássico Superior no sul da Bacia do Paraná (Brasil, possibilitou a identificação de um novo taxon: Sommerxylon spiralosus n.gen. et n.sp. Parâmetros diagnósticos tais como medula heterocelular, composta por células parenquimáticas e esclerenquimáticas, xilema primário endarco, xilema secundário com pontoações areoladas unisseriadas dominantes, espessamentos espiralados nas paredes radiais dos traqueídeos, raios lenhosos homocelulares, ausência de canais resiníferos e de parênquima axial, indicam a sua vinculação à família Taxaceae, constituindo-se em reconhecimento inédito da presença deste grupo no Triássico Superior no sul do Pangea. Esta evidência suporta a hipótese de que a família Taxaceae não estava confinada ao Hemisfério Norte durante o Mesozóico.

  18. Molecular parataxonomy as taxon description: examples from recently named Zoanthidea (Cnidaria: Anthozoa) with revision based on serial histology of microanatomy.

    Science.gov (United States)

    Swain, Timothy D; Swain, Laura M

    2014-05-16

    Current taxonomic practices require corroboration from multiple lines of evidence to provide sufficient rigor for species discovery and description. However, many recently named taxa (species-families) are defined by nucleotide sequence with little or no description of the features that traditionally define higher taxa and link nucleotide-based information to the existing taxonomic system. Without knowledge of form, it may be impossible to identify conspecifics, congeners, and confamiliars of new taxa among the hundreds of specimens and described species for which nucleotide sequencing is not now, and may never be, available. Additionally, some nucleotide sequences are invariant or inconsistently differentiated between congeners; severely limiting the utility of nucleotide-based taxon definitions. Here we use serial histology of paratypes to reveal the microanatomy of internal structures and revise the definitions of the Zoanthidea taxa Corallizoanthus tsukaharai Reimer, Antipathozoanthus hickmani Reimer & Fujii, Parazoanthus darwini Reimer & Fujii, Terrazoanthus onoi Reimer & Fujii, Terrazoanthus sinnigeri Reimer & Fujii, Microzoanthus kagerou Fujii & Reimer, and Zoanthus kuroshio Reimer & Ono; examination of Mesozoanthus lilkweminensis Reimer & Sinniger failed to produce interpretable sections. The results described here, with individual measurements documented in Morphbank (collection 829724) and Encyclopedia of Life (by taxon name), indicate a notably rich diversity of form for an order that is often characterized as depauperate in morphological diversity. One prominent example is a novel marginal muscle structure (cyclically transitional) that is not observable without serial sections. These findings may renew interest in morphological characters and provide the foundation for revision of Zoanthidea higher taxa, particularly now that phylogenetic relationships for these taxa can be inferred.

  19. Species Richness Responses to Structural or Compositional Habitat Diversity between and within Grassland Patches: A Multi-Taxon Approach.

    Directory of Open Access Journals (Sweden)

    Szabolcs Lengyel

    Full Text Available Habitat diversity (spatial heterogeneity within and between habitat patches in a landscape, HD is often invoked as a driver of species diversity at small spatial scales. However, the effect of HD on species richness (SR of multiple taxa is not well understood. We quantified HD and SR in a wet-dry gradient of open grassland habitats in Hortobágy National Park (E-Hungary and tested the effect of compositional and structural factors of HD on SR of flowering plants, orthopterans, true bugs, spiders, ground beetles and birds. Our dataset on 434 grassland species (170 plants, 264 animals showed that the wet-dry gradient (compositional HD at the between-patch scale was primarily related to SR in orthopterans, ground-dwelling arthropods, and all animals combined. The patchiness, or plant association richness, of the vegetation (compositional HD at the within-patch scale was related to SR of vegetation-dwelling arthropods, whereas vegetation height (structural HD at the within-patch scale was related to SR of ground-dwelling arthropods and birds. Patch area was related to SR only in birds, whereas management (grazing, mowing, none was related to SR of plants and true bugs. All relationships between HD and SR were positive, indicating increasing SR with increasing HD. However, total SR was not related to HD because different taxa showed similar positive responses to different HD variables. Our findings, therefore, show that even though HD positively influences SR in a wide range of grassland taxa, each taxon responds to different compositional or structural measures of HD, resulting in the lack of a consistent relationship between HD and SR when taxon responses are pooled. The idiosyncratic responses shown here exemplify the difficulties in detecting general HD-SR relationships over multiple taxa. Our results also suggest that management and restoration aimed specifically to sustain or increase the diversity of habitats are required to conserve

  20. Estudio taxonómico de Centaurea Sect. Acrocentron (Cass.) DC. (Asteraceae) en la Península Ibérica y Baleares

    OpenAIRE

    López, Eusebio; Devesa Alcaraz, Juan Antonio

    2013-01-01

    Se ha efectuado la revisión taxonómica de Centaurea sect. Acrocentron (Cass.) DC. en la Península Ibérica e Islas Baleares. Se reconocen 24 taxones repartidos en 2 subsecciones: Lopholomoides y Chamaecyanus. Se aporta una clave para la identificación de los taxones, así como su descripción morfológica e información sobre la distribución geográfica, apetencias ecológicas, fenología y número cromosómico A taxonomic review of Centaurea sect. Acrocentron (Cass.) DC. in the Iberian Peninsula an...

  1. Estudio taxonómico de Centaurea sect. Acrocentron (Cass.) DC. (Asteraceae) en la Península Ibérica y Baleares

    OpenAIRE

    López, E.; Devesa Alcaraz, Juan Antonio

    2013-01-01

    Se ha efectuado la revisión taxonómica de Centaurea sect. Acrocentron (Cass.) DC. en la Península Ibérica e Islas Baleares. Se reconocen 24 taxones reparti¬dos en 2 subsecciones: Lopholomoides y Chamaecyanus. Se aporta una clave para la identificación de los taxones, así como su descripción morfológica e información sobre la distribución geográfica, apetencias ecológicas, fenología y número cromosómico. Taxonomic study in Centaurea Sect. Acrocentron (Cass.) DC. (Asteraceae) in the Iberian ...

  2. Roadway sampling evaluation : [summary].

    Science.gov (United States)

    2014-09-01

    Asphalt used on Florida roads must meet very : specific standards. Beginning in 1998, the Florida : Department of Transportation (FDOT) moved from : a system in which the department tested asphalt : mixtures for use in road construction to one in : w...

  3. Evaluation of carbon monoxide in blood samples from the second health and nutrition survey. Progress report No. 1

    Energy Technology Data Exchange (ETDEWEB)

    Radford, E.P.

    1976-01-01

    This is a study of carbon monoxide (CO) in the blood of human subjects participating in the Second National Health and Nutrition Survey (HANES II), a detailed study of health indicators in sample populations of many communities throughout the U.S. The purpose of this aspect of the survey is to evaluate the levels of blood carboxyhemoglobin in normal individuals of all ages in typical U.S. communities, from whom accurate histories and clinical studies are available. This report gives results of the first of three years of analyses. A careful calibration of the analytical method has been completed, and more than 3000 blood samples have been analyzed. Although smoking histories are not yet available to permit evaluation of carboxyhemoglobin in non-smokers, in children under 12 years of age, blood COHb has been found to be consistently low, with less than 3% greater than 1.5% COHb. These preliminary results suggest that urban exposure to carbon monoxide among the general population is not now significant in the U.S., at least during the period of these early examinations.

  4. The N-Pact Factor: Evaluating the Quality of Empirical Journals with Respect to Sample Size and Statistical Power

    Science.gov (United States)

    Fraley, R. Chris; Vazire, Simine

    2014-01-01

    The authors evaluate the quality of research reported in major journals in social-personality psychology by ranking those journals with respect to their N-pact Factors (NF)—the statistical power of the empirical studies they publish to detect typical effect sizes. Power is a particularly important attribute for evaluating research quality because, relative to studies that have low power, studies that have high power are more likely to (a) to provide accurate estimates of effects, (b) to produce literatures with low false positive rates, and (c) to lead to replicable findings. The authors show that the average sample size in social-personality research is 104 and that the power to detect the typical effect size in the field is approximately 50%. Moreover, they show that there is considerable variation among journals in sample sizes and power of the studies they publish, with some journals consistently publishing higher power studies than others. The authors hope that these rankings will be of use to authors who are choosing where to submit their best work, provide hiring and promotion committees with a superior way of quantifying journal quality, and encourage competition among journals to improve their NF rankings. PMID:25296159

  5. Comparative evaluation of commercially available point-of-care heartworm antigen tests using well-characterized canine plasma samples

    Directory of Open Access Journals (Sweden)

    Lindsay A. Starkey

    2017-11-01

    Full Text Available Abstract Background Dirofilaria immitis is a worldwide parasite that is endemic in many parts of the United States. There are many commercial assays available for the detection of D. immitis antigen, one of which was modified and has reentered the market. Our objective was to compare the recently reintroduced Witness® Heartworm (HW Antigen test Kit (Zoetis, Florham Park, NJ and the SNAP® Heartworm RT (IDEXX Laboratories, Inc., Westbrook, ME to the well-based ELISA DiroChek® Heartworm Antigen Test Kit (Zoetis, Florham Park, NJ. Methods Canine plasma samples were either received at the Auburn Diagnostic Parasitology Laboratory from veterinarians submitting samples for additional heartworm testing (n = 100 from 2008 to 2016 or purchased from purpose-bred beagles (n = 50, presumed negative in 2016. Samples were categorized as “positive,” “borderline” or “negative” using our established spectrophotometric cutoff value with the DiroChek® assay when a sample was initially received and processed. Three commercially available heartworm antigen tests (DiroChek®, Witness® HW, and SNAP® RT were utilized for simultaneous testing of the 150 samples in random order as per their package insert with the addition of spectrophotometric optical density (OD readings of the DiroChek® assay. Any samples yielding discordant test results between assays were further evaluated by heat treatment of plasma and retesting. Chi-square tests for the equality of proportions were utilized for statistical analyses. Results Concordant results occurred in 140/150 (93.3% samples. Discrepant results occurred in 10/150 samples tested (6.6%: 9/10 occurring in the borderline heartworm (HW category and 1/10 occurring in the negative HW category. The sensitivity and specificity of each test compared to the DiroChek® read by spectrophotometer was similar to what has been reported previously (Witness®: sensitivity 97.0% [94.1–99.4%], specificity 96.4% [95.5–100

  6. Measuring values and committed action with the Engaged Living Scale (ELS): Psychometric evaluation in a nonclinical sample and a chronic pain sample

    NARCIS (Netherlands)

    Trompetter, H.R.; ten Klooster, Peter M.; Schreurs, Karlein Maria Gertrudis; Fledderus, M.; Westerhof, Gerben Johan; Bohlmeijer, Ernst Thomas

    2013-01-01

    This article describes the development and evaluation of the Engaged Living Scale (ELS) as a new self-report, process-specific measure to assess an engaged response style as conceptualized in acceptance and commitment therapy (ACT). The psychometric properties of the ELS test scores were evaluated

  7. Evaluation of ACCMIP ozone simulations and ozonesonde sampling biases using a satellite-based multi-constituent chemical reanalysis

    Science.gov (United States)

    Miyazaki, Kazuyuki; Bowman, Kevin

    2017-07-01

    The Atmospheric Chemistry Climate Model Intercomparison Project (ACCMIP) ensemble ozone simulations for the present day from the 2000 decade simulation results are evaluated by a state-of-the-art multi-constituent atmospheric chemical reanalysis that ingests multiple satellite data including the Tropospheric Emission Spectrometer (TES), the Microwave Limb Sounder (MLS), the Ozone Monitoring Instrument (OMI), and the Measurement of Pollution in the Troposphere (MOPITT) for 2005-2009. Validation of the chemical reanalysis against global ozonesondes shows good agreement throughout the free troposphere and lower stratosphere for both seasonal and year-to-year variations, with an annual mean bias of less than 0.9 ppb in the middle and upper troposphere at the tropics and mid-latitudes. The reanalysis provides comprehensive spatiotemporal evaluation of chemistry-model performance that compliments direct ozonesonde comparisons, which are shown to suffer from significant sampling bias. The reanalysis reveals that the ACCMIP ensemble mean overestimates ozone in the northern extratropics by 6-11 ppb while underestimating by up to 18 ppb in the southern tropics over the Atlantic in the lower troposphere. Most models underestimate the spatial variability of the annual mean lower tropospheric concentrations in the extratropics of both hemispheres by up to 70 %. The ensemble mean also overestimates the seasonal amplitude by 25-70 % in the northern extratropics and overestimates the inter-hemispheric gradient by about 30 % in the lower and middle troposphere. A part of the discrepancies can be attributed to the 5-year reanalysis data for the decadal model simulations. However, these differences are less evident with the current sonde network. To estimate ozonesonde sampling biases, we computed model bias separately for global coverage and the ozonesonde network. The ozonesonde sampling bias in the evaluated model bias for the seasonal mean concentration relative to global

  8. Evaluation of ACCMIP ozone simulations and ozonesonde sampling biases using a satellite-based multi-constituent chemical reanalysis

    Directory of Open Access Journals (Sweden)

    K. Miyazaki

    2017-07-01

    Full Text Available The Atmospheric Chemistry Climate Model Intercomparison Project (ACCMIP ensemble ozone simulations for the present day from the 2000 decade simulation results are evaluated by a state-of-the-art multi-constituent atmospheric chemical reanalysis that ingests multiple satellite data including the Tropospheric Emission Spectrometer (TES, the Microwave Limb Sounder (MLS, the Ozone Monitoring Instrument (OMI, and the Measurement of Pollution in the Troposphere (MOPITT for 2005–2009. Validation of the chemical reanalysis against global ozonesondes shows good agreement throughout the free troposphere and lower stratosphere for both seasonal and year-to-year variations, with an annual mean bias of less than 0.9 ppb in the middle and upper troposphere at the tropics and mid-latitudes. The reanalysis provides comprehensive spatiotemporal evaluation of chemistry-model performance that compliments direct ozonesonde comparisons, which are shown to suffer from significant sampling bias. The reanalysis reveals that the ACCMIP ensemble mean overestimates ozone in the northern extratropics by 6–11 ppb while underestimating by up to 18 ppb in the southern tropics over the Atlantic in the lower troposphere. Most models underestimate the spatial variability of the annual mean lower tropospheric concentrations in the extratropics of both hemispheres by up to 70 %. The ensemble mean also overestimates the seasonal amplitude by 25–70 % in the northern extratropics and overestimates the inter-hemispheric gradient by about 30 % in the lower and middle troposphere. A part of the discrepancies can be attributed to the 5-year reanalysis data for the decadal model simulations. However, these differences are less evident with the current sonde network. To estimate ozonesonde sampling biases, we computed model bias separately for global coverage and the ozonesonde network. The ozonesonde sampling bias in the evaluated model bias for the seasonal mean

  9. Evaluation of Lead Release in a Simulated Lead-Free Premise Plumbing System Using a Sequential Sampling Approach

    Directory of Open Access Journals (Sweden)

    Ding-Quan Ng

    2016-02-01

    Full Text Available In this pilot study, a modified sampling protocol was evaluated for the detection of lead contamination and locating the source of lead release in a simulated premise plumbing system with one-, three- and seven-day stagnation for a total period of 475 days. Copper pipes, stainless steel taps and brass fittings were used to assemble the “lead-free” system. Sequential sampling using 100 mL was used to detect lead contamination while that using 50 mL was used to locate the lead source. Elevated lead levels, far exceeding the World Health Organization (WHO guideline value of 10 µg·L−1, persisted for as long as five months in the system. “Lead-free” brass fittings were identified as the source of lead contamination. Physical disturbances, such as renovation works, could cause short-term spikes in lead release. Orthophosphate was able to suppress total lead levels below 10 µg·L−1, but caused “blue water” problems. When orthophosphate addition was ceased, total lead levels began to spike within one week, implying that a continuous supply of orthophosphate was required to control total lead levels. Occasional total lead spikes were observed in one-day stagnation samples throughout the course of the experiments.

  10. Evaluation of endoscopically obtained duodenal biopsy samples from cats and dogs in an adapter-modified Ussing chamber

    Science.gov (United States)

    DeBiasio, John V.; Suchodolski, Jan S.; Newman, Shelley; Musch, Mark W.; Steiner, Jörg M.

    2014-01-01

    This study was conducted to evaluate an adapter-modified Ussing chamber for assessment of transport physiology in endoscopically obtained duodenal biopsies from healthy cats and dogs, as well as dogs with chronic enteropathies. 17 duodenal biopsies from five cats and 51 duodenal biopsies from 13 dogs were obtained. Samples were transferred into an adapter-modified Ussing chamber and sequentially exposed to various absorbagogues and secretagogues. Overall, 78.6% of duodenal samples obtained from cats responded to at least one compound. In duodenal biopsies obtained from dogs, the rate of overall response ranged from 87.5% (healthy individuals; n = 8), to 63.6% (animals exhibiting clinical signs of gastrointestinal disease and histopathological unremarkable duodenum; n = 15), and 32.1% (animals exhibiting clinical signs of gastrointestinal diseases and moderate to severe histopathological lesions; n = 28). Detailed information regarding the magnitude and duration of the response are provided. The adapter-modified Ussing chamber enables investigation of the absorptive and secretory capacity of endoscopically obtained duodenal biopsies from cats and dogs and has the potential to become a valuable research tool. The response of samples was correlated with histopathological findings. PMID:24378587

  11. Evaluation of lead levels in biological samples of mentally retarded children in different stages using advanced extraction method.

    Science.gov (United States)

    Kazi, Tasneem Gul; Shah, Faheem; Afridi, Hassan Imran; Mughal, Moina Akhtar; Naeemullah; Arain, Sadaf Sadia; Arain, Mohammad Balal

    2013-11-01

    In present study the lead (Pb) levels has been assessed by analyzing the scalp hair and blood samples of mentally retarded/intellectual disabled (MR/ID) children of both genders, age ranged 3-8 years. For comparative purpose, healthy age matched children were also selected. The cloud point extraction of Pb from digested biological samples was carried out by complexed with ammonium pyrrolidinedithiocarbamate. The complexed analyte was subsequently isolated from the aqueous matrix in the micelles of a non-ionic surfactant (Triton X-114). Dilution of the surfactant-rich phase with acidified ethanol was performed after phase separation, and the Pb content was measured by flame atomic absorption spectrometer. Factors affecting the cloud point extraction were evaluated and optimized. The proposed procedure allowed the determination of lead in certified standard and real samples with detection limits of 0.834μgL(-) and enhancement factor 55. The results were compared with those of healthy children have same age, socioeconomic status and residential areas. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Evaluation of immunoassays as an alternative for the rapid determination of pesticides in wine and grape samples.

    Science.gov (United States)

    Argarate, Nerea; Arestin, María; Ramón-Azcón, Javier; Alfaro, Begoña; Barranco, Alejandro; Sánchez-Baeza, Francisco; Marco, M Pilar

    2010-01-01

    The main objective of this paper is to address the performance of immunochemical assays for the detection of the residues of three pesticides [atrazine, bromopropylate, and 2,4,6-trichlorophenol (TCP)] in real winery samples, such as wine, grapes, and grape juice. Different approaches have been evaluated to minimize interferences from the matrixes, and suitable working protocols have been established in order to achieve the necessary LODs, accuracy, and precision for real samples. A simple dilution of the sample proved to be sufficient for the determination of atrazine and bromopropylate in red and white wine and grape juice at the required levels of concentration. However, for TCP, an SPE procedure has been optimized using amino cartridges. The recoveries were above 85% in all cases, and the LOD values were below the parts per billion level, except for bromopropylate, which ranged between 2 and 50 microg/L, depending on the matrix. The grape matrix effect could be resolved by a simple extraction with methanol. Complete recoveries were obtained, and the final measurement procedures were able to determine selected pesticides below their maximum residue levels. The newly developed methods have been compared with standard chromatographic methods.

  13. Comparative Evaluation of Two Venous Sampling Techniques for the Assessment of Pancreatic Insulin and Zinc Release upon Glucose Challenge

    Directory of Open Access Journals (Sweden)

    Anil Kumar Pillai

    2015-01-01

    Full Text Available Advances in noninvasive imaging modalities have provided opportunities to study β cell function through imaging zinc release from insulin secreting β cells. Understanding the temporal secretory pattern of insulin and zinc corelease after a glucose challenge is essential for proper timing of administration of zinc sensing probes. Portal venous sampling is an essential part of pharmacological and nutritional studies in animal models. The purpose of this study was to compare two different percutaneous image-guided techniques: transhepatic ultrasound guided portal vein access and transsplenic fluoroscopy guided splenic vein access for ease of access, safety, and evaluation of temporal kinetics of insulin and zinc release into the venous effluent from the pancreas. Both techniques were safe, reproducible, and easy to perform. The mean time required to obtain desired catheter position for venous sampling was 15 minutes shorter using the transsplenic technique. A clear biphasic insulin release profile was observed in both techniques. Statistically higher insulin concentration but similar zinc release after a glucose challenge was observed from splenic vein samples, as compared to the ones from the portal vein. To our knowledge, this is the first report of percutaneous methods to assess zinc release kinetics from the porcine pancreas.

  14. Biochemical and microbiological evaluation of the water samples collected from different areas of district Kohat and Mohamand Agency, Pakistan.

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    Ayaz Ali

    2013-09-01

    Full Text Available Contamination of drinking water sources mainly due to microorganisms is the major problem in many areas of Pakistan. Pakistan is also facing the problem of contamination of drinking water which greatly affects human health and quality of life. The most important component of human beings for living is water. Therefore, it is important to analyze drinking water quality mostly in developing countries as the local people are mostly unaware of the water pollution. In this study, twenty three samples of water were analyzed during a 3-month period from the well and lake water supplies of different areas of Kohat and Mohamand Agency. The bacteriological evaluation was done and several tests were performed such as Total Plate Count, Coliform, Feacal coliform, Escherichia coli (E. coli and Biochemical test. In this study, thirteen samples were in the normal range and 10 samples were out of safety ranges fixed by World Health Organization (WHO. The water which was not fit for drinking can be a consistent risk of the infectious diseases and continuous assessment and purification strategies should be developed in these areas to reduce the microbial contamination. The proper training by the local public authorities is required to educate the local community about water pollution, their causes and preventive measures in order to improve the health status of the people in the regions.

  15. Genetoxicity of water samples from the scenic Lijang river in the Guilin area, China, evaluated by Tradescantia bioassays.

    Science.gov (United States)

    Jiang, Y G; Yu, Z D; Liu, G Z; Chen, R Z; Peng, G Y

    1999-05-19

    The Lijang river which passes through the Guilin mountains, and Guilin city is a world renowned scenic spot on the southwest border of China. The river and its tributaries receive water from the mountain tops and springs underground. The river water was clean two decades ago before the development of industrial establishments and extra heavy tourism. Deforestation over the mountain tops on the upper stream and its tributaries in the last decades has created serious erosion and increased sedimentation in the river. In the present study, the Tradescantia micronucleus (Trad-MCN) and Tradescantia stamen hair mutation (Trad-SHM) assays were used to evaluate the genetoxicity of water samples collected from 60 different sites along the river. Results indicate that most of the water samples from the tributaries were highly mutagenic, and that pollutants had accumulated in the main river in the Guilin city area from the industrial effluent and city sewage. Both the Trad-MCN and Trad-SHM assays were highly effective for the detection of mutagens in the water samples. Copyright 1999 Elsevier Science B.V.

  16. Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates.

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    Eric D Stein

    Full Text Available Molecular methods, such as DNA barcoding, have the potential to enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biomonitoring using benthic macroinvertebrates. Using higher volumes or concentrations of ethanol, requirements for shorter holding times, or the need to include additional filtering may increase cost and logistical constraints to existing biomonitoring programs. To address this issue we evaluated the efficacy of various ethanol-based sample preservation methods at maintaining DNA integrity. We evaluated a series of methods that were minimally modified from typical field protocols in order to identify an approach that can be readily incorporated into existing monitoring programs. Benthic macroinvertebrates were collected from a minimally disturbed stream in southern California, USA and subjected to one of six preservation treatments. Ten individuals from five taxa were selected from each treatment and processed to produce DNA barcodes from the mitochondrial gene cytochrome c oxidase I (COI. On average, we obtained successful COI sequences (i.e. either full or partial barcodes for between 93-99% of all specimens across all six treatments. As long as samples were initially preserved in 95% ethanol, successful sequencing of COI barcodes was not affected by a low dilution ratio of 2∶1, transfer to 70% ethanol, presence of abundant organic matter, or holding times of up to six months. Barcoding success varied by taxa, with Leptohyphidae (Ephemeroptera producing the lowest barcode success rate, most likely due to poor PCR primer efficiency. Differential barcoding success rates have the potential to introduce spurious results. However, routine preservation methods can largely be used without adverse effects on DNA integrity.

  17. Evaluation of Multiple Linear Regression Limited Sampling Strategies for Enteric-Coated Mycophenolate Sodium in Adult Kidney Transplant Recipients.

    Science.gov (United States)

    Brooks, Emily K; Staatz, Christine E; Tett, Susan E; Isbel, Nicole M; McWhinney, Brett

    2018-02-14

    Although multiple linear regression-based limited sampling strategies (LSS) have been published for enteric-coated mycophenolate sodium (EC-MS), none have been evaluated for the prediction of subsequent mycophenolic acid (MPA) exposure. This study aimed to examine the predictive performance of the published LSS for the estimation of future MPA area under the concentration-time curve from 0 to 12 hours (AUC0-12) in renal transplant recipients. Total MPA plasma concentrations were measured in twenty adult renal transplant patients on two occasions a week apart. All subjects received concomitant tacrolimus and were approximately one-month post transplant. Samples were taken at 0, 0.33, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 6, and 8 hours and 0, 0.25, 0.5, 0.75, 1, 1.25, 1.5, 2, 3, 4, 6, 9, and 12 hours post dose on the first and second sampling occasion, respectively. Predicted MPA AUC0-12 was calculated using nineteen published LSS and data from the first or second sampling occasion for each patient and compared to the second occasion full MPA AUC0-12 calculated using the linear trapezoidal rule. Bias (median percentage prediction error [MPPE]) and imprecision (median absolute prediction error [MAPE]) were determined. MPPE and MAPE for the prediction of full MPA AUC0-12 were multiple linear regression-based LSS was not possible without concentrations up to at least 8 hours after the dose.

  18. Evaluation of a New Primer In Comparison With Microscopy for the Detection of Giardia lamblia Infection in Stool Samples

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    Amir BAIRAMI

    2016-03-01

    Full Text Available Background: Among the most important parasitic disease, causing diarrhea, Gi­ardia lamblia is noteworthy. Nowadays detection methods for these parasites in­clude parasitological methods such as microscopic examination. The sensitivity of these methods relies on the expertise and experience of examiners. In contrast, molecular methods such as PCR are less dependent on the expertise of the exam­iner. Here we developed a PCR for the detection of G. lamblia genome in stool samples in comparison with microscopy, which is the gold standard.Methods:  For the evaluation of primers, 22 positive samples and 47 negative samples were used. QIAamp DNA Stool Mini Kit (QIAGEN, Germany was used for DNA extraction from feces. Primers for PCR were designed using Primer-BLAST which uses Primer 3 to designing specific primers (NCBI/ Primer-BLAST. Results: Sensitivity of the PCR was done with 100% (95%CI: 84.56-100 for the detection of G. lamblia DNA isolated from patients stool samples which were posi­tive for G. lamblia cysts and/or trophozoites using microscopy as gold standard. In comparison with microscopy, PCR had showed the specificity of 97.87% (95%CI: 88.71-99.95.Conclusion: We designed new primers for the Giardia, and PCR method for the rapid and accurate identification of Giardia parasites established. With considera­tion to the routine diagnosis techniques in medical parasitology and their limita­tions such as time consuming, laborious, less sensitivity etc. This G. lamblia PCR is a sensitive and specific application for the diagnosis of G. lamblia and provides us a reliable method in the routine intestinal parasitic infection laboratory diagnosis.

  19. Evaluation of non-invasive biological samples to monitor Staphylococcus aureus colonization in great apes and lemurs.

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    Frieder Schaumburg

    Full Text Available INTRODUCTION: Reintroduction of endangered animals as part of conservational programs bears the risk of importing human pathogens from the sanctuary to the natural habitat. One bacterial pathogen that serves as a model organism to analyze this transmission is Staphylococcus aureus as it can colonize and infect both humans and animals. The aim of this study was to evaluate the utility of various biological samples to monitor S. aureus colonization in great apes and lemurs. METHODS: Mucosal swabs from wild lemurs (n=25, Kirindy, Madagascar, feces, oral and genital swabs from captive chimpanzees (n=58, Ngamba and Entebbe, Uganda and fruit wadges and feces from wild chimpanzees (n=21, Taï National Parc, Côte d'Ivoire were screened for S. aureus. Antimicrobial resistance and selected virulence factors were tested for each isolate. Sequence based genotyping (spa typing, multilocus sequence typing was applied to assess the population structure of S. aureus. RESULTS: Oro-pharyngeal carriage of S. aureus was high in lemurs (72%, n=18 and captive chimpanzees (69.2%, n=27 and 100%, n=6, respectively. Wild chimpanzees shed S. aureus through feces (43.8, n=7 and fruit wadges (54.5, n=12. Analysis of multiple sampling revealed that two samples are sufficient to detect those animals which shed S. aureus through feces or fruit wadges. Genotyping showed that captive animals are more frequently colonized with human-associated S. aureus lineages. CONCLUSION: Oro-pharyngeal swabs are useful to screen for S. aureus colonization in apes and lemurs before reintroduction. Duplicates of stool and fruit wadges reliably detect S. aureus shedding in wild chimpanzees. We propose to apply these sampling strategies in future reintroduction programs to screen for S. aureus colonization. They may also be useful to monitor S. aureus in wild populations.

  20. Evaluation of sorbent materials for the sampling and analysis of phosphine, sulfuryl fluoride and methyl bromide in air.

    Science.gov (United States)

    Magnusson, R; Rittfeldt, L; Åstot, C

    2015-01-02

    Phosphine (PH3), sulfuryl fluoride (SO2F2) and methyl bromide (CH3Br) are highly toxic chemical substances commonly used for fumigation, i.e., pest control with gaseous pesticides. Residues of fumigation agents constitute a health risk for workers affected, and therefore accurate methods for air sampling and analysis are needed. In this study, three commercial adsorbent tubes; Carbosieve SIII™, Air Toxics™ and Tenax TA™, were evaluated for sampling these highly volatile chemicals in air and their subsequent analysis by thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS). The breakthrough volume (BTV) of each fumigant was experimentally determined on the different adsorbents at concentrations at or above their permissible exposure limits, using a method based on frontal chromatography of generated fumigant atmospheres. Carbosieve SIII™, a molecular sieve possessing a very high specific area, proved to be a better adsorbent than both Air Toxics™ and Tenax TA™, resulting in at least a 4-fold increase of the BTV50%. BTV50% for Carbosieve SIII™ at 20°C was measured as 4.7L/g, 5.5L/g and 126L/g for phosphine, sulfuryl fluoride and methyl bromide, respectively, implying safe sampling volumes of 1.9L, 2.2L and 50L, respectively, for a commercial tube packed with 800mg Carbosieve SIII™. The temperature dependence of BTV was strong for Carbosieve SIII™, showing a reduction of 3-5%/°C in breakthrough volume within the range -20 to 40°C. Furthermore, although Carbosieve SIII™ reportedly has a higher affinity for water than most other adsorbents, relative humidity had only a moderate influence on the retention capacity of phosphine. Overall, the applicability of Carbosieve SIII™ adsorbent sampling in combination with TD-GC-MS analysis was demonstrated for highly volatile fumigants. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Evaluation of GeneXpert® system for detection of methicillin-resistant Staphyloccocus aureus in clinical samples

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    Antonella Mencacci

    2011-03-01

    Full Text Available Infections caused by methicillin-resistant Staphyloccocus aureus strains (MRSA have reached epidemic proportions globally, being the major cause of nosocomial infections. Rapid identification of MRSA in nasal swabs or in clinical samples is considered a useful strategy for control and treatment of these infections. GeneXpert system (Cepheid Europe,Vira-Solelch, Maurence-Scopont-France can detect by real-time PCR in approximately one hour methicillin-resistant S. aureus or coagulase-negative staphylococci (CoNS in clinical samples, in comparison with 24 hours for the culture or 48 hours for the antimicrobial susceptibility testing. In this study GeneXpert system was compared with traditional tests for MRSA detection in nasal swabs, bloodcultures and surgical wound swabs. Materials and methods. Eighteen nasal swabs, 23 blood-cultures and 13 surgical wound swabs were tested. The samples were cultured on blood-agar and mannitol-salt agar. Identification of isolates was carried out with traditional tests (Gram staining, catalase, coagulase and automatic Phoenix system. Methicillin-susceptibility was evaluated according to 2010 CLSI guidelines. GeneXpert system was performed according to manufacturers instructions, by using the specific kits and methicillin-resistance was detected by amplification of the genic sequences spa, SCC e mecA. Results. The results showed a 100% accordance between GeneXpert system and traditional tests for detection of methicillin-resistant staphylococci. In particular, among 18 nasal swabs, no MRSA was detected, while 1 bloodculture (4.3% and 4 surgical wound swabs (30.7% were positive for MRSA. Conclusions. GeneXpert system allows a rapid detection of MRSA in clinical samples and shows the same sensitivity and specificity as traditional tests. Therefore, it represents a further effective diagnostic method for prevention and treatment of nosocomial infections due to methicillin-resistant staphylococci.

  2. Evaluation of different parameters affecting the liquid scintillation spectrometry measurement of gross alpha and beta index in water samples

    Energy Technology Data Exchange (ETDEWEB)

    Palomo, M. [Unitat de Radioquimica Ambiental i Sanitaria, Universitat Rovira i Virgili, Tarragona (Spain); Villa, M. [Centro de Investigacion, Tecnologia e Innovacion. Servicio Radioisotopos. Universidad de Sevilla (Spain); Casacuberta, N. [Institut de Ciencia i Tecnologia Ambientals-Departament de Fisica, Universitat Autonoma de Barcelona. Spain (Spain); Penalver, A.; Borrull, F. [Unitat de Radioquimica Ambiental i Sanitaria, Universitat Rovira i Virgili, Tarragona (Spain); Aguilar, C., E-mail: carme.aguilar@urv.cat [Unitat de Radioquimica Ambiental i Sanitaria, Universitat Rovira i Virgili, Tarragona (Spain)

    2011-09-15

    Liquid scintillation spectrometry is a fast competitive technique for the simultaneous evaluation of gross alpha and beta indexes. However, the implementation of this technique should not be considered as straightforward, and the pre-concentration methods to decrease the detection limit together with quenching and alpha, and beta crossover corrections should be carefully chosen according to the needs of the laboratory. Both aspects are being approached in this work as to find an easy and robust method for alpha/beta measurement in water samples, taking into account the quenching and alpha/beta crossover interferences effects. Results showed that most of the pre-concentration methods increased the quenching in the measurement, although HNO{sub 3} 0.05 M points to be the best solution for pre-concentration and re-dissolution of the sample as converges into low quenching and maximum recovery. Subsequently, in the measurement of water samples with different conductivities, the analysis of the raw counts to obtain gross alpha and beta indexes was carried out using different approaches to implement quenching and interference corrections. If quenching and salt content in the sample are relatively low, interference and quenching-efficiency corrections do not improve the accuracy of the results within the usual precision assumed for a result of gross alpha and beta index (25%). Special attention must be paid when corrections are applied to high quenched or saline samples and when alpha and beta activities values are different in several orders of magnitude. - Highlights: > Developed method for simultaneously quantifying gross alpha and gross beta indexes based on LSC was as accurate and precise as the results obtained from methods based on gas proportional counting and ZnS alpha counting. > Alpha/beta crossover and/or quenching corrections were applied and the results obtained did not improve accuracy within 25% dispersion, a widespread acceptance limit for gross alpha and

  3. Evaluation of the imputation performance of the program IMPUTE in an admixed sample from Mexico City using several model designs

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    Krithika S

    2012-05-01

    Full Text Available Abstract Background We explored the imputation performance of the program IMPUTE in an admixed sample from Mexico City. The following issues were evaluated: (a the impact of different reference panels (HapMap vs. 1000 Genomes on imputation; (b potential differences in imputation performance between single-step vs. two-step (phasing and imputation approaches; (c the effect of different INFO score thresholds on imputation performance and (d imputation performance in common vs. rare markers. Methods The sample from Mexico City comprised 1,310 individuals genotyped with the Affymetrix 5.0 array. We randomly masked 5% of the markers directly genotyped on chromosome 12 (n = 1,046 and compared the imputed genotypes with the microarray genotype calls. Imputation was carried out with the program IMPUTE. The concordance rates between the imputed and observed genotypes were used as a measure of imputation accuracy and the proportion of non-missing genotypes as a measure of imputation efficacy. Results The single-step imputation approach produced slightly higher concordance rates than the two-step strategy (99.1% vs. 98.4% when using the HapMap phase II combined panel, but at the expense of a lower proportion of non-missing genotypes (85.5% vs. 90.1%. The 1,000 Genomes reference sample produced similar concordance rates to the HapMap phase II panel (98.4% for both datasets, using the two-step strategy. However, the 1000 Genomes reference sample increased substantially the proportion of non-missing genotypes (94.7% vs. 90.1%. Rare variants ( Conclusions The program IMPUTE had an excellent imputation performance for common alleles in an admixed sample from Mexico City, which has primarily Native American (62% and European (33% contributions. Genotype concordances were higher than 98.4% using all the imputation strategies, in spite of the fact that no Native American samples are present in the HapMap and 1000 Genomes reference panels. The best balance of

  4. Evaluation of the analytical performances of a portable, 18-parameter hemometric system using capillary blood samples for blood donor enrolment.

    Science.gov (United States)

    Pierelli, L; Zennaro, F; Patti, D; Miceli, M; Iudicone, P; Mannella, E

    2010-02-01

    Blood donor enrolment process is frequently based on the sole capillary haemoglobin (Hb) evaluation while platelet donors by apheresis also requires platelet (Plt) count. The 'sole Hb' approach prevents a complete donor evaluation and does not allow Plt donor enrolment. To extend blood counts before donations, we evaluated the performances of a multiparametric counter using capillary blood. The ABX Micros 60 (Micros 60) blood analyzer was employed on capillary blood and compared with venous counts by a reference counter (Coulter AcT 5diff) in a first series of 416 donors and in a second series of 136, after a 3-month period of routine use of this study counter. An average of 50 microl of capillary blood was collected whose 10 microl had been aspirated by Micros 60. High correlations were found between capillary counts using Micros 60 and venous counts using the reference counter. Mean Plt counts differed of 37 x 10(9)/l less for capillary approach in the first series of comparisons, but decreased to 10 x 10(9)/l less in the second series due to a greater expertise of operators in capillary sampling. All other parameters were accurate and never reached clinical relevance albeit they showed statistically significant differences. Data on Micros 60 demonstrated that capillary predonation counts may represent a feasible and effective approach to realize an accurate enrolment process of blood and Plt donors.

  5. Evaluation of a Jugular Venipuncture Alpaca Model to Teach the Technique of Blood Sampling in Adult Alpacas.

    Science.gov (United States)

    Rousseau, Marjolaine; Beauchamp, Guy; Nichols, Sylvain

    2017-01-01

    The effectiveness of teaching aids in veterinary medical education is not often assessed rigorously. The objective in the present study was to evaluate the effectiveness of a commercially available jugular venipuncture alpaca model as a complementary tool to teach veterinary students how to perform venipuncture in adult alpacas. We hypothesized that practicing on the model would allow veterinary students to draw blood in alpacas more rapidly with fewer attempts than students without previous practice on the model. Thirty-six third-year veterinary students were enrolled and randomly allocated to the model (group M; n=18) or the control group (group C; n=18). The venipuncture technique was taught to all students on day 0. Students in group M practiced on the model on day 2. On day 5, an evaluator blinded to group allocation evaluated the students' venipuncture skills during a practical examination using live alpacas. Success was defined as the aspiration of a 6-ml sample of blood. Measured outcomes included number of attempts required to achieve success (success score), total procedural time, and overall qualitative score. Success scores, total procedural time, and overall scores did not differ between groups. Use of restless alpacas reduced performance. The jugular venipuncture alpaca model failed to improve jugular venipuncture skills in this student population. Lack of movement represents a significant weakness of this training model.

  6. International Study to Evaluate PCR Methods for Detection of Trypanosoma cruzi DNA in Blood Samples from Chagas Disease Patients

    Science.gov (United States)

    Schijman, Alejandro G.; Bisio, Margarita; Orellana, Liliana; Sued, Mariela; Duffy, Tomás; Mejia Jaramillo, Ana M.; Cura, Carolina; Auter, Frederic; Veron, Vincent; Qvarnstrom, Yvonne; Deborggraeve, Stijn; Hijar, Gisely; Zulantay, Inés; Lucero, Raúl Horacio; Velazquez, Elsa; Tellez, Tatiana; Sanchez Leon, Zunilda; Galvão, Lucia; Nolder, Debbie; Monje Rumi, María; Levi, José E.; Ramirez, Juan D.; Zorrilla, Pilar; Flores, María; Jercic, Maria I.; Crisante, Gladys; Añez, Néstor; De Castro, Ana M.; Gonzalez, Clara I.; Acosta Viana, Karla; Yachelini, Pedro; Torrico, Faustino; Robello, Carlos; Diosque, Patricio; Triana Chavez, Omar; Aznar, Christine; Russomando, Graciela; Büscher, Philippe; Assal, Azzedine; Guhl, Felipe; Sosa Estani, Sergio; DaSilva, Alexandre; Britto, Constança; Luquetti, Alejandro; Ladzins, Janis

    2011-01-01

    Background A century after its discovery, Chagas disease still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The purpose of this study was to evaluate the performance of PCR methods in detection of Trypanosoma cruzi DNA by an external quality evaluation. Methodology/Findings An international collaborative study was launched by expert PCR laboratories from 16 countries. Currently used strategies were challenged against serial dilutions of purified DNA from stocks representing T. cruzi discrete typing units (DTU) I, IV and VI (set A), human blood spiked with parasite cells (set B) and Guanidine Hidrochloride-EDTA blood samples from 32 seropositive and 10 seronegative patients from Southern Cone countries (set C). Forty eight PCR tests were reported for set A and 44 for sets B and C; 28 targeted minicircle DNA (kDNA), 13 satellite DNA (Sat-DNA) and the remainder low copy number sequences. In set A, commercial master mixes and Sat-DNA Real Time PCR showed better specificity, but kDNA-PCR was more sensitive to detect DTU I DNA. In set B, commercial DNA extraction kits presented better specificity than solvent extraction protocols. Sat-DNA PCR tests had higher specificity, with sensitivities of 0.05–0.5 parasites/mL whereas specific kDNA tests detected 5.10−3 par/mL. Sixteen specific and coherent methods had a Good Performance in both sets A and B (10 fg/µl of DNA from all stocks, 5 par/mL spiked blood). The median values of sensitivities, specificities and accuracies obtained in testing the Set C samples with the 16 tests determined to be good performing by analyzing Sets A and B samples varied considerably. Out of them, four methods depicted the best performing parameters in all three sets of samples, detecting at least 10 fg/µl for each DNA stock, 0.5 par/mL and a sensitivity between 83.3–94.4%, specificity of 85–95

  7. International study to evaluate PCR methods for detection of Trypanosoma cruzi DNA in blood samples from Chagas disease patients.

    Directory of Open Access Journals (Sweden)

    Alejandro G Schijman

    Full Text Available BACKGROUND: A century after its discovery, Chagas disease still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The purpose of this study was to evaluate the performance of PCR methods in detection of Trypanosoma cruzi DNA by an external quality evaluation. METHODOLOGY/FINDINGS: An international collaborative study was launched by expert PCR laboratories from 16 countries. Currently used strategies were challenged against serial dilutions of purified DNA from stocks representing T. cruzi discrete typing units (DTU I, IV and VI (set A, human blood spiked with parasite cells (set B and Guanidine Hidrochloride-EDTA blood samples from 32 seropositive and 10 seronegative patients from Southern Cone countries (set C. Forty eight PCR tests were reported for set A and 44 for sets B and C; 28 targeted minicircle DNA (kDNA, 13 satellite DNA (Sat-DNA and the remainder low copy number sequences. In set A, commercial master mixes and Sat-DNA Real Time PCR showed better specificity, but kDNA-PCR was more sensitive to detect DTU I DNA. In set B, commercial DNA extraction kits presented better specificity than solvent extraction protocols. Sat-DNA PCR tests had higher specificity, with sensitivities of 0.05-0.5 parasites/mL whereas specific kDNA tests detected 5.10(-3 par/mL. Sixteen specific and coherent methods had a Good Performance in both sets A and B (10 fg/µl of DNA from all stocks, 5 par/mL spiked blood. The median values of sensitivities, specificities and accuracies obtained in testing the Set C samples with the 16 tests determined to be good performing by analyzing Sets A and B samples varied considerably. Out of them, four methods depicted the best performing parameters in all three sets of samples, detecting at least 10 fg/µl for each DNA stock, 0.5 par/mL and a sensitivity between 83.3-94.4%, specificity of 85

  8. Psychometric evaluation of the canine brief pain inventory in a Swedish sample of dogs with pain related to osteoarthritis.

    Science.gov (United States)

    Essner, Ann; Zetterberg, Lena; Hellström, Karin; Gustås, Pia; Högberg, Hans; Sjöström, Rita

    2017-07-01

    To evaluate intervention, implement evidence-based practice and enhance the welfare of dogs with naturally occurring osteoarthritis (OA), access to valid, reliable and clinically relevant outcome measures is crucial for researchers, veterinarians and rehabilitation practitioners. The objectives of the present study were to translate and evaluate psychometric properties, in terms of internal consistency and construct validity, of the owner-reported measure canine brief pain inventory (CBPI) in a Swedish sample of dogs with pain related to OA. Twenty-one owners of clinically sound dogs and 58 owners of dogs with pain related to OA were included in this observational and cross-sectional study. After being translated according to the guidelines for patient-reported outcome measures, the CBPI was completed by the canine owners. Construct validity was assessed by confirmatory factor analysis, by repeating the principal component analysis and by assessing for differences between clinically sound dogs and dogs with pain related to OA. Internal consistency was estimated by Cronbach's α. Confirmatory factor analysis was not able to confirm the factor-structure models tested in our sample. Principal component analysis showed a two-component structure, pain severity and pain interference of function. Two components accounted for 76.8% of the total variance, suggesting an acceptable fit of a two-component structure. The ratings from the clinically sound dogs differed from OA dogs and showed significantly lower CBPI total sum. Cronbach's α was 0.94 for the total CBPI, 0.91 for the pain severity and 0.91 for the pain interference of function. The results indicate that the translated version of the CBPI is valid for use in the Swedish language. The findings suggest satisfying psychometric properties in terms of high internal consistencies and ability to discriminate clinically sound dogs from OA dogs. However, based on the confirmatory factor analysis, the original factor

  9. The Influence of Native Language on Auditory-Perceptual Evaluation of Vocal Samples Completed by Brazilian and Canadian SLPs.

    Science.gov (United States)

    Chaves, Cristiane Ribeiro; Campbell, Melanie; Côrtes Gama, Ana Cristina

    2017-03-01

    This study aimed to determine the influence of native language on the auditory-perceptual assessment of voice, as completed by Brazilian and Anglo-Canadian listeners using Brazilian vocal samples and the grade, roughness, breathiness, asthenia, strain (GRBAS) scale. This is an analytical, observational, comparative, and transversal study conducted at the Speech Language Pathology Department of the Federal University of Minas Gerais in Brazil, and at the Communication Sciences and Disorders Department of the University of Alberta in Canada. The GRBAS scale, connected speech, and a sustained vowel were used in this study. The vocal samples were drawn randomly from a database of recorded speech of Brazilian adults, some with healthy voices and some with voice disorders. The database is housed at the Federal University of Minas Gerais. Forty-six samples of connected speech (recitation of days of the week), produced by 35 women and 11 men, and 46 samples of the sustained vowel /a/, produced by 37 women and 9 men, were used in this study. The listeners were divided into two groups of three speech therapists, according to nationality: Brazilian or Anglo-Canadian. The groups were matched according to the years of professional experience of participants. The weighted kappa was used to calculate the intra- and inter-rater agreements, with 95% confidence intervals, respectively. An analysis of the intra-rater agreement showed that Brazilians and Canadians had similar results in auditory-perceptual evaluation of sustained vowel and connected speech. The results of the inter-rater agreement of connected speech and sustained vowel indicated that Brazilians and Canadians had, respectively, moderate agreement on the overall severity (0.57 and 0.50), breathiness (0.45 and 0.45), and asthenia (0.50 and 0.46); poor correlation on roughness (0.19 and 0.007); and weak correlation on strain to connected speech (0.22), and moderate correlation to sustained vowel (0.50). In general

  10. Standardizing operational vector sampling techniques for measuring malaria transmission intensity: evaluation of six mosquito collection methods in western Kenya.

    Science.gov (United States)

    Wong, Jacklyn; Bayoh, Nabie; Olang, George; Killeen, Gerry F; Hamel, Mary J; Vulule, John M; Gimnig, John E

    2013-04-30

    Operational vector sampling methods lack standardization, making quantitative comparisons of malaria transmission across different settings difficult. Human landing catch (HLC) is considered the research gold standard for measuring human-mosquito contact, but is unsuitable for large-scale sampling. This study assessed mosquito catch rates of CDC light trap (CDC-LT), Ifakara tent trap (ITT), window exit trap (WET), pot resting trap (PRT), and box resting trap (BRT) relative to HLC in western Kenya to 1) identify appropriate methods for operational sampling in this region, and 2) contribute to a larger, overarching project comparing standardized evaluations of vector trapping methods across multiple countries. Mosquitoes were collected from June to July 2009 in four districts: Rarieda, Kisumu West, Nyando, and Rachuonyo. In each district, all trapping methods were rotated 10 times through three houses in a 3 × 3 Latin Square design. Anophelines were identified by morphology and females classified as fed or non-fed. Anopheles gambiae s.l. were further identified as Anopheles gambiae s.s. or Anopheles arabiensis by PCR. Relative catch rates were estimated by negative binomial regression. When data were pooled across all four districts, catch rates (relative to HLC indoor) for An. gambiae s.l (95.6% An. arabiensis, 4.4% An. gambiae s.s) were high for HLC outdoor (RR = 1.01), CDC-LT (RR = 1.18), and ITT (RR = 1.39); moderate for WET (RR = 0.52) and PRT outdoor (RR = 0.32); and low for all remaining types of resting traps (PRT indoor, BRT indoor, and BRT outdoor; RR type varied from district to district. ITT, CDC-LT, and WET appear to be effective methods for large-scale vector sampling in western Kenya. Ultimately, choice of collection method for operational surveillance should be driven by trap efficacy and scalability, rather than fine-scale precision with respect to HLC. When compared with recent, similar trap evaluations in Tanzania and Zambia, these data suggest

  11. Evaluating morphometric body mass prediction equations with a juvenile human test sample: accuracy and applicability to small-bodied hominins.

    Science.gov (United States)

    Walker, Christopher S; Yapuncich, Gabriel S; Sridhar, Shilpa; Cameron, Noël; Churchill, Steven E

    2018-02-01

    Body mass is an ecologically and biomechanically important variable in the study of hominin biology. Regression equations derived from recent human samples allow for the reasonable prediction of body mass of later, more human-like, and generally larger hominins from hip joint dimensions, but potential differences in hip biomechanics across hominin taxa render their use questionable with some earlier taxa (i.e., Australopithecus spp.). Morphometric prediction equations using stature and bi-iliac breadth avoid this problem, but their applicability to early hominins, some of which differ in both size and proportions from modern adult humans, has not been demonstrated. Here we use mean stature, bi-iliac breadth, and body mass from a global sample of human juveniles ranging in age from 6 to 12 years (n = 530 age- and sex-specific group annual means from 33 countries/regions) to evaluate the accuracy of several published morphometric prediction equations when applied to small humans. Though the body proportions of modern human juveniles likely differ from those of small-bodied early hominins, human juveniles (like fossil hominins) often differ in size and proportions from adult human reference samples and, accordingly, serve as a useful model for assessing the robustness of morphometric prediction equations. Morphometric equations based on adults systematically underpredict body mass in the youngest age groups and moderately overpredict body mass in the older groups, which fall in the body size range of adult Australopithecus (∼26-46 kg). Differences in body proportions, notably the ratio of lower limb length to stature, influence predictive accuracy. Ontogenetic changes in these body proportions likely influence the shift in prediction error (from under- to overprediction). However, because morphometric equations are reasonably accurate when applied to this juvenile test sample, we argue these equations may be used to predict body mass in small-bodied hominins

  12. pH(stat) vs. single extraction tests to evaluate heavy metals and arsenic leachability in environmental samples.

    Science.gov (United States)

    Rigol, A; Mateu, J; González-Núñez, R; Rauret, G; Vidal, M

    2009-01-19

    Here we compared the pH(stat) test, which examines the leachability of major elements (Ca, Mg, Al, Fe, and Mn), dissolved organic carbon, and trace elements (Cd, Zn, Cu, Pb, and As) in a wide pH range, with single extraction tests based on the use of mild extractants (calcium chloride, acetic acid or EDTA). For this purpose, we examined samples from a variety of environmental conditions (sludges, mineral soils, organic soils, and soils with particulate and/or soluble contamination). Extraction yields obtained with CaCl(2) (0.01 mol L(-1)) and CH(3)COOH (0.43 mol L(-1)) correlated well with those from the pH(stat) at the same pH (r=0.98 and 0.95, respectively), while the use of EDTA (0.05 mol L(-1)) led to systematically higher extraction yields than those quantified with the pH(stat) at the same pH. However, the pH(stat) test had three distinct advantages: (1) it revealed the relationship between the solubility of the main soil phases and pH; (2) it showed the variation in pollutant leachability due to changes in pH; and (3) it better predicted the maximum contaminant availability. Thus we propose that the pH(stat) is the best laboratory tests to evaluate the contaminant leachability over a wide range of sample types (soil, sludge, and sediment).

  13. MyOSD 2014: Evaluating Oceanographic Measurements Contributed by Citizen Scientists in Support of Ocean Sampling Day.

    Science.gov (United States)

    Schnetzer, Julia; Kopf, Anna; Bietz, Matthew J; Buttigieg, Pier Luigi; Fernandez-Guerra, Antonio; Ristov, Aleksandar Pop; Glöckner, Frank Oliver; Kottmann, Renzo

    2016-03-01

    The first Ocean Sampling Day (OSD) took place on June 21, 2014. In a coordinated effort, an internationally distributed group of scientists collected samples from marine surface waters in order to study microbial diversity on a single day with global granularity. Concurrently, citizen scientists enriched the OSD initiative through the MyOSD project, providing additional oceanographic measurements crucial to the contextualization of microbial diversity. Clear protocols, a user-friendly smartphone application, and an online web-form guided citizens in accurate data acquisition, promoting quality submissions to the project's information system. To evaluate the coverage and quality of MyOSD data submissions, we compared the sea surface temperature measurements acquired through OSD, MyOSD, and automatic in situ systems and satellite measurements. Our results show that the quality of citizen-science measurements was comparable to that of scientific measurements. As 79% of MyOSD measurements were conducted in geographic areas not covered by automatic in situ or satellite measurement, citizen scientists contributed significantly to worldwide oceanographic data gathering. Furthermore, survey results indicate that participation in MyOSD made citizens feel more engaged in ocean issues and may have increased their environmental awareness and ocean literacy.

  14. MyOSD 2014: Evaluating Oceanographic Measurements Contributed by Citizen Scientists in Support of Ocean Sampling Day

    Directory of Open Access Journals (Sweden)

    Julia Schnetzer

    2015-11-01

    Full Text Available The first Ocean Sampling Day (OSD took place on June 21, 2014. In a coordinated effort, an internationally distributed group of scientists collected samples from marine surface waters in order to study microbial diversity on a single day with global granularity. Concurrently, citizen scientists enriched the OSD initiative through the MyOSD project, providing additional oceanographic measurements crucial to the contextualization of microbial diversity. Clear protocols, a user-friendly smartphone application, and an online web-form guided citizens in accurate data acquisition, promoting quality submissions to the project’s information system. To evaluate the coverage and quality of MyOSD data submissions, we compared the sea surface temperature measurements acquired through OSD, MyOSD, and automatic in situ systems and satellite measurements. Our results show that the quality of citizen-science measurements was comparable to that of scientific measurements. As 79% of MyOSD measurements were conducted in geographic areas not covered by automatic in situ or satellite measurement, citizen scientists contributed significantly to worldwide oceanographic data gathering. Furthermore, survey results indicate that participation in MyOSD made citizens feel more engaged in ocean issues and may have increased their environmental awareness and ocean literacy.

  15. Evaluation of PCR for cutaneous leishmaniasis diagnosis and species identification using filter paper samples in Panama, Central America.

    Science.gov (United States)

    Miranda, A; Saldaña, A; González, K; Paz, H; Santamaría, G; Samudio, F; Calzada, J E

    2012-09-01

    Cutaneous leishmaniasis (CL) is a major vectorborne disease in Panama. In this study, the diagnostic performance and usefulness of two DNA extraction procedures from skin scraping samples collected on FTA filter paper for subsequent PCR diagnosis of CL was evaluated. A positive CL laboratory diagnosis was based on a positive parasitological test (Giemsa-stained smears or in vitro culture) and/or positive PCR test performed from skin scrapings collected in TE buffer (PCR-TE). Of 100 patients with skin lesions suggestive of CL, 82 (82%) were confirmed as CL positive. The sensitivity was calculated for each of the PCR approaches from samples collected on filter paper. The highest sensitivity was achieved by PCR-FTA processed by Chelex 100 (PCR-Chelex) (0.94). PCR-FTA extracted using the FTA purification reagent presented a lower sensitivity (0.60). Good concordance between routine PCR-TE and PCR-Chelex was observed (percent agreement=0.88, κ index=0.65). In conclusion, use of FTA filter paper for skin scraping collection combined with PCR is a reliable and convenient method for CL diagnosis in Panama, with comparable performance to the routine PCR method and with improved sensitivity compared with those of conventional parasitological methods. Copyright © 2012 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

  16. Development and evaluation of a device for simultaneous uniaxial compression and optical imaging of cartilage samples in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Steinert, Marian; Kratz, Marita; Jones, David B. [Department of Experimental Orthopaedics and Biomechanics, Philipps University Marburg, Baldingerstr., 35043 Marburg (Germany); Jaedicke, Volker; Hofmann, Martin R. [Photonics and Terahertz Technology, Ruhr University Bochum, Universitätsstr. 150, 44801 Bochum (Germany)

    2014-10-15

    In this paper, we present a system that allows imaging of cartilage tissue via optical coherence tomography (OCT) during controlled uniaxial unconfined compression of cylindrical osteochondral cores in vitro. We describe the system design and conduct a static and dynamic performance analysis. While reference measurements yield a full scale maximum deviation of 0.14% in displacement, force can be measured with a full scale standard deviation of 1.4%. The dynamic performance evaluation indicates a high accuracy in force controlled mode up to 25 Hz, but it also reveals a strong effect of variance of sample mechanical properties on the tracking performance under displacement control. In order to counterbalance these disturbances, an adaptive feed forward approach was applied which finally resulted in an improved displacement tracking accuracy up to 3 Hz. A built-in imaging probe allows on-line monitoring of the sample via OCT while being loaded in the cultivation chamber. We show that cartilage topology and defects in the tissue can be observed and demonstrate the visualization of the compression process during static mechanical loading.

  17. Evaluation of Helicobacter pylori antigen positivity in stool samples of patients with dyspeptic complaints in a tertiary care hospital

    Directory of Open Access Journals (Sweden)

    Mehmet Burak Selek

    2013-12-01

    Full Text Available Objective: Helicobacter pylori is a microorganism associatedwith gastritis, peptic ulcer disease and gastriccancer. We aimed to figure out the positivity rate in stoolsamples of outpatients with dyspeptic complaints visitinggastroenterology department and to evaluate its relationwith age, gender and seasonal changes.Methods: Between January 01, 2012 and December 31,2012, stool samples of 330 adult outpatients admitted togastroenterology department are investigated with an immunochromatographictest kit using monoclonal antibodiesfor detection of H. pylori antigen.Results: Among 330 patients’ stool samples tested, 67(20.3% were positive. 18.6% of men and 22.2% of womenwere detected as positive. According to age groups,17.1% patients were positive for 15-35 age groups,27.1% patients were positive for 36-55 age groups and18.2% patients were positive for above 56. Seasonal differenceof H. pylori antigen positivity in stool samples wasstatistically significant (p=0.001. Highest positivity rate29.7% was detected for winter months (December-January-February. According to logistic regression analysis,winter is found as a risk factor with statistically significant2.295 times greater risk [p=0001, Exp (B = 2.925, 95.0%C.I. for EXP (B = 1.668-5.129].Conclusion: H. pylori antigen positivity rate of our study islower than other previously conducted studies in Turkey.But, positivity rates are higher among women comparedto men, concordant with other studies. Even more, detectionof high positivity rates in winter shows primary infectionand/or relapse can be affected by seasonal changes.Key words: Helicobacter pylori, gastroenterology, stool antigen test

  18. Volatilization and oxidative artifacts of PM bound PAHs at low volume sampling (2): Evaluation and comparison of mitigation strategies effects.

    Science.gov (United States)

    Balducci, Catia; Cecinato, Angelo; Paolini, Valerio; Guerriero, Ettore; Perilli, Mattia; Romagnoli, Paola; Tortorella, Carmela; Nacci, Renato Michele; Giove, Aldo; Febo, Antonio

    2017-12-01

    The artifacts induced by oxidative degradation and volatilization were assessed with regards to determination of particulate atmospheric PAHs collected at low volume conditions (2.3 m3 h-1) according to the EU Reference Method EN 12341:2014. In order to evaluate the oxidative degradation, PAH measures carried out through collecting airborne particulate with and without ozone denuders were examined. Simultaneously, the influence of volatilization was investigated by comparing concentrations of PAHs in particulate samples collected over 24-h and 12-h using conventional instruments. Summer and winter/spring campaigns were carried out in order to assess the influence of environmental contour on the artifact processes. Oxidative degradation led to a general decrease of PAH concentrations in both periods; in particular, the highest losses were observed for benzo[a]pyrene and perylene reaching, in average, ca. 20%. In the summer, the effect of volatilization exceeded that of oxidative degradation for light PAHs up to benzo[e]pyrene. In the winter/spring time, the influence of both artifact typologies could be mitigated by splitting the normal 24-h collection interval starting at midnight into two 12-h intervals. A mitigation of the losses could even be obtained by fixing the start time sampling fixed at noon or in the first hours of the day. Finally, the feasibility of collecting PAHs through prolonged sampling (>1 month) at the flow rate of 1.1 L min-1 was preliminarily investigated. Results indicated that this approach is unsuitable for minimizing the oxidative artifacts. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Morphometrics parallel genetics in a newly discovered and endangered taxon of Galápagos tortoise.

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    Ylenia Chiari

    Full Text Available Galápagos tortoises represent the only surviving lineage of giant tortoises that exhibit two different types of shell morphology. The taxonomy of Galápagos tortoises was initially based mainly on diagnostic morphological characters of the shell, but has been clarified by molecular studies indicating that most islands harbor monophyletic lineages, with the exception of Isabela and Santa Cruz. On Santa Cruz there is strong genetic differentiation between the two tortoise populations (Cerro Fatal and La Reserva exhibiting domed shell morphology. Here we integrate nuclear microsatellite and mitochondrial data with statistical analyses of shell shape morphology to evaluate whether the genetic distinction and variability of the two domed tortoise populations is paralleled by differences in shell shape. Based on our results, morphometric analyses support the genetic distinction of the two populations and also reveal that the level of genetic variation is associated with morphological shell shape variation in both populations. The Cerro Fatal population possesses lower levels of morphological and genetic variation compared to the La Reserva population. Because the turtle shell is a complex heritable trait, our results suggest that, for the Cerro Fatal population, non-neutral loci have probably experienced a parallel decrease in variability as that observed for the genetic data.

  20. Classification of avian haemolytic Actinobacillus-like organisms (Bisgaard taxon 26) associated with anseriforme birds as Actinobacillus anseriformium sp. nov.

    Science.gov (United States)

    Bisgaard, M; Christensen, H

    2012-02-01

    Avian haemolytic Actinobacillus-like organisms have tentatively been named Bisgaard taxon 26. Phenotypic information has been published on 65 strains of this taxon. In the current study, 31 isolates were selected for genotypic characterization. Thirty strains had the same rpoB sequence and only one strain diverged in 1 nt. The highest rpoB similarity to members of other taxa was 89.7 % to the type strain of Actinobacillus equuli subsp. haemolyticus and the similarity to the type strain of the type species, Actinobacillus lignieresii, was 88.2 %. The lowest 16S rRNA gene sequence similarity between strains of the group was determined in previous investigations to be 99.6 % and the highest similarities of 96.4 and 96.2 % outside the group were obtained to the reference strain of Actinobacillus genomospecies 2 and to the type strain of A. equuli subsp. equuli, respectively; 95.8-95.3 % similarity was obtained with the type strain of A. lignieresii. recN gene sequence similarities within the group were from 99.5 % (strains F66(T) and F64) to 99.8 % (strains F66(T) and F67) corresponding to genome similarities of 93.9-94.6 %, which are near the upper limit for species compared with other members of the Pasteurellaceae. The highest recN similarity outside the group (83.4 %) was observed to the type strain of Actinobacillus capsulatus, whereas the similarity to the type strain of A. lignieresii was 80.9 %, corresponding to genome similarities of 57.7 and 52.0 %, respectively. All isolates meet the phenotypic characters outlined for Actinobacillus (urease-, phosphatase- and porphyrin-positive, indole-negative, acid production from fructose, sucrose, maltose and dextrin). β-Haemolysis of bovine blood is observed and isolates may demonstrate in vitro satellitic growth, referred to as V-factor or NAD requirement. Isolates have been obtained from the upper respiratory tract of web-footed birds in which they may cause sinusitis, conjunctivitis and

  1. ``Low-cost Electronic nose evaluated on Thai-herb of Northern-Thailand samples using multivariate analysis methods''

    Science.gov (United States)

    na ayudhaya, Paisarn Daungjak; Klinbumrung, Arrak; Jaroensutasinee, Krisanadej; Pratontep, Sirapat; Kerdcharoen, Teerakiat

    2009-05-01

    In case of species of natural and aromatic plant originated from the northern Thailand, sensory characteristics, especially odours, have unique identifiers of herbs. The instruments sensory analysis have performed by several of differential of sensing, so call `electronic nose', to be a significantly and rapidly for chemometrics. The signal responses of the low cost electronic nose were evaluated by principal component analysis (PCA). The aims of this paper evaluated various of Thai-herbs grown in Northern of Thailand as data preprocessing tools of the Low-cost electronic nose (enNU-PYO1). The essential oil groups of Thai herbs such as Garlic, Lemongrass, Shallot (potato onion), Onion, Zanthoxylum limonella (Dennst.) Alston (Thai name is Makaen), and Kaffir lime leaf were compared volatilized from selected fresh herbs. Principal component analysis of the original sensor responses did clearly distinguish either all samples. In all cases more than 97% for cross-validated group were classified correctly. The results demonstrated that it was possible to develop in a model to construct a low-cost electronic nose to provide measurement of odoriferous herbs.

  2. Evaluation of Rhipicephalus (Boophilus microplus (Acari: Ixodidae resistance to different acaricide formulations using samples from Brazilian properties

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    Leandro de Oliveira Souza Higa

    2016-01-01

    Full Text Available Abstract The Rhipicephalus (Boophilus microplus tick is responsible for considerable economic losses in Brazil, causing leather damage, weight loss and reduced milk production in cattle and results in the transmission of pathogens. Currently, the main method for controlling this tick is using acaricides, but their indiscriminate use is one of the major causes of resistance dissemination. In this study, the adult immersion test (AIT was used to evaluate resistance in ticks from 28 properties located in five different states (Mato Grosso do Sul, Mato Grosso, Ceará, São Paulo, e Minas Gerais and the Distrito Federal (DF of Brazil. The resistance was found in 47.64% of the repetitions demonstrating an efficacy of less than 90% in various locations throughout the country. The larvae packet test was used to evaluate samples from ten properties in four states (Mato Grosso do Sul, Mato Grosso, Minas Gerais and Espírito Santo. Spray products belonging to the main classes of acaricides, including combination formulations, were used in both types of test. New cases of resistance were found on properties within the states of Ceará, Espírito Santo and Mato Grosso, where such resistance was not previously reported.

  3. Bias due to sample selection in propensity score matching for a supportive housing program evaluation in New York City.

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    Sungwoo Lim

    Full Text Available OBJECTIVES: Little is known about influences of sample selection on estimation in propensity score matching. The purpose of the study was to assess potential selection bias using one-to-one greedy matching versus optimal full matching as part of an evaluation of supportive housing in New York City (NYC. STUDY DESIGN AND SETTINGS: Data came from administrative data for 2 groups of applicants who were eligible for an NYC supportive housing program in 2007-09, including chronically homeless adults with a substance use disorder and young adults aging out of foster care. We evaluated the 2 matching methods in their ability to balance covariates and represent the original population, and in how those methods affected outcomes related to Medicaid expenditures. RESULTS: In the population with a substance use disorder, only optimal full matching performed well in balancing covariates, whereas both methods created representative populations. In the young adult population, both methods balanced covariates effectively, but only optimal full matching created representative populations. In the young adult population, the impact of the program on Medicaid expenditures was attenuated when one-to-one greedy matching was used, compared with optimal full matching. CONCLUSION: Given covariate balancing with both methods, attenuated program impacts in the young adult population indicated that one-to-one greedy matching introduced selection bias.

  4. Taxon analysis of seed plants used in studies of blood platelet function.

    Science.gov (United States)

    Boncler, Magdalena; Watała, Cezary

    2013-11-28

    The characterization of isolated polyphenolic compounds present in the diet--especially in the context of their therapeutic effect (for instance their antiplatelet activity)--is often based on the generally accepted flavonoid classification. In the case of plant extracts it usually refers to common names of plants rather than scientific botanical nomenclature. Hence, it is often difficult to even roughly estimate how many and which plant taxa exhibit biological activity towards the modulation of blood platelet activity. In this paper, based on a review of literature from the last 50 years (1962-2011), we developed a list of seed plants (Spermatophyta) taxa investigated in studies on blood platelets. We used the PubMed database, as well as the database of species' names--Taxonomy, in order to gather information about the investigated taxa. The review of the literature was made with the use of advanced options, on the basis of keywords (or combinations of keywords) and selected journals. Record search strategies were evaluated on the basis of the sensitivity of search (number of papers meeting the criteria of search strategy) and the specificity of search (number of papers containing in their title and/or abstract information on taxa used in blood platelet research). The publications were considered specific if they reported either Latin or common names of plants (or both). The main search strategy was characterised by high sensitivity, but low specificity. The basis for plant taxonomic specification was the list of 1080 articles, published in 434 journals. The list of taxa used in blood platelet studies covered 98 genera belonging to 47 families of seed plants. The richest in genera, and also in species, appeared to be the families Asteraceae, Fabaceae, and Rosaceae, the most abundant in species all over the world. This study may be a starting point for the selection of plant species to be used for biomedical research and--at the same time--may help in the search

  5. Evaluating the prevalence of DNA mixtures found in fingernail samples from victims and suspects in homicide cases.

    Science.gov (United States)

    Nurit, Bublil; Anat, Gast; Michal, Shenfeld; Lilach, Front; Maya, Freund

    2011-11-01

    An important aspect of homicide investigations is the identification of the persons that had the last contact with the victim prior to death. Violent crimes are frequently characterized by a struggle between the victim and the perpetrator where biological material can be expected to be exchanged between them. Forensic DNA typing enables the generation of genetic profiles by extraction and amplification of cellular material found under fingernails. The evidential value of these samples may be critical if the secondary contributor found in a DNA mixture, can be matched with a potential suspect, or through a DNA database search. The amount of biological material transferred under the fingernails during "casual" activities is not sufficient to genotype reportable mixtures. This may not be the case with homicide victims that may have struggled and died under violent circumstances. The aim of this study was to evaluate the prevalence of DNA mixtures found under the fingernails of both victims and suspected perpetrators of violent deaths. We present a retrospective study of 137 DNA profiles genotyped from fingernail samples of homicide victims and suspects, collected at the Israeli National Center of Forensic Medicine. The majority of the samples produced single source profiles (n=107, 78%) that matched those of the donor's. DNA mixtures (n=30, 22%) were found in increased frequency among victims (n=25/100, 25%) compared to suspects (n=5/37, 13.5%). Mixtures were sub-divided into high level (n=15, 50%), low level (n=9, 30%) and residual (n=6, 20%), according to the number of the foreign contributors' alleles. Thus, this distinctive group of homicide victims was found to express both elevated frequency of DNA mixtures together with highly informative value of the secondary foreign profiles, as compared to other studied populations. These findings support an important aspect for the criminal investigation in murder cases, where a struggle may have ensued and the

  6. Taxon-specific metagenomics of Trichoderma reveals a narrow community of opportunistic species that regulate each other’s development

    Science.gov (United States)

    Friedl, Martina A.

    2012-01-01

    In this paper, we report on the in situ diversity of the mycotrophic fungus Trichoderma (teleomorph Hypocrea, Ascomycota, Dikarya) revealed by a taxon-specific metagenomic approach. We designed a set of genus-specific internal transcribed spacer (ITS)1 and ITS2 rRNA primers and constructed a clone library containing 411 molecular operational taxonomic units (MOTUs). The overall species composition in the soil of the two distinct ecosystems in the Danube floodplain consisted of 15 known species and two potentially novel taxa. The latter taxa accounted for only 1.5 % of all MOTUs, suggesting that almost no hidden or uncultivable Hypocrea/Trichoderma species are present at least in these temperate forest soils. The species were unevenly distributed in vertical soil profiles although no universal factors controlling the distribution of all of them (chemical soil properties, vegetation type and affinity to rhizosphere) were revealed. In vitro experiments simulating infrageneric interactions between the pairs of species that were detected in the same soil horizon showed a broad spectrum of reactions from very strong competition over neutral coexistence to the pronounced synergism. Our data suggest that only a relatively small portion of Hypocrea/Trichoderma species is adapted to soil as a habitat and that the interaction between these species should be considered in a screening for Hypocrea/Trichoderma as an agent(s) of biological control of pests. PMID:22075025

  7. Consideraciones morfológicas y taxonómicas sobre Ischnochiton (Ischnochiton rissoi (Payraudeau, 1826 (Mollusca, Polyplacophora

    Directory of Open Access Journals (Sweden)

    García García, F. J.

    1999-12-01

    Full Text Available The morphological variability of Ischnochiton (Ischnochiton rissoi (Payraudeau, 1826 has produced taxonomic discrepancies. In this paper, besides a taxonomic revision, the morphology of valves, perinotum and radula of several specimens of I. (I. rissoi is studied using Scanning Electron Microscopy. Although a notable morphological variability is present in this species, however, some common features identify all the varieties as an only taxon.La amplia variabilidad de ornamentación de Ischnochiton (Ischnochiton rissoi (Payraudeau, 1826 ha determinado que ejemplares de esta especie se hayan descrito como especies diferentes. En este artículo, además de revisar y discutir las diversas opiniones existentes, se ha realizado un estudio con microscopía electrónica de barrido de numerosos ejemplares y se ha observado la gran heterogeneidad de I. (I. rissoi en relación al tipo de ornamentación de la concha y del perinoto, aunque se han podido determinar ciertos caracteres comunes que permiten identificarlos como pertenecientes a una única especie.

  8. Dispersal and diversity in the earliest North American sauropodomorph dinosaurs, with a description of a new taxon.

    Science.gov (United States)

    Rowe, Timothy B; Sues, Hans-Dieter; Reisz, Robert R

    2011-04-07

    Sauropodomorph dinosaurs originated in the Southern Hemisphere in the Middle or Late Triassic and are commonly portrayed as spreading rapidly to all corners of Pangaea as part of a uniform Late Triassic to Early Jurassic cosmopolitan dinosaur fauna. Under this model, dispersal allegedly inhibited dinosaurian diversification, while vicariance and local extinction enhanced it. However, apomorphy-based analyses of the known fossil record indicate that sauropodomorphs were absent in North America until the Early Jurassic, reframing the temporal context of their arrival. We describe a new taxon from the Kayenta Formation of Arizona that comprises the third diagnosable sauropodomorph from the Early Jurassic of North America. We analysed its relationships to test whether sauropodomorphs reached North America in a single sweepstakes event or in separate dispersals. Our finding of separate arrivals by all three taxa suggests dispersal as a chief factor in dinosaurian diversification during at least the early Mesozoic. It questions whether a 'cosmopolitan' dinosaur fauna ever existed, and corroborates that vicariance, extinction and dispersal did not operate uniformly in time or under uniform conditions during the Mesozoic. Their relative importance is best measured in narrow time slices and circumscribed geographical regions.

  9. Evaluation of 2,6-diacetylpyridinebis-4-phenyl-3-thiosemicarbazone as complexing reagent for zinc in food and environmental samples

    Directory of Open Access Journals (Sweden)

    S. Adi Narayana Reddy

    2016-09-01

    Full Text Available An evaluation of analytical reagent, 2,6-diacetylpyridine-bis-4-phenyl-3-thiosemicarbazone (2,6-DAPBPTSC for traces of Zn(II in foods and environmental samples by the development of a simple, sensitive and selective extractive spectrophotometric method was undertaken. It gave a 1:1(M:L Zn(II–2,6-DAPBPTSC yellowish orange colored complex at pH 4.5, was easily extractable into n-butanol and has shown maximum absorbance at 490 nm. It obeys Beer’s law in the range of 1.06–13.6 μg mL−1 of Zn(II. The molar absorptivity, Sandell’s sensitivity and detection limit were found to be 0.471 × 104 L mol−1 cm−1, 0.0138 μg cm−2 and 0.0081 μg mL−1, respectively. The correlation co-efficient of the complex (r = 0.985 indicates good linearity between two variables such as absorbance of complex and amount of zinc. The proposed procedure was applied to traces of Zn(II in foods and environmental samples. Results were compared with those obtained using an AAS and statical validation of the method was tested in terms of Student ‘T’ test and variance ‘F’ test, which indicate the significance of the present method.

  10. The development and evaluation of a community based model for cervical cancer screening based on self-sampling.

    Science.gov (United States)

    Belinson, Jerome L; Wang, Guixiang; Qu, Xinfeng; Du, Hui; Shen, Jingjing; Xu, Jiajia; Zhong, Liqun; Yi, Ji; Yi, Xin; Wu, Ruifang

    2014-03-01

    To develop and implement a community based model for cervical cancer prevention that allows the communities to manage the screening and the healthcare system to focus resources on evaluation and management of the positives. Using self-sampling and the concepts founded in Community Based Participatory Research (CBPR), we progressively developed a model to efficiently reach the women, especially rural communities; and collect the volume of samples needed to support high throughput centralized low cost per case processing. 8382 eligible women, ages 35 to 59, in 130 rural communities participated. The screening was organized by the local government administration and conducted by the community leaders (CLs). The model used was progressively designed through detailed assessment of key elements at 6 decision points in 26 workshops that were used to train the CLs and the local promoters. The communities were able to accurately conduct the screening; in the final model a local medical worker conducted a 50-minute workshop featuring instructional posters and structured role-play. A manual and a workshop DVD were created for distribution to and implementation by local governments. The average callback rate was 84.3%, without involvement of the local doctors in the management of the positives. An efficient community based model capable of massive screening events was developed. We believe that the callback rate will be further improved when local doctors are trained in the management of the positives. Many elements impact coverage and further research is needed to define the influence of the identified key variables. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Evaluation of an Immunochromatographic Assay for the Rapid and Simultaneous Detection of Rotavirus and Adenovirus in Stool Samples

    Science.gov (United States)

    Kim, Jayoung; Kim, Han-Sung; Kim, Jae-Seok; Song, Wonkeun; Lee, Kyu Man; Lee, Sunhwa; Park, Kyoung Un; Lee, Woochang; Hong, Young Jun

    2014-01-01

    Background We evaluated the analytical and clinical performances of the SD BIOLINE Rota/Adeno Rapid kit (SD Rota/Adeno Rapid; Standard Diagnostics, Inc., Korea), an immunochromatographic assay (ICA), for the simultaneous detection of rotaviruses and adenoviruses in human stool samples. Methods We tested 400 clinical stool samples from patients with acute gastroenteritis and compared the ICA results with the results obtained by using ELISA, enzyme-linked fluorescent assays (ELFA), PCR, and multiplex reverse transcription-PCR (mRT-PCR). To assess the analytical performance of the SD BIOLINE Rota/Adeno Rapid kit, we determined its detection limit, reproducibility, cross-reactivity, and analytical reactivity for adenovirus subtypes, and performed interference studies. Results The overall agreement rates among the tested methods were 91.5% for rotavirus and 85.5% for adenovirus. On the basis of mRT-PCR, the overall agreement, positive agreement, and negative agreement rates of the ICA were 95.6%, 100%, and 94.9% for rotavirus, and 94.0%, 71.4%, and 94.8% for adenovirus, respectively. Using the ICA, we detected all the subtypes of adenovirus tested, but the analytical reactivities for adenovirus subtypes were different between the 4 adenovirus detection methods. The high reproducibility was confirmed, and no cross-reactivity or interference was detected. Conclusions The SD BIOLINE Rota/Adeno Rapid kit showed acceptable analytical and clinical performances. However, interpretation of adenovirus positive/negative result should be cautious because of different detectability for adenovirus subtypes among adenovirus detection methods. PMID:24790909

  12. Murciélagos (Chiroptera: Mammalia del Parque Nacional Yurubí, Venezuela: listado taxonómico y estudio comunitario

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    Mariana Delgado-Jaramillo

    2011-12-01

    Full Text Available Los murciélagos constituyen el grupo de mamíferos más diversificado en la región neotropical y representan un componente clave en la dinámica de muchos ecosistemas terrestres. En este trabajo se describen los resultados de un estudio sobre la quiropterofauna del Parque Nacional Yurubí (ubicado en la zona montañosa del norte de Venezuela, se incluye un listado taxonómico y la caracterización de algunos atributos comunitarios en ambientes predominantemente boscosos. Los datos evaluados fueron obtenidos mediante la revisión de colecciones zoológicas y muestreos diversificados realizados entre febrero y julio del 2009, en un gradiente altitudinal (100-1 500m, que integra a tres unidades ecológicas: bosque semideciduo, bosque siempreverde y selva nublada. Se registraron 64 especies agrupadas en cinco familias, lo que constituye el 63% de los murciélagos conocidos en la Cordillera de la Costa. La familia Phyllostomidae fue dominante (42 especies; 66% del total, seguida por Vespertilionidae, Molossidae, Emballonuridae y Mormoopidae. La comunidad presente a baja elevación fue la más diversificada en términos taxonómicos, mientras que la del piso superior evidenció el menor grado de diversificación. Se identificaron 11 categorías tróficas, con dominancia de los insectívoros en cuanto a la riqueza taxonómica y de los frugívoros en lo que respecta a la abundancia. Nuestros resultados permiten inferir, en un contexto general, que los ecosistemas boscosos del área de estudio muestran un buen estado de conservación, en virtud de la presencia de una proporción relativamente alta de especies pertenecientes a la subfamilia Phyllostominae, cuyos componentes han sido considerados por otros autores como indicadores del grado de conservación de hábitats boscosos primarios, así como la presencia de otras especies con prioridades de conservación. Todos estos aspectos, le confieren a esta área protegida un alto valor proteccionista, en

  13. Sampling Strategies for Evaluating the Rate of Adventitious Transgene Presence in Non-Genetically Modified Crop Fields.

    Science.gov (United States)

    Makowski, David; Bancal, Rémi; Bensadoun, Arnaud; Monod, Hervé; Messéan, Antoine

    2017-09-01

    According to E.U. regulations, the maximum allowable rate of adventitious transgene presence in non-genetically modified (GM) crops is 0.9%. We compared four sampling methods for the detection of transgenic material in agricultural non-GM maize fields: random sampling, stratified sampling, random sampling + ratio reweighting, random sampling + regression reweighting. Random sampling involves simply sampling maize grains from different locations selected at random from the field concerned. The stratified and reweighting sampling methods make use of an auxiliary variable corresponding to the output of a gene-flow model (a zero-inflated Poisson model) simulating cross-pollination as a function of wind speed, wind direction, and distance to the closest GM maize field. With the stratified sampling method, an auxiliary variable is used to define several strata with contrasting transgene presence rates, and grains are then sampled at random from each stratum. With the two methods involving reweighting, grains are first sampled at random from various locations within the field, and the observations are then reweighted according to the auxiliary variable. Data collected from three maize fields were used to compare the four sampling methods, and the results were used to determine the extent to which transgene presence rate estimation was improved by the use of stratified and reweighting sampling methods. We found that transgene rate estimates were more accurate and that substantially smaller samples could be used with sampling strategies based on an auxiliary variable derived from a gene-flow model. © 2017 Society for Risk Analysis.

  14. Diffuse myocardial fibrosis evaluation using cardiac magnetic resonance T1 mapping: sample size considerations for clinical trials

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    Liu Songtao

    2012-12-01

    Full Text Available Abstract Background Cardiac magnetic resonance (CMR T1 mapping has been used to characterize myocardial diffuse fibrosis. The aim of this study is to determine the reproducibility and sample size of CMR fibrosis measurements that would be applicable in clinical trials. Methods A modified Look-Locker with inversion recovery (MOLLI sequence was used to determine myocardial T1 values pre-, and 12 and 25min post-administration of a gadolinium-based contrast agent at 3 Tesla. For 24 healthy subjects (8 men; 29 ± 6 years, two separate scans were obtained a with a bolus of 0.15mmol/kg of gadopentate dimeglumine and b 0.1mmol/kg of gadobenate dimeglumine, respectively, with averaged of 51 ± 34 days between two scans. Separately, 25 heart failure subjects (12 men; 63 ± 14 years, were evaluated after a bolus of 0.15mmol/kg of gadopentate dimeglumine. Myocardial partition coefficient (λ was calculated according to (ΔR1myocardium/ΔR1blood, and ECV was derived from λ by adjusting (1-hematocrit. Results Mean ECV and λ were both significantly higher in HF subjects than healthy (ECV: 0.287 ± 0.034 vs. 0.267 ± 0.028, p=0.002; λ: 0.481 ± 0.052 vs. 442 ± 0.037, p Conclusion ECV and λ quantification have a low variability across scans, and could be a viable tool for evaluating clinical trial outcome.

  15. An evaluation of ICD-11 PTSD and complex PTSD criteria in a sample of adult survivors of childhood institutional abuse

    Directory of Open Access Journals (Sweden)

    Matthias Knefel

    2013-12-01

    Full Text Available Background : The WHO recently launched the proposal for the 11th version of the International Classification of Diseases (ICD-11 that also includes two diagnoses related to traumatic stress. In contrast to the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5, ICD-11 will probably, in addition to posttraumatic stress disorder (PTSD, also define a new diagnosis termed “complex posttraumatic stress disorder” (CPTSD. Objective : We aimed to apply the proposed ICD-11 criteria for PTSD and CPTSD and to compare their prevalence to the ICD-10 (International Classification of Diseases [10th revision] PTSD prevalence. In addition, we compiled a list of symptoms for CPTSD based on subthreshold PTSD so as to include a wider group of individuals. Methods : To evaluate the appropriateness of the WHO ICD-11 proposal compared to the criteria of ICD-10, we applied the newly introduced criteria for PTSD and CPTSD deriving from the Posttraumatic Stress Disorder Checklist – Civilian Version (PCL-C and the Brief Symptom Inventory (BSI scales, to a sample of adult survivors (N=229 of childhood institutional abuse. We evaluated the construct validity of CPTSD using confirmatory factor analysis (CFA. Results : More individuals fulfilled the criteria for PTSD according to ICD-10 (52.8% than the ICD-11 proposal (17% for PTSD only; 38.4% if combined with complex PTSD. The new version of PTSD neutralized the gender effects. The prevalence of CPTSD was 21.4%, and women had a significantly higher rate of CPTSD than men (40.4 and 15.8%, respectively. Those survivors who were diagnosed with CPTSD experienced institutional abuse for a longer time. CFA showed a strong model fit. Conclusion : CPTSD is a highly relevant classification for individuals with complex trauma history, but surprisingly, effects of gender were apparent. Further research should thus address gender effects.

  16. An evaluation of ICD-11 PTSD and complex PTSD criteria in a sample of adult survivors of childhood institutional abuse.

    Science.gov (United States)

    Knefel, Matthias; Lueger-Schuster, Brigitte

    2013-01-01

    The WHO recently launched the proposal for the 11th version of the International Classification of Diseases (ICD-11) that also includes two diagnoses related to traumatic stress. In contrast to the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5), ICD-11 will probably, in addition to posttraumatic stress disorder (PTSD), also define a new diagnosis termed "complex posttraumatic stress disorder" (CPTSD). We aimed to apply the proposed ICD-11 criteria for PTSD and CPTSD and to compare their prevalence to the ICD-10 (International Classification of Diseases [10th revision]) PTSD prevalence. In addition, we compiled a list of symptoms for CPTSD based on subthreshold PTSD so as to include a wider group of individuals. To evaluate the appropriateness of the WHO ICD-11 proposal compared to the criteria of ICD-10, we applied the newly introduced criteria for PTSD and CPTSD deriving from the Posttraumatic Stress Disorder Checklist - Civilian Version (PCL-C) and the Brief Symptom Inventory (BSI) scales, to a sample of adult survivors (N=229) of childhood institutional abuse. We evaluated the construct validity of CPTSD using confirmatory factor analysis (CFA). More individuals fulfilled the criteria for PTSD according to ICD-10 (52.8%) than the ICD-11 proposal (17% for PTSD only; 38.4% if combined with complex PTSD). The new version of PTSD neutralized the gender effects. The prevalence of CPTSD was 21.4%, and women had a significantly higher rate of CPTSD than men (40.4 and 15.8%, respectively). Those survivors who were diagnosed with CPTSD experienced institutional abuse for a longer time. CFA showed a strong model fit. CPTSD is a highly relevant classification for individuals with complex trauma history, but surprisingly, effects of gender were apparent. Further research should thus address gender effects.

  17. Sample Integrity Evaluation and EPA Method 325b Interlaboratory Comparison for Select Volatile Organic Compounds Collected Diffusively on Carbopack X Sorbent Tubes

    Science.gov (United States)

    Sample integrity evaluations and inter-laboratory comparisons were conducted in application of U.S. Environmental Protection Agency (EPA) Methods 325A/B for monitoring benzene and additional selected volatile organic compounds (VOCs) usingpassive-diffusive Carbopack X tube sample...

  18. Application of the SmartSampling Methodology to the Evaluation of Contaminated Landscape Soils at Brookhaven National Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    RAUTMAN,CHRISTOPHER A.

    2000-08-01

    Portions of the SmartSampling{trademark} analysis methodology have been applied to the evaluation of radioactive contaminated landscape soils at Brookhaven National Laboratory. Specifically, the spatial, volumetric distribution of cesium-137 ({sup 137}Cs) contamination within Area of Concern 16E-1 has been modeled probabilistically using a geostatistical methodology, with the purpose of identifying the likelihood of successfully reducing, with respect to a pre-existing, baseline remediation plan, the volume of soil that must be disposed of offsite during clean-up. The principal objective of the analysis was to evaluate the likelihood of successful deployment of the Segmented Gate System (SGS), a novel remediation approach that emphasizes real-time separation of clean from contaminated materials during remediation operations. One primary requirement for successful application of the segmented gate technology investigated is that a variety of contaminant levels exist at the deployment site, which would enable to the SGS to discriminate material above and below a specified remediation threshold value. The results of this analysis indicate that there is potential for significant volume reduction with respect to the baseline remediation plan at a threshold excavation level of 23 pCi/g {sup 137}Cs. A reduction of approximately 50%, from a baseline volume of approximately 1,064.7 yd{sup 3} to less than 550 yd{sup 3}, is possible with acceptance of only a very small level of engineering risk. The vast majority of this volume reduction is obtained by not excavating almost all of levels 3 and 4 (from 12 to 24 inches in depth), which appear to be virtually uncontaminated, based on the available data. Additional volume reductions related to soil materials on levels 1 (depths of 0--6 inches) and 2 (6--12 inches) may be possible, specifically through use of the SGS technology. Level-by-level evaluation of simulation results suggests that as much as 26 percent of level 1 and as

  19. Employing post-DEA cross-evaluation and cluster analysis in a sample of Greek NHS hospitals.

    Science.gov (United States)

    Flokou, Angeliki; Kontodimopoulos, Nick; Niakas, Dimitris

    2011-10-01

    To increase Data Envelopment Analysis (DEA) discrimination of efficient Decision Making Units (DMUs), by complementing "self-evaluated" efficiencies with "peer-evaluated" cross-efficiencies and, based on these results, to classify the DMUs using cluster analysis. Healthcare, which is deprived of such studies, was chosen as the study area. The sample consisted of 27 small- to medium-sized (70-500 beds) NHS general hospitals distributed throughout Greece, in areas where they are the sole NHS representatives. DEA was performed on 2005 data collected from the Ministry of Health and the General Secretariat of the National Statistical Service. Three inputs -hospital beds, physicians and other health professionals- and three outputs -case-mix adjusted hospitalized cases, surgeries and outpatient visits- were included in input-oriented, constant-returns-to-scale (CRS) and variable-returns-to-scale (VRS) models. In a second stage (post-DEA), aggressive and benevolent cross-efficiency formulations and clustering were employed, to validate (or not) the initial DEA scores. The "maverick index" was used to sort the peer-appraised hospitals. All analyses were performed using custom-made software. Ten benchmark hospitals were identified by DEA, but using the aggressive and benevolent formulations showed that two and four of them respectively were at the lower end of the maverick index list. On the other hand, only one 100% efficient (self-appraised) hospital was at the higher end of the list, using either formulation. Cluster analysis produced a hierarchical "tree" structure which dichotomized the hospitals in accordance to the cross-evaluation results, and provided insight on the two-dimensional path to improving efficiency. This is, to our awareness, the first study in the healthcare domain to employ both of these post-DEA techniques (cross efficiency and clustering) at the hospital (i.e. micro) level. The potential benefit for decision-makers is the capability to examine high

  20. Comparison of SVM, RF and ELM on an Electronic Nose for the Intelligent Evaluation of Paraffin Samples

    Directory of Open Access Journals (Sweden)

    Hong Men

    2018-01-01

    Full Text Available Paraffin odor intensity is an important quality indicator when a paraffin inspection is performed. Currently, paraffin odor level assessment is mainly dependent on an artificial sensory evaluation. In this paper, we developed a paraffin odor analysis system to classify and grade four kinds of paraffin samples. The original feature set was optimized using Principal Component Analysis (PCA and Partial Least Squares (PLS. Support Vector Machine (SVM, Random Forest (RF, and Extreme Learning Machine (ELM were applied to three different feature data sets for classification and level assessment of paraffin. For classification, the model based on SVM, with an accuracy rate of 100%, was superior to that based on RF, with an accuracy rate of 98.33–100%, and ELM, with an accuracy rate of 98.01–100%. For level assessment, the R2 related to the training set was above 0.97 and the R2 related to the test set was above 0.87. Through comprehensive comparison, the generalization of the model based on ELM was superior to those based on SVM and RF. The scoring errors for the three models were 0.0016–0.3494, lower than the error of 0.5–1.0 measured by industry standard experts, meaning these methods have a higher prediction accuracy for scoring paraffin level.

  1. A Preliminary Evaluation of the Validity of Binge Eating Disorder Defining Features in a Community-Based Sample

    Science.gov (United States)

    Klein, Kelly M.; Forney, K. Jean; Keel, Pamela K.

    2015-01-01

    Objective Little empirical attention has been paid to the DSM-5 definition of Binge Eating Disorder (BED), particularly to the associated features of binge episodes. The present study sought to determine how the associated features and undue influence of weight/shape on self-evaluation contribute to evidence of a clinically significant eating disorder. Method Secondary analyses were conducted on data (N = 80; 76.3% women, 76.3% Caucasian, ages 18–43) collected through an epidemiological study of eating patterns. Descriptive statistics were used to report the sample prevalence of the features, independently and in combination. Correlations and alpha reliability were employed to examine relationships among associated features, distress regarding bingeing, and clinical diagnosis. Regression models and receiver-operating characteristic (ROC) curves were used to determine the utility of the features for explaining variance in distress. Results Internal consistency reliability for indicators was low, and several features demonstrated low or non-significant associations with distress and diagnosis. Feeling disgusted/depressed/guilty was the only unique predictor of distress (p = 0.001). For the ROC curves, three features was the best threshold for predicting distress. Discussion Results support the need to refine the features to ensure better detection of clinically significant eating pathology for research inclusion and treatment of the illness. PMID:26607858

  2. Evaluation of immunization coverage in the rural area of Pune, Maharashtra, using the 30 cluster sampling technique

    Directory of Open Access Journals (Sweden)

    Pankaj Kumar Gupta

    2013-01-01

    Full Text Available Background: Infectious diseases are a major cause of morbidity and mortality in children. One of the most cost-effective and easy methods for child survival is immunization. Despite all the efforts put in by governmental and nongovernmental institutes for 100% immunization coverage, there are still pockets of low-coverage areas. In India, immunization services are offered free in public health facilities, but, despite rapid increases, the immunization rate remains low in some areas. The Millennium Development Goals (MDG indicators also give importance to immunization. Objective: To assess the immunization coverage in the rural area of Pune. Materials and Methods: A cross-sectional study was conducted in the field practice area of the Rural Health Training Center (RHTC using the WHO′s 30 cluster sampling method for evaluation of immunization coverage. Results: A total of 1913 houses were surveyed. A total of 210 children aged 12-23 months were included in the study. It was found that 86.67% of the children were fully immunized against all the six vaccine-preventable diseases. The proportion of fully immunized children was marginally higher in males (87.61% than in females (85.57%, and the immunization card was available with 60.95% of the subjects. The most common cause for partial immunization was that the time of immunization was inconvenient (36%. Conclusion: Sustained efforts are required to achieve universal coverage of immunization in the rural area of Pune district.

  3. Extending the interview to all medical school candidates--Computer-Based Multiple Sample Evaluation of Noncognitive Skills (CMSENS).

    Science.gov (United States)

    Dore, Kelly L; Reiter, Harold I; Eva, Kevin W; Krueger, Sharyn; Scriven, Edward; Siu, Eric; Hilsden, Shannon; Thomas, Jennifer; Norman, Geoffrey R

    2009-10-01

    Most medical school candidates are excluded without benefit of noncognitive skills assessment. Is development of a noncognitive preinterview screening test that correlates with the well-validated Multiple Mini-Interview (MMI) possible? Study 1: 110 medical school candidates completed MMI and Computer-based Multiple Sample Evaluation of Noncognitive Skills (CMSENS)-eight 1-minute video-based scenarios and four self-descriptive questions, with short-answer-response format. Seventy-eight responses were audiotaped, 32 typewritten; all were scored by two independent raters. Study 2: 167 candidates completed CMSENS-eight videos, six self-descriptive questions, typewritten responses only, scored by two raters; 88 of 167 underwent the MMI. Results for overall test generalizability, interrater reliability, and correlation with MMI, respectively, were, for Study 1, audio-responders: 0.86, 0.82, 0.15; typewritten-responders: 0.72, 0.81, 0.51; and for Study 2, 0.83, 0.95, 0.46 (correlation with disattenuation was 0.60). Strong psychometric properties, including MMI correlation, of CMSENS warrant investigation into future widespread implementation as a preinterview noncognitive screening test.

  4. Immunological and histological evaluation of clinical samples from psoriasis patients treated with anti-CD6 itolizumab.

    Science.gov (United States)

    Aira, Lazaro E; López-Requena, Alejandro; Fuentes, Dasha; Sánchez, Liset; Pérez, Teresita; Urquiza, Aleida; Bautista, Heber; Falcón, Leopoldina; Hernández, Patricia; Mazorra, Zaima

    2014-01-01

    Psoriasis is a chronic inflammatory disease with a prevalence of approximately 2-3% in the general population. The majority of diagnosed patients have plaque psoriasis, and about 20% have moderate-to-severe disease. Itolizumab, a new monoclonal antibody specific for the CD6 molecule mainly expressed on T lymphocytes, has demonstrated to inhibit in vitro ligand-induced proliferation and pro-inflammatory cytokine production. We assessed the immunological and histopathological effect of the antibody using clinical samples taken from 26 patients with moderate-to-severe psoriasis included in a clinical trial. The precursor frequency of lymphocytes activated with anti-CD2/CD3/CD28 beads, as well as the number of interferon (IFN)-γ-secreting T cells after stimulation, were measured at different time points of the study. Serum cytokine levels and anti-idiotypic antibody response to itolizumab were also evaluated. Additionally, lymphocyte infiltration and epidermis hyperplasia were studied in five patients. A significant reduction in T cell proliferation capacity and number of IFN-γ-producing T cells was found in treated patients. Serum levels of interleukin-6, tumor necrosis factor and IFN-γ showed an overall trend toward reduction. No anti-idiotypic antibody response was detected. A significant reduction in the epidermis hyperplasia was observed in analyzed patients. These results support the relevance of the CD6 molecule as a therapeutic target for the treatment of this disease.

  5. A preliminary evaluation of the validity of binge-eating disorder defining features in a community-based sample.

    Science.gov (United States)

    Klein, Kelly M; Forney, K Jean; Keel, Pamela K

    2016-05-01

    Little empirical attention has been paid to the DSM-5 definition of binge-eating disorder (BED), particularly to the associated features of binge episodes. The present study sought to determine how the associated features and undue influence of weight/shape on self-evaluation contribute to evidence of a clinically significant eating disorder. Secondary analyses were conducted on data (N = 80; 76.3% women, 76.3% Caucasian, ages 18-43) collected through an epidemiological study of eating patterns. Descriptive statistics were used to report the sample prevalence of the features, independently and in combination. Correlations and alpha reliability were employed to examine relationships among associated features, distress regarding bingeing, and clinical diagnosis. Regression models and receiver-operating characteristic (ROC) curves were used to determine the utility of the features for explaining variance in distress. Internal consistency reliability for indicators was low, and several features demonstrated low or nonsignificant associations with distress and diagnosis. Feeling disgusted/depressed/guilty was the only unique predictor of distress (p = 0.001). For the ROC curves, three features was the best threshold for predicting distress. Results support the need to refine the features to ensure better detection of clinically significant eating pathology for research inclusion and treatment of the illness. © 2015 Wiley Periodicals, Inc. (Int J Eat Disord 2016; 49:524-528). © 2015 Wiley Periodicals, Inc.

  6. Metal Concentrations in Samples of Frozen Cephalopods (Cuttlefish, Octopus, Squid, and Shortfin Squid): An Evaluation of Dietary Intake.

    Science.gov (United States)

    Sangiuliano, D; Rubio, C; Gutiérrez, A J; González-Weller, D; Revert, C; Hardisson, A; Zanardi, E; Paz, S

    2017-10-10

    Cephalopods are an important source of nutrients and some of the most widely consumed marine foods. However, because of contamination of the oceans and the bioaccumulative nature of toxic metals, these foods may pose a health risk. For this reason, the concentrations of some trace elements (chromium [Cr], lithium, strontium [Sr], copper [Cu], and nickel) and toxic metals (aluminum [Al], cadmium, and lead) were determined in 65 frozen samples of cuttlefish, octopus, common squid, and shortfin squid by inductively coupled plasma optical emission spectrometry to evaluate dietary intake and toxic risk. Sr was the major trace element (3.03 mg/kg) in cuttlefish; however, Cu (1.57 mg/kg) was found in the highest concentration in common squid. Among the toxic metals, Al had the highest concentration (3.09 mg/kg) in common squid. Al can pose an important health risk to individuals with kidney problems and to children because these groups are most vulnerable to the toxic effects. Significant differences among the four cephalopod types were found in the concentrations of most of the metals examined. Taking into account the average consumption of cephalopods, the contribution of toxic metals does not pose a risk to the health of adults.

  7. Comparison of SVM, RF and ELM on an Electronic Nose for the Intelligent Evaluation of Paraffin Samples

    Science.gov (United States)

    Men, Hong; Fu, Songlin; Yang, Jialin; Cheng, Meiqi; Shi, Yan

    2018-01-01

    Paraffin odor intensity is an important quality indicator when a paraffin inspection is performed. Currently, paraffin odor level assessment is mainly dependent on an artificial sensory evaluation. In this paper, we developed a paraffin odor analysis system to classify and grade four kinds of paraffin samples. The original feature set was optimized using Principal Component Analysis (PCA) and Partial Least Squares (PLS). Support Vector Machine (SVM), Random Forest (RF), and Extreme Learning Machine (ELM) were applied to three different feature data sets for classification and level assessment of paraffin. For classification, the model based on SVM, with an accuracy rate of 100%, was superior to that based on RF, with an accuracy rate of 98.33–100%, and ELM, with an accuracy rate of 98.01–100%. For level assessment, the R2 related to the training set was above 0.97 and the R2 related to the test set was above 0.87. Through comprehensive comparison, the generalization of the model based on ELM was superior to those based on SVM and RF. The scoring errors for the three models were 0.0016–0.3494, lower than the error of 0.5–1.0 measured by industry standard experts, meaning these methods have a higher prediction accuracy for scoring paraffin level. PMID:29346328

  8. The relative congruence of cranial and genetic estimates of hominoid taxon relationships: implications for the reconstruction of hominin phylogeny.

    Science.gov (United States)

    von Cramon-Taubadel, Noreen; Smith, Heather F

    2012-05-01

    Previous analyses of extant catarrhine craniodental morphology have often failed to recover their molecular relationships, casting doubt on the accuracy of hominin phylogenies based on anatomical data. However, on the basis of genetic, morphometric and environmental affinity patterns, a growing body of literature has demonstrated that particular aspects of cranial morphology are remarkably reliable proxies for neutral modern human population history. Hence, it is important to test whether these intra-specific patterns can be extrapolated to a broader primate taxon level such that inference rules for understanding the morphological evolution of the extinct hominins may be devised. Here, we use a matrix of molecular distances between 15 hominoid taxa to test the genetic congruence of 14 craniomandibular regions, defined and morphometrically delineated on the basis of previous modern human analyses. This methodology allowed us to test directly whether the cranial regions found to be reliable indicators of population history were also more reliable proxies for hominoid genetic relationships. Cranial regions were defined on the basis of three criteria: developmental-functional units, individual bones, and regions differentially affected by masticatory stress. The results found that all regions tested were significantly and strongly correlated with the molecular matrix. However, the modern human predictions regarding the relative congruence of particular regions did not hold true, as the face was statistically the most reliable indicator of hominoid genetic distances, as opposed to the vault or basicranium. Moreover, when modern humans were removed from the analysis, all cranial regions improved in their genetic congruence, suggesting that it is the inclusion of morphologically-derived humans that has the largest effect on incongruence between morphological and molecular estimates of hominoid relationships. Therefore, it may be necessary to focus on smaller intra

  9. Observaciones sobre algunos caracteres de valor taxonómico en el grupo de los carófitos

    Directory of Open Access Journals (Sweden)

    Pedrola, J.

    1990-05-01

    Full Text Available The variability of the microstructurals characters and mineralogical composition of the oogonia of some charophytes extant and fossils is described. Two types of microstructures (W & V are find. These are conservative into populations and are not able to change by the environmental factors. Moreover, these structures are quite constant in some of the phylogenetics groups studied. Consequently it is proposed its utilization in taxonomy. The apparition of original compounds in the Charophyta (vaterite. whewelite, aragonite, etc. is important because it supports an old idea that considerates the Charophyta as an autonomous class between the Clorophyta and the Traqueophyta.

    Se describe la variabilidad de los caracteres microestructurales y la composición mineralógica de las células espirales del oogonio en diversas especies actuales y fósiles del grupo de los carófitos. Se encuentran así, dos tipos de microestructuras diferentes (W y V que se muestran conservativas en el seno de las poblaciones, no moldeables por el ambiente y relativamente constantes dentro de los distintos grupos filogenéticos. En consecuencia, se propone su utilización con fines taxonómicos. La aparición de ciertos elementos mineralógicos (vaterita, whewelita, aragonito etc. resulta remarcable por su originalidad y su apoyo al viejo criterio que consideraba los carófitos como una clase autónoma y quizás de "enlace" entre clorófitos y traqueófitos.

  10. Evaluation of natural radioactivity in soil, sediment and water samples of Niger Delta (Biseni) flood plain lakes, Nigeria.

    Science.gov (United States)

    Agbalagba, E O; Onoja, R A

    2011-07-01

    This paper presents the findings of a baseline study undertaken to evaluate the natural radioactivity levels in soil, sediment and water samples in four flood plain lakes of the Niger Delta using a hyper pure germanium (HPGe) detector. The activity profile of radionuclides shows low activity across the study area. The mean activity level of the natural radionuclides (226)Ra, (232)Th and (40)K is 20 ± 3, 20 ± 3 and 180 ± 50 Bq kg(-1), respectively. These values are well within values reported elsewhere in the country and in other countries with similar environments. The study also examined some radiation hazard indices. The mean values obtained are, 76 ± 14 Bq kg(-1), 30 ± 5.5 ηGy h(-1), 37 ± 6.8 μSv y(-1), 0.17 and 0.23 for Radium Equivalent Activity (Ra(eq)), Absorbed Dose Rates (D), Annual Effective Dose Rates (E(ff) Dose), External Hazard Index (H(ex)) and Internal Hazard Index (H(in)) respectively. All the health hazard indices are well below their recommended limits. The soil and sediments from the study area provide no excessive exposures for inhabitants and can be used as constructi