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Sample records for methods analyses revealed

  1. A review of bioinformatic methods for forensic DNA analyses.

    Science.gov (United States)

    Liu, Yao-Yuan; Harbison, SallyAnn

    2018-03-01

    Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Quantitative methods for analysing cumulative effects on fish migration success: a review.

    Science.gov (United States)

    Johnson, J E; Patterson, D A; Martins, E G; Cooke, S J; Hinch, S G

    2012-07-01

    It is often recognized, but seldom addressed, that a quantitative assessment of the cumulative effects, both additive and non-additive, of multiple stressors on fish survival would provide a more realistic representation of the factors that influence fish migration. This review presents a compilation of analytical methods applied to a well-studied fish migration, a more general review of quantitative multivariable methods, and a synthesis on how to apply new analytical techniques in fish migration studies. A compilation of adult migration papers from Fraser River sockeye salmon Oncorhynchus nerka revealed a limited number of multivariable methods being applied and the sub-optimal reliance on univariable methods for multivariable problems. The literature review of fisheries science, general biology and medicine identified a large number of alternative methods for dealing with cumulative effects, with a limited number of techniques being used in fish migration studies. An evaluation of the different methods revealed that certain classes of multivariable analyses will probably prove useful in future assessments of cumulative effects on fish migration. This overview and evaluation of quantitative methods gathered from the disparate fields should serve as a primer for anyone seeking to quantify cumulative effects on fish migration survival. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

  3. Methods and procedures for shielding analyses for the SNS

    International Nuclear Information System (INIS)

    Popova, I.; Ferguson, F.; Gallmeier, F.X.; Iverson, E.; Lu, Wei

    2011-01-01

    In order to provide radiologically safe Spallation Neutron Source operation, shielding analyses are performed according to Oak Ridge National Laboratory internal regulations and to comply with the Code of Federal Regulations. An overview of on-going shielding work for the accelerator facility and neutrons beam lines, methods used for the analyses, and associated procedures and regulations are presented. Methods used to perform shielding analyses are described as well. (author)

  4. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development

    Directory of Open Access Journals (Sweden)

    Heidi G. Parker

    2017-04-01

    Full Text Available There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds.

  5. Study of thermal-hydraulic analyses with CIP method

    International Nuclear Information System (INIS)

    Doi, Yoshihiro

    1996-09-01

    New type of numerical scheme CIP has been proposed for solving hyperbolic type equations and the CIP is focused on as a less numerical diffusive scheme. C-CUP method with the CIP scheme is adopted to numerical simulations that treat compressible and incompressible fluids, phase change phenomena and Mixture fluids. To evaluate applicabilities of the CIP scheme and C-CUP method for thermal hydraulic analyses related to Fast Breeder Reactors (FBRs), the scheme and the method were reviewed. Feature of the CIP scheme and procedure of the C-CUP method were presented. The CIP scheme is used to solve linear hyperbolic type equations for advection term in basic equations of fluids. Key issues of the scheme is that profile between grid points is described to solve the equation by cubic polynomial and spatial derivatives of the polynomial. The scheme can capture steep change of solution and suppress numerical error. In the C-CUP method, the basic equations of fluids are divided into advection terms and the other terms. The advection terms is solved with CIP scheme and the other terms is solved with difference method. The C-CUP method is robust for numerical instability, but mass of fluid will be in unfair preservation with nonconservative equations for fluids. Numerical analyses with the CIP scheme and the C-CUP method has been performed for phase change, mixture and moving object. These analyses are depend on characteristics of that the scheme and the method are robust for steep change of density and useful for interface tracking. (author)

  6. Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food.

    Science.gov (United States)

    Lim, Shu Yong; Yap, Kien-Pong; Thong, Kwai Lin

    2016-01-01

    Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia. The genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively. Our virulence profiling indicated a total of 31 virulence genes shared by both analysed strains. These shared genes included those that encode for internalins and L. monocytogenes pathogenicity island 1 (LIPI-1). Both the Malaysian L. monocytogenes strains also harboured several genes associated with stress tolerance to counter the adverse conditions. Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolone, tetracycline, and penicillin, and macrolides were identified in the genomes of both strains. Whole genome sequencing and comparative genomics analyses revealed two virulent L. monocytogenes strains isolated from ready-to-eat foods in Malaysia. The identification of strains with pathogenic, persistent, and antibiotic resistant potentials from minimally processed food warrant close attention from both healthcare and food industry.

  7. Comparative analyses reveal discrepancies among results of commonly used methods for Anopheles gambiaemolecular form identification

    Directory of Open Access Journals (Sweden)

    Pinto João

    2011-08-01

    Full Text Available Abstract Background Anopheles gambiae M and S molecular forms, the major malaria vectors in the Afro-tropical region, are ongoing a process of ecological diversification and adaptive lineage splitting, which is affecting malaria transmission and vector control strategies in West Africa. These two incipient species are defined on the basis of single nucleotide differences in the IGS and ITS regions of multicopy rDNA located on the X-chromosome. A number of PCR and PCR-RFLP approaches based on form-specific SNPs in the IGS region are used for M and S identification. Moreover, a PCR-method to detect the M-specific insertion of a short interspersed transposable element (SINE200 has recently been introduced as an alternative identification approach. However, a large-scale comparative analysis of four widely used PCR or PCR-RFLP genotyping methods for M and S identification was never carried out to evaluate whether they could be used interchangeably, as commonly assumed. Results The genotyping of more than 400 A. gambiae specimens from nine African countries, and the sequencing of the IGS-amplicon of 115 of them, highlighted discrepancies among results obtained by the different approaches due to different kinds of biases, which may result in an overestimation of MS putative hybrids, as follows: i incorrect match of M and S specific primers used in the allele specific-PCR approach; ii presence of polymorphisms in the recognition sequence of restriction enzymes used in the PCR-RFLP approaches; iii incomplete cleavage during the restriction reactions; iv presence of different copy numbers of M and S-specific IGS-arrays in single individuals in areas of secondary contact between the two forms. Conclusions The results reveal that the PCR and PCR-RFLP approaches most commonly utilized to identify A. gambiae M and S forms are not fully interchangeable as usually assumed, and highlight limits of the actual definition of the two molecular forms, which might

  8. A vector matching method for analysing logic Petri nets

    Science.gov (United States)

    Du, YuYue; Qi, Liang; Zhou, MengChu

    2011-11-01

    Batch processing function and passing value indeterminacy in cooperative systems can be described and analysed by logic Petri nets (LPNs). To directly analyse the properties of LPNs, the concept of transition enabling vector sets is presented and a vector matching method used to judge the enabling transitions is proposed in this article. The incidence matrix of LPNs is defined; an equation about marking change due to a transition's firing is given; and a reachable tree is constructed. The state space explosion is mitigated to a certain extent from directly analysing LPNs. Finally, the validity and reliability of the proposed method are illustrated by an example in electronic commerce.

  9. ObStruct: a method to objectively analyse factors driving population structure using Bayesian ancestry profiles.

    Directory of Open Access Journals (Sweden)

    Velimir Gayevskiy

    Full Text Available Bayesian inference methods are extensively used to detect the presence of population structure given genetic data. The primary output of software implementing these methods are ancestry profiles of sampled individuals. While these profiles robustly partition the data into subgroups, currently there is no objective method to determine whether the fixed factor of interest (e.g. geographic origin correlates with inferred subgroups or not, and if so, which populations are driving this correlation. We present ObStruct, a novel tool to objectively analyse the nature of structure revealed in Bayesian ancestry profiles using established statistical methods. ObStruct evaluates the extent of structural similarity between sampled and inferred populations, tests the significance of population differentiation, provides information on the contribution of sampled and inferred populations to the observed structure and crucially determines whether the predetermined factor of interest correlates with inferred population structure. Analyses of simulated and experimental data highlight ObStruct's ability to objectively assess the nature of structure in populations. We show the method is capable of capturing an increase in the level of structure with increasing time since divergence between simulated populations. Further, we applied the method to a highly structured dataset of 1,484 humans from seven continents and a less structured dataset of 179 Saccharomyces cerevisiae from three regions in New Zealand. Our results show that ObStruct provides an objective metric to classify the degree, drivers and significance of inferred structure, as well as providing novel insights into the relationships between sampled populations, and adds a final step to the pipeline for population structure analyses.

  10. Toward a unified method for analysing and teaching Human Robot Interaction

    DEFF Research Database (Denmark)

    Dinesen, Jens Vilhelm

    , drawing on key theories and methods from both communications- and interaction-theory. The aim is to provide a single unified method for analysing interaction, through means of video analysis and then applying theories, with proven mutual compatibility, to reach a desired granularity of study.......This abstract aims to present key aspect of a future paper, which outlines the ongoing development ofa unified method for analysing and teaching Human-Robot-Interaction. The paper will propose a novel method for analysing both HRI, interaction with other forms of technologies and fellow humans...

  11. Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

    Directory of Open Access Journals (Sweden)

    Dmitri Papatsenko

    2015-08-01

    Full Text Available Analyses of gene expression in single mouse embryonic stem cells (mESCs cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM. In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

  12. Trial sequential analysis reveals insufficient information size and potentially false positive results in many meta-analyses

    DEFF Research Database (Denmark)

    Brok, J.; Thorlund, K.; Gluud, C.

    2008-01-01

    in 80% (insufficient information size). TSA(15%) and TSA(LBHIS) found that 95% and 91% had absence of evidence. The remaining nonsignificant meta-analyses had evidence of lack of effect. CONCLUSION: TSA reveals insufficient information size and potentially false positive results in many meta......OBJECTIVES: To evaluate meta-analyses with trial sequential analysis (TSA). TSA adjusts for random error risk and provides the required number of participants (information size) in a meta-analysis. Meta-analyses not reaching information size are analyzed with trial sequential monitoring boundaries...... analogous to interim monitoring boundaries in a single trial. STUDY DESIGN AND SETTING: We applied TSA on meta-analyses performed in Cochrane Neonatal reviews. We calculated information sizes and monitoring boundaries with three different anticipated intervention effects of 30% relative risk reduction (TSA...

  13. Time-Series Analyses of Transcriptomes and Proteomes Reveal Molecular Networks Underlying Oil Accumulation in Canola.

    Science.gov (United States)

    Wan, Huafang; Cui, Yixin; Ding, Yijuan; Mei, Jiaqin; Dong, Hongli; Zhang, Wenxin; Wu, Shiqi; Liang, Ying; Zhang, Chunyu; Li, Jiana; Xiong, Qing; Qian, Wei

    2016-01-01

    Understanding the regulation of lipid metabolism is vital for genetic engineering of canola ( Brassica napus L.) to increase oil yield or modify oil composition. We conducted time-series analyses of transcriptomes and proteomes to uncover the molecular networks associated with oil accumulation and dynamic changes in these networks in canola. The expression levels of genes and proteins were measured at 2, 4, 6, and 8 weeks after pollination (WAP). Our results show that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. We found that genes in almost every node of fatty acid synthesis pathway were significantly up-regulated during oil accumulation. Moreover, significant expression changes of two genes, acetyl-CoA carboxylase and acyl-ACP desaturase, were detected on both transcriptomic and proteomic levels. We confirmed the temporal expression patterns revealed by the transcriptomic analyses using quantitative real-time PCR experiments. The gene set association analysis show that the biosynthesis of fatty acids and unsaturated fatty acids are the most significant biological processes from 2-4 WAP and 4-6 WAP, respectively, which is consistent with the results of time-series analyses. These results not only provide insight into the mechanisms underlying lipid metabolism, but also reveal novel candidate genes that are worth further investigation for their values in the genetic engineering of canola.

  14. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

    Directory of Open Access Journals (Sweden)

    Gareth D Westrop

    Full Text Available Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

  15. Individual-based analyses reveal limited functional overlap in a coral reef fish community.

    Science.gov (United States)

    Brandl, Simon J; Bellwood, David R

    2014-05-01

    Detailed knowledge of a species' functional niche is crucial for the study of ecological communities and processes. The extent of niche overlap, functional redundancy and functional complementarity is of particular importance if we are to understand ecosystem processes and their vulnerability to disturbances. Coral reefs are among the most threatened marine systems, and anthropogenic activity is changing the functional composition of reefs. The loss of herbivorous fishes is particularly concerning as the removal of algae is crucial for the growth and survival of corals. Yet, the foraging patterns of the various herbivorous fish species are poorly understood. Using a multidimensional framework, we present novel individual-based analyses of species' realized functional niches, which we apply to a herbivorous coral reef fish community. In calculating niche volumes for 21 species, based on their microhabitat utilization patterns during foraging, and computing functional overlaps, we provide a measurement of functional redundancy or complementarity. Complementarity is the inverse of redundancy and is defined as less than 50% overlap in niche volumes. The analyses reveal extensive complementarity with an average functional overlap of just 15.2%. Furthermore, the analyses divide herbivorous reef fishes into two broad groups. The first group (predominantly surgeonfishes and parrotfishes) comprises species feeding on exposed surfaces and predominantly open reef matrix or sandy substrata, resulting in small niche volumes and extensive complementarity. In contrast, the second group consists of species (predominantly rabbitfishes) that feed over a wider range of microhabitats, penetrating the reef matrix to exploit concealed surfaces of various substratum types. These species show high variation among individuals, leading to large niche volumes, more overlap and less complementarity. These results may have crucial consequences for our understanding of herbivorous processes on

  16. Dynamics of energy systems: Methods of analysing technology change

    Energy Technology Data Exchange (ETDEWEB)

    Neij, Lena

    1999-05-01

    Technology change will have a central role in achieving a sustainable energy system. This calls for methods of analysing the dynamics of energy systems in view of technology change and policy instruments for effecting and accelerating technology change. In this thesis, such methods have been developed, applied, and assessed. Two types of methods have been considered, methods of analysing and projecting the dynamics of future technology change and methods of evaluating policy instruments effecting technology change, i.e. market transformation programmes. Two methods are focused on analysing the dynamics of future technology change; vintage models and experience curves. Vintage models, which allow for complex analysis of annual streams of energy and technological investments, are applied to the analysis of the time dynamics of electricity demand for lighting and air-distribution in Sweden. The results of the analyses show that the Swedish electricity demand for these purposes could decrease over time, relative to a reference scenario, if policy instruments are used. Experience curves are used to provide insight into the prospects of diffusion of wind turbines and photo voltaic (PV) modules due to cost reduction. The results show potential for considerable cost reduction for wind-generated electricity, which, in turn, could lead to major diffusion of wind turbines. The results also show that major diffusion of PV modules, and a reduction of PV generated electricity down to the level of conventional base-load electricity, will depend on large investments in bringing the costs down (through R D and D, market incentives and investments in niche markets) or the introduction of new generations of PV modules (e.g. high-efficiency mass-produced thin-film cells). Moreover, a model has been developed for the evaluation of market transformation programmes, i.e. policy instruments that effect technology change and the introduction and commercialisation of energy

  17. Methods for analysing cardiovascular studies with repeated measures

    NARCIS (Netherlands)

    Cleophas, T. J.; Zwinderman, A. H.; van Ouwerkerk, B. M.

    2009-01-01

    Background. Repeated measurements in a single subject are generally more similar than unrepeated measurements in different subjects. Unrepeated analyses of repeated data cause underestimation of the treatment effects. Objective. To review methods adequate for the analysis of cardiovascular studies

  18. Uncertainty Analyses for Back Projection Methods

    Science.gov (United States)

    Zeng, H.; Wei, S.; Wu, W.

    2017-12-01

    So far few comprehensive error analyses for back projection methods have been conducted, although it is evident that high frequency seismic waves can be easily affected by earthquake depth, focal mechanisms and the Earth's 3D structures. Here we perform 1D and 3D synthetic tests for two back projection methods, MUltiple SIgnal Classification (MUSIC) (Meng et al., 2011) and Compressive Sensing (CS) (Yao et al., 2011). We generate synthetics for both point sources and finite rupture sources with different depths, focal mechanisms, as well as 1D and 3D structures in the source region. The 3D synthetics are generated through a hybrid scheme of Direct Solution Method and Spectral Element Method. Then we back project the synthetic data using MUSIC and CS. The synthetic tests show that the depth phases can be back projected as artificial sources both in space and time. For instance, for a source depth of 10km, back projection gives a strong signal 8km away from the true source. Such bias increases with depth, e.g., the error of horizontal location could be larger than 20km for a depth of 40km. If the array is located around the nodal direction of direct P-waves the teleseismic P-waves are dominated by the depth phases. Therefore, back projections are actually imaging the reflection points of depth phases more than the rupture front. Besides depth phases, the strong and long lasted coda waves due to 3D effects near trench can lead to additional complexities tested here. The strength contrast of different frequency contents in the rupture models also produces some variations to the back projection results. In the synthetic tests, MUSIC and CS derive consistent results. While MUSIC is more computationally efficient, CS works better for sparse arrays. In summary, our analyses indicate that the impact of various factors mentioned above should be taken into consideration when interpreting back projection images, before we can use them to infer the earthquake rupture physics.

  19. Special analyses reveal coke-deposit structure

    International Nuclear Information System (INIS)

    Albright, L.F.

    1988-01-01

    A scanning electron microscope (SEM) and an energy dispersive X-ray analyzer (EDAX) have been used to obtain information that clarifies the three mechanisms of coke formation in ethylene furnaces, and to analyze the metal condition at the exit of furnace. The results can be used to examine furnace operations and develop improved ethylene plant practices. In this first of four articles on the analyses of coke and metal samples, the coking mechanisms and coke deposits in a section of tube from an actual ethylene furnace (Furnace A) from a plant on the Texas Gulf Coast are discussed. The second articles in the series will analyze the condition of the tube metal in the same furnace. To show how coke deposition and metal condition dependent on the operating parameters of an ethylene furnace, the third article in the series will show the coke deposition in a Texas Gulf Coast furnace tube (Furnace B) that operated at shorter residence time. The fourth article discusses the metal condition in that furnace. Some recommendations, based on the analyses and findings, are offered in the fourth article that could help extend the life of ethylene furnace tubes, and also improve overall ethylene plant operations

  20. Comparative analyses of genetic risk prediction methods reveal ...

    Indian Academy of Sciences (India)

    2015-03-12

    Mar 12, 2015 ... 1National Institute of Biomedical Genomics, Netaji Subhas Sanatorium (T. B. ... 2Institute of Post Graduate Medical Education and Research, J. C. Bose Road, ...... Torres D. M. and Harrison S. A 2008 Diagnosis and therapy of.

  1. Comparative analyses of genetic risk prediction methods reveal ...

    Indian Academy of Sciences (India)

    0.85. 0.8. 0.95. 0.93. 0.81 rs1227756. 0.5. 0.56. 0.75. 0.55. 0.7. 0.71. 0.58. 0.81. 0.25. 0.5. 0.53. 0.48. 0.64. 0.58. 0.58. 0.8. 0.68. 0.78. 0.48. 0.65. NA. NA. NA. NA rs1501299. 0.64. 0.78. 0.75. 0.83. 0.83. 0.89. 0.83. 0.72. 0.63. 0.73. 0.78. 0.75. 0.84. 0.79. 0.61. 0.78. 0.78. 0.7. 0.73. 0.73. NA. NA. NA. NA rs16944. 0.64. 0.72. 0.68.

  2. Genome-wide analyses reveal a role for peptide hormones in planarian germline development.

    Directory of Open Access Journals (Sweden)

    James J Collins

    Full Text Available Bioactive peptides (i.e., neuropeptides or peptide hormones represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites.

  3. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

    Science.gov (United States)

    Lai, Yiling; Liu, Keke; Zhang, Xinyu; Zhang, Xiaoling; Li, Kuan; Wang, Niuniu; Shu, Chi; Wu, Yunpeng; Wang, Chengshu; Bushley, Kathryn E.; Xiang, Meichun; Liu, Xingzhong

    2014-01-01

    Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. PMID:25359922

  4. Phylogeographic analyses of the pampas cat (Leopardus colocola; Carnivora, Felidae) reveal a complex demographic history

    Science.gov (United States)

    da Silva Santos, Anelisie; Trigo, Tatiane Campos; de Oliveira, Tadeu Gomes; Silveira, Leandro

    2018-01-01

    Abstract The pampas cat is a small felid that occurs in open habitats throughout much of South America. Previous studies have revealed intriguing patterns of morphological differentiation and genetic structure among its populations, as well as molecular evidence for hybridization with the closely related L. tigrinus. Here we report phylogeographic analyses encompassing most of its distribution (focusing particularly on Brazilian specimens, which had been poorly sampled in previous studies), using a novel dataset comprising 2,143 bp of the mitogenome, along with previously reported mtDNA sequences. Our data revealed strong population strutucture and supported a west-to-east colonization process in this species’ history. We detected two population expansion events, one older (ca. 200 thousand years ago [kya]) in western South America and another more recent (ca. 60-50 kya) in eastern areas, coinciding with the expansion of savanna environments in Brazil. Analyses including L. tigrinus individuals bearing introgressed mtDNA from L. colocola showed a complete lack of shared haplotypes between species, indicating that their hybridization was ancient. Finally, we observed a close relationship between Brazilian/Uruguayan L. colocola haplotypes and those sampled in L. tigrinus, indicating that their hybridization was likely related to the demographic expansion of L. colocola into eastern South America. PMID:29668017

  5. The 'revealed preferences' theory: Assumptions and conjectures

    International Nuclear Information System (INIS)

    Green, C.H.

    1983-01-01

    Being kind of intuitive psychology the 'Revealed-Preferences'- theory based approaches towards determining the acceptable risks are a useful method for the generation of hypotheses. In view of the fact that reliability engineering develops faster than methods for the determination of reliability aims the Revealed-Preferences approach is a necessary preliminary help. Some of the assumptions on which the 'Revealed-Preferences' theory is based will be identified and analysed and afterwards compared with experimentally obtained results. (orig./DG) [de

  6. A Methodology for Conducting Integrative Mixed Methods Research and Data Analyses

    Science.gov (United States)

    Castro, Felipe González; Kellison, Joshua G.; Boyd, Stephen J.; Kopak, Albert

    2011-01-01

    Mixed methods research has gained visibility within the last few years, although limitations persist regarding the scientific caliber of certain mixed methods research designs and methods. The need exists for rigorous mixed methods designs that integrate various data analytic procedures for a seamless transfer of evidence across qualitative and quantitative modalities. Such designs can offer the strength of confirmatory results drawn from quantitative multivariate analyses, along with “deep structure” explanatory descriptions as drawn from qualitative analyses. This article presents evidence generated from over a decade of pilot research in developing an integrative mixed methods methodology. It presents a conceptual framework and methodological and data analytic procedures for conducting mixed methods research studies, and it also presents illustrative examples from the authors' ongoing integrative mixed methods research studies. PMID:22167325

  7. Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members

    Science.gov (United States)

    Palmblad, Magnus; van Eck, Nees Jan

    2018-03-01

    We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or `hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics). [Figure not available: see fulltext.

  8. Fast and accurate methods for phylogenomic analyses

    Directory of Open Access Journals (Sweden)

    Warnow Tandy

    2011-10-01

    Full Text Available Abstract Background Species phylogenies are not estimated directly, but rather through phylogenetic analyses of different gene datasets. However, true gene trees can differ from the true species tree (and hence from one another due to biological processes such as horizontal gene transfer, incomplete lineage sorting, and gene duplication and loss, so that no single gene tree is a reliable estimate of the species tree. Several methods have been developed to estimate species trees from estimated gene trees, differing according to the specific algorithmic technique used and the biological model used to explain differences between species and gene trees. Relatively little is known about the relative performance of these methods. Results We report on a study evaluating several different methods for estimating species trees from sequence datasets, simulating sequence evolution under a complex model including indels (insertions and deletions, substitutions, and incomplete lineage sorting. The most important finding of our study is that some fast and simple methods are nearly as accurate as the most accurate methods, which employ sophisticated statistical methods and are computationally quite intensive. We also observe that methods that explicitly consider errors in the estimated gene trees produce more accurate trees than methods that assume the estimated gene trees are correct. Conclusions Our study shows that highly accurate estimations of species trees are achievable, even when gene trees differ from each other and from the species tree, and that these estimations can be obtained using fairly simple and computationally tractable methods.

  9. Mitochondrial DNA analyses reveal low genetic diversity in Culex quinquefasciatus from residential areas in Malaysia.

    Science.gov (United States)

    Low, V L; Lim, P E; Chen, C D; Lim, Y A L; Tan, T K; Norma-Rashid, Y; Lee, H L; Sofian-Azirun, M

    2014-06-01

    The present study explored the intraspecific genetic diversity, dispersal patterns and phylogeographic relationships of Culex quinquefasciatus Say (Diptera: Culicidae) in Malaysia using reference data available in GenBank in order to reveal this species' phylogenetic relationships. A statistical parsimony network of 70 taxa aligned as 624 characters of the cytochrome c oxidase subunit I (COI) gene and 685 characters of the cytochrome c oxidase subunit II (COII) gene revealed three haplotypes (A1-A3) and four haplotypes (B1-B4), respectively. The concatenated sequences of both COI and COII genes with a total of 1309 characters revealed seven haplotypes (AB1-AB7). Analysis using tcs indicated that haplotype AB1 was the common ancestor and the most widespread haplotype in Malaysia. The genetic distance based on concatenated sequences of both COI and COII genes ranged from 0.00076 to 0.00229. Sequence alignment of Cx. quinquefasciatus from Malaysia and other countries revealed four haplotypes (AA1-AA4) by the COI gene and nine haplotypes (BB1-BB9) by the COII gene. Phylogenetic analyses demonstrated that Malaysian Cx. quinquefasciatus share the same genetic lineage as East African and Asian Cx. quinquefasciatus. This study has inferred the genetic lineages, dispersal patterns and hypothetical ancestral genotypes of Cx. quinquefasciatus. © 2013 The Royal Entomological Society.

  10. Methodical treatment of dependent failures in risk analyses

    International Nuclear Information System (INIS)

    Hennings, W.; Mertens, J.

    1987-06-01

    In this report the state-of-the-art regarding dependent failures is compiled and commented on. Among others the following recommendations are infered: The term 'common mode failures' should be restricted to failures of redundant, similar components; the generic term is 'dependent failures' with the subsets 'causal failures' and 'common cause failures'. In risk studies, dependent failures should be covered as far as possible by 'explicit methods'. Nevertheless an uncovered rest remains, which should be accounted for by sensitivity analyses using 'implicit methods'. For this the homogeneous Marshall-Olkin model is recommended. Because the available reports on operating experiences only record 'common mode failures' systematically, it is recommended to additionally apply other methods, e.g. carry out a 'precursor study'. (orig.) [de

  11. Fossil-based comparative analyses reveal ancient marine ancestry erased by extinction in ray-finned fishes.

    Science.gov (United States)

    Betancur-R, Ricardo; Ortí, Guillermo; Pyron, Robert Alexander

    2015-05-01

    The marine-freshwater boundary is a major biodiversity gradient and few groups have colonised both systems successfully. Fishes have transitioned between habitats repeatedly, diversifying in rivers, lakes and oceans over evolutionary time. However, their history of habitat colonisation and diversification is unclear based on available fossil and phylogenetic data. We estimate ancestral habitats and diversification and transition rates using a large-scale phylogeny of extant fish taxa and one containing a massive number of extinct species. Extant-only phylogenetic analyses indicate freshwater ancestry, but inclusion of fossils reveal strong evidence of marine ancestry in lineages now restricted to freshwaters. Diversification and colonisation dynamics vary asymmetrically between habitats, as marine lineages colonise and flourish in rivers more frequently than the reverse. Our study highlights the importance of including fossils in comparative analyses, showing that freshwaters have played a role as refuges for ancient fish lineages, a signal erased by extinction in extant-only phylogenies. © 2015 John Wiley & Sons Ltd/CNRS.

  12. APPLYING SPECTROSCOPIC METHODS ON ANALYSES OF HAZARDOUS WASTE

    OpenAIRE

    Dobrinić, Julijan; Kunić, Marija; Ciganj, Zlatko

    2000-01-01

    Abstract The paper presents results of measuring the content of heavy and other metals in waste samples from the hazardous waste disposal site of Sovjak near Rijeka. The preliminary design elaboration and the choice of the waste disposal sanification technology were preceded by the sampling and physico-chemical analyses of disposed waste, enabling its categorization. The following spectroscopic methods were applied on metal content analysis: Atomic absorption spectroscopy (AAS) and plas...

  13. The intervals method: a new approach to analyse finite element outputs using multivariate statistics

    Directory of Open Access Journals (Sweden)

    Jordi Marcé-Nogué

    2017-10-01

    Full Text Available Background In this paper, we propose a new method, named the intervals’ method, to analyse data from finite element models in a comparative multivariate framework. As a case study, several armadillo mandibles are analysed, showing that the proposed method is useful to distinguish and characterise biomechanical differences related to diet/ecomorphology. Methods The intervals’ method consists of generating a set of variables, each one defined by an interval of stress values. Each variable is expressed as a percentage of the area of the mandible occupied by those stress values. Afterwards these newly generated variables can be analysed using multivariate methods. Results Applying this novel method to the biological case study of whether armadillo mandibles differ according to dietary groups, we show that the intervals’ method is a powerful tool to characterize biomechanical performance and how this relates to different diets. This allows us to positively discriminate between specialist and generalist species. Discussion We show that the proposed approach is a useful methodology not affected by the characteristics of the finite element mesh. Additionally, the positive discriminating results obtained when analysing a difficult case study suggest that the proposed method could be a very useful tool for comparative studies in finite element analysis using multivariate statistical approaches.

  14. The intervals method: a new approach to analyse finite element outputs using multivariate statistics

    Science.gov (United States)

    De Esteban-Trivigno, Soledad; Püschel, Thomas A.; Fortuny, Josep

    2017-01-01

    Background In this paper, we propose a new method, named the intervals’ method, to analyse data from finite element models in a comparative multivariate framework. As a case study, several armadillo mandibles are analysed, showing that the proposed method is useful to distinguish and characterise biomechanical differences related to diet/ecomorphology. Methods The intervals’ method consists of generating a set of variables, each one defined by an interval of stress values. Each variable is expressed as a percentage of the area of the mandible occupied by those stress values. Afterwards these newly generated variables can be analysed using multivariate methods. Results Applying this novel method to the biological case study of whether armadillo mandibles differ according to dietary groups, we show that the intervals’ method is a powerful tool to characterize biomechanical performance and how this relates to different diets. This allows us to positively discriminate between specialist and generalist species. Discussion We show that the proposed approach is a useful methodology not affected by the characteristics of the finite element mesh. Additionally, the positive discriminating results obtained when analysing a difficult case study suggest that the proposed method could be a very useful tool for comparative studies in finite element analysis using multivariate statistical approaches. PMID:29043107

  15. Revealing climate modes in steric sea levels: lessons learned from satellite geodesy, objective analyses and ocean reanalyses

    Science.gov (United States)

    Pfeffer, J.; Tregoning, P.; Purcell, A. P.

    2017-12-01

    Due to increased greenhouse gases emissions, the oceans are accumulating heat. In response to the ocean circulation and atmospheric forcing, the heat is irregularly redistributed within the oceans, causing sea level to rise at variable rates in space and time. These rates of steric expansion are extremely difficult to assess because of the sparsity of in-situ hydrographic observations available within the course of the 20th century. We compare here three methods to reconstruct the steric sea levels over the past 13, 25 and 58 years based on satellite geodesy, objective analyses and ocean reanalyses. The interannual to decadal variability of each dataset is explored with a model merging six climate indices representative of the natural variability of the ocean and climate system. Consistent regional patterns are identified for the Pacific Decadal Oscillation (PDO) and El Niño Southern Oscillation (ENSO) in all datasets at all timescales. Despite the short time coverage (13 years), the combination of satellite geodetic data (altimetry and GRACE) also reveals significant steric responses to the North Pacific Gyre Oscillation (NPGO), Indian Dipole (IOD) and Indian ocean basinwide (IOBM) mode. The richer information content in the ocean reanalyses allows us to recover the regional fingerprints of the PDO, ENSO, NPGO, IOD and IOBM, but also of the Atlantic Multidecadal Oscillation (AMO) acting over longer time scales (40 to 60 years). Therefore, ocean reanalyses, coupled with climate mode analyses, constitute innovative and promising tools to investigate the mechanisms triggering the variability of sea level rise over the past decades.

  16. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

    Directory of Open Access Journals (Sweden)

    Tod W Reeder

    Full Text Available Squamate reptiles (lizards and snakes are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa. Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia. These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses without considering the possible impact of molecular data on their placement.

  17. Integrated analyses resolve conflicts over squamate reptile phylogeny and reveal unexpected placements for fossil taxa.

    Science.gov (United States)

    Reeder, Tod W; Townsend, Ted M; Mulcahy, Daniel G; Noonan, Brice P; Wood, Perry L; Sites, Jack W; Wiens, John J

    2015-01-01

    Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.

  18. Integrated Analyses Resolve Conflicts over Squamate Reptile Phylogeny and Reveal Unexpected Placements for Fossil Taxa

    Science.gov (United States)

    Reeder, Tod W.; Townsend, Ted M.; Mulcahy, Daniel G.; Noonan, Brice P.; Wood, Perry L.; Sites, Jack W.; Wiens, John J.

    2015-01-01

    Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phylogeny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement. PMID:25803280

  19. Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

    Directory of Open Access Journals (Sweden)

    Maris Hindrikson

    Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

  20. Comparative proteomic analyses reveal that FlbA down-regulates gliT expression and SOD activity in Aspergillus fumigatus.

    Science.gov (United States)

    Shin, Kwang-Soo; Park, Hee-Soo; Kim, Young-Hwan; Yu, Jae-Hyuk

    2013-07-11

    FlbA is a regulator of G-protein signaling protein that plays a central role in attenuating heterotrimeric G-protein mediated vegetative growth signaling in Aspergillus. The deletion of flbA (∆flbA) in the opportunistic human pathogen Aspergillus fumigatus results in accelerated cell death and autolysis in submerged culture. To further investigate the effects of ∆flbA on intracellular protein levels we carried out 2-D proteome analyses of 2-day old submerged cultures of ∆flbA and wild type (WT) strains and observed 160 differentially expressed proteins. Via nano-LC-ESI-MS/MS analyses, we revealed the identity of 10 and 2 proteins exhibiting high and low level accumulation, respectively, in ∆flbA strain. Notably, the GliT protein is accumulated at about 1800-fold higher levels in ∆flbA than WT. Moreover, GliT is secreted at high levels from ∆flbA strain, whereas Sod1 (superoxide dismutase) is secreted at a higher level in WT. Northern blot analyses reveal that ∆flbA results in elevated accumulation of gliT mRNA. Consequently, ∆flbA strain exhibits enhanced tolerance to gliotoxin toxicity. Finally, ∆flbA strain displayed enhanced SOD activity and elevated resistance to menadione and paraquat. In summary, FlbA-mediated signaling control negatively affects cellular responses associated with detoxification of reactive oxygen species and of exogenous gliotoxin in A. fumigatus. Regulator of G protein Signaling (RGS) proteins play crucial roles in fundamental biological processes in filamentous fungi. FlbA is the first studied filamentous fungal RGS protein, yet much remains to be understood about its roles in the opportunistic human pathogen Aspergillus fumigatus. In the present study, we examined the effects of the deletion of flbA using comprehensive analyses of the intra- and extracellular proteomes of A. fumigatus wild type and the flbA deletion mutant. Via MS analyses, we identified 10 proteins exhibiting high level accumulation in the flbA deletion

  1. Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Shan Goh

    Full Text Available BACKGROUND: Genes essential for bacterial growth are of particular scientific interest. Many putative essential genes have been identified or predicted in several species, however, little is known about gene expression requirement stringency, which may be an important aspect of bacterial physiology and likely a determining factor in drug target development. METHODOLOGY/PRINCIPAL FINDINGS: Working from the premise that essential genes differ in absolute requirement for growth, we describe silencing of putative essential genes in E. coli to obtain a titration of declining growth rates and transcript levels by using antisense peptide nucleic acids (PNA and expressed antisense RNA. The relationship between mRNA decline and growth rate decline reflects the degree of essentiality, or stringency, of an essential gene, which is here defined by the minimum transcript level for a 50% reduction in growth rate (MTL(50. When applied to four growth essential genes, both RNA silencing methods resulted in MTL(50 values that reveal acpP as the most stringently required of the four genes examined, with ftsZ the next most stringently required. The established antibacterial targets murA and fabI were less stringently required. CONCLUSIONS: RNA silencing can reveal stringent requirements for gene expression with respect to growth. This method may be used to validate existing essential genes and to quantify drug target requirement.

  2. Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation.

    Directory of Open Access Journals (Sweden)

    Stéphane Uroz

    Full Text Available In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France. The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource

  3. Molecular analyses reveal high species diversity of trematodes in a sub-Arctic lake

    Science.gov (United States)

    Soldánová, Miroslava; Georgieva, Simona; Roháčováa, Jana; Knudsen, Rune; Kuhn, Jesper A.; Henriksen, Eirik H.; Siwertsson, Anna; Shaw, Jenny C.; Kuris, Armand M.; Amundsen, Per-Arne; Scholz, Tomáš; Lafferty, Kevin D.; Kostadinova, Aneta

    2017-01-01

    To identify trematode diversity and life-cycles in the sub-Arctic Lake Takvatn, Norway, we characterised 120 trematode isolates from mollusc first intermediate hosts, metacercariae from second intermediate host fishes and invertebrates, and adults from fish and invertebrate definitive hosts, using molecular techniques. Phylogenies based on nuclear and/or mtDNA revealed high species richness (24 species or species-level genetic lineages), and uncovered trematode diversity (16 putative new species) from five families typical in lake ecosystems (Allocreadiidae, Diplostomidae, Plagiorchiidae, Schistosomatidae and Strigeidae). Sampling potential invertebrate hosts allowed matching of sequence data for different stages, thus achieving molecular elucidation of trematode life-cycles and exploration of host-parasite interactions. Phylogenetic analyses also helped identify three major mollusc intermediate hosts (Radix balthica, Pisidium casertanum and Sphaerium sp.) in the lake. Our findings increase the known trematode diversity at the sub-Arctic Lake Takvatn, showing that digenean diversity is high in this otherwise depauperate sub-Arctic freshwater ecosystem, and indicating that sub-Arctic and Arctic ecosystems may be characterised by unique trematode assemblages.

  4. Genetic Diversity among Rhizobium leguminosarum bv. Trifolii Strains Revealed by Allozyme and Restriction Fragment Length Polymorphism Analyses

    Science.gov (United States)

    Demezas, David H.; Reardon, Terry B.; Watson, John M.; Gibson, Alan H.

    1991-01-01

    Allozyme electrophoresis and restriction fragment length polymorphism (RFLP) analyses were used to examine the genetic diversity of a collection of 18 Rhizobium leguminosarum bv. trifolii, 1 R. leguminosarum bv. viciae, and 2 R. meliloti strains. Allozyme analysis at 28 loci revealed 16 electrophoretic types. The mean genetic distance between electrophoretic types of R. leguminosarum and R. meliloti was 0.83. Within R. leguminosarum, the single strain of bv. viciae differed at an average of 0.65 from strains of bv. trifolii, while electrophoretic types of bv. trifolii differed at a range of 0.23 to 0.62. Analysis of RFLPs around two chromosomal DNA probes also delineated 16 unique RFLP patterns and yielded genetic diversity similar to that revealed by the allozyme data. Analysis of RFLPs around three Sym (symbiotic) plasmid-derived probes demonstrated that the Sym plasmids reflect genetic divergence similar to that of their bacterial hosts. The large genetic distances between many strains precluded reliable estimates of their genetic relationships. PMID:16348600

  5. Personality psychology: lexical approaches, assessment methods, and trait concepts reveal only half of the story--why it is time for a paradigm shift.

    Science.gov (United States)

    Uher, Jana

    2013-03-01

    This article develops a comprehensive philosophy-of-science for personality psychology that goes far beyond the scope of the lexical approaches, assessment methods, and trait concepts that currently prevail. One of the field's most important guiding scientific assumptions, the lexical hypothesis, is analysed from meta-theoretical viewpoints to reveal that it explicitly describes two sets of phenomena that must be clearly differentiated: 1) lexical repertoires and the representations that they encode and 2) the kinds of phenomena that are represented. Thus far, personality psychologists largely explored only the former, but have seriously neglected studying the latter. Meta-theoretical analyses of these different kinds of phenomena and their distinct natures, commonalities, differences, and interrelations reveal that personality psychology's focus on lexical approaches, assessment methods, and trait concepts entails a) erroneous meta-theoretical assumptions about what the phenomena being studied actually are, and thus how they can be analysed and interpreted, b) that contemporary personality psychology is largely based on everyday psychological knowledge, and c) a fundamental circularity in the scientific explanations used in trait psychology. These findings seriously challenge the widespread assumptions about the causal and universal status of the phenomena described by prominent personality models. The current state of knowledge about the lexical hypothesis is reviewed, and implications for personality psychology are discussed. Ten desiderata for future research are outlined to overcome the current paradigmatic fixations that are substantially hampering intellectual innovation and progress in the field.

  6. Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes.

    Science.gov (United States)

    Ball, Robyn L; Fujiwara, Yasuhiro; Sun, Fengyun; Hu, Jianjun; Hibbs, Matthew A; Handel, Mary Ann; Carter, Gregory W

    2016-08-12

    The continuous and non-synchronous nature of postnatal male germ-cell development has impeded stage-specific resolution of molecular events of mammalian meiotic prophase in the testis. Here the juvenile onset of spermatogenesis in mice is analyzed by combining cytological and transcriptomic data in a novel computational analysis that allows decomposition of the transcriptional programs of spermatogonia and meiotic prophase substages. Germ cells from testes of individual mice were obtained at two-day intervals from 8 to 18 days post-partum (dpp), prepared as surface-spread chromatin and immunolabeled for meiotic stage-specific protein markers (STRA8, SYCP3, phosphorylated H2AFX, and HISTH1T). Eight stages were discriminated cytologically by combinatorial antibody labeling, and RNA-seq was performed on the same samples. Independent principal component analyses of cytological and transcriptomic data yielded similar patterns for both data types, providing strong evidence for substage-specific gene expression signatures. A novel permutation-based maximum covariance analysis (PMCA) was developed to map co-expressed transcripts to one or more of the eight meiotic prophase substages, thereby linking distinct molecular programs to cytologically defined cell states. Expression of meiosis-specific genes is not substage-limited, suggesting regulation of substage transitions at other levels. This integrated analysis provides a general method for resolving complex cell populations. Here it revealed not only features of meiotic substage-specific gene expression, but also a network of substage-specific transcription factors and relationships to potential target genes.

  7. A method for reducing memory errors in the isotopic analyses of uranium hexafluoride by mass spectrometry; Methode de reduction des erreurs de memoire dans les analyses isotopiques de l'hexafluorure d'uranium par spectrometrie de masse

    Energy Technology Data Exchange (ETDEWEB)

    Bir, R [Commissariat a l' Energie Atomique, Saclay (France).Centre d' Etudes Nucleaires

    1961-07-01

    One of the most serious causes of systematic error in isotopic analyses of uranium from UF{sub 6} is the tendency of this material to become fixed in various ways in the mass spectrometer. As a result the value indicated by the instrument is influenced by the isotopic composition of the substances previously analysed. The resulting error is called a memory error. Making use of an elementary mathematical theory, the various methods used to reduce memory errors are analysed and compared. A new method is then suggested, which reduces the memory errors to an extent where they become negligible over a wide range of {sup 235}U concentration. The method is given in full, together with examples of its application. (author) [French] Une des causes d'erreurs systematiques les plus graves dans les analyses isotopiques d'uranium a partir d'UF{sub 6} est l'aptitude de ce produit a se fixer de diverses manieres dans le spectrometre de masse. Il en resulte une influence de la composition isotopique des produits precedemment analyses sur la valeur indiquee par l'appareil. L'erreur resultante est appelee erreur de memoire. A partir d'une theorie mathematique elementaire, on analyse et on compare les differentes methodes utilisees pour reduire les erreurs de memoire. On suggere ensuite une nouvelle methode qui reduit les erreurs de memoire dans une proportion telle qu'elles deviennent negligeables dans un grand domaine de concentration en {sup 235}U. On donne le mode operatoire complet et des exemples d'application. (auteur)

  8. Performing dynamic time history analyses by extension of the response spectrum method

    International Nuclear Information System (INIS)

    Hulbert, G.M.

    1983-01-01

    A method is presented to calculate the dynamic time history response of finite-element models using results from response spectrum analyses. The proposed modified time history method does not represent a new mathamatical approach to dynamic analysis but suggests a more efficient ordering of the analytical equations and procedures. The modified time history method is considerably faster and less expensive to use than normal time hisory methods. This paper presents the theory and implementation of the modified time history approach along with comparisons of the modified and normal time history methods for a prototypic seismic piping design problem

  9. Physical analytical methods for uranium hexafluoride; Methodes physiques d'analyse de l'hexafluorure d'uranium

    Energy Technology Data Exchange (ETDEWEB)

    Vandenbussche, G [Commissariat a l' Energie Atomique, Fontenay-aux-Roses (France). Centre d' Etudes Nucleaires

    1965-12-15

    Various physical methods of analysis currently used or still under investigation such as: sound analysis, vapor pressure measurements, fractional distillation, cryogenics, micro-sublimation, ultra-violet, visible and infra-red absorption spectrophotometry, nuclear magnetic resonance and mass spectrometry are reviewed. For each method, principle and applications are given, and results obtained concerning reproducibility, application limits and rapidity are discussed. (author) [French] On passe en revue les differentes methodes physiques d'analyse utilisees ou en cours d'etude actuellement: par mesure de la vitesse du son, de la pression de vapeur, par distillation fractionnee, cryometrie, microsublimation, spectrometrie d'absorption dans l'ultraviolet, le visible et l'infrarouge, par resonance magnetique nucleaire et par spectrometrie de masse. Pour chaque methode, on donne le principe et son application et on examine les resultats obtenus concernant la reproductibilite, le domaine d'application et la duree des mesures. (auteur)

  10. Statistical parameters of random heterogeneity estimated by analysing coda waves based on finite difference method

    Science.gov (United States)

    Emoto, K.; Saito, T.; Shiomi, K.

    2017-12-01

    Short-period (2 s) seismograms. We found that the energy of the coda of long-period seismograms shows a spatially flat distribution. This phenomenon is well known in short-period seismograms and results from the scattering by small-scale heterogeneities. We estimate the statistical parameters that characterize the small-scale random heterogeneity by modelling the spatiotemporal energy distribution of long-period seismograms. We analyse three moderate-size earthquakes that occurred in southwest Japan. We calculate the spatial distribution of the energy density recorded by a dense seismograph network in Japan at the period bands of 8-16 s, 4-8 s and 2-4 s and model them by using 3-D finite difference (FD) simulations. Compared to conventional methods based on statistical theories, we can calculate more realistic synthetics by using the FD simulation. It is not necessary to assume a uniform background velocity, body or surface waves and scattering properties considered in general scattering theories. By taking the ratio of the energy of the coda area to that of the entire area, we can separately estimate the scattering and the intrinsic absorption effects. Our result reveals the spectrum of the random inhomogeneity in a wide wavenumber range including the intensity around the corner wavenumber as P(m) = 8πε2a3/(1 + a2m2)2, where ε = 0.05 and a = 3.1 km, even though past studies analysing higher-frequency records could not detect the corner. Finally, we estimate the intrinsic attenuation by modelling the decay rate of the energy. The method proposed in this study is suitable for quantifying the statistical properties of long-wavelength subsurface random inhomogeneity, which leads the way to characterizing a wider wavenumber range of spectra, including the corner wavenumber.

  11. Partial differential equation techniques for analysing animal movement: A comparison of different methods.

    Science.gov (United States)

    Wang, Yi-Shan; Potts, Jonathan R

    2017-03-07

    Recent advances in animal tracking have allowed us to uncover the drivers of movement in unprecedented detail. This has enabled modellers to construct ever more realistic models of animal movement, which aid in uncovering detailed patterns of space use in animal populations. Partial differential equations (PDEs) provide a popular tool for mathematically analysing such models. However, their construction often relies on simplifying assumptions which may greatly affect the model outcomes. Here, we analyse the effect of various PDE approximations on the analysis of some simple movement models, including a biased random walk, central-place foraging processes and movement in heterogeneous landscapes. Perhaps the most commonly-used PDE method dates back to a seminal paper of Patlak from 1953. However, our results show that this can be a very poor approximation in even quite simple models. On the other hand, more recent methods, based on transport equation formalisms, can provide more accurate results, as long as the kernel describing the animal's movement is sufficiently smooth. When the movement kernel is not smooth, we show that both the older and newer methods can lead to quantitatively misleading results. Our detailed analysis will aid future researchers in the appropriate choice of PDE approximation for analysing models of animal movement. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Comparative analyses reveal different consequences of two oxidative stress inducers, gamma irradiation and potassium tellurite, in the extremophile Deinococcus radiodurans

    International Nuclear Information System (INIS)

    Narasimha, Anaganti; Basu, Bhakti; Apte, Shree Kumar

    2014-01-01

    Proteomic and mass spectrometric analyses revealed differential responses of D. radiodurans to two oxidative stressors. While both elicited oxidative stress alleviation response, major divergence was observed at the level of DNA repair, metabolic pathways and protein homeostasis. Response to gamma irradiation was focused on DNA repair and ROS scavenging but supported metabolism as well as protein homeostasis. Tellurite, induced oxidative stress alleviation but decreased reducing affected and adversely affected metabolism and protein homeostasis

  13. Forward-Weighted CADIS Method for Variance Reduction of Monte Carlo Reactor Analyses

    International Nuclear Information System (INIS)

    Wagner, John C.; Mosher, Scott W.

    2010-01-01

    Current state-of-the-art tools and methods used to perform 'real' commercial reactor analyses use high-fidelity transport codes to produce few-group parameters at the assembly level for use in low-order methods applied at the core level. Monte Carlo (MC) methods, which allow detailed and accurate modeling of the full geometry and energy details and are considered the 'gold standard' for radiation transport solutions, are playing an ever-increasing role in correcting and/or verifying the several-decade-old methodology used in current practice. However, the prohibitive computational requirements associated with obtaining fully converged system-wide solutions restrict the role of MC to benchmarking deterministic results at a limited number of state-points for a limited number of relevant quantities. A goal of current research at Oak Ridge National Laboratory (ORNL) is to change this paradigm by enabling the direct use of MC for full-core reactor analyses. The most significant of the many technical challenges that must be overcome is the slow non-uniform convergence of system-wide MC estimates and the memory requirements associated with detailed solutions throughout a reactor (problems involving hundreds of millions of different material and tally regions due to fuel irradiation, temperature distributions, and the needs associated with multi-physics code coupling). To address these challenges, research has focused on development in the following two areas: (1) a hybrid deterministic/MC method for determining high-precision fluxes throughout the problem space in k-eigenvalue problems and (2) an efficient MC domain-decomposition algorithm that partitions the problem phase space onto multiple processors for massively parallel systems, with statistical uncertainty estimation. The focus of this paper is limited to the first area mentioned above. It describes the FW-CADIS method applied to variance reduction of MC reactor analyses and provides initial results for calculating

  14. Application of the Random Forest method to analyse epidemiological and phenotypic characteristics of Salmonella 4,[5],12:i:- and Salmonella Typhimurium strains

    DEFF Research Database (Denmark)

    Barco, L.; Mancin, M.; Ruffa, M.

    2012-01-01

    in Italy, particularly as far as veterinary isolates are concerned. For this reason, a data set of 877 strains isolated in the north-east of Italy from foodstuffs, animals and environment was analysed during 2005-2010. The Random Forests (RF) method was used to identify the most important epidemiological...... and phenotypic variables to show the difference between the two serovars. Both descriptive analysis and RF revealed that S. 4,[5],12:i:- is less heterogeneous than S. Typhimurium. RF highlighted that phage type was the most important variable to differentiate the two serovars. The most common phage types...

  15. Global terrestrial water storage connectivity revealed using complex climate network analyses

    Science.gov (United States)

    Sun, A. Y.; Chen, J.; Donges, J.

    2015-07-01

    Terrestrial water storage (TWS) exerts a key control in global water, energy, and biogeochemical cycles. Although certain causal relationship exists between precipitation and TWS, the latter quantity also reflects impacts of anthropogenic activities. Thus, quantification of the spatial patterns of TWS will not only help to understand feedbacks between climate dynamics and the hydrologic cycle, but also provide new insights and model calibration constraints for improving the current land surface models. This work is the first attempt to quantify the spatial connectivity of TWS using the complex network theory, which has received broad attention in the climate modeling community in recent years. Complex networks of TWS anomalies are built using two global TWS data sets, a remote sensing product that is obtained from the Gravity Recovery and Climate Experiment (GRACE) satellite mission, and a model-generated data set from the global land data assimilation system's NOAH model (GLDAS-NOAH). Both data sets have 1° × 1° grid resolutions and cover most global land areas except for permafrost regions. TWS networks are built by first quantifying pairwise correlation among all valid TWS anomaly time series, and then applying a cutoff threshold derived from the edge-density function to retain only the most important features in the network. Basinwise network connectivity maps are used to illuminate connectivity of individual river basins with other regions. The constructed network degree centrality maps show the TWS anomaly hotspots around the globe and the patterns are consistent with recent GRACE studies. Parallel analyses of networks constructed using the two data sets reveal that the GLDAS-NOAH model captures many of the spatial patterns shown by GRACE, although significant discrepancies exist in some regions. Thus, our results provide further measures for constraining the current land surface models, especially in data sparse regions.

  16. Revisit of analytical methods for the process and plant control analyses during reprocessing of fast reactor fuels

    International Nuclear Information System (INIS)

    Subba Rao, R.V.

    2016-01-01

    CORAL (COmpact facility for Reprocessing of Advanced fuels in Lead cell) is an experimental facility for demonstrating the reprocessing of irradiated fast reactor fuels discharged from the Fast Breeder Test Reactor (FBTR). The objective of the reprocessing plant is to achieve nuclear grade plutonium and uranium oxides with minimum process waste volumes. The process flow sheet for the reprocessing of spent Fast Reactor Fuel consists of Transport of spent fuel, Chopping, Dissolution, Feed conditioning, Solvent Extraction cycle, Partitioning Cycle and Re-conversion of Plutonium nitrate and uranium nitrate to respective oxides. The efficiency and performance of the plant to achieve desired objective depends on the analyses of various species in the different steps adopted during reprocessing of fuels. The analytical requirements in the plant can be broadly classified as 1. Process control Analyses (Analyses which effect the performance of the plant- PCA); 2. Plant control Analyses (Analyses which indicates efficiency of the plant-PLCA); 3. Nuclear Material Accounting samples (Analyses which has bearing on nuclear material accounting in the plant - NUMAC) and Quality control Analyses (Quality of the input bulk chemicals as well as products - QCA). The analytical methods selected are based on the duration of analyses, precision and accuracies required for each type analytical requirement classified earlier. The process and plant control analyses requires lower precision and accuracies as compared to NUMAC analyses, which requires very high precision accuracy. The time taken for analyses should be as lower as possible for process and plant control analyses as compared to NUMAC analyses. The analytical methods required for determining U and Pu in process and plant samples from FRFR will be different as compared to samples from TRFR (Thermal Reactor Fuel Reprocessing) due to higher Pu to U ratio in FRFR as compared TRFR and they should be such that they can be easily

  17. A Method to Reveal Fine-Grained and Diverse Conceptual Progressions during Learning

    Science.gov (United States)

    Lombard, François; Merminod, Marie; Widmer, Vincent; Schneider, Daniel K.

    2018-01-01

    Empirical data on learners' conceptual progression is required to design curricula and guide students. In this paper, we present the Reference Map Change Coding (RMCC) method for revealing students' progression at a fine-grained level. The method has been developed and tested through the analysis of successive versions of the productions of eight…

  18. Quantitative numerical method for analysing slip traces observed by AFM

    International Nuclear Information System (INIS)

    Veselý, J; Cieslar, M; Coupeau, C; Bonneville, J

    2013-01-01

    Atomic force microscopy (AFM) is used more and more routinely to study, at the nanometre scale, the slip traces produced on the surface of deformed crystalline materials. Taking full advantage of the quantitative height data of the slip traces, which can be extracted from these observations, requires however an adequate and robust processing of the images. In this paper an original method is presented, which allows the fitting of AFM scan-lines with a specific parameterized step function without any averaging treatment of the original data. This yields a quantitative and full description of the changes in step shape along the slip trace. The strength of the proposed method is established on several typical examples met in plasticity by analysing nano-scale structures formed on the sample surface by emerging dislocations. (paper)

  19. Statistical methods for analysing the relationship between bank profitability and liquidity

    OpenAIRE

    Boguslaw Guzik

    2006-01-01

    The article analyses the most popular methods for the empirical estimation of the relationship between bank profitability and liquidity. Owing to the fact that profitability depends on various factors (both economic and non-economic), a simple correlation coefficient, two-dimensional (profitability/liquidity) graphs or models where profitability depends only on liquidity variable do not provide good and reliable results. Quite good results can be obtained only when multifactorial profitabilit...

  20. International intercalibration as a method for control of radiochemical analyses

    International Nuclear Information System (INIS)

    Angelova, A.; Totseva, R.; Karaivanova, R.; Dandulova, Z.; Botsova, L.

    1994-01-01

    The participation of the Radioecology Section at the National Centre for Radiology and Radiation Protection (NCRRP) in the International Interlaboratory Comparison of radiochemical analyses organized by WHO is reported. The method of evaluating accuracy of the results from inter calibrations concerning radionuclide determination of environmental samples is outlined. The data from analysis of cesium 137, strontium 90 and radium 226 in milk, sediments, soil and seaweed made by 21 laboratories are presented. They show a good accuracy values of the results from NCRRP. 1 tab. 2 figs., 6 refs

  1. Validation of Method Performance of pH, PCO2, PO2, Na(+), K(+) of Cobas b121 ABG Analyser.

    Science.gov (United States)

    Nanda, Sunil Kumar; Ray, Lopamudra; Dinakaran, Asha

    2014-06-01

    The introduction of a new method or new analyser is a common occurrence in clinical biochemistry laboratory. Blood gas measurements and electrolytes are often performed in Point-of-Care (POC) settings. When a new POC analyser is obtained, the performance of the analyser should be evaluated by comparison to the measurements with the reference analyser in the laboratory. Evaluation of method performance of pH, PCO2, PO2, Na(+), K(+) of cobas b121 ABG analyser. The evaluation of method performance of pH, PO2, PCO2, Na(+), K(+) of cobas b121 ABG analyser was done by comparing the results of 50 patient samples run on cobas b121 with the results obtained from Rapid lab values (reference analyser). Correlation coefficient was calculated from the results obtained from both the analysers. Precision was calculated by running biorad ABG control samples. The correlation coefficient values obtained for parameters were close to 1.0 indicating good correlation. The CV obtained for all the parameters were less than 5 indicating good precision. The new ABG analyser, Cobas b121 correlated well with the reference ABG analyser (Rapid Lab) and could be used to run on patient samples.

  2. Conserved regulators of nucleolar size revealed by global phenotypic analyses.

    Science.gov (United States)

    Neumüller, Ralph A; Gross, Thomas; Samsonova, Anastasia A; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

    2013-08-20

    Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I-mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I-mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry-based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules.

  3. Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses

    Science.gov (United States)

    Neumüller, Ralph A.; Gross, Thomas; Samsonova, Anastasia A.; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P.; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

    2014-01-01

    Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I–mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I–mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry–based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules. PMID:23962978

  4. Mitochondrial dysfunction, oxidative stress and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson’s disease

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Mark H.; Qian, Weijun; Wang, Haixing; Petyuk, Vladislav A.; Bloom, Joshua S.; Sforza, Daniel M.; Lacan, Goran; Liu, Dahai; Khan, Arshad H.; Cantor, Rita M.; Bigelow, Diana J.; Melega, William P.; Camp, David G.; Smith, Richard D.; Smith, Desmond J.

    2008-02-10

    The molecular mechanisms underlying the changes in the nigrostriatal pathway in Parkinson disease (PD) are not completely understood. Here we use mass spectrometry and microarrays to study the proteomic and transcriptomic changes in the striatum of two mouse models of PD, induced by the distinct neurotoxins 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and methamphetamine (METH). Proteomic analyses resulted in the identification and relative quantification of 912 proteins with two or more unique peptides and 85 proteins with significant abundance changes following neurotoxin treatment. Similarly, microarray analyses revealed 181 genes with significant changes in mRNA following neurotoxin treatment. The combined protein and gene list provides a clearer picture of the potential mechanisms underlying neurodegeneration observed in PD. Functional analysis of this combined list revealed a number of significant categories, including mitochondrial dysfunction, oxidative stress response and apoptosis. Additionally, codon usage and miRNAs may play an important role in translational control in the striatum. These results constitute one of the largest datasets integrating protein and transcript changes for these neurotoxin models with many similar endpoint phenotypes but distinct mechanisms.

  5. A quantitative method to analyse an open answer questionnaire: A case study about the Boltzmann Factor

    International Nuclear Information System (INIS)

    Battaglia, Onofrio Rosario; Di Paola, Benedetto

    2015-01-01

    This paper describes a quantitative method to analyse an openended questionnaire. Student responses to a specially designed written questionnaire are quantitatively analysed by not hierarchical clustering called k-means method. Through this we can characterise behaviour students with respect their expertise to formulate explanations for phenomena or processes and/or use a given model in the different context. The physics topic is about the Boltzmann Factor, which allows the students to have a unifying view of different phenomena in different contexts.

  6. Analytical methods used by the geochemical section: water; Methodes d'analyses utilisees par la section de geochimie: les eaux

    Energy Technology Data Exchange (ETDEWEB)

    Berthollet, P; Cavalier, G [Commissariat a l' Energie Atomique, Fontenay-aux-Roses (France). Centre d' Etudes Nucleaires

    1971-07-01

    The authors describe the analytical methods used by the C.E.A. Geochemical Section to determine the chemical composition of natural waters encountered during the prospecting of uraniferous deposits or in the course of mining operations. Because of the diversity of the samples and the different items of information requested, methods were selected and adapted to answer to the demands peculiar to mining research. Methods and know-how concerning the quantitative analysis of natural water to find out the concentration of the following chemicals are reviewed: carbonates and bicarbonates, calcium, magnesium, chlorides, sodium and potassium, sulfates, nitrates, silica, phosphates, iron, manganese, aluminium, fluorides, dissolved oxygen, CO{sub 2}, SH{sub 2} and sulphur, and uranium. (authors) [French] Les auteurs decrivent les methodes d'analyses utilisees par la Section de Geochimie du C.E.A., pour la determination de la composition chimique des eaux naturelles rencontrees au cours de prospections de gites uraniferes ou de travaux miniers. La diversite des echantillons et les differents renseignements demandes a l'analyse les ont conduit a selectionner et a adapter des methodes afin qu'elles repondent aux exigences particulieres de la recherche miniere. Les methodes concernant le dosage dans les eaux superficielles et eaux souterraines des elements qui suivent sont presentees : carbonates and bicarbonates, calcium, magnesium, chlorures, sodium et potassium, sulfates, nitrates, silice, phosphates, fer ferreus et ferrique, manganese, aluminium, fluorures, oxygene dissous, CO{sub 2} libre, SH{sub 2} et soufre total, et uranium. (auteurs)

  7. A Fuzzy Logic Based Method for Analysing Test Results

    Directory of Open Access Journals (Sweden)

    Le Xuan Vinh

    2017-11-01

    Full Text Available Network operators must perform many tasks to ensure smooth operation of the network, such as planning, monitoring, etc. Among those tasks, regular testing of network performance, network errors and troubleshooting is very important. Meaningful test results will allow the operators to evaluate network performanceof any shortcomings and to better plan for network upgrade. Due to the diverse and mainly unquantifiable nature of network testing results, there is a needs to develop a method for systematically and rigorously analysing these results. In this paper, we present STAM (System Test-result Analysis Method which employs a bottom-up hierarchical processing approach using Fuzzy logic. STAM is capable of combining all test results into a quantitative description of the network performance in terms of network stability, the significance of various network erros, performance of each function blocks within the network. The validity of this method has been successfully demonstrated in assisting the testing of a VoIP system at the Research Instiute of Post and Telecoms in Vietnam. The paper is organized as follows. The first section gives an overview of fuzzy logic theory the concepts of which will be used in the development of STAM. The next section describes STAM. The last section, demonstrating STAM’s capability, presents a success story in which STAM is successfully applied.

  8. LITERATURE SEARCH FOR METHODS FOR HAZARD ANALYSES OF AIR CARRIER OPERATIONS.

    Energy Technology Data Exchange (ETDEWEB)

    MARTINEZ - GURIDI,G.; SAMANTA,P.

    2002-07-01

    Representatives of the Federal Aviation Administration (FAA) and several air carriers under Title 14 of the Code of Federal Regulations (CFR) Part 121 developed a system-engineering model of the functions of air-carrier operations. Their analyses form the foundation or basic architecture upon which other task areas are based: hazard analyses, performance measures, and risk indicator design. To carry out these other tasks, models may need to be developed using the basic architecture of the Air Carrier Operations System Model (ACOSM). Since ACOSM encompasses various areas of air-carrier operations and can be used to address different task areas with differing but interrelated objectives, the modeling needs are broad. A literature search was conducted to identify and analyze the existing models that may be applicable for pursuing the task areas in ACOSM. The intent of the literature search was not necessarily to identify a specific model that can be directly used, but rather to identify relevant ones that have similarities with the processes and activities defined within ACOSM. Such models may provide useful inputs and insights in structuring ACOSM models. ACOSM simulates processes and activities in air-carrier operation, but, in a general framework, it has similarities with other industries where attention also has been paid to hazard analyses, emphasizing risk management, and in designing risk indicators. To assure that efforts in other industries are adequately considered, the literature search includes publications from other industries, e.g., chemical, nuclear, and process industries. This report discusses the literature search, the relevant methods identified and provides a preliminary assessment of their use in developing the models needed for the ACOSM task areas. A detailed assessment of the models has not been made. Defining those applicable for ACOSM will need further analyses of both the models and tools identified. The report is organized in four chapters

  9. Advanced computational tools and methods for nuclear analyses of fusion technology systems

    International Nuclear Information System (INIS)

    Fischer, U.; Chen, Y.; Pereslavtsev, P.; Simakov, S.P.; Tsige-Tamirat, H.; Loughlin, M.; Perel, R.L.; Petrizzi, L.; Tautges, T.J.; Wilson, P.P.H.

    2005-01-01

    An overview is presented of advanced computational tools and methods developed recently for nuclear analyses of Fusion Technology systems such as the experimental device ITER ('International Thermonuclear Experimental Reactor') and the intense neutron source IFMIF ('International Fusion Material Irradiation Facility'). These include Monte Carlo based computational schemes for the calculation of three-dimensional shut-down dose rate distributions, methods, codes and interfaces for the use of CAD geometry models in Monte Carlo transport calculations, algorithms for Monte Carlo based sensitivity/uncertainty calculations, as well as computational techniques and data for IFMIF neutronics and activation calculations. (author)

  10. Structural analyses of Legionella LepB reveal a new GAP fold that catalytically mimics eukaryotic RasGAP.

    Science.gov (United States)

    Yu, Qin; Hu, Liyan; Yao, Qing; Zhu, Yongqun; Dong, Na; Wang, Da-Cheng; Shao, Feng

    2013-06-01

    Rab GTPases are emerging targets of diverse bacterial pathogens. Here, we perform biochemical and structural analyses of LepB, a Rab GTPase-activating protein (GAP) effector from Legionella pneumophila. We map LepB GAP domain to residues 313-618 and show that the GAP domain is Rab1 specific with a catalytic activity higher than the canonical eukaryotic TBC GAP and the newly identified VirA/EspG family of bacterial RabGAP effectors. Exhaustive mutation analyses identify Arg444 as the arginine finger, but no catalytically essential glutamine residues. Crystal structures of LepB313-618 alone and the GAP domain of Legionella drancourtii LepB in complex with Rab1-GDP-AlF3 support the catalytic role of Arg444, and also further reveal a 3D architecture and a GTPase-binding mode distinct from all known GAPs. Glu449, structurally equivalent to TBC RabGAP glutamine finger in apo-LepB, undergoes a drastic movement upon Rab1 binding, which induces Rab1 Gln70 side-chain flipping towards GDP-AlF3 through a strong ionic interaction. This conformationally rearranged Gln70 acts as the catalytic cis-glutamine, therefore uncovering an unexpected RasGAP-like catalytic mechanism for LepB. Our studies highlight an extraordinary structural and catalytic diversity of RabGAPs, particularly those from bacterial pathogens.

  11. Towards an Industrial Application of Statistical Uncertainty Analysis Methods to Multi-physical Modelling and Safety Analyses

    International Nuclear Information System (INIS)

    Zhang, Jinzhao; Segurado, Jacobo; Schneidesch, Christophe

    2013-01-01

    Since 1980's, Tractebel Engineering (TE) has being developed and applied a multi-physical modelling and safety analyses capability, based on a code package consisting of the best estimate 3D neutronic (PANTHER), system thermal hydraulic (RELAP5), core sub-channel thermal hydraulic (COBRA-3C), and fuel thermal mechanic (FRAPCON/FRAPTRAN) codes. A series of methodologies have been developed to perform and to license the reactor safety analysis and core reload design, based on the deterministic bounding approach. Following the recent trends in research and development as well as in industrial applications, TE has been working since 2010 towards the application of the statistical sensitivity and uncertainty analysis methods to the multi-physical modelling and licensing safety analyses. In this paper, the TE multi-physical modelling and safety analyses capability is first described, followed by the proposed TE best estimate plus statistical uncertainty analysis method (BESUAM). The chosen statistical sensitivity and uncertainty analysis methods (non-parametric order statistic method or bootstrap) and tool (DAKOTA) are then presented, followed by some preliminary results of their applications to FRAPCON/FRAPTRAN simulation of OECD RIA fuel rod codes benchmark and RELAP5/MOD3.3 simulation of THTF tests. (authors)

  12. Multiple spectroscopic analyses reveal the fate and metabolism of sulfamide herbicide triafamone in agricultural environments

    International Nuclear Information System (INIS)

    Wang, Mengcen; Qian, Yuan; Liu, Xiaoyu; Wei, Peng; Deng, Man; Wang, Lei; Wu, Huiming; Zhu, Guonian

    2017-01-01

    Triafamone, a sulfamide herbicide, has been extensively utilized for weed control in rice paddies in Asia. However, its fate and transformation in the environment have not been established. Through a rice paddy microcosm-based simulation trial combined with multiple spectroscopic analyses, we isolated and identified three novel metabolites of triafamone, including hydroxyl triafamone (HTA), hydroxyl triafamone glycoside (HTAG), and oxazolidinedione triafamone (OTA). When triafamone was applied to rice paddies at a concentration of 34.2 g active ingredient/ha, this was predominantly distributed in the paddy soil and water, and then rapidly dissipated in accordance with the first-order rate model, with half-lives of 4.3–11.0 days. As the main transformation pathway, triafamone was assimilated by the rice plants and was detoxified into HTAG, whereas the rest was reduced into HTA with subsequent formation of OTA. At the senescence stage, brown rice had incurred triafamone at a concentration of 0.0016 mg/kg, but the hazard quotient was <1, suggesting that long-term consumption of the triafamone-containing brown rice is relatively safe. The findings of the present study indicate that triafamone is actively metabolized in the agricultural environment, and elucidation of the link between environmental exposure to these triazine or oxazolidinedione moieties that contain metabolites and their potential impacts is warranted. - Highlights: • Multiple spectroscopic analyses were applied to investigate agrochemicals transformation in environment. • Three novel compounds were isolated and identified as triafamone metabolites. • The fate and transformation pathway of triafamone in rice paddy were revealed. • Long-term consumption of the triafamone-containing brown rice is relatively safe. • Elucidation of environmental impacts by exposure to these triazine or oxazolidinedione metabolites is warranted. - Triafamone rapidly dissipates in agricultural environments

  13. On stream radioisotope X-ray fluorescence analyser and a method for the determination of copper in slurry

    International Nuclear Information System (INIS)

    Holynska, B.; Lankosz, M.; Lacki, E.; Ostachowicz, J.; Baran, W.; Owsiak, T.

    1975-01-01

    The paper presents an ''on stream'' analyser and a radioisotope X-ray fluorescence method for the continuous determination of copper content in feed 0.5-2.5% Cu, concentrates 15-25% Cu and tailings 0.01-0.03% Cu. The analyser consists essentially of a radioisotope X-ray fluorescence measuring head, γ-density gauge, electronic unit, analog processor and recorders. The method is based on the measurement of the characteristic radiation of Cu series, selected by nickel-cobalt filters. The total relative error (1s) of the determination of copper in feed is 6-8%, in concentrates 5-7% and in tailings about 18%. The ''on stream'' analyser has been succesfully operated in a pilot plant. (author)

  14. Stress and deflection analyses of floating roofs based on a load-modifying method

    International Nuclear Information System (INIS)

    Sun Xiushan; Liu Yinghua; Wang Jianbin; Cen Zhangzhi

    2008-01-01

    This paper proposes a load-modifying method for the stress and deflection analyses of floating roofs used in cylindrical oil storage tanks. The formulations of loads and deformations are derived according to the equilibrium analysis of floating roofs. Based on these formulations, the load-modifying method is developed to conduct a geometrically nonlinear analysis of floating roofs with the finite element (FE) simulation. In the procedure with the load-modifying method, the analysis is carried out through a series of iterative computations until a convergence is achieved within the error tolerance. Numerical examples are given to demonstrate the validity and reliability of the proposed method, which provides an effective and practical numerical solution to the design and analysis of floating roofs

  15. The use of bootstrap methods for analysing health-related quality of life outcomes (particularly the SF-36

    Directory of Open Access Journals (Sweden)

    Campbell Michael J

    2004-12-01

    Full Text Available Abstract Health-Related Quality of Life (HRQoL measures are becoming increasingly used in clinical trials as primary outcome measures. Investigators are now asking statisticians for advice on how to analyse studies that have used HRQoL outcomes. HRQoL outcomes, like the SF-36, are usually measured on an ordinal scale. However, most investigators assume that there exists an underlying continuous latent variable that measures HRQoL, and that the actual measured outcomes (the ordered categories, reflect contiguous intervals along this continuum. The ordinal scaling of HRQoL measures means they tend to generate data that have discrete, bounded and skewed distributions. Thus, standard methods of analysis such as the t-test and linear regression that assume Normality and constant variance may not be appropriate. For this reason, conventional statistical advice would suggest that non-parametric methods be used to analyse HRQoL data. The bootstrap is one such computer intensive non-parametric method for analysing data. We used the bootstrap for hypothesis testing and the estimation of standard errors and confidence intervals for parameters, in four datasets (which illustrate the different aspects of study design. We then compared and contrasted the bootstrap with standard methods of analysing HRQoL outcomes. The standard methods included t-tests, linear regression, summary measures and General Linear Models. Overall, in the datasets we studied, using the SF-36 outcome, bootstrap methods produce results similar to conventional statistical methods. This is likely because the t-test and linear regression are robust to the violations of assumptions that HRQoL data are likely to cause (i.e. non-Normality. While particular to our datasets, these findings are likely to generalise to other HRQoL outcomes, which have discrete, bounded and skewed distributions. Future research with other HRQoL outcome measures, interventions and populations, is required to

  16. Revealing barriers and facilitators to use a new genetic test: comparison of three user involvement methods.

    Science.gov (United States)

    Rhebergen, Martijn D F; Visser, Maaike J; Verberk, Maarten M; Lenderink, Annet F; van Dijk, Frank J H; Kezic, Sanja; Hulshof, Carel T J

    2012-10-01

    We compared three common user involvement methods in revealing barriers and facilitators from intended users that might influence their use of a new genetic test. The study was part of the development of a new genetic test on the susceptibility to hand eczema for nurses. Eighty student nurses participated in five focus groups (n = 33), 15 interviews (n = 15) or questionnaires (n = 32). For each method, data were collected until saturation. We compared the mean number of items and relevant remarks that could influence the use of the genetic test obtained per method, divided by the number of participants in that method. Thematic content analysis was performed using MAXQDA software. The focus groups revealed 30 unique items compared to 29 in the interviews and 21 in the questionnaires. The interviews produced more items and relevant remarks per participant (1.9 and 8.4 pp) than focus groups (0.9 and 4.8 pp) or questionnaires (0.7 and 2.3 pp). All three involvement methods revealed relevant barriers and facilitators to use a new genetic test. Focus groups and interviews revealed substantially more items than questionnaires. Furthermore, this study suggests a preference for the use of interviews because the number of items per participant was higher than for focus groups and questionnaires. This conclusion may be valid for other genetic tests as well.

  17. Hybrid and Parallel Domain-Decomposition Methods Development to Enable Monte Carlo for Reactor Analyses

    International Nuclear Information System (INIS)

    Wagner, John C.; Mosher, Scott W.; Evans, Thomas M.; Peplow, Douglas E.; Turner, John A.

    2010-01-01

    This paper describes code and methods development at the Oak Ridge National Laboratory focused on enabling high-fidelity, large-scale reactor analyses with Monte Carlo (MC). Current state-of-the-art tools and methods used to perform real commercial reactor analyses have several undesirable features, the most significant of which is the non-rigorous spatial decomposition scheme. Monte Carlo methods, which allow detailed and accurate modeling of the full geometry and are considered the gold standard for radiation transport solutions, are playing an ever-increasing role in correcting and/or verifying the deterministic, multi-level spatial decomposition methodology in current practice. However, the prohibitive computational requirements associated with obtaining fully converged, system-wide solutions restrict the role of MC to benchmarking deterministic results at a limited number of state-points for a limited number of relevant quantities. The goal of this research is to change this paradigm by enabling direct use of MC for full-core reactor analyses. The most significant of the many technical challenges that must be overcome are the slow, non-uniform convergence of system-wide MC estimates and the memory requirements associated with detailed solutions throughout a reactor (problems involving hundreds of millions of different material and tally regions due to fuel irradiation, temperature distributions, and the needs associated with multi-physics code coupling). To address these challenges, our research has focused on the development and implementation of (1) a novel hybrid deterministic/MC method for determining high-precision fluxes throughout the problem space in k-eigenvalue problems and (2) an efficient MC domain-decomposition (DD) algorithm that partitions the problem phase space onto multiple processors for massively parallel systems, with statistical uncertainty estimation. The hybrid method development is based on an extension of the FW-CADIS method, which

  18. Hybrid and parallel domain-decomposition methods development to enable Monte Carlo for reactor analyses

    International Nuclear Information System (INIS)

    Wagner, J.C.; Mosher, S.W.; Evans, T.M.; Peplow, D.E.; Turner, J.A.

    2010-01-01

    This paper describes code and methods development at the Oak Ridge National Laboratory focused on enabling high-fidelity, large-scale reactor analyses with Monte Carlo (MC). Current state-of-the-art tools and methods used to perform 'real' commercial reactor analyses have several undesirable features, the most significant of which is the non-rigorous spatial decomposition scheme. Monte Carlo methods, which allow detailed and accurate modeling of the full geometry and are considered the 'gold standard' for radiation transport solutions, are playing an ever-increasing role in correcting and/or verifying the deterministic, multi-level spatial decomposition methodology in current practice. However, the prohibitive computational requirements associated with obtaining fully converged, system-wide solutions restrict the role of MC to benchmarking deterministic results at a limited number of state-points for a limited number of relevant quantities. The goal of this research is to change this paradigm by enabling direct use of MC for full-core reactor analyses. The most significant of the many technical challenges that must be overcome are the slow, non-uniform convergence of system-wide MC estimates and the memory requirements associated with detailed solutions throughout a reactor (problems involving hundreds of millions of different material and tally regions due to fuel irradiation, temperature distributions, and the needs associated with multi-physics code coupling). To address these challenges, our research has focused on the development and implementation of (1) a novel hybrid deterministic/MC method for determining high-precision fluxes throughout the problem space in k-eigenvalue problems and (2) an efficient MC domain-decomposition (DD) algorithm that partitions the problem phase space onto multiple processors for massively parallel systems, with statistical uncertainty estimation. The hybrid method development is based on an extension of the FW-CADIS method

  19. A new automated assign and analysing method for high-resolution rotationally resolved spectra using genetic algorithms

    NARCIS (Netherlands)

    Meerts, W.L.; Schmitt, M.

    2006-01-01

    This paper describes a numerical technique that has recently been developed to automatically assign and fit high-resolution spectra. The method makes use of genetic algorithms (GA). The current algorithm is compared with previously used analysing methods. The general features of the GA and its

  20. Novel method for equivalent stiffness and Coulomb's damping ratio analyses of leaf spring

    International Nuclear Information System (INIS)

    Wen Jun, Wu; Yu, Xiang; Le Mei, Zhu; Li Jun, He

    2012-01-01

    The leaf spring is a representative type of laminated structure. Based on the linear theories of curve beams, the first derivatives of the leave's status vector of the leaf spring are provided. The first derivatives of the combination status-vector are obtained by properly dealing with the nonlinear interacted forces between adjacent leaves. Moreover, the precise integration technology and the transform matrix method are introduced to solve the equations. The force displacement curve of a leaf spring is then calculated separately by using the present method and the finite element software ANSYS. From the results, the precision and advantages of the present methods for analyzing the leaf spring are revealed. The Coulomb's damping ratio of the leaf spring is studied by using the present method

  1. Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses

    Science.gov (United States)

    Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from UK, South Korea, Brazil and USA revealed four novel large-scale structural variations of at least 2,000...

  2. On the superconvergence of the SBB method

    International Nuclear Information System (INIS)

    Franca, L.P.

    1988-05-01

    Written in a mixed form a simple two-point boundary value problem is shown to have superconvergence characteristics under the SBB method. Convergence and accuracy analyses reveal superior performance of the method compared to the usual Galerkin method. (author) [pt

  3. Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality

    Directory of Open Access Journals (Sweden)

    Hyun-Seob Song

    2015-03-01

    Full Text Available Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as “topologically important.” Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as “functionally important” genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.

  4. Standard method for economic analyses of inertial confinement fusion power plants

    International Nuclear Information System (INIS)

    Meier, W.R.

    1986-01-01

    A standard method for calculating the total capital cost and the cost of electricity for a typical inertial confinement fusion electric power plant has been developed. A standard code of accounts at the two-digit level is given for the factors making up the total capital cost of the power plant. Equations are given for calculating the indirect capital costs, the project contingency, and the time-related costs. Expressions for calculating the fixed charge rate, which is necessary to determine the cost of electricity, are also described. Default parameters are given to define a reference case for comparative economic analyses

  5. Combined metabolomic and correlation networks analyses reveal fumarase insufficiency altered amino acid metabolism.

    Science.gov (United States)

    Hou, Entai; Li, Xian; Liu, Zerong; Zhang, Fuchang; Tian, Zhongmin

    2018-04-01

    Fumarase catalyzes the interconversion of fumarate and l-malate in the tricarboxylic acid cycle. Fumarase insufficiencies were associated with increased levels of fumarate, decreased levels of malate and exacerbated salt-induced hypertension. To gain insights into the metabolism profiles induced by fumarase insufficiency and identify key regulatory metabolites, we applied a GC-MS based metabolomics platform coupled with a network approach to analyze fumarase insufficient human umbilical vein endothelial cells (HUVEC) and negative controls. A total of 24 altered metabolites involved in seven metabolic pathways were identified as significantly altered, and enriched for the biological module of amino acids metabolism. In addition, Pearson correlation network analysis revealed that fumaric acid, l-malic acid, l-aspartic acid, glycine and l-glutamic acid were hub metabolites according to Pagerank based on their three centrality indices. Alanine aminotransferase and glutamate dehydrogenase activities increased significantly in fumarase deficiency HUVEC. These results confirmed that fumarase insufficiency altered amino acid metabolism. The combination of metabolomics and network methods would provide another perspective on expounding the molecular mechanism at metabolomics level. Copyright © 2017 John Wiley & Sons, Ltd.

  6. Novel citation-based search method for scientific literature: application to meta-analyses.

    Science.gov (United States)

    Janssens, A Cecile J W; Gwinn, M

    2015-10-13

    Finding eligible studies for meta-analysis and systematic reviews relies on keyword-based searching as the gold standard, despite its inefficiency. Searching based on direct citations is not sufficiently comprehensive. We propose a novel strategy that ranks articles on their degree of co-citation with one or more "known" articles before reviewing their eligibility. In two independent studies, we aimed to reproduce the results of literature searches for sets of published meta-analyses (n = 10 and n = 42). For each meta-analysis, we extracted co-citations for the randomly selected 'known' articles from the Web of Science database, counted their frequencies and screened all articles with a score above a selection threshold. In the second study, we extended the method by retrieving direct citations for all selected articles. In the first study, we retrieved 82% of the studies included in the meta-analyses while screening only 11% as many articles as were screened for the original publications. Articles that we missed were published in non-English languages, published before 1975, published very recently, or available only as conference abstracts. In the second study, we retrieved 79% of included studies while screening half the original number of articles. Citation searching appears to be an efficient and reasonably accurate method for finding articles similar to one or more articles of interest for meta-analysis and reviews.

  7. Chemistry and liquid chromatography methods for the analyses of primary oxidation products of triacylglycerols.

    Science.gov (United States)

    Zeb, A

    2015-05-01

    Triacylglycerols (TAGs) are one of the major components of the cells in higher biological systems, which can act as an energy reservoir in the living cells. The unsaturated fatty acid moiety is the key site of oxidation and formation of oxidation compounds. The TAG free radical generates several primary oxidation compounds. These include hydroperoxides, hydroxides, epidioxides, hydroperoxy epidioxides, hydroxyl epidioxides, and epoxides. The presence of these oxidized TAGs in the cell increases the chances of several detrimental processes. For this purpose, several liquid chromatography (LC) methods were reported in their analyses. This review is therefore focused on the chemistry, oxidation, extraction, and the LC methods reported in the analyses of oxidized TAGs. The studies on thin-layer chromatography were mostly focused on the total oxidized TAGs separation and employ hexane as major solvent. High-performance LC (HPLC) methods were discussed in details along with their merits and demerits. It was found that most of the HPLC methods employed isocratic elution with methanol and acetonitrile as major solvents with an ultraviolet detector. The coupling of HPLC with mass spectrometry (MS) highly increases the efficiency of analysis as well as enables reliable structural elucidation. The use of MS was found to be helpful in studying the oxidation chemistry of TAGs and needs to be extended to the complex biological systems.

  8. Individualising Chronic Care Management by Analysing Patients’ Needs – A Mixed Method Approach

    Directory of Open Access Journals (Sweden)

    P. Timpel

    2017-11-01

    Full Text Available Background: Modern health systems are increasingly faced with the challenge to provide effective, affordable and accessible health care for people with chronic conditions. As evidence on the specific unmet needs and their impact on health outcomes is limited, practical research is needed to tailor chronic care to individual needs of patients with diabetes. Qualitative approaches to describe professional and informal caregiving will support understanding the complexity of chronic care. Results are intended to provide practical recommendations to be used for systematic implementation of sustainable chronic care models. Method: A mixed method study was conducted. A standardised survey (n = 92 of experts in chronic care using mail responses to open-ended questions was conducted to analyse existing chronic care programs focusing on effective, problematic and missing components. An expert workshop (n = 22 of professionals and scientists of a European funded research project MANAGE CARE was used to define a limited number of unmet needs and priorities of elderly patients with type 2 diabetes mellitus and comorbidities. This list was validated and ranked using a multilingual online survey (n = 650. Participants of the online survey included patients, health care professionals and other stakeholders from 56 countries. Results: The survey indicated that current care models need to be improved in terms of financial support, case management and the consideration of social care. The expert workshop identified 150 patient needs which were summarised in 13 needs dimensions. The online survey of these pre-defined dimensions revealed that financial issues, education of both patients and professionals, availability of services as well as health promotion are the most important unmet needs for both patients and professionals. Conclusion: The study uncovered competing demands which are not limited to medical conditions. The findings emphasise that future care

  9. A method for energy and exergy analyses of product transformation processes in industry

    International Nuclear Information System (INIS)

    Abou Khalil, B.

    2008-12-01

    After a literature survey enabling the determination of the advantages and drawbacks of existing methods of assessment of the potential energy gains of an industrial site, this research report presents a newly developed method, named Energy and Exergy Analysis of Transformation Processes (or AEEP for Analyse energetique et exergetique des procedes de transformation), while dealing with actual industrial operations, in order to demonstrate the systematic character of this method. The different steps of the method are presented and detailed, one of them, the process analysis, being critical for the application of the developed method. This particular step is then applied to several industrial unitary operations in order to be a base for future energy audits in the concerned industry sectors, as well as to demonstrate its generic and systematic character. The method is the then applied in a global manner to a cheese manufacturing plant, all the different steps of the AEEP being applied. The author demonstrates that AEEP is a systematic method and can be applied to all energy audit levels, moreover to the lowest levels which have a relatively low cost

  10. Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

    Directory of Open Access Journals (Sweden)

    Eunyoung Seo

    2016-08-01

    Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

  11. Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks.

    Science.gov (United States)

    Mai, Hans-Jörg; Pateyron, Stéphanie; Bauer, Petra

    2016-10-03

    FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes. 448 genes were found FIT-regulated. Out of these, 34 genes were robustly FIT-regulated in root and seedling samples and included 13 novel FIT-dependent genes. Three hundred thirty-one genes showed differential regulation in response to the presence and absence of FIT only in the root samples, while this was the case for 83 genes in the seedling samples. We assembled a virtual dataset of iron-regulated genes based on a total of 14 transcriptomic analyses of iron-deficient and iron-sufficient wild-type plants to pinpoint the best marker genes for iron deficiency and analyzed this dataset in depth. Co-expression analysis of this dataset revealed 13 distinct regulons part of which predominantly contained functionally related genes. We could enlarge the list of FIT-dependent genes and discriminate between genes that are robustly FIT-regulated in roots and seedlings or only in one of those. FIT-regulated genes were mostly induced, few of them were repressed by FIT. With the analysis of a virtual dataset we could filter out and pinpoint new candidates among the most reliable marker genes for iron deficiency. Moreover, co-expression and functional analysis of this virtual dataset revealed iron deficiency-induced and functionally distinct regulons.

  12. Findings from analysing and quantifying human error using current methods

    International Nuclear Information System (INIS)

    Dang, V.N.; Reer, B.

    1999-01-01

    In human reliability analysis (HRA), the scarcity of data means that, at best, judgement must be applied to transfer to the domain of the analysis what data are available for similar tasks. In particular for the quantification of tasks involving decisions, the analyst has to choose among quantification approaches that all depend to a significant degree on expert judgement. The use of expert judgement can be made more reliable by eliciting relative judgements rather than absolute judgements. These approaches, which are based on multiple criterion decision theory, focus on ranking the tasks to be analysed by difficulty. While these approaches remedy at least partially the poor performance of experts in the estimation of probabilities, they nevertheless require the calibration of the relative scale on which the actions are ranked in order to obtain the probabilities of interest. This paper presents some results from a comparison of some current HRA methods performed in the frame of a study of SLIM calibration options. The HRA quantification methods THERP, HEART, and INTENT were applied to derive calibration human error probabilities for two groups of operator actions. (author)

  13. Analysing mass balance of viruses in a coagulation-ceramic microfiltration hybrid system by a combination of the polymerase chain reaction (PCR) method and the plaque forming units (PFU) method.

    Science.gov (United States)

    Matsushita, T; Matsui, Y; Shirasaki, N

    2006-01-01

    Virus removal experiments using river water spiked with bacteriophages were conducted by an in-line coagulation-ceramic microfiltration hybrid system to investigate the effects of filtration flux (62.5 and 125 L/(m2 x h)) and type of virus (Qbeta and MS2) on virus removal. In addition, the mass balance of viruses through the hybrid system was analysed by quantifying the infectious and inactive viruses by a combination of the polymerase chain reaction (PCR) method and the plaque forming units (PFU) method. Even when the system was operated at high filtration flux (125 L/(m2 x h)), high virus removal (> 6 log) with short coagulation time (2.4 s) was successfully achieved by dosing polyaluminium chloride (PACI) at more than 1.08 mg-Al/L. Removal performances were different between Qbeta and MS2, although their diameters are almost the same: greater virus removal was achieved for MS2 at PACI dosing of 0.54 mg-Al/L, and for Qbeta at PACI dosing of more than 1.08 mg-Al/L. The combination of the PCR and PFU methods revealed that two phenomena, adsorption to/entrapment in aluminium floc and virucidal activity of PACI, partially account for the high virus removal in the coagulation-MF hybrid system.

  14. Sobol method application in dimensional sensitivity analyses of different AFM cantilevers for biological particles

    Science.gov (United States)

    Korayem, M. H.; Taheri, M.; Ghahnaviyeh, S. D.

    2015-08-01

    Due to the more delicate nature of biological micro/nanoparticles, it is necessary to compute the critical force of manipulation. The modeling and simulation of reactions and nanomanipulator dynamics in a precise manipulation process require an exact modeling of cantilevers stiffness, especially the stiffness of dagger cantilevers because the previous model is not useful for this investigation. The stiffness values for V-shaped cantilevers can be obtained through several methods. One of them is the PBA method. In another approach, the cantilever is divided into two sections: a triangular head section and two slanted rectangular beams. Then, deformations along different directions are computed and used to obtain the stiffness values in different directions. The stiffness formulations of dagger cantilever are needed for this sensitivity analyses so the formulations have been driven first and then sensitivity analyses has been started. In examining the stiffness of the dagger-shaped cantilever, the micro-beam has been divided into two triangular and rectangular sections and by computing the displacements along different directions and using the existing relations, the stiffness values for dagger cantilever have been obtained. In this paper, after investigating the stiffness of common types of cantilevers, Sobol sensitivity analyses of the effects of various geometric parameters on the stiffness of these types of cantilevers have been carried out. Also, the effects of different cantilevers on the dynamic behavior of nanoparticles have been studied and the dagger-shaped cantilever has been deemed more suitable for the manipulation of biological particles.

  15. A simplified method for obtaining high-purity perchlorate from groundwater for isotope analyses.

    Energy Technology Data Exchange (ETDEWEB)

    vonKiparski, G; Hillegonds, D

    2011-04-04

    Investigations into the occurrence and origin of perchlorate (ClO{sub 4}{sup -}) found in groundwater from across North America have been sparse until recent years, and there is mounting evidence that natural formation mechanisms are important. New opportunities for identifying groundwater perchlorate and its origin have arisen with the utilization of improved detection methods and sampling techniques. Additionally, application of the forensic potential of isotopic measurements has begun to elucidate sources, potential formation mechanisms and natural attenuation processes. Procedures developed appear to be amenable to enable high precision stable isotopic analyses, as well as lower precision AMS analyses of {sup 36}Cl. Immediate work is in analyzing perchlorate isotope standards and developing full analytical accuracy and uncertainty expectations. Field samples have also been collected, and will be analyzed when final qa/qc samples are deemed acceptable.

  16. Kinds of access: Different methods for report reveal different kinds of metacognitive access

    DEFF Research Database (Denmark)

    Overgaard, Morten; Sandberg, Kristian

    2012-01-01

    that there is not only a theoretical, but also an empirical difference between different methods of reporting. We hypothesize that differences in the sensitivity of different scales may reveal that different types of access are used to issue direct reports about experiences and metacognitive reports about...

  17. Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes.

    Science.gov (United States)

    Zhang, Qi-Peng; Hu, Wen-Fang; Zhou, Ting-Ting; Kong, Shen-Shen; Liu, Zhi-Fang; Zheng, Rong-Quan

    2018-01-01

    Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa . In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa , evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini . Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini . By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa , and a cryptic species may also exist in Q. boulengeri . However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri . Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa .

  18. Computational methods, tools and data for nuclear analyses of fusion technology systems

    International Nuclear Information System (INIS)

    Fischer, U.

    2006-01-01

    An overview is presented of the Research and Development work conducted at Forschungszentrum Karlsruhe in co-operation with other associations in the framework of the European Fusion Technology Programme on the development and qualification of computational tools and data for nuclear analyses of Fusion Technology systems. The focus is on the development of advanced methods and tools based on the Monte Carlo technique for particle transport simulations, and the evaluation and qualification of dedicated nuclear data to satisfy the needs of the ITER and the IFMIF projects. (author)

  19. Comprehensive analyses of imprinted differentially methylated regions reveal epigenetic and genetic characteristics in hepatoblastoma

    International Nuclear Information System (INIS)

    Rumbajan, Janette Mareska; Aoki, Shigehisa; Kohashi, Kenichi; Oda, Yoshinao; Hata, Kenichiro; Saji, Tsutomu; Taguchi, Tomoaki; Tajiri, Tatsuro; Soejima, Hidenobu; Joh, Keiichiro; Maeda, Toshiyuki; Souzaki, Ryota; Mitsui, Kazumasa; Higashimoto, Ken; Nakabayashi, Kazuhiko; Yatsuki, Hitomi; Nishioka, Kenichi; Harada, Ryoko

    2013-01-01

    Aberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma. However, the methylation status of imprinted DMRs in imprinted loci scattered through the human genome has not been analyzed yet in any tumors. The methylation statuses of 33 imprinted DMRs were analyzed in 12 hepatoblastomas and adjacent normal liver tissue by MALDI-TOF MS and pyrosequencing. Uniparental disomy (UPD) and copy number abnormalities were investigated with DNA polymorphisms. Among 33 DMRs analyzed, 18 showed aberrant methylation in at least 1 tumor. There was large deviation in the incidence of aberrant methylation among the DMRs. KvDMR1 and IGF2-DMR0 were the most frequently hypomethylated DMRs. INPP5Fv2-DMR and RB1-DMR were hypermethylated with high frequencies. Hypomethylation was observed at certain DMRs not only in tumors but also in a small number of adjacent histologically normal liver tissue, whereas hypermethylation was observed only in tumor samples. The methylation levels of long interspersed nuclear element-1 (LINE-1) did not show large differences between tumor tissue and normal liver controls. Chromosomal abnormalities were also found in some tumors. 11p15.5 and 20q13.3 loci showed the frequent occurrence of both genetic and epigenetic alterations. Our analyses revealed tumor-specific aberrant hypermethylation at some imprinted DMRs in 12 hepatoblastomas with additional suggestion for the possibility of hypomethylation prior to tumor development. Some loci showed both genetic and epigenetic alterations with high frequencies. These findings will aid in understanding the development of hepatoblastoma

  20. A norm knockout method on indirect reciprocity to reveal indispensable norms

    Science.gov (United States)

    Yamamoto, Hitoshi; Okada, Isamu; Uchida, Satoshi; Sasaki, Tatsuya

    2017-03-01

    Although various norms for reciprocity-based cooperation have been suggested that are evolutionarily stable against invasion from free riders, the process of alternation of norms and the role of diversified norms remain unclear in the evolution of cooperation. We clarify the co-evolutionary dynamics of norms and cooperation in indirect reciprocity and also identify the indispensable norms for the evolution of cooperation. Inspired by the gene knockout method, a genetic engineering technique, we developed the norm knockout method and clarified the norms necessary for the establishment of cooperation. The results of numerical investigations revealed that the majority of norms gradually transitioned to tolerant norms after defectors are eliminated by strict norms. Furthermore, no cooperation emerges when specific norms that are intolerant to defectors are knocked out.

  1. Three genetic stocks of frigate tuna Auxis thazard thazard (Lacepede, 1800) along the Indian coast revealed from sequence analyses of mitochondrial DNA D-loop region

    Digital Repository Service at National Institute of Oceanography (India)

    GirishKumar; Kunal, S.P.; Menezes, M.R.; Meena, R.M.

    revealed from sequence analyses of mitochondrial DNA D-loop region Name of authors: 1. Girish Kumar* Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: girishkumar....nio@gmail.com Tel: +919766548060 2. Swaraj Priyaranjan Kunal Biological Oceanography Division (BOD) National Institute of Oceanography (NIO) Dona Paula, Goa 403004, India. Email: swar.mbt@gmail.com 3. Maria Rosalia Menezes Biological Oceanography...

  2. Analysing E-Services and Mobile Applications with Companied Conjoint Analysis and fMRI Technique

    OpenAIRE

    Heinonen, Jarmo

    2015-01-01

    Previous research has shown that neuromarketing and conjoint analysis have been used in many areas of consumer research, and to provide for further understanding of consumer behaviour. Together these two methods may reveal more information about hidden desires, expectations and restrains of consumers’ brain. This paper attempts to examine these two research methods together as a companied analysis. More specifically this study utilizes fMRI and conjoint analysis is a tool for analysing consum...

  3. Less is less: a systematic review of graph use in meta-analyses.

    Science.gov (United States)

    Schild, Anne H E; Voracek, Martin

    2013-09-01

    Graphs are an essential part of scientific communication. Complex datasets, of which meta-analyses are textbook examples, benefit the most from visualization. Although a number of graph options for meta-analyses exist, the extent to which these are used was hitherto unclear. A systematic review on graph use in meta-analyses in three disciplines (medicine, psychology, and business) and nine journals was conducted. Interdisciplinary differences, which are mirrored in the respective journals, were revealed, that is, graph use correlates with external factors rather than methodological considerations. There was only limited variation in graph types (with forest plots as the most important representatives), and diagnostic plots were very rare. Although an increase in graph use over time could be observed, it is unlikely that this phenomenon is specific to meta-analyses. There is a gaping discrepancy between available graphic methods and their application in meta-analyses. This may be rooted in a number of factors, namely, (i) insufficient dissemination of new developments, (ii) unsatisfactory implementation in software packages, and (iii) minor attention on graphics in meta-analysis reporting guidelines. Using visualization methods to their full capacity is a further step in using meta-analysis to its full potential. Copyright © 2013 John Wiley & Sons, Ltd.

  4. HIGH THROUGHPUT SCREENING METHOD AND APPARATUS FOR ANALYSING INTERACTIONS BETWEEN SURFACES WITH DIFFERENT TOPOGRAPHY AND THE ENVIRONMENT

    NARCIS (Netherlands)

    de Boer, Jan; van Blitterswijk, Clemens; Unadkat, H.V.; Stamatialis, Dimitrios; Papenburg, B.J.; Wessling, Matthias

    2009-01-01

    The invention is directed to a high throughput screening method for analysing and interaction between a surface of a material and an environment. The screening method of the invention comprises: providing a micro-array comprising said material and having a multitude of units at least part of which

  5. [Methods, challenges and opportunities for big data analyses of microbiome].

    Science.gov (United States)

    Sheng, Hua-Fang; Zhou, Hong-Wei

    2015-07-01

    Microbiome is a novel research field related with a variety of chronic inflamatory diseases. Technically, there are two major approaches to analysis of microbiome: metataxonome by sequencing the 16S rRNA variable tags, and metagenome by shot-gun sequencing of the total microbial (mainly bacterial) genome mixture. The 16S rRNA sequencing analyses pipeline includes sequence quality control, diversity analyses, taxonomy and statistics; metagenome analyses further includes gene annotation and functional analyses. With the development of the sequencing techniques, the cost of sequencing will decrease, and big data analyses will become the central task. Data standardization, accumulation, modeling and disease prediction are crucial for future exploit of these data. Meanwhile, the information property in these data, and the functional verification with culture-dependent and culture-independent experiments remain the focus in future research. Studies of human microbiome will bring a better understanding of the relations between the human body and the microbiome, especially in the context of disease diagnosis and therapy, which promise rich research opportunities.

  6. Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota.

    Science.gov (United States)

    Ahlgren, N.; Parada, A. E.; Fuhrman, J. A.

    2016-02-01

    Marine Thaumarchaea are an abundant, important group of marine microbial communities as they fix carbon, oxidize ammonium, and thus contribute to key N and C cycles in the oceans. From an enrichment culture, we have sequenced the complete genome of a new Thaumarchaeota strain, SPOT01. Analysis of this genome and other Thaumarchaeal genomes contributes new insight into its role in N cycling and clarifies the broader biogeography of marine Thaumarchaeal genera. Phylogenomics of Thaumarchaeota genomes reveal coherent separation into clusters roughly equivalent to the genus level, and SPOT01 represents a new genus of marine Thaumarchaea. Competitive fragment recruitment of globally distributed metagenomes from TARA, Ocean Sampling Day, and those generated from a station off California shows that the SPOT01 genus is often the most abundant genus, especially where total Thaumarchaea are most abundant in the overall community. The SPOT01 genome contains urease genes allowing it to use an alternative form of N. Genomic and metagenomic analysis also reveal that among planktonic genomes and populations, the urease genes in general are more frequently found in members of the SPOT01 genus and another genus dominant in deep waters, thus we predict these two genera contribute most significantly to urea utilization among marine Thaumarchaea. Recruitment also revealed broader biogeographic and ecological patterns of the putative genera. The SPOT01 genus was most abundant at colder temperatures (45 degrees). The genus containing Nitrosopumilus maritimus had the highest temperature range, and the genus containing Candidatus Nitrosopelagicus brevis was typically most abundant at intermediate temperatures and intermediate latitudes ( 35-45 degrees). Together these genome and metagenome enabled analyses provide significant new insight into the ecology and biogeochemical contributions of marine archaea.

  7. Two-step extraction method for lead isotope fractionation to reveal anthropogenic lead pollution.

    Science.gov (United States)

    Katahira, Kenshi; Moriwaki, Hiroshi; Kamura, Kazuo; Yamazaki, Hideo

    2018-05-28

    This study developed the 2-step extraction method which eluted the Pb adsorbing on the surface of sediments in the first solution by aqua regia and extracted the Pb absorbed inside particles into the second solution by mixed acid of nitric acid, hydrofluoric acid and hydrogen peroxide solution. We applied the method to sediments in the enclosed water area and found out that the isotope ratios of Pb in the second solution represented those of natural origin. This advantage of the method makes it possible to distinguish the Pb between natural origin and anthropogenic source on the basis of the isotope ratios. The results showed that the method was useful to discuss the Pb sources and that anthropogenic Pb in the sediment samples analysed was mainly derived from China because of transboundary air pollution.

  8. Proteomic and physiological analyses reveal the role of exogenous spermidine on cucumber roots in response to Ca(NO3)2 stress.

    Science.gov (United States)

    Du, Jing; Guo, Shirong; Sun, Jin; Shu, Sheng

    2018-05-01

    The mechanism of exogenous Spd-induced Ca(NO 3 ) 2 stress tolerance in cucumber was studied by proteomics and physiological analyses. Protein-protein interaction network revealed 13 key proteins involved in Spd-induced Ca(NO 3 ) 2 stress resistance. Ca(NO 3 ) 2 stress is one of the major reasons for secondary salinization that limits cucumber plant development in greenhouse. The conferred protective role of exogenous Spd on cucumber in response to Ca(NO 3 ) 2 stress cues involves changes at the cellular and physiological levels. To investigate the molecular foundation of exogenous Spd in Ca(NO 3 ) 2 stress tolerance, a proteomic approach was performed in our work. After a 9 days period of Ca(NO 3 ) 2 stress and/or exogenous Spd, 71 differential protein spots were confidently identified. The resulting proteins were enriched in seven different categories of biological processes, including protein metabolism, carbohydrate and energy metabolism, ROS homeostasis and stress defense, cell wall related, transcription, others and unknown. Protein metabolism (31.2%), carbohydrate and energy metabolism (15.6%), ROS homeostasis and stress defense (32.5%) were the three largest functional categories in cucumber root and most of them were significantly increased by exogenous Spd. The Spd-responsive protein interaction network revealed 13 key proteins, whose accumulation changes could be critical for Spd-induced resistance; all 13 proteins were upregulated by Spd at transcriptional and protein levels in response to Ca(NO 3 ) 2 stress. Furthermore, accumulation of antioxidant enzymes, non-enzymatic antioxidant and polyamines, along with reduction of H 2 O 2 and MDA, were detected after exogenous Spd application during Ca(NO 3 ) 2 stress. The results of these proteomic and physiological analyses in cucumber root may facilitate a better understanding of the underlying mechanism of Ca(NO 3 ) 2 stress tolerance mediated by exogenous Spd.

  9. Individualising Chronic Care Management by Analysing Patients' Needs - A Mixed Method Approach.

    Science.gov (United States)

    Timpel, P; Lang, C; Wens, J; Contel, J C; Gilis-Januszewska, A; Kemple, K; Schwarz, P E

    2017-11-13

    Modern health systems are increasingly faced with the challenge to provide effective, affordable and accessible health care for people with chronic conditions. As evidence on the specific unmet needs and their impact on health outcomes is limited, practical research is needed to tailor chronic care to individual needs of patients with diabetes. Qualitative approaches to describe professional and informal caregiving will support understanding the complexity of chronic care. Results are intended to provide practical recommendations to be used for systematic implementation of sustainable chronic care models. A mixed method study was conducted. A standardised survey (n = 92) of experts in chronic care using mail responses to open-ended questions was conducted to analyse existing chronic care programs focusing on effective, problematic and missing components. An expert workshop (n = 22) of professionals and scientists of a European funded research project MANAGE CARE was used to define a limited number of unmet needs and priorities of elderly patients with type 2 diabetes mellitus and comorbidities. This list was validated and ranked using a multilingual online survey (n = 650). Participants of the online survey included patients, health care professionals and other stakeholders from 56 countries. The survey indicated that current care models need to be improved in terms of financial support, case management and the consideration of social care. The expert workshop identified 150 patient needs which were summarised in 13 needs dimensions. The online survey of these pre-defined dimensions revealed that financial issues, education of both patients and professionals, availability of services as well as health promotion are the most important unmet needs for both patients and professionals. The study uncovered competing demands which are not limited to medical conditions. The findings emphasise that future care models need to focus stronger on individual patient needs and

  10. Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

    Science.gov (United States)

    Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z.; Tyagi, Anil K.

    2014-01-01

    ABSTRACT Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size—their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. PMID:25370496

  11. Bliss and Loewe interaction analyses of clinically relevant drug combinations in human colon cancer cell lines reveal complex patterns of synergy and antagonism.

    Science.gov (United States)

    Kashif, Muhammad; Andersson, Claes; Mansoori, Sharmineh; Larsson, Rolf; Nygren, Peter; Gustafsson, Mats G

    2017-11-28

    We analyzed survival effects for 15 different pairs of clinically relevant anti-cancer drugs in three iso-genic pairs of human colorectal cancer carcinoma cell lines, by applying for the first time our novel software (R package) called COMBIA. In our experiments iso-genic pairs of cell lines were used, differing only with respect to a single clinically important KRAS or BRAF mutation. Frequently, concentration dependent but mutation independent joint Bliss and Loewe synergy/antagonism was found statistically significant. Four combinations were found synergistic/antagonistic specifically to the parental (harboring KRAS or BRAF mutation) cell line of the corresponding iso-genic cell lines pair. COMBIA offers considerable improvements over established software for synergy analysis such as MacSynergy™ II as it includes both Bliss (independence) and Loewe (additivity) analyses, together with a tailored non-parametric statistical analysis employing heteroscedasticity, controlled resampling, and global (omnibus) testing. In many cases Loewe analyses found significant synergistic as well as antagonistic effects in a cell line at different concentrations of a tested drug combination. By contrast, Bliss analysis found only one type of significant effect per cell line. In conclusion, the integrated Bliss and Loewe interaction analysis based on non-parametric statistics may provide more robust interaction analyses and reveal complex patterns of synergy and antagonism.

  12. Dry-air drying at room temperature - a practical pre-treatment method of tree leaves for quantitative analyses of phenolics?

    Science.gov (United States)

    Tegelberg, Riitta; Virjamo, Virpi; Julkunen-Tiitto, Riitta

    2018-03-09

    In ecological experiments, storage of plant material is often needed between harvesting and laboratory analyses when the number of samples is too large for immediate, fresh analyses. Thus, accuracy and comparability of the results call for pre-treatment methods where the chemical composition remains unaltered and large number of samples can be treated efficiently. To study if a fast dry-air drying provides an efficient pre-treatment method for quantitative analyses of phenolics. Dry-air drying of mature leaves was done in a drying room equipped with dehumifier (10% relative humidity, room temperature) and results were compared to freeze-drying or freeze-drying after pre-freezing in liquid nitrogen. The quantities of methanol-soluble phenolics of Betula pendula Roth, Betula pubescens Ehrh., Salix myrsinifolia Salisb., Picea abies L. Karsten and Pinus sylvestris L. were analysed with HPLC and condensed tannins were analysed using the acid-butanol test. In deciduous tree leaves (Betula, Salix), the yield of most of the phenolic compounds was equal or higher in samples dried in dry-air room than the yield from freeze-dried samples. In Picea abies needles, however, dry-air drying caused severe reductions in picein, stilbenes, condensed tannin and (+)-catechin concentrations compared to freeze-drying. In Pinus sylvestris highest yields of neolignans but lowest yields of acetylated flavonoids were obtained from samples freeze-dried after pre-freezing. Results show that dry-air drying provides effective pre-treatment method for quantifying the soluble phenolics for deciduous tree leaves, but when analysing coniferous species, the different responses between structural classes of phenolics should be taken into account. Copyright © 2018 John Wiley & Sons, Ltd.

  13. An application of the explicit method for analysing intersystem dependencies in the evaluation of event trees

    International Nuclear Information System (INIS)

    Oliveira, L.F.S.; Frutuoso e Melo, P.F.; Lima, J.E.P.; Stal, I.L.

    1985-01-01

    We discuss in this paper a computational application of the explicit method for analyzing event trees in the context of probabilistic risk assessments. A detailed analysis of the explicit method is presented, including the train level analysis (TLA) of safety systems and the impact vector method. It is shown that the penalty for not adopting TLA is that in some cases non-conservative results may be reached. The impact vector method can significantly reduce the number of sequences to be considered, and its use has inspired the definition of a dependency matrix, which enables the proper running of a computer code especially developed for analysing event trees. This code constructs and quantifies the event trees in the fashion just discussed, by receiving as input the construction and quantification dependencies defined in the dependency matrix. The code has been extensively used in the Angra 1 PRA currently underway. In its present version it gives as output the dominant sequences for each given initiator, properly classifying them in core-degradation classes as specified by the user. This calculation is made in a pointwise fashion. Extensions of this code are being developed in order to perform uncertainty analyses on the dominant sequences and also risk importance measures of the safety systems envolved. (orig.)

  14. Do regional methods really help reduce uncertainties in flood frequency analyses?

    Science.gov (United States)

    Cong Nguyen, Chi; Payrastre, Olivier; Gaume, Eric

    2013-04-01

    Flood frequency analyses are often based on continuous measured series at gauge sites. However, the length of the available data sets is usually too short to provide reliable estimates of extreme design floods. To reduce the estimation uncertainties, the analyzed data sets have to be extended either in time, making use of historical and paleoflood data, or in space, merging data sets considered as statistically homogeneous to build large regional data samples. Nevertheless, the advantage of the regional analyses, the important increase of the size of the studied data sets, may be counterbalanced by the possible heterogeneities of the merged sets. The application and comparison of four different flood frequency analysis methods to two regions affected by flash floods in the south of France (Ardèche and Var) illustrates how this balance between the number of records and possible heterogeneities plays in real-world applications. The four tested methods are: (1) a local statistical analysis based on the existing series of measured discharges, (2) a local analysis valuating the existing information on historical floods, (3) a standard regional flood frequency analysis based on existing measured series at gauged sites and (4) a modified regional analysis including estimated extreme peak discharges at ungauged sites. Monte Carlo simulations are conducted to simulate a large number of discharge series with characteristics similar to the observed ones (type of statistical distributions, number of sites and records) to evaluate to which extent the results obtained on these case studies can be generalized. These two case studies indicate that even small statistical heterogeneities, which are not detected by the standard homogeneity tests implemented in regional flood frequency studies, may drastically limit the usefulness of such approaches. On the other hand, these result show that the valuation of information on extreme events, either historical flood events at gauged

  15. ATHENA/INTRA analyses for ITER, NSSR-2

    International Nuclear Information System (INIS)

    Shen, Kecheng; Eriksson, John; Sjoeberg, A.

    1999-02-01

    The present report is a summary report including thermal-hydraulic analyses made at Studsvik Eco and Safety AB for the ITER NSSR-2 safety documentation. The objective of the analyses was to reveal the safety characteristics of various heat transfer systems at specified operating conditions and to indicate the conditions for which there were obvious risks of jeopardising the structural integrity of the coolant systems. In the latter case also some analyses were made to indicate conceivable mitigating measures for maintaining the integrity.The analyses were primarily concerned with the First Wall and Divertor heat transfer systems. Several enveloping transients were analysed with associated specific flow and heat load boundary conditions. The analyses were performed with the ATHENA and INTRA codes

  16. ATHENA/INTRA analyses for ITER, NSSR-2

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Kecheng; Eriksson, John; Sjoeberg, A

    1999-02-01

    The present report is a summary report including thermal-hydraulic analyses made at Studsvik Eco and Safety AB for the ITER NSSR-2 safety documentation. The objective of the analyses was to reveal the safety characteristics of various heat transfer systems at specified operating conditions and to indicate the conditions for which there were obvious risks of jeopardising the structural integrity of the coolant systems. In the latter case also some analyses were made to indicate conceivable mitigating measures for maintaining the integrity.The analyses were primarily concerned with the First Wall and Divertor heat transfer systems. Several enveloping transients were analysed with associated specific flow and heat load boundary conditions. The analyses were performed with the ATHENA and INTRA codes 8 refs, 14 figs, 15 tabs

  17. Underestimation of species richness in neotropical frogs revealed by mtDNA analyses.

    Directory of Open Access Journals (Sweden)

    Antoine Fouquet

    2007-10-01

    Full Text Available Amphibians are rapidly vanishing. At the same time, it is most likely that the number of amphibian species is highly underestimated. Recent DNA barcoding work has attempted to define a threshold between intra- and inter-specific genetic distances to help identify candidate species. In groups with high extinction rates and poorly known species boundaries, like amphibians, such tools may provide a way to rapidly evaluate species richness.Here we analyse published and new 16S rDNA sequences from 60 frog species of Amazonia-Guianas to obtain a minimum estimate of the number of undescribed species in this region. We combined isolation by distance, phylogenetic analyses, and comparison of molecular distances to evaluate threshold values for the identification of candidate species among these frogs.In most cases, geographically distant populations belong to genetically highly distinct lineages that could be considered as candidate new species. This was not universal among the taxa studied and thus widespread species of Neotropical frogs really do exist, contrary to previous assumptions. Moreover, the many instances of paraphyly and the wide overlap between distributions of inter- and intra-specific distances reinforce the hypothesis that many cryptic species remain to be described. In our data set, pairwise genetic distances below 0.02 are strongly correlated with geographical distances. This correlation remains statistically significant until genetic distance is 0.05, with no such relation thereafter. This suggests that for higher distances allopatric and sympatric cryptic species prevail. Based on our analyses, we propose a more inclusive pairwise genetic distance of 0.03 between taxa to target lineages that could correspond to candidate species.Using this approach, we identify 129 candidate species, two-fold greater than the 60 species included in the current study. This leads to estimates of around 170 to 460 frog taxa unrecognized in Amazonia

  18. SQA of finite element method (FEM) codes used for analyses of pit storage/transport packages

    Energy Technology Data Exchange (ETDEWEB)

    Russel, E. [Lawrence Livermore National Lab., CA (United States)

    1997-11-01

    This report contains viewgraphs on the software quality assurance of finite element method codes used for analyses of pit storage and transport projects. This methodology utilizes the ISO 9000-3: Guideline for application of 9001 to the development, supply, and maintenance of software, for establishing well-defined software engineering processes to consistently maintain high quality management approaches.

  19. Metabarcoding and metabolome analyses of copepod grazing reveal feeding preference and linkage to metabolite classes in dynamic microbial plankton communities.

    Science.gov (United States)

    Ray, Jessica L; Althammer, Julia; Skaar, Katrine S; Simonelli, Paolo; Larsen, Aud; Stoecker, Diane; Sazhin, Andrey; Ijaz, Umer Z; Quince, Christopher; Nejstgaard, Jens C; Frischer, Marc; Pohnert, Georg; Troedsson, Christofer

    2016-11-01

    In order to characterize copepod feeding in relation to microbial plankton community dynamics, we combined metabarcoding and metabolome analyses during a 22-day seawater mesocosm experiment. Nutrient amendment of mesocosms promoted the development of haptophyte (Phaeocystis pouchetii)- and diatom (Skeletonema marinoi)-dominated plankton communities in mesocosms, in which Calanus sp. copepods were incubated for 24 h in flow-through chambers to allow access to prey particles (<500 μm). Copepods and mesocosm water sampled six times spanning the experiment were analysed using metabarcoding, while intracellular metabolite profiles of mesocosm plankton communities were generated for all experimental days. Taxon-specific metabarcoding ratios (ratio of consumed prey to available prey in the surrounding seawater) revealed diverse and dynamic copepod feeding selection, with positive selection on large diatoms, heterotrophic nanoflagellates and fungi, while smaller phytoplankton, including P. pouchetii, were passively consumed or even negatively selected according to our indicator. Our analysis of the relationship between Calanus grazing ratios and intracellular metabolite profiles indicates the importance of carbohydrates and lipids in plankton succession and copepod-prey interactions. This molecular characterization of Calanus sp. grazing therefore provides new evidence for selective feeding in mixed plankton assemblages and corroborates previous findings that copepod grazing may be coupled to the developmental and metabolic stage of the entire prey community rather than to individual prey abundances. © 2016 John Wiley & Sons Ltd.

  20. Advanced exergy-based analyses applied to a system including LNG regasification and electricity generation

    Energy Technology Data Exchange (ETDEWEB)

    Morosuk, Tatiana; Tsatsaronis, George; Boyano, Alicia; Gantiva, Camilo [Technische Univ. Berlin (Germany)

    2012-07-01

    Liquefied natural gas (LNG) will contribute more in the future than in the past to the overall energy supply in the world. The paper discusses the application of advanced exergy-based analyses to a recently developed LNG-based cogeneration system. These analyses include advanced exergetic, advanced exergoeconomic, and advanced exergoenvironmental analyses in which thermodynamic inefficiencies (exergy destruction), costs, and environmental impacts have been split into avoidable and unavoidable parts. With the aid of these analyses, the potentials for improving the thermodynamic efficiency and for reducing the overall cost and the overall environmental impact are revealed. The objectives of this paper are to demonstrate (a) the potential for generating electricity while regasifying LNG and (b) some of the capabilities associated with advanced exergy-based methods. The most important subsystems and components are identified, and suggestions for improving them are made. (orig.)

  1. The quality of reporting methods and results of cost-effectiveness analyses in Spain: a methodological systematic review.

    Science.gov (United States)

    Catalá-López, Ferrán; Ridao, Manuel; Alonso-Arroyo, Adolfo; García-Altés, Anna; Cameron, Chris; González-Bermejo, Diana; Aleixandre-Benavent, Rafael; Bernal-Delgado, Enrique; Peiró, Salvador; Tabarés-Seisdedos, Rafael; Hutton, Brian

    2016-01-07

    Cost-effectiveness analysis has been recognized as an important tool to determine the efficiency of healthcare interventions and services. There is a need for evaluating the reporting of methods and results of cost-effectiveness analyses and establishing their validity. We describe and examine reporting characteristics of methods and results of cost-effectiveness analyses conducted in Spain during more than two decades. A methodological systematic review was conducted with the information obtained through an updated literature review in PubMed and complementary databases (e.g. Scopus, ISI Web of Science, National Health Service Economic Evaluation Database (NHS EED) and Health Technology Assessment (HTA) databases from Centre for Reviews and Dissemination (CRD), Índice Médico Español (IME) Índice Bibliográfico Español en Ciencias de la Salud (IBECS)). We identified cost-effectiveness analyses conducted in Spain that used quality-adjusted life years (QALYs) as outcome measures (period 1989-December 2014). Two reviewers independently extracted the data from each paper. The data were analysed descriptively. In total, 223 studies were included. Very few studies (10; 4.5 %) reported working from a protocol. Most studies (200; 89.7 %) were simulation models and included a median of 1000 patients. Only 105 (47.1 %) studies presented an adequate description of the characteristics of the target population. Most study interventions were categorized as therapeutic (189; 84.8 %) and nearly half (111; 49.8 %) considered an active alternative as the comparator. Effectiveness of data was derived from a single study in 87 (39.0 %) reports, and only few (40; 17.9 %) used evidence synthesis-based estimates. Few studies (42; 18.8 %) reported a full description of methods for QALY calculation. The majority of the studies (147; 65.9 %) reported that the study intervention produced "more costs and more QALYs" than the comparator. Most studies (200; 89.7 %) reported favourable

  2. Neurolinguistics Programming: Method or Myth?

    Science.gov (United States)

    Gumm, W. B.; And Others

    1982-01-01

    The preferred modality by which 50 right-handed female college students encoded experience was assessed by recordings of conjugate eye movements, content analysis of the subject's verbal report, and the subject's self-report. Kappa analyses failed to reveal any agreement of the three assessment methods. (Author)

  3. The Effect of Pleistocene Climate Fluctuations on Distribution of European Abalone (Haliotis tuberculata), Revealed by Combined Mitochondrial and Nuclear Marker Analyses.

    Science.gov (United States)

    Roussel, Valérie; Van Wormhoudt, Alain

    2017-04-01

    The genetic differentiation among the populations of the European abalone Haliotis tuberculata was investigated using different markers to better understand the evolutionary history and exchanges between populations. Three markers were used: mitochondrial cytochrome oxidase I (COI), the sperm lysin nuclear gene, and eight nuclear microsatellites. These markers present different characteristics concerning mutation rate and inheritance, which provided complementary information about abalone history and gene diversity. Genetic diversity and relationships among subspecies were calculated from a sample of approximately 500 individuals, collected from 17 different locations in the north-eastern Atlantic Ocean, Macaronesia, and Mediterranean Sea. COI marker was used to explore the phylogeny of the species with a network analysis and two phylogenetic methods. The analysis revealed 18 major haplotypes grouped into two distinct clades with a pairwise sequence divergence up to 3.5 %. These clades do not correspond to subspecies but revealed many contacts along Atlantic coast during the Pleistocene interglaciations. The sperm lysin gene analysis separated two different subtaxa: one associated to Macaronesian islands, and the other to all other populations. Moreover, a small population of the northern subtaxon was isolated in the Adriatic Sea-probably before the separation of the two lineages-and evolved independently. Microsatellites were analyzed by different genetics methods, including the Bayesian clustering method and migration patterns analysis. It revealed genetically distinct microsatellite patterns among populations from Mediterranean Sea, Brittany and Normandy, Morocco, and Canary and Balearic islands. Gene flow is asymmetric among the regions; the Azores and the Canary Islands are particularly isolated and have low effective population sizes. Our results support the hypothesis that climate changes since the Pleistocene glaciations have played a major role in the

  4. Revealed Preference Methods for Studying Bicycle Route Choice—A Systematic Review

    Directory of Open Access Journals (Sweden)

    Ray Pritchard

    2018-03-01

    Full Text Available One fundamental aspect of promoting utilitarian bicycle use involves making modifications to the built environment to improve the safety, efficiency and enjoyability of cycling. Revealed preference data on bicycle route choice can assist greatly in understanding the actual behaviour of a highly heterogeneous group of users, which in turn assists the prioritisation of infrastructure or other built environment initiatives. This systematic review seeks to compare the relative strengths and weaknesses of the empirical approaches for evaluating whole journey route choices of bicyclists. Two electronic databases were systematically searched for a selection of keywords pertaining to bicycle and route choice. In total seven families of methods are identified: GPS devices, smartphone applications, crowdsourcing, participant-recalled routes, accompanied journeys, egocentric cameras and virtual reality. The study illustrates a trade-off in the quality of data obtainable and the average number of participants. Future additional methods could include dockless bikeshare, multiple camera solutions using computer vision and immersive bicycle simulator environments.

  5. Stepwise multiphoton activation fluorescence reveals a new method of melanin detection

    Science.gov (United States)

    Lai, Zhenhua; Kerimo, Josef; Mega, Yair; DiMarzio, Charles A.

    2013-06-01

    The stepwise multiphoton activated fluorescence (SMPAF) of melanin, activated by a continuous-wave mode near infrared (NIR) laser, reveals a broad spectrum extending from the visible spectra to the NIR and has potential application for a low-cost, reliable method of detecting melanin. SMPAF images of melanin in mouse hair and skin are compared with conventional multiphoton fluorescence microscopy and confocal reflectance microscopy (CRM). By combining CRM with SMPAF, we can locate melanin reliably. However, we have the added benefit of eliminating background interference from other components inside mouse hair and skin. The melanin SMPAF signal from the mouse hair is a mixture of a two-photon process and a third-order process. The melanin SMPAF emission spectrum is activated by a 1505.9-nm laser light, and the resulting spectrum has a peak at 960 nm. The discovery of the emission peak may lead to a more energy-efficient method of background-free melanin detection with less photo-bleaching.

  6. Structural Analyses of Avocado sunblotch viroid Reveal Differences in the Folding of Plus and Minus RNA Strands

    Directory of Open Access Journals (Sweden)

    Clémentine Delan-Forino

    2014-01-01

    Full Text Available Viroids are small pathogenic circular single-stranded RNAs, present in two complementary sequences, named plus and minus, in infected plant cells. A high degree of complementarities between different regions of the RNAs allows them to adopt complex structures. Since viroids are naked non-coding RNAs, interactions with host factors appear to be closely related to their structural and catalytic characteristics. Avocado sunblotch viroid (ASBVd, a member of the family Avsunviroidae, replicates via a symmetric RNA-dependant rolling-circle process, involving self-cleavage via hammerhead ribozymes. Consequently, it is assumed that ASBVd plus and minus strands adopt similar structures. Moreover, by computer analyses, a quasi-rod-like secondary structure has been predicted. Nevertheless, secondary and tertiary structures of both polarities of ASBVd remain unsolved. In this study, we analyzed the characteristic of each strand of ASBVd through biophysical analyses. We report that ASBVd transcripts of plus and minus polarities exhibit differences in electrophoretic mobility under native conditions and in thermal denaturation profiles. Subsequently, the secondary structures of plus and minus polarities of ASBVd were probed using the RNA-selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE method. The models obtained show that both polarities fold into different structures. Moreover, our results suggest the existence of a kissing-loop interaction within the minus strand that may play a role in in vivo viroid life cycle.

  7. Development of an ellipse fitting method with which to analyse selected area electron diffraction patterns

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, D.R.G., E-mail: dmitchel@uow.edu.au [Electron Microscopy Centre, Australian Institute for Innovative Materials, Innovation Campus, University of Wollongong, North Wollongong, NSW 2500 (Australia); Van den Berg, J.A. [Electron Microscopy Centre, Australian Institute for Innovative Materials, Innovation Campus, University of Wollongong, North Wollongong, NSW 2500 (Australia); Catalyst Fundamentals, Fischer-Tropsch and Syngas Conversion Research, Sasol Technology R & D, Sasolburg 1947 (South Africa)

    2016-01-15

    A software method has been developed which uses ellipse fitting to analyse electron diffraction patterns from polycrystalline materials. The method, which requires minimal user input, can determine the pattern centre and the diameter of diffraction rings with sub-pixel precision. This enables accurate crystallographic information to be obtained in a rapid and consistent manner. Since the method fits ellipses, it can detect, quantify and correct any elliptical distortion introduced by the imaging system. Distortion information derived from polycrystalline patterns as a function of camera length can be subsequently recalled and applied to single crystal patterns, resulting in improved precision and accuracy. The method has been implemented as a plugin for the DigitalMicrograph software by Gatan, and is a freely available via the internet. - Highlights: • A robust ellipse fitting method is developed. • Freely available software for automated diffraction pattern analysis is demonstrated. • Measurement and correction of elliptical distortion is routinely achieved.

  8. The surface analysis methods; Les methodes d`analyse des surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Deville, J.P. [Institut de Physique et Chimie, 67 - Strasbourg (France)

    1998-11-01

    Nowadays, there are a lot of surfaces analysis methods, each having its specificity, its qualities, its constraints (for instance vacuum) and its limits. Expensive in time and in investment, these methods have to be used deliberately. This article appeals to non specialists. It gives some elements of choice according to the studied information, the sensitivity, the use constraints or the answer to a precise question. After having recalled the fundamental principles which govern these analysis methods, based on the interaction between radiations (ultraviolet, X) or particles (ions, electrons) with matter, two methods will be more particularly described: the Auger electron spectroscopy (AES) and x-rays photoemission spectroscopy (ESCA or XPS). Indeed, they are the most widespread methods in laboratories, the easier for use and probably the most productive for the analysis of surface of industrial materials or samples submitted to treatments in aggressive media. (O.M.) 11 refs.

  9. Mitochondrial DNA analyses revealed low genetic diversity in the endangered Indian wild ass Equus hemionus khur.

    Science.gov (United States)

    Khaire, Devendra; Atkulwar, Ashwin; Farah, Sameera; Baig, Mumtaz

    2017-09-01

    The Indian wild ass Equus hemionus khur, belonging to ass-like equid branch, inhabits the dry and arid desert of the Little Rann of Kutch, Gujarat. The E. h. khur is the sole survivor of Asiatic wild ass species/subspecies in South Asia. To provide first ever insights into the genetic diversity, phylogeny, and demography of the endangered Indian wild ass, we sampled 52 free-ranging individuals from the Little Rann of Kutch by using a non-invasive methodology. The sequencing of 230 bp in cytochrome b (Cyt b) and displacement loop (D-loop) region revealed that current ∼4000 extant population of Indian wild ass harbours low genetic diversity. Phylogenetic analyses confirmed that E. h. khur, E. h. onager, and E. h. kulan belong to a single strict monophyletic clade. Therefore, we suggest the delimitation of the five E. hemionus subspecies in vogue to a single species E. hemionus. The application of molecular clock confirmed that the Asiatic wild ass had undergone diversification 0.65 Million years ago. Demographic measurements assessed using a Bayesian skyline plot demonstrated decline in the maternal effective population size of the Indian wild ass during different periods; these periods coincided with the origin and rise of the Indus civilization in the northwest of the Indian subcontinent during the Neolithic. In conclusion, maintaining high genetic diversity in the existing isolated population of 4000 Indian wild asses inhabiting the wild ass sanctuary is important compared with subspecies preservation alone.

  10. How Do We Know What Is Happening Online?: A Mixed Methods Approach to Analysing Online Activity

    Science.gov (United States)

    Charalampidi, Marina; Hammond, Michael

    2016-01-01

    Purpose: The purpose of this paper is to discuss the process of analysing online discussion and argue for the merits of mixed methods. Much research of online participation and e-learning has been either message-focused or person-focused. The former covers methodologies such as content and discourse analysis, the latter interviewing and surveys.…

  11. Method to perform radioimmunological analyses

    International Nuclear Information System (INIS)

    Friedel, R.

    1976-01-01

    The invention concerns a method for the radioimmunoligcal detection of antigens. According to the invention, antibodies are adsorbed on water-insoluble high-polymeric compounds on the inner surfaces of a capillary device, a labelled antigen is then added and, following incubation, suching off of the test mixture and washing of the coated surfaces, the latter is measured for radioactivity. (VJ) [de

  12. Application of geostatistical methods to long-term safety analyses for radioactive waste repositories

    International Nuclear Information System (INIS)

    Roehlig, K.J.

    2001-01-01

    Long-term safety analyses are an important part of the design and optimisation process as well as of the licensing procedure for final repositories for radioactive waste in deep geological formations. For selected scenarios describing possible evolutions of the repository system in the post-closure phase, quantitative consequence analyses are performed. Due to the complexity of the phenomena of concern and the large timeframes under consideration, several types of uncertainties have to be taken into account. The modelling work for the far-field (geosphere) surrounding or overlaying the repository is based on model calculations concerning the groundwater movement and the resulting migration of radionuclides which possibly will be released from the repository. In contrast to engineered systems, the geosphere shows a strong spatial variability of facies, materials and material properties. The paper presented here describes the first steps towards a quantitative approach for an uncertainty assessment taking into account this variability. Due to the availability of a large amount of data and information of several types, the Gorleben site (Germany) has been used for a case study in order to demonstrate the method. (orig.)

  13. Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53.

    Directory of Open Access Journals (Sweden)

    Kristina Kirschner

    2015-03-01

    Full Text Available The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage and chronically activated (in senescent or pro-apoptotic conditions p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.

  14. Hemoglobin analyses in the Netherlands reveal more than 80 different variants including six novel ones.

    Science.gov (United States)

    van Zwieten, Rob; Veldthuis, Martijn; Delzenne, Barend; Berghuis, Jeffrey; Groen, Joke; Ait Ichou, Fatima; Clifford, Els; Harteveld, Cornelis L; Stroobants, An K

    2014-01-01

    More than 20,000 blood samples of individuals living in The Netherlands and suspected of hemolytic anemia or diabetes were analyzed by high resolution cation exchange high performance liquid chromatography (HPLC). Besides common disease-related hemoglobins (Hbs), rare variants were also detected. The variant Hbs were retrospectively analyzed by capillary zone electrophoresis (CZE) and by isoelectric focusing (IEF). For unambiguous identification, the globin genes were sequenced. Most of the 80 Hb variants detected by initial screening on HPLC were also separated by capillary electrophoresis (CE), but a few variants were only detectable with one of these methods. Some variants were unstable, had thalassemic properties or increased oxygen affinity, and some interfered with Hb A2 measurement, detection of sickle cell Hb or Hb A1c quantification. Two of the six novel variants, Hb Enschede (HBA2: c.308G  > A, p.Ser103Asn) and Hb Weesp (HBA1: c.301C > T, p.Leu101Phe), had no clinical consequences. In contrast, two others appeared clinically significant: Hb Ede (HBB: c.53A > T, p.Lys18Met) caused thalassemia and Hb Waterland (HBB: c.428C > T, pAla143Val) was related to mild polycytemia. Hb A2-Venlo (HBD: c.193G > A, p.Gly65Ser) and Hb A2-Rotterdam (HBD: c.38A > C, p.Asn13Thr) interfered with Hb A2 quantification. This survey shows that HPLC analysis followed by globin gene sequencing of rare variants is an effective method to reveal Hb variants.

  15. Big data analyses reveal patterns and drivers of the movements of southern elephant seals

    KAUST Repository

    Rodrí guez, J. P.; Ferná ndez-Gracia, Juan; Thums, Michele; Hindell, Mark A.; Sequeira, Ana M. M.; Meekan, Mark G.; Costa, Daniel P.; Guinet, Christophe; Harcourt, R.; McMahon, Clive R.; Muelbert, Monica; Duarte, Carlos M.; Eguí luz, V. M.

    2017-01-01

    The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with

  16. Big data analyses reveal patterns and drivers of the movements of southern elephant seals

    KAUST Repository

    Rodríguez, Jorge P.

    2017-03-02

    The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with

  17. Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin

    Science.gov (United States)

    Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-xian; Reiter, Russel J.; Zhang, Heng; Liu, Renyi; Chan, Zhulong

    2015-01-01

    Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. PMID:25225478

  18. Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis.

    Directory of Open Access Journals (Sweden)

    Jason Abernathy

    Full Text Available Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation. After a 12-week feeding trial with our selected strain and a control trout strain fed either a fishmeal-based diet or an all-plant protein diet, high-throughput RNA sequencing was completed on both liver and muscle tissues. Differential gene expression analyses, weighted correlation network analyses and further functional characterization were performed. A strain-by-diet design revealed differential expression ranging from a few dozen to over one thousand genes among the various comparisons and tissues. Major gene ontology groups identified between comparisons included those encompassing central, intermediary and foreign molecule metabolism, associated biosynthetic pathways as well as immunity. A systems approach indicated that genes involved in purine metabolism were highly perturbed. Systems analysis among the tissues tested further suggests the interplay between selection for growth, dietary utilization and protein tolerance may also have implications for nonspecific immunity. By combining data from differential gene expression and co-expression networks using selected trout, along with ontology and pathway analyses, a set of 63 candidate genes for plant diet tolerance was found. Risk loci in human inflammatory bowel diseases were also found in our datasets, indicating rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model.

  19. RNA-seq analyses reveal insights into the function of respiratory nitrate reductase of the diazotroph Herbaspirillum seropedicae.

    Science.gov (United States)

    Bonato, Paloma; Batista, Marcelo B; Camilios-Neto, Doumit; Pankievicz, Vânia C S; Tadra-Sfeir, Michelle Z; Monteiro, Rose Adele; Pedrosa, Fabio O; Souza, Emanuel M; Chubatsu, Leda S; Wassem, Roseli; Rigo, Liu Un

    2016-09-01

    Herbaspirillum seropedicae is a nitrogen-fixing β-proteobacterium that associates with roots of gramineous plants. In silico analyses revealed that H. seropedicae genome has genes encoding a putative respiratory (NAR) and an assimilatory nitrate reductase (NAS). To date, little is known about nitrate metabolism in H. seropedicae, and, as this bacterium cannot respire nitrate, the function of NAR remains unknown. This study aimed to investigate the function of NAR in H. seropedicae and how it metabolizes nitrate in a low aerated-condition. RNA-seq transcriptional profiling in the presence of nitrate allowed us to pinpoint genes important for nitrate metabolism in H. seropedicae, including nitrate transporters and regulatory proteins. Additionally, both RNA-seq data and physiological characterization of a mutant in the catalytic subunit of NAR (narG mutant) showed that NAR is not required for nitrate assimilation but is required for: (i) production of high levels of nitrite, (ii) production of NO and (iii) dissipation of redox power, which in turn lead to an increase in carbon consumption. In addition, wheat plants showed an increase in shoot dry weight only when inoculated with H. seropedicae wild type, but not with the narG mutant, suggesting that NAR is important to H. seropedicae-wheat interaction. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  20. Refining cost-effectiveness analyses using the net benefit approach and econometric methods: an example from a trial of anti-depressant treatment.

    Science.gov (United States)

    Sabes-Figuera, Ramon; McCrone, Paul; Kendricks, Antony

    2013-04-01

    Economic evaluation analyses can be enhanced by employing regression methods, allowing for the identification of important sub-groups and to adjust for imperfect randomisation in clinical trials or to analyse non-randomised data. To explore the benefits of combining regression techniques and the standard Bayesian approach to refine cost-effectiveness analyses using data from randomised clinical trials. Data from a randomised trial of anti-depressant treatment were analysed and a regression model was used to explore the factors that have an impact on the net benefit (NB) statistic with the aim of using these findings to adjust the cost-effectiveness acceptability curves. Exploratory sub-samples' analyses were carried out to explore possible differences in cost-effectiveness. Results The analysis found that having suffered a previous similar depression is strongly correlated with a lower NB, independent of the outcome measure or follow-up point. In patients with previous similar depression, adding an selective serotonin reuptake inhibitors (SSRI) to supportive care for mild-to-moderate depression is probably cost-effective at the level used by the English National Institute for Health and Clinical Excellence to make recommendations. This analysis highlights the need for incorporation of econometric methods into cost-effectiveness analyses using the NB approach.

  1. Application of digital image correlation method for analysing crack ...

    Indian Academy of Sciences (India)

    centrated strain by imitating the treatment of micro-cracks using the finite element ... water and moisture to penetrate the concrete leading to serious rust of the ... The correlations among various grey values of digital images are analysed for ...

  2. DNA sequence analyses reveal abundant diversity, endemism and evidence for Asian origin of the porcini mushrooms.

    Directory of Open Access Journals (Sweden)

    Bang Feng

    Full Text Available The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions.

  3. DNA Sequence Analyses Reveal Abundant Diversity, Endemism and Evidence for Asian Origin of the Porcini Mushrooms

    Science.gov (United States)

    Feng, Bang; Xu, Jianping; Wu, Gang; Zeng, Nian-Kai; Li, Yan-Chun; Tolgor, Bau; Kost, Gerhard W.; Yang, Zhu L.

    2012-01-01

    The wild gourmet mushroom Boletus edulis and its close allies are of significant ecological and economic importance. They are found throughout the Northern Hemisphere, but despite their ubiquity there are still many unresolved issues with regard to the taxonomy, systematics and biogeography of this group of mushrooms. Most phylogenetic studies of Boletus so far have characterized samples from North America and Europe and little information is available on samples from other areas, including the ecologically and geographically diverse regions of China. Here we analyzed DNA sequence variation in three gene markers from samples of these mushrooms from across China and compared our findings with those from other representative regions. Our results revealed fifteen novel phylogenetic species (about one-third of the known species) and a newly identified lineage represented by Boletus sp. HKAS71346 from tropical Asia. The phylogenetic analyses support eastern Asia as the center of diversity for the porcini sensu stricto clade. Within this clade, B. edulis is the only known holarctic species. The majority of the other phylogenetic species are geographically restricted in their distributions. Furthermore, molecular dating and geological evidence suggest that this group of mushrooms originated during the Eocene in eastern Asia, followed by dispersal to and subsequent speciation in other parts of Asia, Europe, and the Americas from the middle Miocene through the early Pliocene. In contrast to the ancient dispersal of porcini in the strict sense in the Northern Hemisphere, the occurrence of B. reticulatus and B. edulis sensu lato in the Southern Hemisphere was probably due to recent human-mediated introductions. PMID:22629418

  4. Combustion water purification techniques influence on OBT analysing using liquid scintillation counting method

    International Nuclear Information System (INIS)

    Varlam, C.; Vagner, I.; Faurescu, I.; Faurescu, D.

    2015-01-01

    In order to determine organically bound tritium (OBT) from environmental samples, these must be converted into water, measurable by liquid scintillation counting (LSC). For this purpose we conducted some experiments to determine OBT level of a grass sample collected from an uncontaminated area. The studied grass sample was combusted in a Parr bomb. However usual interfering phenomena were identified: color or chemical quench, chemiluminescence, overlap over tritium spectrum because of other radionuclides presence as impurities ( 14 C from organically compounds, 36 Cl as chloride and free chlorine, 40 K as potassium cations) and emulsion separation. So the purification of the combustion water before scintillation counting appeared to be essential. 5 purification methods were tested: distillation with chemical treatment (Na 2 O 2 and KMnO 4 ), lyophilization, chemical treatment (Na 2 O 2 and KMnO 4 ) followed by lyophilization, azeotropic distillation with toluene and treatment with a volcanic tuff followed by lyophilization. After the purification step each sample was measured and the OBT measured concentration, together with physico-chemical analysis of the water analyzed, revealed that the most efficient method applied for purification of the combustion water was the method using chemical treatment followed by lyophilization

  5. An on-line potentiometric sequential injection titration process analyser for the determination of acetic acid.

    Science.gov (United States)

    van Staden, J F; Mashamba, Mulalo G; Stefan, Raluca I

    2002-09-01

    An on-line potentiometric sequential injection titration process analyser for the determination of acetic acid is proposed. A solution of 0.1 mol L(-1) sodium chloride is used as carrier. Titration is achieved by aspirating acetic acid samples between two strong base-zone volumes into a holding coil and by channelling the stack of well-defined zones with flow reversal through a reaction coil to a potentiometric sensor where the peak widths were measured. A linear relationship between peak width and logarithm of the acid concentration was obtained in the range 1-9 g/100 mL. Vinegar samples were analysed without any sample pre-treatment. The method has a relative standard deviation of 0.4% with a sample frequency of 28 samples per hour. The results revealed good agreement between the proposed sequential injection and an automated batch titration method.

  6. Analyses of the internal structure of the oscillating vibro-packed fuels by the micro focus X-rays CT method

    International Nuclear Information System (INIS)

    Mizuta, Yasutoshi

    2003-02-01

    The purpose of this study is to support the development of vibro-packed fuel technology at Japan Nuclear Cycle Development Institute. 3-dimensional (3-D) data was built from the multi-cross sectional images obtained by the micro focus X-rays CT method in the vibro-packed fuel models. The structural analyses were carried out about the obtained 3-D CT images. The packing-rate distribution and the density distribution were measured as well as the number distribution of particles, etc. Consequently, it is obtained that vibrate conditions and a vibrating state have strong correlation, and it is also shown that the 3-D analyses of the internal structure by the micro focus X-rays CT method are effective in performance evaluation of vibro-packed fuels. (author)

  7. 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 10 2 CFU/100 cm 2 . 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.

  8. Application of annual ring analyses to the detection of smoke damage. I. A methodical contribution to the treatment of annual ring analyses

    Energy Technology Data Exchange (ETDEWEB)

    Vins, B

    1961-01-01

    Losses in growth of silvicultural stands caused by smoke can be measured by annual ring analysis. The method is advantageous mainly because the annual gains can be checked far into the past and thus compared with gains before the onset of the pollution. Experience gained in the Krusne Hory area of Czechoslovakia with the methodical processing of 2000 annual ring analyses is reviewed. The principal problem was that more than half the trees exposed to pollution failed to grow annual rings. At first no rings are added from the ground up to a certain height; then the defect spreads all the way into the crowns of the affected trees. This observation is of fundamental importance in the calculation of losses in growth gains due to industrial emissions because hitherto the last annual ring next to the bark was always identified with the test year, while in reality a number of annual rings might already have failed to grow due to the effects of pollution. Errors far exceeding permissible limits might have occurred in the analysis.

  9. The secondary stress analyses in the fuel pin cladding due to the swelling gradient across the wall thickness

    International Nuclear Information System (INIS)

    Uwaba, Tomoyuki; Ukai, Shigeharu

    2002-01-01

    Irradiation deformation analyses of FBR fuel cladding were made by using the finite element method. In these analyses the history of the stress occurred in the cladding was evaluated paying attention to the secondary stress induced by the swelling difference across the wall thickness. It was revealed that the difference of the swelling incubation dose in the direction of the thickness and the irradiation creep deformation play an important role in the history of the secondary stress. The effect of the stress-enhanced swelling was also analyzed in this study

  10. A comparative study between xerographic, computer-assisted overlay generation and animated-superimposition methods in bite mark analyses.

    Science.gov (United States)

    Tai, Meng Wei; Chong, Zhen Feng; Asif, Muhammad Khan; Rahmat, Rabiah A; Nambiar, Phrabhakaran

    2016-09-01

    This study was to compare the suitability and precision of xerographic and computer-assisted methods for bite mark investigations. Eleven subjects were asked to bite on their forearm and the bite marks were photographically recorded. Alginate impressions of the subjects' dentition were taken and their casts were made using dental stone. The overlays generated by xerographic method were obtained by photocopying the subjects' casts and the incisal edge outlines were then transferred on a transparent sheet. The bite mark images were imported into Adobe Photoshop® software and printed to life-size. The bite mark analyses using xerographically generated overlays were done by comparing an overlay to the corresponding printed bite mark images manually. In computer-assisted method, the subjects' casts were scanned into Adobe Photoshop®. The bite mark analyses using computer-assisted overlay generation were done by matching an overlay and the corresponding bite mark images digitally using Adobe Photoshop®. Another comparison method was superimposing the cast images with corresponding bite mark images employing the Adobe Photoshop® CS6 and GIF-Animator©. A score with a range of 0-3 was given during analysis to each precision-determining criterion and the score was increased with better matching. The Kruskal Wallis H test showed significant difference between the three sets of data (H=18.761, p<0.05). In conclusion, bite mark analysis using the computer-assisted animated-superimposition method was the most accurate, followed by the computer-assisted overlay generation and lastly the xerographic method. The superior precision contributed by digital method is discernible despite the human skin being a poor recording medium of bite marks. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  11. Integrative analyses of human reprogramming reveal dynamic nature of induced pluripotency

    Science.gov (United States)

    Cacchiarelli, Davide; Trapnell, Cole; Ziller, Michael J.; Soumillon, Magali; Cesana, Marcella; Karnik, Rahul; Donaghey, Julie; Smith, Zachary D.; Ratanasirintrawoot, Sutheera; Zhang, Xiaolan; Ho Sui, Shannan J.; Wu, Zhaoting; Akopian, Veronika; Gifford, Casey A.; Doench, John; Rinn, John L.; Daley, George Q.; Meissner, Alexander; Lander, Eric S.; Mikkelsen, Tarjei S.

    2015-01-01

    Summary Induced pluripotency is a promising avenue for disease modeling and therapy, but the molecular principles underlying this process, particularly in human cells, remain poorly understood due to donor-to-donor variability and intercellular heterogeneity. Here we constructed and characterized a clonal, inducible human reprogramming system that provides a reliable source of cells at any stage of the process. This system enabled integrative transcriptional and epigenomic analysis across the human reprogramming timeline at high resolution. We observed distinct waves of gene network activation, including the ordered reactivation of broad developmental regulators followed by early embryonic patterning genes and culminating in the emergence of a signature reminiscent of pre-implantation stages. Moreover, complementary functional analyses allowed us to identify and validate novel regulators of the reprogramming process. Altogether, this study sheds light on the molecular underpinnings of induced pluripotency in human cells and provides a robust cell platform for further studies. PMID:26186193

  12. Non-invasive genetics outperforms morphological methods in faecal dietary analysis, revealing wild boar as a considerable conservation concern for ground-nesting birds.

    Science.gov (United States)

    Oja, Ragne; Soe, Egle; Valdmann, Harri; Saarma, Urmas

    2017-01-01

    Capercaillie (Tetrao urogallus) and other grouse species represent conservation concerns across Europe due to their negative abundance trends. In addition to habitat deterioration, predation is considered a major factor contributing to population declines. While the role of generalist predators on grouse predation is relatively well known, the impact of the omnivorous wild boar has remained elusive. We hypothesize that wild boar is an important predator of ground-nesting birds, but has been neglected as a bird predator because traditional morphological methods underestimate the proportion of birds in wild boar diet. To distinguish between different mammalian predator species, as well as different grouse prey species, we developed a molecular method based on the analysis of mitochondrial DNA that allows accurate species identification. We collected 109 wild boar faeces at protected capercaillie leks and surrounding areas and analysed bird consumption using genetic methods and classical morphological examination. Genetic analysis revealed that the proportion of birds in wild boar faeces was significantly higher (17.3%; 4.5×) than indicated by morphological examination (3.8%). Moreover, the genetic method allowed considerably more precise taxonomic identification of consumed birds compared to morphological analysis. Our results demonstrate: (i) the value of using genetic approaches in faecal dietary analysis due to their higher sensitivity, and (ii) that wild boar is an important predator of ground-nesting birds, deserving serious consideration in conservation planning for capercaillie and other grouse.

  13. Methods in pharmacoepidemiology: a review of statistical analyses and data reporting in pediatric drug utilization studies.

    Science.gov (United States)

    Sequi, Marco; Campi, Rita; Clavenna, Antonio; Bonati, Maurizio

    2013-03-01

    To evaluate the quality of data reporting and statistical methods performed in drug utilization studies in the pediatric population. Drug utilization studies evaluating all drug prescriptions to children and adolescents published between January 1994 and December 2011 were retrieved and analyzed. For each study, information on measures of exposure/consumption, the covariates considered, descriptive and inferential analyses, statistical tests, and methods of data reporting was extracted. An overall quality score was created for each study using a 12-item checklist that took into account the presence of outcome measures, covariates of measures, descriptive measures, statistical tests, and graphical representation. A total of 22 studies were reviewed and analyzed. Of these, 20 studies reported at least one descriptive measure. The mean was the most commonly used measure (18 studies), but only five of these also reported the standard deviation. Statistical analyses were performed in 12 studies, with the chi-square test being the most commonly performed test. Graphs were presented in 14 papers. Sixteen papers reported the number of drug prescriptions and/or packages, and ten reported the prevalence of the drug prescription. The mean quality score was 8 (median 9). Only seven of the 22 studies received a score of ≥10, while four studies received a score of statistical methods and reported data in a satisfactory manner. We therefore conclude that the methodology of drug utilization studies needs to be improved.

  14. Combined metabonomic and quantitative real-time PCR analyses reveal systems metabolic changes in Jurkat T-cells treated with HIV-1 Tat protein.

    Science.gov (United States)

    Liao, Wenting; Tan, Guangguo; Zhu, Zhenyu; Chen, Qiuli; Lou, Ziyang; Dong, Xin; Zhang, Wei; Pan, Wei; Chai, Yifeng

    2012-11-02

    HIV-1 Tat protein is released by infected cells and can affect bystander uninfected T cells and induce numerous biological responses which contribute to its pathogenesis. To elucidate the complex pathogenic mechanism, we conducted a comprehensive investigation on Tat protein-related extracellular and intracellular metabolic changes in Jurkat T-cells using combined gas chromatography-mass spectrometry (GC-MS), reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) and a hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS)-based metabonomics approach. Quantitative real-time PCR (qRT-PCR) analyses were further employed to measure expressions of several relevant enzymes together with perturbed metabolic pathways. Combined metabonomic and qRT-PCR analyses revealed that HIV-1 Tat caused significant and comprehensive metabolic changes, as represented by significant changes of 37 metabolites and 10 relevant enzymes in HIV-1 Tat-treated cells. Using MetaboAnalyst 2.0, it was found that 11 pathways (Impact-value >0.10) among the regulated pathways were acutely perturbed, including sphingolipid metabolism, glycine, serine and threonine metabolism, pyruvate metabolism, inositol phosphate metabolism, arginine and proline metabolism, citrate cycle, phenylalanine metabolism, tryptophan metabolism, pentose phosphate pathway, glycerophospholipid metabolism, glycolysis or gluconeogenesis. These results provide metabolic evidence of the complex pathogenic mechanism of HIV-1 Tat protein as a "viral toxin", and would help obligate Tat protein as "an important target" for therapeutic intervention and vaccine development.

  15. Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of improved abiotic stress resistance in bermudagrass [Cynodon dactylon (L). Pers.] by exogenous melatonin.

    Science.gov (United States)

    Shi, Haitao; Jiang, Chuan; Ye, Tiantian; Tan, Dun-Xian; Reiter, Russel J; Zhang, Heng; Liu, Renyi; Chan, Zhulong

    2015-02-01

    Melatonin (N-acetyl-5-methoxytryptamine), a well-known animal hormone, is also involved in plant development and abiotic stress responses. In this study, it is shown that exogenous application of melatonin conferred improved salt, drought, and cold stress resistances in bermudagrass. Moreover, exogenous melatonin treatment alleviated reactive oxygen species (ROS) burst and cell damage induced by abiotic stress; this involved activation of several antioxidants. Additionally, melatonin-pre-treated plants exhibited higher concentrations of 54 metabolites, including amino acids, organic acids, sugars, and sugar alcohols, than non-treated plants under abiotic stress conditions. Genome-wide transcriptomic profiling identified 3933 transcripts (2361 up-regulated and 1572 down-regulated) that were differentially expressed in melatonin-treated plants versus controls. Pathway and gene ontology (GO) term enrichment analyses revealed that genes involved in nitrogen metabolism, major carbohydrate metabolism, tricarboxylic acid (TCA)/org transformation, transport, hormone metabolism, metal handling, redox, and secondary metabolism were over-represented after melatonin pre-treatment. Taken together, this study provides the first evidence of the protective roles of exogenous melatonin in the bermudagrass response to abiotic stresses, partially via activation of antioxidants and modulation of metabolic homeostasis. Notably, metabolic and transcriptomic analyses showed that the underlying mechanisms of melatonin could involve major reorientation of photorespiratory and carbohydrate and nitrogen metabolism. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  16. An application of the explicit method for analysing intersystem dependencies in the evaluation of event trees

    International Nuclear Information System (INIS)

    Oliveira, L.F.S. de; Frutuoso e Melo, P.F.F.; Lima, J.E.P.; Stal, I.L.

    1985-01-01

    A computacional application of the explicit method for analyzing event trees in the context of probabilistic risk assessments is discussed. A detailed analysis of the explicit method is presented, including the train level analysis (TLA) of safety systems and the impact vector method. It is shown that the penalty for not adopting TLA is that in some cases non-conservative results may be reached. The impact vector method can significantly reduce the number of sequences to be considered, and its use has inspired the definition of a dependency matrix, which enables the proper running of a computer code especially developed for analysing event trees. The code has been extensively used in the Angra 1 PRA currently underway. In its present version it gives as output the dominant sequences for each given initiator, properly classiying them in core-degradation classes as specified by the user. (Author) [pt

  17. Analysis of the accuracy of certain methods used for measuring very low reactivities; Analyse de la precision de certaines methodes de mesure de tres basses reactivites

    Energy Technology Data Exchange (ETDEWEB)

    Valat, J; Stern, T E

    1964-07-01

    The rapid measurement of anti-reactivities, in particular very low ones (i.e. a few tens of {beta}) appears to be an interesting method for the automatic start-up a reactor and its optimisation. With this in view, the present report explores the various methods studied essentially from the point of view of the time required for making the measurement with a given statistical accuracy, especially as far as very low activities are concerned. The statistical analysis is applied in turn to: the methods for the natural background noise (auto-correlation and spectral density); the sinusoidal excitation methods for the reactivity or the source, with synchronous detection ; the periodic source excitation method using pulsed neutrons. Finally, the statistical analysis leads to the suggestion of a new method of source excitation using neutronic random square waves combined with an intercorrelation between the random excitation and the resulting output. (authors) [French] La mesure rapide des antireactivites, en particulier celle des tres basses (soit quelques dizaines de {beta}), apparait comme une voie interessante pour le demarrage automatique d'un reacteur et son optimalisation. Dans cette optique, le present rapport explore diverses methodes etudiees essentiellement sous l'angle de la duree de mesure necessaire a une precision relative statistique donnee, plus particulierement en ce qui concerne les tres basses reactivites. L'analyse statistique porte successivement sur: les methodes du bruit de fond naturel (autocorrelation et densite spectrale); les methodes d'excitation sinusoidale de reactivite ou de source, avec detection synchrone; la methode d'excitation periodique de source par neutrons pulses. Enfin l'analyse statistique amene a proposer une methode nouvelle d'excitation de source par creneaux neutroniques aleatoires alliee a une intercorrelation entre l'excitation aleatoire et la sortie resultante. (auteurs)

  18. Utilisation of best estimate system codes and best estimate methods in safety analyses of VVER reactors in the Czech Republic

    International Nuclear Information System (INIS)

    Macek, Jiri; Kral, Pavel

    2010-01-01

    The content of the presentation was as follows: Conservative versus best estimate approach, Brief description and selection of methodology, Description of uncertainty methods, Examples of the BE methodology. It is concluded that where BE computer codes are used, uncertainty and sensitivity analyses should be included; if best estimate codes + uncertainty are used, the safety margins increase; and BE + BSA is the next step in licensing analyses. (P.A.)

  19. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks

    Science.gov (United States)

    Glicksberg, Benjamin S.; Li, Li; Badgeley, Marcus A.; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D.; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L.; Hoffman, Gabriel E.; Dan Li, Shuyu; Schadt, Eric E.; Patel, Chirag J.; Chen, Rong; Dudley, Joel T.

    2016-01-01

    Motivation: Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). Results: We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key ‘hub’ diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. Contacts: rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307606

  20. Exploratory Metabolomic Analyses Reveal Compounds Correlated with Lutein Concentration in Frontal Cortex, Hippocampus, and Occipital Cortex of Human Infant Brain.

    Directory of Open Access Journals (Sweden)

    Jacqueline C Lieblein-Boff

    Full Text Available Lutein is a dietary carotenoid well known for its role as an antioxidant in the macula, and recent reports implicate a role for lutein in cognitive function. Lutein is the dominant carotenoid in both pediatric and geriatric brain tissue. In addition, cognitive function in older adults correlated with macular and postmortem brain lutein concentrations. Furthermore, lutein was found to preferentially accumulate in the infant brain in comparison to other carotenoids that are predominant in diet. While lutein is consistently related to cognitive function, the mechanisms by which lutein may influence cognition are not clear. In an effort to identify potential mechanisms through which lutein might influence neurodevelopment, an exploratory study relating metabolite signatures and lutein was completed. Post-mortem metabolomic analyses were performed on human infant brain tissues in three regions important for learning and memory: the frontal cortex, hippocampus, and occipital cortex. Metabolomic profiles were compared to lutein concentration, and correlations were identified and reported here. A total of 1276 correlations were carried out across all brain regions. Of 427 metabolites analyzed, 257 were metabolites of known identity. Unidentified metabolite correlations (510 were excluded. In addition, moderate correlations with xenobiotic relationships (2 or those driven by single outliers (3 were excluded from further study. Lutein concentrations correlated with lipid pathway metabolites, energy pathway metabolites, brain osmolytes, amino acid neurotransmitters, and the antioxidant homocarnosine. These correlations were often brain region-specific. Revealing relationships between lutein and metabolic pathways may help identify potential candidates on which to complete further analyses and may shed light on important roles of lutein in the human brain during development.

  1. Combustion water purification techniques influence on OBT analysing using liquid scintillation counting method

    Energy Technology Data Exchange (ETDEWEB)

    Varlam, C.; Vagner, I.; Faurescu, I.; Faurescu, D. [National Institute for Cryogenics and Isotopic Technologies, Valcea (Romania)

    2015-03-15

    In order to determine organically bound tritium (OBT) from environmental samples, these must be converted into water, measurable by liquid scintillation counting (LSC). For this purpose we conducted some experiments to determine OBT level of a grass sample collected from an uncontaminated area. The studied grass sample was combusted in a Parr bomb. However usual interfering phenomena were identified: color or chemical quench, chemiluminescence, overlap over tritium spectrum because of other radionuclides presence as impurities ({sup 14}C from organically compounds, {sup 36}Cl as chloride and free chlorine, {sup 40}K as potassium cations) and emulsion separation. So the purification of the combustion water before scintillation counting appeared to be essential. 5 purification methods were tested: distillation with chemical treatment (Na{sub 2}O{sub 2} and KMnO{sub 4}), lyophilization, chemical treatment (Na{sub 2}O{sub 2} and KMnO{sub 4}) followed by lyophilization, azeotropic distillation with toluene and treatment with a volcanic tuff followed by lyophilization. After the purification step each sample was measured and the OBT measured concentration, together with physico-chemical analysis of the water analyzed, revealed that the most efficient method applied for purification of the combustion water was the method using chemical treatment followed by lyophilization.

  2. A DNA microarray-based methylation-sensitive (MS)-AFLP hybridization method for genetic and epigenetic analyses.

    Science.gov (United States)

    Yamamoto, F; Yamamoto, M

    2004-07-01

    We previously developed a PCR-based DNA fingerprinting technique named the Methylation Sensitive (MS)-AFLP method, which permits comparative genome-wide scanning of methylation status with a manageable number of fingerprinting experiments. The technique uses the methylation sensitive restriction enzyme NotI in the context of the existing Amplified Fragment Length Polymorphism (AFLP) method. Here we report the successful conversion of this gel electrophoresis-based DNA fingerprinting technique into a DNA microarray hybridization technique (DNA Microarray MS-AFLP). By performing a total of 30 (15 x 2 reciprocal labeling) DNA Microarray MS-AFLP hybridization experiments on genomic DNA from two breast and three prostate cancer cell lines in all pairwise combinations, and Southern hybridization experiments using more than 100 different probes, we have demonstrated that the DNA Microarray MS-AFLP is a reliable method for genetic and epigenetic analyses. No statistically significant differences were observed in the number of differences between the breast-prostate hybridization experiments and the breast-breast or prostate-prostate comparisons.

  3. Development and verification of an efficient spatial neutron kinetics method for reactivity-initiated event analyses

    International Nuclear Information System (INIS)

    Ikeda, Hideaki; Takeda, Toshikazu

    2001-01-01

    A space/time nodal diffusion code based on the nodal expansion method (NEM), EPISODE, was developed in order to evaluate transient neutron behavior in light water reactor cores. The present code employs the improved quasistatic (IQS) method for spatial neutron kinetics, and neutron flux distribution is numerically obtained by solving the neutron diffusion equation with the nonlinear iteration scheme to achieve fast computation. A predictor-corrector (PC) method developed in the present study enabled to apply a coarse time mesh to the transient spatial neutron calculation than that applicable in the conventional IQS model, which improved computational efficiency further. Its computational advantage was demonstrated by applying to the numerical benchmark problems that simulate reactivity-initiated events, showing reduction of computational times up to a factor of three than the conventional IQS. The thermohydraulics model was also incorporated in EPISODE, and the capability of realistic reactivity event analyses was verified using the SPERT-III/E-Core experimental data. (author)

  4. Comparative Genome Analyses of Serratia marcescens FS14 Reveals Its High Antagonistic Potential

    Science.gov (United States)

    Li, Pengpeng; Kwok, Amy H. Y.; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C.

    2015-01-01

    S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens. PMID:25856195

  5. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

    Science.gov (United States)

    Li, Pengpeng; Kwok, Amy H Y; Jiang, Jingwei; Ran, Tingting; Xu, Dongqing; Wang, Weiwu; Leung, Frederick C

    2015-01-01

    S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs) in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

  6. Kinds of access: different methods for report reveal different kinds of metacognitive access

    Science.gov (United States)

    Overgaard, Morten; Sandberg, Kristian

    2012-01-01

    In experimental investigations of consciousness, participants are asked to reflect upon their own experiences by issuing reports about them in different ways. For this reason, a participant needs some access to the content of her own conscious experience in order to report. In such experiments, the reports typically consist of some variety of ratings of confidence or direct descriptions of one's own experiences. Whereas different methods of reporting are typically used interchangeably, recent experiments indicate that different results are obtained with different kinds of reporting. We argue that there is not only a theoretical, but also an empirical difference between different methods of reporting. We hypothesize that differences in the sensitivity of different scales may reveal that different types of access are used to issue direct reports about experiences and metacognitive reports about the classification process. PMID:22492747

  7. A New Optimization Method for Centrifugal Compressors Based on 1D Calculations and Analyses

    Directory of Open Access Journals (Sweden)

    Pei-Yuan Li

    2015-05-01

    Full Text Available This paper presents an optimization design method for centrifugal compressors based on one-dimensional calculations and analyses. It consists of two parts: (1 centrifugal compressor geometry optimization based on one-dimensional calculations and (2 matching optimization of the vaned diffuser with an impeller based on the required throat area. A low pressure stage centrifugal compressor in a MW level gas turbine is optimized by this method. One-dimensional calculation results show that D3/D2 is too large in the original design, resulting in the low efficiency of the entire stage. Based on the one-dimensional optimization results, the geometry of the diffuser has been redesigned. The outlet diameter of the vaneless diffuser has been reduced, and the original single stage diffuser has been replaced by a tandem vaned diffuser. After optimization, the entire stage pressure ratio is increased by approximately 4%, and the efficiency is increased by approximately 2%.

  8. Neuroanatomical heterogeneity of schizophrenia revealed by semi-supervised machine learning methods.

    Science.gov (United States)

    Honnorat, Nicolas; Dong, Aoyan; Meisenzahl-Lechner, Eva; Koutsouleris, Nikolaos; Davatzikos, Christos

    2017-12-20

    Schizophrenia is associated with heterogeneous clinical symptoms and neuroanatomical alterations. In this work, we aim to disentangle the patterns of neuroanatomical alterations underlying a heterogeneous population of patients using a semi-supervised clustering method. We apply this strategy to a cohort of patients with schizophrenia of varying extends of disease duration, and we describe the neuroanatomical, demographic and clinical characteristics of the subtypes discovered. We analyze the neuroanatomical heterogeneity of 157 patients diagnosed with Schizophrenia, relative to a control population of 169 subjects, using a machine learning method called CHIMERA. CHIMERA clusters the differences between patients and a demographically-matched population of healthy subjects, rather than clustering patients themselves, thereby specifically assessing disease-related neuroanatomical alterations. Voxel-Based Morphometry was conducted to visualize the neuroanatomical patterns associated with each group. The clinical presentation and the demographics of the groups were then investigated. Three subgroups were identified. The first two differed substantially, in that one involved predominantly temporal-thalamic-peri-Sylvian regions, whereas the other involved predominantly frontal regions and the thalamus. Both subtypes included primarily male patients. The third pattern was a mix of these two and presented milder neuroanatomic alterations and comprised a comparable number of men and women. VBM and statistical analyses suggest that these groups could correspond to different neuroanatomical dimensions of schizophrenia. Our analysis suggests that schizophrenia presents distinct neuroanatomical variants. This variability points to the need for a dimensional neuroanatomical approach using data-driven, mathematically principled multivariate pattern analysis methods, and should be taken into account in clinical studies. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis

    Directory of Open Access Journals (Sweden)

    Couturier Marie

    2012-02-01

    Full Text Available Abstract Background Filamentous fungi are potent biomass degraders due to their ability to thrive in ligno(hemicellulose-rich environments. During the last decade, fungal genome sequencing initiatives have yielded abundant information on the genes that are putatively involved in lignocellulose degradation. At present, additional experimental studies are essential to provide insights into the fungal secreted enzymatic pools involved in lignocellulose degradation. Results In this study, we performed a wide analysis of 20 filamentous fungi for which genomic data are available to investigate their biomass-hydrolysis potential. A comparison of fungal genomes and secretomes using enzyme activity profiling revealed discrepancies in carbohydrate active enzymes (CAZymes sets dedicated to plant cell wall. Investigation of the contribution made by each secretome to the saccharification of wheat straw demonstrated that most of them individually supplemented the industrial Trichoderma reesei CL847 enzymatic cocktail. Unexpectedly, the most striking effect was obtained with the phytopathogen Ustilago maydis that improved the release of total sugars by 57% and of glucose by 22%. Proteomic analyses of the best-performing secretomes indicated a specific enzymatic mechanism of U. maydis that is likely to involve oxido-reductases and hemicellulases. Conclusion This study provides insight into the lignocellulose-degradation mechanisms by filamentous fungi and allows for the identification of a number of enzymes that are potentially useful to further improve the industrial lignocellulose bioconversion process.

  10. Analyses in zebrafish embryos reveal that nanotoxicity profiles are dependent on surface-functionalization controlled penetrance of biological membranes.

    Science.gov (United States)

    Paatero, Ilkka; Casals, Eudald; Niemi, Rasmus; Özliseli, Ezgi; Rosenholm, Jessica M; Sahlgren, Cecilia

    2017-08-21

    Mesoporous silica nanoparticles (MSNs) are extensively explored as drug delivery systems, but in depth understanding of design-toxicity relationships is still scarce. We used zebrafish (Danio rerio) embryos to study toxicity profiles of differently surface functionalized MSNs. Embryos with the chorion membrane intact, or dechoroniated embryos, were incubated or microinjected with amino (NH 2 -MSNs), polyethyleneimine (PEI-MSNs), succinic acid (SUCC-MSNs) or polyethyleneglycol (PEG-MSNs) functionalized MSNs. Toxicity was assessed by viability and cardiovascular function. NH 2 -MSNs, SUCC-MSNs and PEG-MSNs were well tolerated, 50 µg/ml PEI-MSNs induced 100% lethality 48 hours post fertilization (hpf). Dechoroniated embryos were more sensitive and 10 µg/ml PEI-MSNs reduced viability to 5% at 96hpf. Sensitivity to PEG- and SUCC-, but not NH 2 -MSNs, was also enhanced. Typically cardiovascular toxicity was evident prior to lethality. Confocal microscopy revealed that PEI-MSNs penetrated into the embryos whereas PEG-, NH2- and SUCC-MSNs remained aggregated on the skin surface. Direct exposure of inner organs by microinjecting NH 2 -MSNs and PEI-MSNs demonstrated that the particles displayed similar toxicity indicating that functionalization affects the toxicity profile by influencing penetrance through biological barriers. The data emphasize the need for careful analyses of toxicity mechanisms in relevant models and constitute an important knowledge step towards the development of safer and sustainable nanotherapies.

  11. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain.

    Directory of Open Access Journals (Sweden)

    Rajini Sreenivasan

    Full Text Available BACKGROUND: Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs. METHODOLOGY/PRINCIPAL FINDINGS: We have identified 116638 gonad-derived zebrafish expressed sequence tags (ESTs, 21% of which were isolated in our lab. Following in silico normalization, we constructed a gonad-derived microarray comprising 6370 unique, full-length cDNAs from differentiating and adult gonads. Labeled targets from adult gonad, brain, kidney and 'rest-of-body' from both sexes were hybridized onto the microarray. Our analyses revealed 1366, 881 and 656 differentially expressed transcripts (34.7% novel that showed highest expression in ovary, testis and both gonads respectively. Hierarchical clustering showed correlation of the two gonadal transcriptomes and their similarities to those of the brains. In addition, we have identified 276 genes showing sexually dimorphic expression both between the brains and between the gonads. By in situ hybridization, we showed that the gonadal transcripts with the strongest array signal intensities were germline-expressed. We found that five members of the GTP-binding septin gene family, from which only one member (septin 4 has previously been implicated in reproduction in mice, were all strongly expressed in the gonads. CONCLUSIONS/SIGNIFICANCE: We have generated a gonad-derived zebrafish cDNA microarray and demonstrated its usefulness in identifying genes with sexually dimorphic co-expression in both the gonads and the brains. We have also provided the first evidence of large-scale differential gene expression between female and male brains of a teleost. Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations. Since several genes have been shown to play similar

  12. Comparative genome analyses of Serratia marcescens FS14 reveals its high antagonistic potential.

    Directory of Open Access Journals (Sweden)

    Pengpeng Li

    Full Text Available S. marcescens FS14 was isolated from an Atractylodes macrocephala Koidz plant that was infected by Fusarium oxysporum and showed symptoms of root rot. With the completion of the genome sequence of FS14, the first comprehensive comparative-genomic analysis of the Serratia genus was performed. Pan-genome and COG analyses showed that the majority of the conserved core genes are involved in basic cellular functions, while genomic factors such as prophages contribute considerably to genome diversity. Additionally, a Type I restriction-modification system, a Type III secretion system and tellurium resistance genes are found in only some Serratia species. Comparative analysis further identified that S. marcescens FS14 possesses multiple mechanisms for antagonism against other microorganisms, including the production of prodigiosin, bacteriocins, and multi-antibiotic resistant determinants as well as chitinases. The presence of two evolutionarily distinct Type VI secretion systems (T6SSs in FS14 may provide further competitive advantages for FS14 against other microbes. To our knowledge, this is the first report of comparative analysis on T6SSs in the genus, which identifies four types of T6SSs in Serratia spp.. Competition bioassays of FS14 against the vital plant pathogenic bacterium Ralstonia solanacearum and fungi Fusarium oxysporum and Sclerotinia sclerotiorum were performed to support our genomic analyses, in which FS14 demonstrated high antagonistic activities against both bacterial and fungal phytopathogens.

  13. Measurement System Analyses - Gauge Repeatability and Reproducibility Methods

    Science.gov (United States)

    Cepova, Lenka; Kovacikova, Andrea; Cep, Robert; Klaput, Pavel; Mizera, Ondrej

    2018-02-01

    The submitted article focuses on a detailed explanation of the average and range method (Automotive Industry Action Group, Measurement System Analysis approach) and of the honest Gauge Repeatability and Reproducibility method (Evaluating the Measurement Process approach). The measured data (thickness of plastic parts) were evaluated by both methods and their results were compared on the basis of numerical evaluation. Both methods were additionally compared and their advantages and disadvantages were discussed. One difference between both methods is the calculation of variation components. The AIAG method calculates the variation components based on standard deviation (then a sum of variation components does not give 100 %) and the honest GRR study calculates the variation components based on variance, where the sum of all variation components (part to part variation, EV & AV) gives the total variation of 100 %. Acceptance of both methods among the professional society, future use, and acceptance by manufacturing industry were also discussed. Nowadays, the AIAG is the leading method in the industry.

  14. Practicable methods for histological section thickness measurement in quantitative stereological analyses.

    Science.gov (United States)

    Matenaers, Cyrill; Popper, Bastian; Rieger, Alexandra; Wanke, Rüdiger; Blutke, Andreas

    2018-01-01

    The accuracy of quantitative stereological analysis tools such as the (physical) disector method substantially depends on the precise determination of the thickness of the analyzed histological sections. One conventional method for measurement of histological section thickness is to re-embed the section of interest vertically to its original section plane. The section thickness is then measured in a subsequently prepared histological section of this orthogonally re-embedded sample. However, the orthogonal re-embedding (ORE) technique is quite work- and time-intensive and may produce inaccurate section thickness measurement values due to unintentional slightly oblique (non-orthogonal) positioning of the re-embedded sample-section. Here, an improved ORE method is presented, allowing for determination of the factual section plane angle of the re-embedded section, and correction of measured section thickness values for oblique (non-orthogonal) sectioning. For this, the analyzed section is mounted flat on a foil of known thickness (calibration foil) and both the section and the calibration foil are then vertically (re-)embedded. The section angle of the re-embedded section is then calculated from the deviation of the measured section thickness of the calibration foil and its factual thickness, using basic geometry. To find a practicable, fast, and accurate alternative to ORE, the suitability of spectral reflectance (SR) measurement for determination of plastic section thicknesses was evaluated. Using a commercially available optical reflectometer (F20, Filmetrics®, USA), the thicknesses of 0.5 μm thick semi-thin Epon (glycid ether)-sections and of 1-3 μm thick plastic sections (glycolmethacrylate/ methylmethacrylate, GMA/MMA), as regularly used in physical disector analyses, could precisely be measured within few seconds. Compared to the measured section thicknesses determined by ORE, SR measures displayed less than 1% deviation. Our results prove the applicability

  15. Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks.

    Science.gov (United States)

    Glicksberg, Benjamin S; Li, Li; Badgeley, Marcus A; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L; Hoffman, Gabriel E; Dan Li, Shuyu; Schadt, Eric E; Patel, Chirag J; Chen, Rong; Dudley, Joel T

    2016-06-15

    Underrepresentation of racial groups represents an important challenge and major gap in phenomics research. Most of the current human phenomics research is based primarily on European populations; hence it is an important challenge to expand it to consider other population groups. One approach is to utilize data from EMR databases that contain patient data from diverse demographics and ancestries. The implications of this racial underrepresentation of data can be profound regarding effects on the healthcare delivery and actionability. To the best of our knowledge, our work is the first attempt to perform comparative, population-scale analyses of disease networks across three different populations, namely Caucasian (EA), African American (AA) and Hispanic/Latino (HL). We compared susceptibility profiles and temporal connectivity patterns for 1988 diseases and 37 282 disease pairs represented in a clinical population of 1 025 573 patients. Accordingly, we revealed appreciable differences in disease susceptibility, temporal patterns, network structure and underlying disease connections between EA, AA and HL populations. We found 2158 significantly comorbid diseases for the EA cohort, 3265 for AA and 672 for HL. We further outlined key disease pair associations unique to each population as well as categorical enrichments of these pairs. Finally, we identified 51 key 'hub' diseases that are the focal points in the race-centric networks and of particular clinical importance. Incorporating race-specific disease comorbidity patterns will produce a more accurate and complete picture of the disease landscape overall and could support more precise understanding of disease relationships and patient management towards improved clinical outcomes. rong.chen@mssm.edu or joel.dudley@mssm.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  16. Development of the evaluation methods in reactor safety analyses and core characteristics

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-08-15

    In order to support the safety reviews by NRA on reactor safety design including the phenomena with multiple failures, the computer codes are developed and the safety evaluations with analyses are performed in the areas of thermal hydraulics and core characteristics evaluation. In the code preparation of safety analyses, the TRACE and RELAP5 code were prepared to conduct the safety analyses of LOCA and beyond design basis accidents with multiple failures. In the core physics code preparation, the functions of sensitivity and uncertainty analysis were incorporated in the lattice physics code CASMO-4. The verification of improved CASMO-4 /SIMULATE-3 was continued by using core physics data. (author)

  17. Combined Metabonomic and Quantitative RT-PCR Analyses Revealed Metabolic Reprogramming Associated with Fusarium graminearum Resistance in Transgenic Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Fangfang Chen

    2018-01-01

    Full Text Available Fusarium head blight disease resulting from Fusarium graminearum (FG infection causes huge losses in global production of cereals and development of FG-resistant plants is urgently needed. To understand biochemistry mechanisms for FG resistance, here, we have systematically investigated the plant metabolomic phenotypes associated with FG resistance for transgenic Arabidopsis thaliana expressing a class-I chitinase (Chi, a Fusarium-specific recombinant antibody gene (CWP2 and fused Chi-CWP2. Plant disease indices, mycotoxin levels, metabonomic characteristics, and expression levels of several key genes were measured together with their correlations. We found that A. thaliana expressing Chi-CWP2 showed higher FG resistance with much lower disease indices and mycotoxin levels than the wild-type and the plants expressing Chi or CWP2 alone. The combined metabonomic and quantitative RT-PCR analyses revealed that such FG-resistance was closely associated with the promoted biosynthesis of secondary metabolites (phenylpropanoids, alkanoids and organic osmolytes (proline, betaine, glucose, myo-inositol together with enhanced TCA cycle and GABA shunt. These suggest that the concurrently enhanced biosyntheses of the shikimate-mediated secondary metabolites and organic osmolytes be an important strategy for A. thaliana to develop and improve FG resistance. These findings provide essential biochemical information related to FG resistance which is important for developing FG-resistant cereals.

  18. Normalization Methods and Selection Strategies for Reference Materials in Stable Isotope Analyses - Review

    International Nuclear Information System (INIS)

    Skrzypek, G.; Sadler, R.; Paul, D.; Forizs, I.

    2011-01-01

    A stable isotope analyst has to make a number of important decisions regarding how to best determine the 'true' stable isotope composition of analysed samples in reference to an international scale. It has to be decided which reference materials should be used, the number of reference materials and how many repetitions of each standard is most appropriate for a desired level of precision, and what normalization procedure should be selected. In this paper we summarise what is known about propagation of uncertainties associated with normalization procedures and propagation of uncertainties associated with reference materials used as anchors for the determination of 'true' values for δ''1''3C and δ''1''8O. Normalization methods Several normalization methods transforming the 'raw' value obtained from mass spectrometers to one of the internationally recognized scales has been developed. However, as summarised by Paul et al. different normalization transforms alone may lead to inconsistencies between laboratories. The most common normalization procedures are: single-point anchoring (versus working gas and certified reference standard), modified single-point normalization, linear shift between the measured and the true isotopic composition of two certified reference standards, two-point and multipoint linear normalization methods. The accuracy of these various normalization methods has been compared by using analytical laboratory data by Paul et al., with the single-point and normalization versus tank calibrations resulting in the largest normalization errors, and that also exceed the analytical uncertainty recommended for δ 13 C. The normalization error depends greatly on the relative differences between the stable isotope composition of the reference material and the sample. On the other hand, the normalization methods using two or more certified reference standards produces a smaller normalization error, if the reference materials are bracketing the whole range of

  19. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    KAUST Repository

    Ferreira, Ari J S

    2014-06-12

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world\\'s oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  20. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    KAUST Repository

    Ferreira, Ari J S; Siam, Rania; Setubal, Joã o C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvä slaiho, Heikki; Ramadan, Eman; Antunes, André ; Stingl, Ulrich; Archer, John A.C.; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

    2014-01-01

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  1. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    Directory of Open Access Journals (Sweden)

    Ari J S Ferreira

    Full Text Available Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

  2. Multiple Spectral Ratio Analyses Reveal Earthquake Source Spectra of Small Earthquakes and Moment Magnitudes of Microearthquakes

    Science.gov (United States)

    Uchide, T.; Imanishi, K.

    2016-12-01

    Spectral studies for macroscopic earthquake source parameters are helpful for characterizing earthquake rupture process and hence understanding earthquake source physics and fault properties. Those studies require us mute wave propagation path and site effects in spectra of seismograms to accentuate source effect. We have recently developed the multiple spectral ratio method [Uchide and Imanishi, BSSA, 2016] employing many empirical Green's function (EGF) events to reduce errors from the choice of EGF events. This method helps us estimate source spectra more accurately as well as moment ratios among reference and EGF events, which are useful to constrain the seismic moment of microearthquakes. First, we focus on earthquake source spectra. The source spectra have generally been thought to obey the omega-square model with single corner-frequency. However recent studies imply the existence of another corner frequency for some earthquakes. We analyzed small shallow inland earthquakes (3.5 multiple spectral ratio analyses. For 20000 microearthquakes in Fukushima Hamadori and northern Ibaraki prefecture area, we found that the JMA magnitudes (Mj) based on displacement or velocity amplitude are systematically below Mw. The slope of the Mj-Mw relation is 0.5 for Mj 5. We propose a fitting curve for the obtained relationship as Mw = (1/2)Mj + (1/2)(Mjγ + Mcorγ)1/γ+ c, where Mcor is a corner magnitude, γ determines the sharpness of the corner, and c denotes an offset. We obtained Mcor = 4.1, γ = 5.6, and c = -0.47 to fit the observation. The parameters are useful for characterizing the Mj-Mw relationship. This non-linear relationship affects the b-value of the Gutenberg-Richter law. Quantitative discussions on b-values are affected by the definition of magnitude to use.

  3. Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

    Science.gov (United States)

    Studt, Lena; Niehaus, Eva-Maria; Espino, Jose J.; Huß, Kathleen; Michielse, Caroline B.; Albermann, Sabine; Wagner, Dominik; Bergner, Sonja V.; Connolly, Lanelle R.; Fischer, Andreas; Reuter, Gunter; Kleigrewe, Karin; Bald, Till; Wingfield, Brenda D.; Ophir, Ron; Freeman, Stanley; Hippler, Michael; Smith, Kristina M.; Brown, Daren W.; Proctor, Robert H.; Münsterkötter, Martin; Freitag, Michael; Humpf, Hans-Ulrich; Güldener, Ulrich; Tudzynski, Bettina

    2013-01-01

    The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F

  4. "Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses".

    Science.gov (United States)

    Eveno, Emmanuelle; Collada, Carmen; Guevara, M Angeles; Léger, Valérie; Soto, Alvaro; Díaz, Luis; Léger, Patrick; González-Martínez, Santiago C; Cervera, M Teresa; Plomion, Christophe; Garnier-Géré, Pauline H

    2008-02-01

    The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognized. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analyzed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared 3 coalescent-based methods: 2 frequentist-like, including 1 approach specifically developed for biallelic single nucleotide polymorphisms (SNPs) here and 1 Bayesian. Five genes showed outlier patterns that were robust across methods at the haplotype level for 2 of them. Two genes presented higher F(ST) values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, 3 genes presented lower F(ST) values than expected (dhn-1, dhn2, and lp3-1), which could represent signatures of homogenizing selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favorable situations for local adaptation. Outlier patterns are discussed

  5. Random error in cardiovascular meta-analyses

    DEFF Research Database (Denmark)

    Albalawi, Zaina; McAlister, Finlay A; Thorlund, Kristian

    2013-01-01

    BACKGROUND: Cochrane reviews are viewed as the gold standard in meta-analyses given their efforts to identify and limit systematic error which could cause spurious conclusions. The potential for random error to cause spurious conclusions in meta-analyses is less well appreciated. METHODS: We exam...

  6. Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855 (Mollusca, Ommastrephidae in the eastern tropical Atlantic.

    Directory of Open Access Journals (Sweden)

    Véronique Merten

    Full Text Available In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855 (Cephalopoda, Ommastrephidae is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding were combined with stable isotope data (∂15N and ∂13C of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid's gladius-the chitinous spiniform structure supporting the muscles and organs-were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp., but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae, crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid's trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and

  7. Diet and stable isotope analyses reveal the feeding ecology of the orangeback squid Sthenoteuthis pteropus (Steenstrup 1855) (Mollusca, Ommastrephidae) in the eastern tropical Atlantic.

    Science.gov (United States)

    Merten, Véronique; Christiansen, Bernd; Javidpour, Jamileh; Piatkowski, Uwe; Puebla, Oscar; Gasca, Rebeca; Hoving, Henk-Jan T

    2017-01-01

    In the eastern tropical Atlantic, the orangeback flying squid Sthenoteuthis pteropus (Steenstrup 1855) (Cephalopoda, Ommastrephidae) is a dominant species of the epipelagic nekton community. This carnivore squid has a short lifespan and is one of the fastest-growing squids. In this study, we characterise the role of S. pteropus in the pelagic food web of the eastern tropical Atlantic by investigating its diet and the dynamics of its feeding habits throughout its ontogeny and migration. During three expeditions in the eastern tropical Atlantic in 2015, 129 specimens were caught by hand jigging. Stomach content analyses (via visual identification and DNA barcoding) were combined with stable isotope data (∂15N and ∂13C) of muscle tissue to describe diet, feeding habits and trophic ecology of S. pteropus. Additionally, stable isotope analyses of incremental samples along the squid's gladius-the chitinous spiniform structure supporting the muscles and organs-were carried out to explore possible diet shifts through ontogeny and migration. Our results show that S. pteropus preys mainly on myctophid fishes (e.g. Myctophum asperum, Myctophum nitidulum, Vinciguerria spp.), but also on other teleost species, cephalopods (e.g. Enoploteuthidae, Bolitinidae, Ommastrephidae), crustaceans and possibly on gelatinous zooplankton as well. The squid shows a highly opportunistic feeding behaviour that includes cannibalism. Our study indicates that the trophic position of S. pteropus may increase by approximately one trophic level from a mantle length of 15 cm to 47 cm. The reconstructed isotope-based feeding chronologies of the gladii revealed high intra- and inter-individual variability in the squid's trophic position and foraging area. These findings are not revealed by diet or muscle tissue stable isotope analysis. This suggests a variable and complex life history involving individual variation and migration. The role of S. pteropus in transferring energy and nutrients from

  8. Analyses of Crime Patterns in NIBRS Data Based on a Novel Graph Theory Clustering Method: Virginia as a Case Study

    Directory of Open Access Journals (Sweden)

    Peixin Zhao

    2014-01-01

    Full Text Available This paper suggests a novel clustering method for analyzing the National Incident-Based Reporting System (NIBRS data, which include the determination of correlation of different crime types, the development of a likelihood index for crimes to occur in a jurisdiction, and the clustering of jurisdictions based on crime type. The method was tested by using the 2005 assault data from 121 jurisdictions in Virginia as a test case. The analyses of these data show that some different crime types are correlated and some different crime parameters are correlated with different crime types. The analyses also show that certain jurisdictions within Virginia share certain crime patterns. This information assists with constructing a pattern for a specific crime type and can be used to determine whether a jurisdiction may be more likely to see this type of crime occur in their area.

  9. 18F-FDG PET Reveals Fronto-temporal Dysfunction in Children with Fever-Induced Refractory Epileptic Encephalopathy

    International Nuclear Information System (INIS)

    Mazzuca, M.; Dulac, O.; Chiron, C.; Jambaque, I.; Hertz-Pannier, L.; Bouilleret, V.; Archambaud, F.; Rodrigo, S.; Dulac, O.; Chiron, C.; Jambaque, I.; Hertz-Pannier, L.; Bouilleret, V.; Archambaud, F.; Rodrigo, S.; Chiron, C.; Hertz-Pannier, L.; Rodrigo, S.; Dulac, O.; Chiron, C.; Caviness, V.

    2011-01-01

    Fever-induced refractory epileptic encephalopathy in school-age children (FIRES) is a recently described epileptic entity whose etiology remains unknown. Brain abnormalities shown by MRI are usually limited to mesial-temporal structures and do not account for the catastrophic neuro-psychologic findings. Methods: We conducted FIRES studies in 8 patients, aged 6-13 y, using 18 F-FDG PET to disclose eventual neo-cortical dysfunction. Voxel-based analyses of cerebral glucose metabolism were performed using statistical parametric mapping and an age-matched control group. Results: Group analysis revealed a widespread inter-ictal hypo-metabolic network including the temporo-parietal and orbito-frontal cortices bilaterally. The individual analyses in patients identified hypo-metabolic areas corresponding to the predominant electroencephalograph foci and neuro-psychologic deficits involving language, behavior, and memory. Conclusion: Despite clinical heterogeneity, 18 F-FDG PET reveals a common network dysfunction in patients with sequelae due to fever-induced refractory epileptic encephalopathy. (authors)

  10. Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree (Olea europaea L.) Cultivars.

    Science.gov (United States)

    Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Rebai, Ahmed

    2016-12-01

    The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation coefficient, indicating the usefulness of the UPGMA method for clustering plant genotypes. Based on principal coordinate analysis using a similarity matrix, the first two coordinates, revealed 54.94 % of the total variance. This work provides a more comprehensive explanation of the diversity available in Tunisia olive cultivars, and an important contribution for olive breeding and olive oil authenticity.

  11. Statistical analyses in the study of solar wind-magnetosphere coupling

    International Nuclear Information System (INIS)

    Baker, D.N.

    1985-01-01

    Statistical analyses provide a valuable method for establishing initially the existence (or lack of existence) of a relationship between diverse data sets. Statistical methods also allow one to make quantitative assessments of the strengths of observed relationships. This paper reviews the essential techniques and underlying statistical bases for the use of correlative methods in solar wind-magnetosphere coupling studies. Techniques of visual correlation and time-lagged linear cross-correlation analysis are emphasized, but methods of multiple regression, superposed epoch analysis, and linear prediction filtering are also described briefly. The long history of correlation analysis in the area of solar wind-magnetosphere coupling is reviewed with the assessments organized according to data averaging time scales (minutes to years). It is concluded that these statistical methods can be very useful first steps, but that case studies and various advanced analysis methods should be employed to understand fully the average response of the magnetosphere to solar wind input. It is clear that many workers have not always recognized underlying assumptions of statistical methods and thus the significance of correlation results can be in doubt. Long-term averages (greater than or equal to 1 hour) can reveal gross relationships, but only when dealing with high-resolution data (1 to 10 min) can one reach conclusions pertinent to magnetospheric response time scales and substorm onset mechanisms

  12. Simplified elastoplastic methods of analysing fatigue in notches

    International Nuclear Information System (INIS)

    Autrusson, B.

    1993-01-01

    The aim of this study is to show the state of the art concerning methods of mechanical analysis available in the literature for evaluating notch root elastoplastic strain. The components of fast breeder reactors are subjected to numerous thermal transients, which can cause fatigue failure. To prevent this from happening, it is necessary to know the local strain range and to use it to estimate the number of cycles to crack initiation. Practical methods have been developed for the calculation of the local strain range, and have led to the drafting of design rules. Direct methods of determining the local strain range of the 'inelastic analysis' type have also been described. In conclusion a series of recommendations is made on the applicability and the conservatism of these methods

  13. Genome size analyses of Pucciniales reveal the largest fungal genomes.

    Science.gov (United States)

    Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

    2014-01-01

    Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

  14. Development and application of neutron transport methods and uncertainty analyses for reactor core calculations. Technical report; Entwicklung und Einsatz von Neutronentransportmethoden und Unsicherheitsanalysen fuer Reaktorkernberechnungen. Technischer Bericht

    Energy Technology Data Exchange (ETDEWEB)

    Zwermann, W.; Aures, A.; Bernnat, W.; and others

    2013-06-15

    This report documents the status of the research and development goals reached within the reactor safety research project RS1503 ''Development and Application of Neutron Transport Methods and Uncertainty Analyses for Reactor Core Calculations'' as of the 1{sup st} quarter of 2013. The superordinate goal of the project is the development, validation, and application of neutron transport methods and uncertainty analyses for reactor core calculations. These calculation methods will mainly be applied to problems related to the core behaviour of light water reactors and innovative reactor concepts. The contributions of this project towards achieving this goal are the further development, validation, and application of deterministic and stochastic calculation programmes and of methods for uncertainty and sensitivity analyses, as well as the assessment of artificial neutral networks, for providing a complete nuclear calculation chain. This comprises processing nuclear basis data, creating multi-group data for diffusion and transport codes, obtaining reference solutions for stationary states with Monte Carlo codes, performing coupled 3D full core analyses in diffusion approximation and with other deterministic and also Monte Carlo transport codes, and implementing uncertainty and sensitivity analyses with the aim of propagating uncertainties through the whole calculation chain from fuel assembly, spectral and depletion calculations to coupled transient analyses. This calculation chain shall be applicable to light water reactors and also to innovative reactor concepts, and therefore has to be extensively validated with the help of benchmarks and critical experiments.

  15. Analysing radio-frequency coil arrays in high-field magnetic resonance imaging by the combined field integral equation method

    Energy Technology Data Exchange (ETDEWEB)

    Wang Shumin; Duyn, Jeff H [Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke, National Institutes of Health, 10 Center Drive, 10/B1D728, Bethesda, MD 20892 (United States)

    2006-06-21

    We present the combined field integral equation (CFIE) method for analysing radio-frequency coil arrays in high-field magnetic resonance imaging (MRI). Three-dimensional models of coils and the human body were used to take into account the electromagnetic coupling. In the method of moments formulation, we applied triangular patches and the Rao-Wilton-Glisson basis functions to model arbitrarily shaped geometries. We first examined a rectangular loop coil to verify the CFIE method and also demonstrate its efficiency and accuracy. We then studied several eight-channel receive-only head coil arrays for 7.0 T SENSE functional MRI. Numerical results show that the signal dropout and the average SNR are two major concerns in SENSE coil array design. A good design should be a balance of these two factors.

  16. Kernel based eigenvalue-decomposition methods for analysing ham

    DEFF Research Database (Denmark)

    Christiansen, Asger Nyman; Nielsen, Allan Aasbjerg; Møller, Flemming

    2010-01-01

    methods, such as PCA, MAF or MNF. We therefore investigated the applicability of kernel based versions of these transformation. This meant implementing the kernel based methods and developing new theory, since kernel based MAF and MNF is not described in the literature yet. The traditional methods only...... have two factors that are useful for segmentation and none of them can be used to segment the two types of meat. The kernel based methods have a lot of useful factors and they are able to capture the subtle differences in the images. This is illustrated in Figure 1. You can see a comparison of the most...... useful factor of PCA and kernel based PCA respectively in Figure 2. The factor of the kernel based PCA turned out to be able to segment the two types of meat and in general that factor is much more distinct, compared to the traditional factor. After the orthogonal transformation a simple thresholding...

  17. Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii

    Directory of Open Access Journals (Sweden)

    Johnson David R

    2011-11-01

    opposite effect and decreased after perturbation with PEG8000. Conclusions A combination of growth assays, transcriptome profiling, and membrane fatty acid analyses revealed that permeating and non-permeating solutes trigger different adaptive responses in strain RW1, suggesting these solutes affect cells in fundamentally different ways. Future work is now needed that connects these responses with the responses observed in more realistic scenarios of soil desiccation.

  18. Calculation methods for analysing nuclear power plant accidents and its qualification

    International Nuclear Information System (INIS)

    Sacco, W.

    1986-01-01

    A methodology of transient and accident analyses able to carried out calculations for all transients and accidents required to support operation and operation licensing of Angra-1 reactor reload, is presented. (M.C.K.) [pt

  19. Analyses of Dynamics in Dairy Products and Identification of Lactic Acid Bacteria Population by Molecular Methods

    Directory of Open Access Journals (Sweden)

    Aytül Sofu

    2017-01-01

    Full Text Available Lactic acid bacteria (LAB with different ecological niches are widely seen in fermented meat, vegetables, dairy products and cereals as well as in fermented beverages. Lactic acid bacteria are the most important group of bacteria in dairy industry due to their probiotic characteristics and fermentation agents as starter culture. In the taxonomy of the lactic acid bacteria; by means of rep-PCR, which is the analysis of repetitive sequences that are based on 16S ribosomal RNA (rRNA gene sequence, it is possible to conduct structural microbial community analyses such as Restriction Fragment Length Polymorphism (RFLP analysis of DNA fragments of different sizes cut with enzymes, Random Amplified Polymorphic DNA (RAPD polymorphic DNA amplified randomly at low temperatures and Amplified Fragment-Length Polymorphism (AFLP-PCR of cut genomic DNA. Besides, in the recent years, non-culture-based molecular methods such as Pulse Field Gel Electrophoresis (PFGE, Denaturing Gradient Gel Electrophoresis (DGGE, Thermal Gradient Gel Electrophoresis (TGGE, and Fluorescence In-situ Hybridization (FISH have replaced classical methods once used for the identification of LAB. Identification of lactic acid bacteria culture independent regardless of the method will be one of the most important methods used in the future pyrosequencing as a Next Generation Sequencing (NGS techniques. This paper reviews molecular-method based studies conducted on the identification of LAB species in dairy products.

  20. Ab initio O(N) elongation-counterpoise method for BSSE-corrected interaction energy analyses in biosystems

    Energy Technology Data Exchange (ETDEWEB)

    Orimoto, Yuuichi; Xie, Peng; Liu, Kai [Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Yamamoto, Ryohei [Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Imamura, Akira [Hiroshima Kokusai Gakuin University, 6-20-1 Nakano, Aki-ku, Hiroshima 739-0321 (Japan); Aoki, Yuriko, E-mail: aoki.yuriko.397@m.kyushu-u.ac.jp [Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012 (Japan)

    2015-03-14

    An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs’ inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligibly small energy error in the total energy calculations (in the order of 10{sup −7}–10{sup −8} hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. −290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for

  1. Multiple-scattering and DV-Xα analyses of a Cl-passivated Ge(111) surface

    International Nuclear Information System (INIS)

    Cao, S; Tang, J-C; Shen, S-L

    2003-01-01

    The multiple-scattering cluster and DV-Xα methods have been employed to analyse the chlorine 1s near edge x-ray absorption fine structure (NEXAFS) of a Cl-passivated Ge(111) surface. Our detailed analysis demonstrates how the chlorine atoms form a perfect monochloride structure with Cl bonding to the topmost Ge atom. Our calculation reveals the interaction in the chlorine layer is multipolar electrostatic forces. Furthermore, the DV-Xα cluster calculation shows that the orbital contour of the sharp Cl-Ge resonance exhibits a global symmetry, which confirms it to be σ * -like. The above studies are found to enrich previous experimental NEXAFS investigations

  2. Ancient ancestry of KFDV and AHFV revealed by complete genome analyses of viruses isolated from ticks and mammalian hosts.

    Directory of Open Access Journals (Sweden)

    Kimberly A Dodd

    2011-10-01

    Full Text Available BACKGROUND: Alkhurma hemorrhagic fever virus (AHFV and Kyasanur forest disease virus (KFDV cause significant human disease and mortality in Saudi Arabia and India, respectively. Despite their distinct geographic ranges, AHFV and KFDV share a remarkably high sequence identity. Given its emergence decades after KFDV, AHFV has since been considered a variant of KFDV and thought to have arisen from an introduction of KFDV to Saudi Arabia from India. To gain a better understanding of the evolutionary history of AHFV and KFDV, we analyzed the full length genomes of 16 AHFV and 3 KFDV isolates. METHODOLOGY/PRINCIPAL FINDINGS: Viral genomes were sequenced and compared to two AHFV sequences available in GenBank. Sequence analyses revealed higher genetic diversity within AHFVs isolated from ticks than human AHFV isolates. A Bayesian coalescent phylogenetic analysis demonstrated an ancient divergence of AHFV and KFDV of approximately 700 years ago. CONCLUSIONS/SIGNIFICANCE: The high sequence diversity within tick populations and the presence of competent tick vectors in the surrounding regions, coupled with the recent identification of AHFV in Egypt, indicate possible viral range expansion or a larger geographic range than previously thought. The divergence of AHFV from KFDV nearly 700 years ago suggests other AHFV/KFDV-like viruses might exist in the regions between Saudi Arabia and India. Given the human morbidity and mortality associated with these viruses, these results emphasize the importance of more focused study of these significant public health threats.

  3. Integrative analyses reveal novel strategies in HPV11,-16 and-45 early infection

    DEFF Research Database (Denmark)

    Kaczkowski, Bogumil; Rossing, Maria; Andersen, Ditte

    2012-01-01

    of genes not previously implicated in HPV biology, such as the PSG family and ANKRD1, and of genes implicated in the biology of other viruses, e. g. MX1, IFI44 and DDX60. Carcinogenesis-related genes, e. g. ABL2, MGLL and CYR61, were upregulated by high-risk HPV16 and -45. The integrative analysis revealed...... the suppression of DNA repair by HPV11 and -16, and downregulation of cytoskeleton genes by all HPV types. Various signalling pathways were affected by the HPVs: IL-2 by HPV11; JAK-STAT by HPV16; and TGF-beta, NOTCH and tyrosine kinase signalling by HPV45. This study uncovered novel strategies employed by HPV...... to establish infection and promote uncontrolled growth....

  4. Application of artificial neural network method to exergy and energy analyses of fluidized bed dryer for potato cubes

    International Nuclear Information System (INIS)

    Azadbakht, Mohsen; Aghili, Hajar; Ziaratban, Armin; Torshizi, Mohammad Vahedi

    2017-01-01

    Drying the samples was performed in the inlet temperatures of 45, 50, and 55 °C, air velocity of 3.2, 6.8, and 9.1 m s"−"1, and bed depth of 1.5, 2.2, and 3 cm. The effects of these parameters were evaluated on energy utilization, energy efficiency and utilization ratio and exergy loss and efficiency. Furthermore, artificial neural network was employed in order to predict the energy and exergy parameters, and simulation of thermodynamic drying process was carried out, using the ANN created. A network was constructed from learning algorithms and transfer functions that could predict, with good accuracy, the exergy and energy parameters related to the drying process. The results revealed that energy utilization, efficiency, and utilization ratio increased by increasing the air velocity and depth of the bed; however, energy utilization and efficiency were augmented by increasing the temperature; additionally, energy utilization ratio decreased along with the rise in temperature. Also was found that exergy loss and efficiency improved by increasing the air velocity, temperature, and depth of the bed. Finally, the results of the statistical analyses indicated that neural networks can be utilized in intelligent drying process which has a large share of energy utilization in the food industry. - Highlights: • Energy utilization increased by increasing temperature, air velocity and depth of the bed. • Exergy loss increased with increasing the air velocity, temperature and depth of the bed. • Prediction by a trained neural network is faster than usual mathematical models. • ANN it is a suitable method to predict the energy and exergy in various driers.

  5. Chemicals of emerging concern in water and bottom sediment in Great Lakes areas of concern, 2010 to 2011-Collection methods, analyses methods, quality assurance, and data

    Science.gov (United States)

    Lee, Kathy E.; Langer, Susan K.; Menheer, Michael A.; Foreman, William T.; Furlong, Edward T.; Smith, Steven G.

    2012-01-01

    The U.S. Geological Survey (USGS) cooperated with the U.S. Environmental Protection Agency and the U.S. Fish and Wildlife Service on a study to identify the occurrence of chemicals of emerging concern (CECs) in water and bottom-sediment samples collected during 2010–11 at sites in seven areas of concern (AOCs) throughout the Great Lakes. Study sites include tributaries to the Great Lakes in AOCs located near Duluth, Minn.; Green Bay, Wis.; Roches­ter, N.Y.; Detroit, Mich.; Toledo, Ohio; Milwaukee, Wis.; and Ashtabula, Ohio. This report documents the collection meth­ods, analyses methods, quality-assurance data and analyses, and provides the data for this study. Water and bottom-sediment samples were analyzed at the USGS National Water Quality Laboratory in Denver, Colo., for a broad suite of CECs. During this study, 135 environmental and 23 field dupli­cate samples of surface water and wastewater effluent, 10 field blank water samples, and 11 field spike water samples were collected and analyzed. Sixty-one of the 69 wastewater indicator chemicals (laboratory method 4433) analyzed were detected at concentrations ranging from 0.002 to 11.2 micrograms per liter. Twenty-eight of the 48 pharmaceuticals (research method 8244) analyzed were detected at concentrations ranging from 0.0029 to 22.0 micro­grams per liter. Ten of the 20 steroid hormones and sterols analyzed (research method 4434) were detected at concentrations ranging from 0.16 to 10,000 nanograms per liter. During this study, 75 environmental, 13 field duplicate samples, and 9 field spike samples of bottom sediment were collected and analyzed for a wide variety of CECs. Forty-seven of the 57 wastewater indicator chemicals (laboratory method 5433) analyzed were detected at concentrations ranging from 0.921 to 25,800 nanograms per gram. Seventeen of the 20 steroid hormones and sterols (research method 6434) analyzed were detected at concentrations ranging from 0.006 to 8,921 nanograms per gram. Twelve of

  6. Conventional and advanced exergetic analyses applied to a combined cycle power plant

    International Nuclear Information System (INIS)

    Petrakopoulou, Fontina; Tsatsaronis, George; Morosuk, Tatiana; Carassai, Anna

    2012-01-01

    Conventional exergy-based methods pinpoint components and processes with high irreversibilities. However, they lack certain insight. For a given advanced technological state, there is a minimum level of exergy destruction related to technological and/or economic constraints that is unavoidable. Furthermore, in any thermodynamic system, exergy destruction stems from both component interactions (exogenous) and component inefficiencies (endogenous). To overcome the limitations of the conventional analyses and to increase our knowledge about a plant, advanced exergy-based analyses have been developed. In this paper, a combined cycle power plant is analyzed using both conventional and advanced exergetic analyses. Except for the expander of the gas turbine system and the high-pressure steam turbine, most of the exergy destruction in the plant components is unavoidable. This unavoidable part is constrained by internal technological limitations, i.e. each component’s endogenous exergy destruction. High levels of endogenous exergy destruction show that component interactions do not contribute significantly to the thermodynamic inefficiencies. In addition, these inefficiencies are unavoidable to a large extent. With the advanced analysis, new improvement strategies are revealed that could not otherwise be found. -- Highlights: ► This is the first application of a complete advanced exergetic analysis to a complex power plant. ► In the three-pressure-level combined cycle power plant studied here, the improvement potential of the majority of the components is low, since most of the exergy destruction is unavoidable. ► Component interactions are generally of lower importance for the considered plant. ► Splitting the exogenous exergy destruction reveals one-to-one component interactions and improvement strategies. ► The advanced exergetic analysis is a necessary supplement to the conventional analysis in improving a complex system.

  7. Development of modern methods with respect to neutron transport and uncertainty analyses for reactor core calculations. Interim report; Weiterentwicklung moderner Verfahren zu Neutronentransport und Unsicherheitsanalysen fuer Kernberechnungen. Zwischenbericht

    Energy Technology Data Exchange (ETDEWEB)

    Zwermann, Winfried; Aures, Alexander; Bostelmann, Friederike; Pasichnyk, Ihor; Perin, Yann; Velkov, Kiril; Zilly, Matias

    2016-12-15

    This report documents the status of the research and development goals reached within the reactor safety research project RS1536 ''Development of modern methods with respect to neutron transport and uncertainty analyses for reactor core calculations'' as of the 3{sup rd} quarter of 2016. The superordinate goal of the project is the development, validation, and application of neutron transport methods and uncertainty analyses for reactor core calculations. These calculation methods will mainly be applied to problems related to the core behaviour of light water reactors and innovative reactor concepts, in particular fast reactors cooled by liquid metal. The contributing individual goals are the further optimization and validation of deterministic calculation methods with high spatial and energy resolution, the development of a coupled calculation system using the Monte Carlo method for the neutron transport to describe time-dependent reactor core states, the processing and validation of nuclear data, particularly with regard to covariance data, the development, validation, and application of sampling-based methods for uncertainty and sensitivity analyses, the creation of a platform for performing systematic uncertainty analyses for fast reactor systems, as well as the description of states of severe core damage with the Monte Carlo method. Moreover, work regarding the European NURESAFE project, started in the preceding project RS1503, are being continued and completed.

  8. A geometric buckling expression for regular polygons: II. Analyses based on the multiple reciprocity boundary element method

    International Nuclear Information System (INIS)

    Itagaki, Masafumi; Miyoshi, Yoshinori; Hirose, Hideyuki

    1993-01-01

    A procedure is presented for the determination of geometric buckling for regular polygons. A new computation technique, the multiple reciprocity boundary element method (MRBEM), has been applied to solve the one-group neutron diffusion equation. The main difficulty in applying the ordinary boundary element method (BEM) to neutron diffusion problems has been the need to compute a domain integral, resulting from the fission source. The MRBEM has been developed for transforming this type of domain integral into an equivalent boundary integral. The basic idea of the MRBEM is to apply repeatedly the reciprocity theorem (Green's second formula) using a sequence of higher order fundamental solutions. The MRBEM requires discretization of the boundary only rather than of the domain. This advantage is useful for extensive survey analyses of buckling for complex geometries. The results of survey analyses have indicated that the general form of geometric buckling is B g 2 = (a n /R c ) 2 , where R c represents the radius of the circumscribed circle of the regular polygon under consideration. The geometric constant A n depends on the type of regular polygon and takes the value of π for a square and 2.405 for a circle, an extreme case that has an infinite number of sides. Values of a n for a triangle, pentagon, hexagon, and octagon have been calculated as 4.190, 2.281, 2.675, and 2.547, respectively

  9. On Rigorous Drought Assessment Using Daily Time Scale: Non-Stationary Frequency Analyses, Revisited Concepts, and a New Method to Yield Non-Parametric Indices

    Directory of Open Access Journals (Sweden)

    Charles Onyutha

    2017-10-01

    Full Text Available Some of the problems in drought assessments are that: analyses tend to focus on coarse temporal scales, many of the methods yield skewed indices, a few terminologies are ambiguously used, and analyses comprise an implicit assumption that the observations come from a stationary process. To solve these problems, this paper introduces non-stationary frequency analyses of quantiles. How to use non-parametric rescaling to obtain robust indices that are not (or minimally skewed is also introduced. To avoid ambiguity, some concepts on, e.g., incidence, extremity, etc., were revisited through shift from monthly to daily time scale. Demonstrations on the introduced methods were made using daily flow and precipitation insufficiency (precipitation minus potential evapotranspiration from the Blue Nile basin in Africa. Results show that, when a significant trend exists in extreme events, stationarity-based quantiles can be far different from those when non-stationarity is considered. The introduced non-parametric indices were found to closely agree with the well-known standardized precipitation evapotranspiration indices in many aspects but skewness. Apart from revisiting some concepts, the advantages of the use of fine instead of coarse time scales in drought assessment were given. The links for obtaining freely downloadable tools on how to implement the introduced methods were provided.

  10. Analytical procedures used by the uranium - radon - radium geochemistry group; Methodes d'analyses utilisees par la section de geochimie uranium, radon, radium

    Energy Technology Data Exchange (ETDEWEB)

    Berthollet, P [Commissariat a l' Energie Atomique, Fontenay-aux-Roses (France). Centre d' Etudes Nucleaires

    1968-07-01

    The analytical methods described are applied to the geochemical prospecting of uranium. The nature of the material under investigation, which may be soil, alluvium, rock, plant or water, and the particular requirements of geochemical exploration, have prompted us to adjust the widely used conventional methods to the demands of large scale operation, without lowering their standards of accuracy and reliability. These procedures are explained in great detail. Though most of this technical information may appear superfluous to the chemical engineer well versed in trace element determination, it will, however, serve a useful purpose both with the operator in charge of routine testing and with the chemist called upon to interpret results. (author) [French] Les methodes d'analyses decrites sont utilisees pour la prospection geochimique de l'uranium. La nature des materiaux: sols, alluvions, roches, vegetaux, eaux, et les exigences propres a la prospection geochimique, nous ont conduit a adapter des methodes classique couramment utilisees pour les rendre aptes a etre executees en grande serie, sans abandonner leurs qualites de precision et de fidelite. Ces methodes sont presentees avec un maximum de details operatoires qui paraitront superflus aux chimistes habitues aux dosages de traces, mais seront utiles aussi bien aux manipulateurs charges des analyses qu'aux geochimistes appeles a exploiter les resultats. (auteur)

  11. Analysing malaria drug trials on a per-individual or per-clone basis: a comparison of methods.

    Science.gov (United States)

    Jaki, Thomas; Parry, Alice; Winter, Katherine; Hastings, Ian

    2013-07-30

    There are a variety of methods used to estimate the effectiveness of antimalarial drugs in clinical trials, invariably on a per-person basis. A person, however, may have more than one malaria infection present at the time of treatment. We evaluate currently used methods for analysing malaria trials on a per-individual basis and introduce a novel method to estimate the cure rate on a per-infection (clone) basis. We used simulated and real data to highlight the differences of the various methods. We give special attention to classifying outcomes as cured, recrudescent (infections that never fully cleared) or ambiguous on the basis of genetic markers at three loci. To estimate cure rates on a per-clone basis, we used the genetic information within an individual before treatment to determine the number of clones present. We used the genetic information obtained at the time of treatment failure to classify clones as recrudescence or new infections. On the per-individual level, we find that the most accurate methods of classification label an individual as newly infected if all alleles are different at the beginning and at the time of failure and as a recrudescence if all or some alleles were the same. The most appropriate analysis method is survival analysis or alternatively for complete data/per-protocol analysis a proportion estimate that treats new infections as successes. We show that the analysis of drug effectiveness on a per-clone basis estimates the cure rate accurately and allows more detailed evaluation of the performance of the treatment. Copyright © 2012 John Wiley & Sons, Ltd.

  12. Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling.

    Science.gov (United States)

    Schluttenhofer, Craig; Pattanaik, Sitakanta; Patra, Barunava; Yuan, Ling

    2014-06-20

    To combat infection to biotic stress plants elicit the biosynthesis of numerous natural products, many of which are valuable pharmaceutical compounds. Jasmonate is a central regulator of defense response to pathogens and accumulation of specialized metabolites. Catharanthus roseus produces a large number of terpenoid indole alkaloids (TIAs) and is an excellent model for understanding the regulation of this class of valuable compounds. Recent work illustrates a possible role for the Catharanthus WRKY transcription factors (TFs) in regulating TIA biosynthesis. In Arabidopsis and other plants, the WRKY TF family is also shown to play important role in controlling tolerance to biotic and abiotic stresses, as well as secondary metabolism. Here, we describe the WRKY TF families in response to jasmonate in Arabidopsis and Catharanthus. Publically available Arabidopsis microarrays revealed at least 30% (22 of 72) of WRKY TFs respond to jasmonate treatments. Microarray analysis identified at least six jasmonate responsive Arabidopsis WRKY genes (AtWRKY7, AtWRKY20, AtWRKY26, AtWRKY45, AtWRKY48, and AtWRKY72) that have not been previously reported. The Catharanthus WRKY TF family is comprised of at least 48 members. Phylogenetic clustering reveals 11 group I, 32 group II, and 5 group III WRKY TFs. Furthermore, we found that at least 25% (12 of 48) were jasmonate responsive, and 75% (9 of 12) of the jasmonate responsive CrWRKYs are orthologs of AtWRKYs known to be regulated by jasmonate. Overall, the CrWRKY family, ascertained from transcriptome sequences, contains approximately 75% of the number of WRKYs found in other sequenced asterid species (pepper, tomato, potato, and bladderwort). Microarray and transcriptomic data indicate that expression of WRKY TFs in Arabidopsis and Catharanthus are under tight spatio-temporal and developmental control, and potentially have a significant role in jasmonate signaling. Profiling of CrWRKY expression in response to jasmonate treatment

  13. Method of accounting for code safety valve setpoint drift in safety analyses

    International Nuclear Information System (INIS)

    Rousseau, K.R.; Bergeron, P.A.

    1989-01-01

    In performing the safety analyses for transients that result in a challenge to the reactor coolant system (RCS) pressure boundary, the general acceptance criterion is that the peak RCS pressure not exceed the American Society of Mechanical Engineers limit of 110% of the design pressure. Without crediting non-safety-grade pressure mitigating systems, protection from this limit is mainly provided by the primary and secondary code safety valves. In theory, the combination of relief capacity and setpoints for these valves is designed to provide this protection. Generally, banks of valves are set at varying setpoints staggered by 15- to 20-psid increments to minimize the number of valves that would open by an overpressure challenge. In practice, however, when these valves are removed and tested (typically during a refueling outage), setpoints are sometimes found to have drifted by >50 psid. This drift should be accounted for during the performance of the safety analysis. This paper describes analyses performed by Yankee Atomic Electric Company (YAEC) to account for setpoint drift in safety valves from testing. The results of these analyses are used to define safety valve operability or acceptance criteria

  14. Field trip method as an effort to reveal student environmental literacy on biodiversity issue and context

    Science.gov (United States)

    Rijal, M.; Saefudin; Amprasto

    2018-05-01

    Field trip method through investigation of local biodiversity cases can give educational experiences for students. This learning activity was efforts to reveal students environmental literacy on biodiversity. The aim of study were (1) to describe the activities of students get information about the biodiversity issue and its context through field trip, (2) to describe the students findings during field trip, and (3) to reveal students environmental literacy based on pre test and post test. The research method used weak-experiment and involved 34 participants at senior high school students in Bandung-Indonesia. The research instruments for collecting data were environmental literacy test, observation sheets and questionnaire sheets for students. The analysis of data was quantitative descriptive. The results show that more than 79% of the students gave positive view for each field trip activity, i.e students activity during work (97%-100%); students activity during gather information (79%- 100%); students activity during exchange information with friend (82%-100%); and students interested to Biodiversity after field trip activity (85%-100%). Students gain knowledge about the diversity of animal vertebrate and its characteristics, the status and condition of animals, and the source of animal with the cases of animal diversity. The students environmental literacy tends to be moderate level based on test. Meanwhile, the average of the attitudes and action greater than the components of knowledge and cognitive skills.

  15. Transcriptome, expression, and activity analyses reveal a vital heat shock protein 70 in the stress response of stony coral Pocillopora damicornis.

    Science.gov (United States)

    Zhang, Yidan; Zhou, Zhi; Wang, Lingui; Huang, Bo

    2018-02-12

    Coral bleaching occurs worldwide with increasing frequencies and intensities, which is caused by the stress response of stony coral to environmental change, especially increased sea surface temperature. In the present study, transcriptome, expression, and activity analyses were employed to illustrate the underlying molecular mechanisms of heat shock protein 70 (HSP70) in the stress response of coral to environmental changes. The domain analyses of assembled transcripts revealed 30 HSP70 gene contigs in stony coral Pocillopora damicornis. One crucial HSP70 (PdHSP70) was observed, whose expressions were induced by both elevated temperature and ammonium after expression difference analysis. The complete complementary DNA (cDNA) sequence of PdHSP70 was identified, which encoded a polypeptide of 650 amino acids with a molecular weight of 71.93 kDa. The deduced amino acid sequence of PdHSP70 contained a HSP70 domain (from Pro8 to Gly616), and it shared the highest similarity (95%) with HSP70 from Stylophora pistillata. The expression level of PdHSP70 gene increased significantly at 12 h, and returned to the initial level at 24 h after the stress of high temperature (32 °C). The cDNA fragment encoding the mature peptide of PdHSP70 was recombined and expressed in the prokaryotic expression system. The ATPase activity of recombinant PdHSP70 protein was determined, and it did not change significantly in a wide range of temperature from 25 to 40 °C. These results collectively suggested that PdHSP70 was a vital heat shock protein 70 in the stony coral P. damicornis, whose mRNA expression could be induced by diverse environmental stress and whose activity could remain stable under heat stress. PdHSP70 might be involved in the regulation of the bleaching owing to heat stress in the stony coral P. damicornis.

  16. Possible Factors Promoting Car Evacuation in the 2011 Tohoku Tsunami Revealed by Analysing a Large-Scale Questionnaire Survey in Kesennuma City

    Directory of Open Access Journals (Sweden)

    Fumiyasu Makinoshima

    2017-11-01

    Full Text Available Excessive car evacuation can cause severe traffic jams that can lead to large numbers of casualties during tsunami disasters. Investigating the possible factors that lead to unnecessary car evacuation can ensure smoother tsunami evacuations and mitigate casualty damages in future tsunami events. In this study, we quantitatively investigated the possible factors that promote car evacuation, including both necessary and unnecessary usages, by statistically analysing a large amount of data on actual tsunami evacuation behaviours surveyed in Kesennuma, where devastating damage occurred during the 2011 Tohoku Tsunami. A straightforward statistical analysis revealed a high percentage of car evacuations (approx. 50%; however, this fraction includes a high number of unnecessary usage events that were distinguished based on mode choice reasons. In addition, a binary logistic regression was conducted to quantitatively evaluate the effects of several factors and to identify the dominant factor that affected evacuation mode choice. The regression results suggested that the evacuation distance was the dominant factor for choosing car evacuation relative to other factors, such as age and sex. The cross-validation test of the regression model demonstrated that the considered factors were useful for decision making and the prediction of evacuation mode choice in the target area.

  17. Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

    Directory of Open Access Journals (Sweden)

    Weerachai Jaratlerdsiri

    Full Text Available The major histocompatibility complex (MHC is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. The MHC is generally divided into subregions (classes I, II and III containing genes of similar function across species, but with different gene number and organisation. Crocodylia (crocodilians are widely distributed and represent an evolutionary distinct group among higher vertebrates, but the genomic organisation of MHC within this lineage has been largely unexplored. Here, we studied the MHC region of the saltwater crocodile (Crocodylus porosus and compared it with that of other taxa. We characterised genomic clusters encompassing MHC class I and class II genes in the saltwater crocodile based on sequencing of bacterial artificial chromosomes. Six gene clusters spanning ∼452 kb were identified to contain nine MHC class I genes, six MHC class II genes, three TAP genes, and a TRIM gene. These MHC class I and class II genes were in separate scaffold regions and were greater in length (2-6 times longer than their counterparts in well-studied fowl B loci, suggesting that the compaction of avian MHC occurred after the crocodilian-avian split. Comparative analyses between the saltwater crocodile MHC and that from the alligator and gharial showed large syntenic areas (>80% identity with similar gene order. Comparisons with other vertebrates showed that the saltwater crocodile had MHC class I genes located along with TAP, consistent with birds studied. Linkage between MHC class I and TRIM39 observed in the saltwater crocodile resembled MHC in eutherians compared, but absent in avian MHC, suggesting that the saltwater crocodile MHC appears to have gene organisation intermediate between these two lineages. These observations suggest that the structure of the saltwater crocodile MHC, and other crocodilians, can help determine the MHC that was present in the ancestors of archosaurs.

  18. Systematic Derivation of Static Analyses for Software Product Lines

    DEFF Research Database (Denmark)

    Midtgaard, Jan; Brabrand, Claus; Wasowski, Andrzej

    2014-01-01

    A recent line of work lifts particular verification and analysis methods to Software Product Lines (SPL). In an effort to generalize such case-by-case approaches, we develop a systematic methodology for lifting program analyses to SPLs using abstract interpretation. Abstract interpretation...... for lifting analyses and Galois connections. We prove that for analyses developed using our method, the soundness of lifting follows by construction. Finally, we discuss approximating variability in an analysis and we derive variational data-flow equations for an example analysis, a constant propagation...

  19. Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signalling dynamics

    Science.gov (United States)

    Lee, Hong-Won; Kyung, Taeyoon; Yoo, Janghyun; Kim, Tackhoon; Chung, Chaeuk; Ryu, Ji Young; Lee, Hanki; Park, Kihyun; Lee, Sangkyu; Jones, Walton D.; Lim, Dae-Sik; Hyeon, Changbong; Do Heo, Won; Yoon, Tae-Young

    2013-01-01

    Co-immunoprecipitation (co-IP) has become a standard technique, but its protein-band output provides only static, qualitative information about protein–protein interactions. Here we demonstrate a real-time single-molecule co-IP technique that generates real-time videos of individual protein–protein interactions as they occur in unpurified cell extracts. By analysing single Ras–Raf interactions with a 50-ms time resolution, we have observed transient intermediates of the protein–protein interaction and determined all the essential kinetic rates. Using this technique, we have quantified the active fraction of native Ras proteins in xenograft tumours, normal tissue and cancer cell lines. We demonstrate that the oncogenic Ras mutations selectively increase the active-Ras fraction by one order of magnitude, without affecting total Ras levels or single-molecule signalling kinetics. Our approach allows us to probe the previously hidden, dynamic aspects of weak protein–protein interactions. It also suggests a path forward towards precision molecular diagnostics at the protein–protein interaction level. PMID:23422673

  20. Complex analyses of inverted repeats in mitochondrial genomes revealed their importance and variability.

    Science.gov (United States)

    Cechová, Jana; Lýsek, Jirí; Bartas, Martin; Brázda, Václav

    2018-04-01

    The NCBI database contains mitochondrial DNA (mtDNA) genomes from numerous species. We investigated the presence and locations of inverted repeat sequences (IRs) in these mtDNA sequences, which are known to be important for regulating nuclear genomes. IRs were identified in mtDNA in all species. IR lengths and frequencies correlate with evolutionary age and the greatest variability was detected in subgroups of plants and fungi and the lowest variability in mammals. IR presence is non-random and evolutionary favoured. The frequency of IRs generally decreased with IR length, but not for IRs 24 or 30 bp long, which are 1.5 times more abundant. IRs are enriched in sequences from the replication origin, followed by D-loop, stem-loop and miscellaneous sequences, pointing to the importance of IRs in regulatory regions of mitochondrial DNA. Data were produced using Palindrome analyser, freely available on the web at http://bioinformatics.ibp.cz. vaclav@ibp.cz. Supplementary data are available at Bioinformatics online.

  1. Evaluation Of Three Methods Of Sugar Analyses For Determination ...

    African Journals Online (AJOL)

    Chemical methods developed by Lane and Eynon, Knight and Allen, and colorimetric method by Dubois et al were used to determine reducing sugar in eight fruit samples. The methods showed detection limits as follows: Lane and Eynon (1ppt); Knight and Allen (0.1ppt); and Dubois et al (<2ppm). The coefficients of ...

  2. Non-Statistical Methods of Analysing of Bankruptcy Risk

    Directory of Open Access Journals (Sweden)

    Pisula Tomasz

    2015-06-01

    Full Text Available The article focuses on assessing the effectiveness of a non-statistical approach to bankruptcy modelling in enterprises operating in the logistics sector. In order to describe the issue more comprehensively, the aforementioned prediction of the possible negative results of business operations was carried out for companies functioning in the Polish region of Podkarpacie, and in Slovakia. The bankruptcy predictors selected for the assessment of companies operating in the logistics sector included 28 financial indicators characterizing these enterprises in terms of their financial standing and management effectiveness. The purpose of the study was to identify factors (models describing the bankruptcy risk in enterprises in the context of their forecasting effectiveness in a one-year and two-year time horizon. In order to assess their practical applicability the models were carefully analysed and validated. The usefulness of the models was assessed in terms of their classification properties, and the capacity to accurately identify enterprises at risk of bankruptcy and healthy companies as well as proper calibration of the models to the data from training sample sets.

  3. Physiological and Proteomics Analyses Reveal Low-Phosphorus Stress Affected the Regulation of Photosynthesis in Soybean.

    Science.gov (United States)

    Chu, Shanshan; Li, Hongyan; Zhang, Xiangqian; Yu, Kaiye; Chao, Maoni; Han, Suoyi; Zhang, Dan

    2018-06-06

    Previous studies have revealed a significant genetic relationship between phosphorus (P)-efficiency and photosynthesis-related traits in soybean. In this study, we used proteome profiling in combination with expression analysis, biochemical investigations, and leaf ultrastructural analysis to identify the underlying physiological and molecular responses. The expression analysis and ultrastructural analysis showed that the photosynthesis key genes were decreased at transcript levels and the leaf mesophyll and chloroplast were severely damaged after low-P stress. Approximately 55 protein spots showed changes under low-P condition by mass spectrometry, of which 17 were involved in various photosynthetic processes. Further analysis revealed the depression of photosynthesis caused by low-P stress mainly involves the regulation of leaf structure, adenosine triphosphate (ATP) synthesis, absorption and transportation of CO₂, photosynthetic electron transport, production of assimilatory power, and levels of enzymes related to the Calvin cycle. In summary, our findings indicated that the existence of a stringent relationship between P supply and the genomic control of photosynthesis in soybean. As an important strategy to protect soybean photosynthesis, P could maintain the stability of cell structure, up-regulate the enzymes’ activities, recover the process of photosystem II (PSII), and induce the expression of low-P responsive genes and proteins.

  4. Improving the safety of a body composition analyser based on the PGNAA method

    Energy Technology Data Exchange (ETDEWEB)

    Miri-Hakimabad, Hashem; Izadi-Najafabadi, Reza; Vejdani-Noghreiyan, Alireza; Panjeh, Hamed [FUM Radiation Detection And Measurement Laboratory, Ferdowsi University of Mashhad (Iran, Islamic Republic of)

    2007-12-15

    The {sup 252}Cf radioisotope and {sup 241}Am-Be are intense neutron emitters that are readily encapsulated in compact, portable and sealed sources. Some features such as high flux of neutron emission and reliable neutron spectrum of these sources make them suitable for the prompt gamma neutron activation analysis (PGNAA) method. The PGNAA method can be used in medicine for neutron radiography and body chemical composition analysis. {sup 252}Cf and {sup 241}Am-Be sources generate not only neutrons but also are intense gamma emitters. Furthermore, the sample in medical treatments is a human body, so it may be exposed to the bombardments of these gamma-rays. Moreover, accumulations of these high-rate gamma-rays in the detector volume cause simultaneous pulses that can be piled up and distort the spectra in the region of interest (ROI). In order to remove these disadvantages in a practical way without being concerned about losing the thermal neutron flux, a gamma-ray filter made of Pb must be employed. The paper suggests a relatively safe body chemical composition analyser (BCCA) machine that uses a spherical Pb shield, enclosing the neutron source. Gamma-ray shielding effects and the optimum radius of the spherical Pb shield have been investigated, using the MCNP-4C code, and compared with the unfiltered case, the bare source. Finally, experimental results demonstrate that an optimised gamma-ray shield for the neutron source in a BCCA can reduce effectively the risk of exposure to the {sup 252}Cf and {sup 241}Am-Be sources.

  5. Fracture analyses of WWER reactor pressure vessels

    International Nuclear Information System (INIS)

    Sievers, J.; Liu, X.

    1997-01-01

    In the paper first the methodology of fracture assessment based on finite element (FE) calculations is described and compared with simplified methods. The FE based methodology was verified by analyses of large scale thermal shock experiments in the framework of the international comparative study FALSIRE (Fracture Analyses of Large Scale Experiments) organized by GRS and ORNL. Furthermore, selected results from fracture analyses of different WWER type RPVs with postulated cracks under different loading transients are presented. 11 refs, 13 figs, 1 tab

  6. Fracture analyses of WWER reactor pressure vessels

    Energy Technology Data Exchange (ETDEWEB)

    Sievers, J; Liu, X [Gesellschaft fuer Anlagen- und Reaktorsicherheit mbH (GRS), Koeln (Germany)

    1997-09-01

    In the paper first the methodology of fracture assessment based on finite element (FE) calculations is described and compared with simplified methods. The FE based methodology was verified by analyses of large scale thermal shock experiments in the framework of the international comparative study FALSIRE (Fracture Analyses of Large Scale Experiments) organized by GRS and ORNL. Furthermore, selected results from fracture analyses of different WWER type RPVs with postulated cracks under different loading transients are presented. 11 refs, 13 figs, 1 tab.

  7. Researcher’s Perspective of Substitution Method on Text Steganography

    Science.gov (United States)

    Zamir Mansor, Fawwaz; Mustapha, Aida; Azah Samsudin, Noor

    2017-08-01

    The linguistic steganography studies are still in the stage of development and empowerment practices. This paper will present several text steganography on substitution methods based on the researcher’s perspective, all scholar paper will analyse and compared. The objective of this paper is to give basic information in the substitution method of text domain steganography that has been applied by previous researchers. The typical ways of this method also will be identified in this paper to reveal the most effective method in text domain steganography. Finally, the advantage of the characteristic and drawback on these techniques in generally also presented in this paper.

  8. Stochastic methods for the quantification of sensitivities and uncertainties in criticality analyses; Stochastische Methoden zur Quantifizierung von Sensitivitaeten und Unsicherheiten in Kritikalitaetsanalysen

    Energy Technology Data Exchange (ETDEWEB)

    Behler, Matthias; Bock, Matthias; Stuke, Maik; Wagner, Markus

    2014-06-15

    This work describes statistical analyses based on Monte Carlo sampling methods for criticality safety analyses. The methods analyse a large number of calculations of a given problem with statistically varied model parameters to determine uncertainties and sensitivities of the computed results. The GRS development SUnCISTT (Sensitivities and Uncertainties in Criticality Inventory and Source Term Tool) is a modular, easily extensible abstract interface program, designed to perform such Monte Carlo sampling based uncertainty and sensitivity analyses in the field of criticality safety. It couples different criticality and depletion codes commonly used in nuclear criticality safety assessments to the well-established GRS tool SUSA for sensitivity and uncertainty analyses. For uncertainty analyses of criticality calculations, SunCISTT couples various SCALE sequences developed at Oak Ridge National Laboratory and the general Monte Carlo N-particle transport code MCNP from Los Alamos National Laboratory to SUSA. The impact of manufacturing tolerances of a fuel assembly configuration on the neutron multiplication factor for the various sequences is shown. Uncertainties in nuclear inventories, dose rates, or decay heat can be investigated via the coupling of the GRS depletion system OREST to SUSA. Some results for a simplified irradiated Pressurized Water Reactor (PWR) UO{sub 2} fuel assembly are shown. SUnCISTT also combines the two aforementioned modules for burnup credit criticality analysis of spent nuclear fuel to ensures an uncertainty and sensitivity analysis using the variations of manufacturing tolerances in the burn-up code and criticality code simultaneously. Calculations and results for a storage cask loaded with typical irradiated PWR UO{sub 2} fuel are shown, including Monte Carlo sampled axial burn-up profiles. The application of SUnCISTT in the field of code validation, specifically, how it is applied to compare a simulation model to available benchmark

  9. Method of chemical analysis of silicate rocks (1962); Methode d'analyse chimique des roches silicatees (1962)

    Energy Technology Data Exchange (ETDEWEB)

    Pouget, R [Commissariat a l' Energie Atomique, Fontenay-aux-Roses (France). Centre d' Etudes Nucleaires

    1962-07-01

    A rapid method of analysis for the physical and chemical determination of the major constituents of silicate rocks is described. Water losses at 100 deg. C and losses of volatile elements at 1000 deg. C are estimated after staying in oven for these temperatures, or by mean of a thermo-balance. The determination of silica is made by a double insolubilization with hydrochloric acid on attack solution with sodium carbonate; total iron and aluminium, both with calcium and magnesium, after ammoniacal precipitation of Fe and Al, are determined on the filtration product of silica by titrimetry-photometry of their complexes with EDTA. The alkalis Na and K by flame spectrophotometry, Mn by colorimetry of the permanganate, and Ti by mean of his complex with H{sub 2}O{sub 2}, are determined on fluosulfuric attack solution. Phosphorus is determined by his complex with 'molybdenum blue' on a fluoro-nitro-boric attack solution; iron is estimated by potentiometry, with the help of bichromate on hydrofluoric solution. (author) [French] Une methode d'analyse rapide est decrite pour la determination physico-chimique des constituants principaux des roches silicatees. Les pertes en eau a 100 deg. C et en matieres volatiles a 1000 deg. C sont evaluees apres passage au four a ces temperatures, ou a l'aide d'une thermobalance. La determination de la silice se fait par double insolubilisation a l'acide chlorhydrique, sur une attaque au carbonate de sodium; le fer total et l'aluminium ainsi que le calcium et le magnesium, apres precipitation a l'ammoniaque des deux premiers metaux, sont determines sur le filtrat de la silice par titrimetrie-photometrie de leurs complexes avec l'E.D.T.A. Les alcalins sodium et potassium par spectrophotometrie de flamme, le manganese par colorimetrie du permanganate, le titane a l'aide de son complexe avec l'eau oxygenee, sont determines sur une attaque fluosulfurique. Le phosphore est determine par son complexe du 'bleu de molybdene' sur une attaque fluo

  10. Dose Assessment using Chromosome Aberration Analyses in Human Peripheral Blood Lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Ryu, Tae Ho; Kim, Jin-Hong; Kim, Jin Kyu [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2015-10-15

    The healthy five donors were recruited to establish the dose-response calibration curve for chromosomal aberrations by ionizing radiation exposure. Our cytogenetic results revealed that the mean frequency of chromosome aberration increased with increasing radiation dose. In this study, dicentric assay and CBMN assay were compared considering the sensitivity and accuracy of dose estimation. Therefore, these chromosome aberration analyses will be the foundation for biological dosimetric analysis with additional research methods such as translocation and PCC assay. The conventional analysis of dicentric chromosomes in HPBL was suggested by Bender and Gooch in 1962. This assay has been for many years, the golden standard and the most specific method for ionizing radiation damage. The dicentric assay technique in HPBL has been shown as the most sensitive biological method and reliable bio-indicator of quantifying the radiation dose. In contrast, the micronucleus assay has advantages over the dicentric assay since it is rapid and requires less specialized expertise, and accordingly it can be applied to monitor a big population. The cytokinesis-block micronucleus (CBMN) assay is a suitable method for micronuceli measurement in cultured human as well as mammalian cells. The aim of our study was to establish the dose response curve of radiation-induced chromosome aberrations in HPBL by analyzing the frequency of dicentrics and micronuclei.

  11. On statistical methods for analysing the geographical distribution of cancer cases near nuclear installations

    International Nuclear Information System (INIS)

    Bithell, J.F.; Stone, R.A.

    1989-01-01

    This paper sets out to show that epidemiological methods most commonly used can be improved. When analysing geographical data it is necessary to consider location. The most obvious quantification of location is ranked distance, though other measures which may be more meaningful in relation to aetiology may be substituted. A test based on distance ranks, the ''Poisson maximum test'', depends on the maximum of observed relative risk in regions of increasing size, but with significance level adjusted for selection. Applying this test to data from Sellafield and Sizewell shows that the excess of leukaemia incidence observed at Seascale, near Sellafield, is not an artefact due to data selection by region, and that the excess probably results from a genuine, if as yet unidentified cause (there being little evidence of any other locational association once the Seascale cases have been removed). So far as Sizewell is concerned, geographical proximity to the nuclear power station does not seen particularly important. (author)

  12. Statistical reliability analyses of two wood plastic composite extrusion processes

    International Nuclear Information System (INIS)

    Crookston, Kevin A.; Mark Young, Timothy; Harper, David; Guess, Frank M.

    2011-01-01

    Estimates of the reliability of wood plastic composites (WPC) are explored for two industrial extrusion lines. The goal of the paper is to use parametric and non-parametric analyses to examine potential differences in the WPC metrics of reliability for the two extrusion lines that may be helpful for use by the practitioner. A parametric analysis of the extrusion lines reveals some similarities and disparities in the best models; however, a non-parametric analysis reveals unique and insightful differences between Kaplan-Meier survival curves for the modulus of elasticity (MOE) and modulus of rupture (MOR) of the WPC industrial data. The distinctive non-parametric comparisons indicate the source of the differences in strength between the 10.2% and 48.0% fractiles [3,183-3,517 MPa] for MOE and for MOR between the 2.0% and 95.1% fractiles [18.9-25.7 MPa]. Distribution fitting as related to selection of the proper statistical methods is discussed with relevance to estimating the reliability of WPC. The ability to detect statistical differences in the product reliability of WPC between extrusion processes may benefit WPC producers in improving product reliability and safety of this widely used house-decking product. The approach can be applied to many other safety and complex system lifetime comparisons.

  13. Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus revealed by analyses of multiple mitochondrial and nuclear DNA loci

    Directory of Open Access Journals (Sweden)

    Wu Shi-Fang

    2011-07-01

    Full Text Available Abstract Background Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. Results Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. Conclusion This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.

  14. Short-wavelength magnetic recording new methods and analyses

    CERN Document Server

    Ruigrok, JJM

    2013-01-01

    Short-wavelength magnetic recording presents a series of practical solutions to a wide range of problems in the field of magnetic recording. It features many new and original results, all derived from fundamental principles as a result of up-to-date research.A special section is devoted to the playback process, including the calculations of head efficiency and head impedance, derived from new theorems.Features include:A simple and fast method for measuring efficiency; a simple method for the accurate separation of the read and write behaviour of magnetic heads; a new concept - the bandpass hea

  15. Infra-Red Gas Analysers of Liquid Crystal Type for Environmental Monitoring

    Directory of Open Access Journals (Sweden)

    V. I. Nazarov

    2004-01-01

    Full Text Available The paper reveals an opportunity to use infra-red gas analysers on the basis of the developed dichroic liquid crystal cells for investigation of absorption bands of various gases in the near infrared spectral region.

  16. Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera.

    Science.gov (United States)

    Meganathan, P R; Pagan, Heidi J T; McCulloch, Eve S; Stevens, Richard D; Ray, David A

    2012-01-15

    Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes. Copyright © 2011 Elsevier B.V. All rights reserved.

  17. A Rapid Colorimetric Method Reveals Fraudulent Substitutions in Sea Urchin Roe Marketed in Sardinia (Italy).

    Science.gov (United States)

    Meloni, Domenico; Spina, Antonio; Satta, Gianluca; Chessa, Vittorio

    2016-06-25

    In recent years, besides the consumption of fresh sea urchin specimens, the demand of minimally-processed roe has grown considerably. This product has made frequent consumption in restaurants possible and frauds are becoming widespread with the partial replacement of sea urchin roe with surrogates that are similar in colour. One of the main factors that determines the quality of the roe is its colour and small differences in colour scale cannot be easily discerned by the consumers. In this study we have applied a rapid colorimetric method for reveal the fraudulent partial substitution of semi-solid sea urchin roe with liquid egg yolk. Objective assessment of whiteness (L*), redness (a*), yellowness (b*), hue (h*), and chroma (C*) was carried out with a digital spectrophotometer using the CIE L*a*b* colour measurement system. The colorimetric method highlighted statistically significant differences among sea urchin roe and liquid egg yolk that could be easily discerned quantitatively.

  18. Reliability of the k{sub 0}-standardization method using geological sample analysed in a proficiency test

    Energy Technology Data Exchange (ETDEWEB)

    Pelaes, Ana Clara O.; Menezes, Maria Ângela de B.C., E-mail: anacpelaes@gmail.com, E-mail: menezes@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil)

    2017-11-01

    The Neutron Activation Analysis (NAA) is an analytical technique to determine the elemental chemical composition in samples of several matrices, that has been applied by the Laboratory for Neutron Activation Analysis, located at Centro de Desenvolvimento da Tecnologia Nuclear /Comissão Nacional de Energia Nuclear (Nuclear Technology Development Center/Brazilian Commission for Nuclear Energy), CDTN/CNEN, since the starting up of the TRIGA MARK I IPR-R1 reactor, in 1960. Among the methods of application of the technique, the k{sub 0}-standardization method, which was established at CDTN in 1995, is the most efficient and in 2003 it was reestablished and optimized. In order to verify the reproducibility of the results generated by the application of the k{sub 0}-standardization method at CDTN, aliquots of a geological sample sent by WEPAL (Wageningen Evaluating Programs for Analytical Laboratories) were analysed and its results were compared with the results obtained through the Intercomparison of Results organized by the International Atomic Energy Agency in 2015. WEPAL is an accredited institution for the organisation of interlaboratory studies, preparing and organizing proficiency testing schemes all over the world. Therefore, the comparison with the results provided aims to contribute to the continuous improvement of the quality of the results obtained by the CDTN. The objective of this study was to verify the reliability of the method applied two years after the intercomparison round. (author)

  19. Who runs public health? A mixed-methods study combining qualitative and network analyses.

    Science.gov (United States)

    Oliver, Kathryn; de Vocht, Frank; Money, Annemarie; Everett, Martin

    2013-09-01

    Persistent health inequalities encourage researchers to identify new ways of understanding the policy process. Informal relationships are implicated in finding evidence and making decisions for public health policy (PHP), but few studies use specialized methods to identify key actors in the policy process. We combined network and qualitative data to identify the most influential individuals in PHP in a UK conurbation and describe their strategies to influence policy. Network data were collected by asking for nominations of powerful and influential people in PHP (n = 152, response rate 80%), and 23 semi-structured interviews were analysed using a framework approach. The most influential PHP makers in this conurbation were mid-level managers in the National Health Service and local government, characterized by managerial skills: controlling policy processes through gate keeping key organizations, providing policy content and managing selected experts and executives to lead on policies. Public health professionals and academics are indirectly connected to policy via managers. The most powerful individuals in public health are managers, not usually considered targets for research. As we show, they are highly influential through all stages of the policy process. This study shows the importance of understanding the daily activities of influential policy individuals.

  20. Publication bias in dermatology systematic reviews and meta-analyses.

    Science.gov (United States)

    Atakpo, Paul; Vassar, Matt

    2016-05-01

    Systematic reviews and meta-analyses in dermatology provide high-level evidence for clinicians and policy makers that influence clinical decision making and treatment guidelines. One methodological problem with systematic reviews is the under representation of unpublished studies. This problem is due in part to publication bias. Omission of statistically non-significant data from meta-analyses may result in overestimation of treatment effect sizes which may lead to clinical consequences. Our goal was to assess whether systematic reviewers in dermatology evaluate and report publication bias. Further, we wanted to conduct our own evaluation of publication bias on meta-analyses that failed to do so. Our study considered systematic reviews and meta-analyses from ten dermatology journals from 2006 to 2016. A PubMed search was conducted, and all full-text articles that met our inclusion criteria were retrieved and coded by the primary author. 293 articles were included in our analysis. Additionally, we formally evaluated publication bias in meta-analyses that failed to do so using trim and fill and cumulative meta-analysis by precision methods. Publication bias was mentioned in 107 articles (36.5%) and was formally evaluated in 64 articles (21.8%). Visual inspection of a funnel plot was the most common method of evaluating publication bias. Publication bias was present in 45 articles (15.3%), not present in 57 articles (19.5%) and not determined in 191 articles (65.2%). Using the trim and fill method, 7 meta-analyses (33.33%) showed evidence of publication bias. Although the trim and fill method only found evidence of publication bias in 7 meta-analyses, the cumulative meta-analysis by precision method found evidence of publication bias in 15 meta-analyses (71.4%). Many of the reviews in our study did not mention or evaluate publication bias. Further, of the 42 articles that stated following PRISMA reporting guidelines, 19 (45.2%) evaluated for publication bias. In

  1. Comparative metagenomic and metatranscriptomic analyses of microbial communities in acid mine drainage.

    Science.gov (United States)

    Chen, Lin-xing; Hu, Min; Huang, Li-nan; Hua, Zheng-shuang; Kuang, Jia-liang; Li, Sheng-jin; Shu, Wen-sheng

    2015-07-01

    The microbial communities in acid mine drainage have been extensively studied to reveal their roles in acid generation and adaption to this environment. Lacking, however, are integrated community- and organism-wide comparative gene transcriptional analyses that could reveal the response and adaptation mechanisms of these extraordinary microorganisms to different environmental conditions. In this study, comparative metagenomics and metatranscriptomics were performed on microbial assemblages collected from four geochemically distinct acid mine drainage (AMD) sites. Taxonomic analysis uncovered unexpectedly high microbial biodiversity of these extremely acidophilic communities, and the abundant taxa of Acidithiobacillus, Leptospirillum and Acidiphilium exhibited high transcriptional activities. Community-wide comparative analyses clearly showed that the AMD microorganisms adapted to the different environmental conditions via regulating the expression of genes involved in multiple in situ functional activities, including low-pH adaptation, carbon, nitrogen and phosphate assimilation, energy generation, environmental stress resistance, and other functions. Organism-wide comparative analyses of the active taxa revealed environment-dependent gene transcriptional profiles, especially the distinct strategies used by Acidithiobacillus ferrivorans and Leptospirillum ferrodiazotrophum in nutrients assimilation and energy generation for survival under different conditions. Overall, these findings demonstrate that the gene transcriptional profiles of AMD microorganisms are closely related to the site physiochemical characteristics, providing clues into the microbial response and adaptation mechanisms in the oligotrophic, extremely acidic environments.

  2. High overlap of CNVs and selection signatures revealed by varLD analyses of taurine and zebu cattle

    Science.gov (United States)

    Selection Signatures (SS) assessed through analysis of genomic data are being widely studied to discover population specific regions selected via artificial or natural selection. Different methodologies have been proposed for these analyses, each having specific limitations as to the age of the sele...

  3. Log sampling methods and software for stand and landscape analyses.

    Science.gov (United States)

    Lisa J. Bate; Torolf R. Torgersen; Michael J. Wisdom; Edward O. Garton; Shawn C. Clabough

    2008-01-01

    We describe methods for efficient, accurate sampling of logs at landscape and stand scales to estimate density, total length, cover, volume, and weight. Our methods focus on optimizing the sampling effort by choosing an appropriate sampling method and transect length for specific forest conditions and objectives. Sampling methods include the line-intersect method and...

  4. Family-based Association Analyses of Imputed Genotypes Reveal Genome-Wide Significant Association of Alzheimer’s disease with OSBPL6, PTPRG and PDCL3

    Science.gov (United States)

    Herold, Christine; Hooli, Basavaraj V.; Mullin, Kristina; Liu, Tian; Roehr, Johannes T; Mattheisen, Manuel; Parrado, Antonio R.; Bertram, Lars; Lange, Christoph; Tanzi, Rudolph E.

    2015-01-01

    The genetic basis of Alzheimer's disease (AD) is complex and heterogeneous. Over 200 highly penetrant pathogenic variants in the genes APP, PSEN1 and PSEN2 cause a subset of early-onset familial Alzheimer's disease (EOFAD). On the other hand, susceptibility to late-onset forms of AD (LOAD) is indisputably associated to the ε4 allele in the gene APOE, and more recently to variants in more than two-dozen additional genes identified in the large-scale genome-wide association studies (GWAS) and meta-analyses reports. Taken together however, although the heritability in AD is estimated to be as high as 80%, a large proportion of the underlying genetic factors still remain to be elucidated. In this study we performed a systematic family-based genome-wide association and meta-analysis on close to 15 million imputed variants from three large collections of AD families (~3,500 subjects from 1,070 families). Using a multivariate phenotype combining affection status and onset age, meta-analysis of the association results revealed three single nucleotide polymorphisms (SNPs) that achieved genome-wide significance for association with AD risk: rs7609954 in the gene PTPRG (P-value = 3.98·10−08), rs1347297 in the gene OSBPL6 (P-value = 4.53·10−08), and rs1513625 near PDCL3 (P-value = 4.28·10−08). In addition, rs72953347 in OSBPL6 (P-value = 6.36·10−07) and two SNPs in the gene CDKAL1 showed marginally significant association with LOAD (rs10456232, P-value: 4.76·10−07; rs62400067, P-value: 3.54·10−07). In summary, family-based GWAS meta-analysis of imputed SNPs revealed novel genomic variants in (or near) PTPRG, OSBPL6, and PDCL3 that influence risk for AD with genome-wide significance. PMID:26830138

  5. Diet of Tollund Man. Stable isotope analyses of an Iron Age bog body from Denmark

    DEFF Research Database (Denmark)

    Helt Nielsen, Nina; Philippsen, Bente; Jensen, L. V.

    Tollund Man is one of the world’s most famous bog bodies due to his exceptionally well-preserved head. He was found in 1950 by peat cutters in a bog near Bjældskovdal, c. 10 km west of Silkeborg. During the years, several analyses have been performed on the body to shed light on the life and deat...... to dry out, and the bone sample could therefore be analysed without special pretreatment. The hair, on the other hand, had been treated with wax, which needed to be removed prior to analysis. The successful method of pre-treatment will be presented....... and hair of Tollund Man. The analysis of the isotopes of C, N and S reveals the diet on long and short time scales: The isotope signature in the bone sample reflects the average diet in the years prior to death; the isotope signature in the hair reflects the diet in the last months of his life. Any...

  6. Methods and Techniques Used to Convey Total System Performance Assessment Analyses and Results for Site Recommendation at Yucca Mountain, Nevada, USA

    International Nuclear Information System (INIS)

    Mattie, Patrick D.; McNeish, Jerry A.; Sevougian, S. David; Andrews, Robert W.

    2001-01-01

    Total System Performance Assessment (TSPA) is used as a key decision-making tool for the potential geologic repository of high level radioactive waste at Yucca Mountain, Nevada USA. Because of the complexity and uncertainty involved in a post-closure performance assessment, an important goal is to produce a transparent document describing the assumptions, the intermediate steps, the results, and the conclusions of the analyses. An important objective for a TSPA analysis is to illustrate confidence in performance projections of the potential repository given a complex system of interconnected process models, data, and abstractions. The methods and techniques used for the recent TSPA analyses demonstrate an effective process to portray complex models and results with transparency and credibility

  7. ALBEDO PATTERN RECOGNITION AND TIME-SERIES ANALYSES IN MALAYSIA

    Directory of Open Access Journals (Sweden)

    S. A. Salleh

    2012-07-01

    Full Text Available Pattern recognition and time-series analyses will enable one to evaluate and generate predictions of specific phenomena. The albedo pattern and time-series analyses are very much useful especially in relation to climate condition monitoring. This study is conducted to seek for Malaysia albedo pattern changes. The pattern recognition and changes will be useful for variety of environmental and climate monitoring researches such as carbon budgeting and aerosol mapping. The 10 years (2000–2009 MODIS satellite images were used for the analyses and interpretation. These images were being processed using ERDAS Imagine remote sensing software, ArcGIS 9.3, the 6S code for atmospherical calibration and several MODIS tools (MRT, HDF2GIS, Albedo tools. There are several methods for time-series analyses were explored, this paper demonstrates trends and seasonal time-series analyses using converted HDF format MODIS MCD43A3 albedo land product. The results revealed significance changes of albedo percentages over the past 10 years and the pattern with regards to Malaysia's nebulosity index (NI and aerosol optical depth (AOD. There is noticeable trend can be identified with regards to its maximum and minimum value of the albedo. The rise and fall of the line graph show a similar trend with regards to its daily observation. The different can be identified in term of the value or percentage of rises and falls of albedo. Thus, it can be concludes that the temporal behavior of land surface albedo in Malaysia have a uniform behaviours and effects with regards to the local monsoons. However, although the average albedo shows linear trend with nebulosity index, the pattern changes of albedo with respects to the nebulosity index indicates that there are external factors that implicates the albedo values, as the sky conditions and its diffusion plotted does not have uniform trend over the years, especially when the trend of 5 years interval is examined, 2000 shows high

  8. Expression and phylogenetic analyses reveal paralogous lineages of putatively classical and non-classical MHC-I genes in three sparrow species (Passer).

    Science.gov (United States)

    Drews, Anna; Strandh, Maria; Råberg, Lars; Westerdahl, Helena

    2017-06-26

    The Major Histocompatibility Complex (MHC) plays a central role in immunity and has been given considerable attention by evolutionary ecologists due to its associations with fitness-related traits. Songbirds have unusually high numbers of MHC class I (MHC-I) genes, but it is not known whether all are expressed and equally important for immune function. Classical MHC-I genes are highly expressed, polymorphic and present peptides to T-cells whereas non-classical MHC-I genes have lower expression, are more monomorphic and do not present peptides to T-cells. To get a better understanding of the highly duplicated MHC genes in songbirds, we studied gene expression in a phylogenetic framework in three species of sparrows (house sparrow, tree sparrow and Spanish sparrow), using high-throughput sequencing. We hypothesize that sparrows could have classical and non-classical genes, as previously indicated though never tested using gene expression. The phylogenetic analyses reveal two distinct types of MHC-I alleles among the three sparrow species, one with high and one with low level of polymorphism, thus resembling classical and non-classical genes, respectively. All individuals had both types of alleles, but there was copy number variation both within and among the sparrow species. However, the number of highly polymorphic alleles that were expressed did not vary between species, suggesting that the structural genomic variation is counterbalanced by conserved gene expression. Overall, 50% of the MHC-I alleles were expressed in sparrows. Expression of the highly polymorphic alleles was very variable, whereas the alleles with low polymorphism had uniformly low expression. Interestingly, within an individual only one or two alleles from the polymorphic genes were highly expressed, indicating that only a single copy of these is highly expressed. Taken together, the phylogenetic reconstruction and the analyses of expression suggest that sparrows have both classical and non

  9. Congruence between distribution modelling and phylogeographical analyses reveals Quaternary survival of a toadflax species (Linaria elegans) in oceanic climate areas of a mountain ring range.

    Science.gov (United States)

    Fernández-Mazuecos, Mario; Vargas, Pablo

    2013-06-01

    · The role of Quaternary climatic shifts in shaping the distribution of Linaria elegans, an Iberian annual plant, was investigated using species distribution modelling and molecular phylogeographical analyses. Three hypotheses are proposed to explain the Quaternary history of its mountain ring range. · The distribution of L. elegans was modelled using the maximum entropy method and projected to the last interglacial and to the last glacial maximum (LGM) using two different paleoclimatic models: the Community Climate System Model (CCSM) and the Model for Interdisciplinary Research on Climate (MIROC). Two nuclear and three plastid DNA regions were sequenced for 24 populations (119 individuals sampled). Bayesian phylogenetic, phylogeographical, dating and coalescent-based population genetic analyses were conducted. · Molecular analyses indicated the existence of northern and southern glacial refugia and supported two routes of post-glacial recolonization. These results were consistent with the LGM distribution as inferred under the CCSM paleoclimatic model (but not under the MIROC model). Isolation between two major refugia was dated back to the Riss or Mindel glaciations, > 100 kyr before present (bp). · The Atlantic distribution of inferred refugia suggests that the oceanic (buffered)-continental (harsh) gradient may have played a key and previously unrecognized role in determining Quaternary distribution shifts of Mediterranean plants. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  10. Safety analyses for reprocessing and waste processing

    International Nuclear Information System (INIS)

    1983-03-01

    Presentation of an incident analysis of process steps of the RP, simplified considerations concerning safety, and safety analyses of the storage and solidification facilities of the RP. A release tree method is developed and tested. An incident analysis of process steps, the evaluation of the SRL-study and safety analyses of the storage and solidification facilities of the RP are performed in particular. (DG) [de

  11. Trend analyses of transformer problems in the U.S. nuclear power plants

    International Nuclear Information System (INIS)

    Shimada, Yoshio

    2009-01-01

    Up to 2007, the authors have conducted the trend analyses of trouble events related to main generators, emergency diesel generators, breakers and motors, which are more likely to cause problems than other electric equipments in nuclear power plants. The frequency of trouble events in transformers in domestic nuclear power plants at present is approximately one third of the publicly reported cases in the U.S. However, as the situation of maintenance in Japan in the future will become similar to those in the U.S. if the operating period is extended or the maintenance method is to be shifted from preventive maintenance to condition based maintenance, there is a concern that the frequency of transformer events in Japan will increase in Japan, also. Thus, trend analyses were conducted on transformers events which had not been subject to such analyses, from among electrical equipments which are likely to cause problems. The trend analyses were performed on 23 transformer events which had occurred in the U.S. nuclear power plants in five years from 2003 through 2007 among events reported in the Licensee Event Reports (LERs: event reports submitted to NRC by U.S. nuclear power plants) which have been registered in the nuclear information database of the Institute of Nuclear Safety System, Incorporated's (INSS), as well as 8 events registered in the Nuclear Information Archives (NUCIA), which had occurred in domestic nuclear power plants in five from 2003 through 2007. Lessons learned from the trend analyses of the transformer trouble events in the U.S. revealed that for transformers in general, the maintenance management of tap changers is important, while for the main transformers which are most likely to cause problems, it is vital to prevent the deterioration of insulation and insulating oil. (author)

  12. Pathway-based analyses.

    Science.gov (United States)

    Kent, Jack W

    2016-02-03

    New technologies for acquisition of genomic data, while offering unprecedented opportunities for genetic discovery, also impose severe burdens of interpretation and penalties for multiple testing. The Pathway-based Analyses Group of the Genetic Analysis Workshop 19 (GAW19) sought reduction of multiple-testing burden through various approaches to aggregation of highdimensional data in pathways informed by prior biological knowledge. Experimental methods testedincluded the use of "synthetic pathways" (random sets of genes) to estimate power and false-positive error rate of methods applied to simulated data; data reduction via independent components analysis, single-nucleotide polymorphism (SNP)-SNP interaction, and use of gene sets to estimate genetic similarity; and general assessment of the efficacy of prior biological knowledge to reduce the dimensionality of complex genomic data. The work of this group explored several promising approaches to managing high-dimensional data, with the caveat that these methods are necessarily constrained by the quality of external bioinformatic annotation.

  13. Lactococcus lactis Diversity in Undefined Mixed Dairy Starter Cultures as Revealed by Comparative Genome Analyses and Targeted Amplicon Sequencing of epsD.

    Science.gov (United States)

    Frantzen, Cyril A; Kleppen, Hans Petter; Holo, Helge

    2018-02-01

    Undefined mesophilic mixed (DL) starter cultures are used in the production of continental cheeses and contain unknown strain mixtures of Lactococcus lactis and leuconostocs. The choice of starter culture affects the taste, aroma, and quality of the final product. To gain insight into the diversity of Lactococcus lactis strains in starter cultures, we whole-genome sequenced 95 isolates from three different starter cultures. Pan-genomic analyses, which included 30 publically available complete genomes, grouped the strains into 21 L. lactis subsp . lactis and 28 L. lactis subsp. cremoris lineages. Only one of the 95 isolates grouped with previously sequenced strains, and the three starter cultures showed no overlap in lineage distributions. The culture diversity was assessed by targeted amplicon sequencing using purR , a core gene, and epsD , present in 93 of the 95 starter culture isolates but absent in most of the reference strains. This enabled an unprecedented discrimination of starter culture Lactococcus lactis and revealed substantial differences between the three starter cultures and compositional shifts during the cultivation of cultures in milk. IMPORTANCE In contemporary cheese production, standardized frozen seed stock starter cultures are used to ensure production stability, reproducibility, and quality control of the product. The dairy industry experiences significant disruptions of cheese production due to phage attacks, and one commonly used countermeasure to phage attack is to employ a starter rotation strategy, in which two or more starters with minimal overlap in phage sensitivity are used alternately. A culture-independent analysis of the lactococcal diversity in complex undefined starter cultures revealed large differences between the three starter cultures and temporal shifts in lactococcal composition during the production of bulk starters. A better understanding of the lactococcal diversity in starter cultures will enable the development of

  14. Sensitivity in risk analyses with uncertain numbers.

    Energy Technology Data Exchange (ETDEWEB)

    Tucker, W. Troy; Ferson, Scott

    2006-06-01

    Sensitivity analysis is a study of how changes in the inputs to a model influence the results of the model. Many techniques have recently been proposed for use when the model is probabilistic. This report considers the related problem of sensitivity analysis when the model includes uncertain numbers that can involve both aleatory and epistemic uncertainty and the method of calculation is Dempster-Shafer evidence theory or probability bounds analysis. Some traditional methods for sensitivity analysis generalize directly for use with uncertain numbers, but, in some respects, sensitivity analysis for these analyses differs from traditional deterministic or probabilistic sensitivity analyses. A case study of a dike reliability assessment illustrates several methods of sensitivity analysis, including traditional probabilistic assessment, local derivatives, and a ''pinching'' strategy that hypothetically reduces the epistemic uncertainty or aleatory uncertainty, or both, in an input variable to estimate the reduction of uncertainty in the outputs. The prospects for applying the methods to black box models are also considered.

  15. Identifying null meta-analyses that are ripe for updating

    Directory of Open Access Journals (Sweden)

    Fang Manchun

    2003-07-01

    Full Text Available Abstract Background As an increasingly large number of meta-analyses are published, quantitative methods are needed to help clinicians and systematic review teams determine when meta-analyses are not up to date. Methods We propose new methods for determining when non-significant meta-analytic results might be overturned, based on a prediction of the number of participants required in new studies. To guide decision making, we introduce the "new participant ratio", the ratio of the actual number of participants in new studies to the predicted number required to obtain statistical significance. A simulation study was conducted to study the performance of our methods and a real meta-analysis provides further evidence. Results In our three simulation configurations, our diagnostic test for determining whether a meta-analysis is out of date had sensitivity of 55%, 62%, and 49% with corresponding specificity of 85%, 80%, and 90% respectively. Conclusions Simulations suggest that our methods are able to detect out-of-date meta-analyses. These quick and approximate methods show promise for use by systematic review teams to help decide whether to commit the considerable resources required to update a meta-analysis. Further investigation and evaluation of the methods is required before they can be recommended for general use.

  16. An efficient method for studying and analysing the propagation ...

    African Journals Online (AJOL)

    The paper describes a method, based on the solution of travelling-wave phenomena in polyphase systems by the use of matrix methods, of deriving the basic matrices of the conductor system taking into account the effect of conductor geometry, conductor internal impedance and the earth-return path. It is then shown how ...

  17. Post-facta Analyses of Fukushima Accident and Lessons Learned

    Energy Technology Data Exchange (ETDEWEB)

    Tanabe, Fumiya [Sociotechnical Systems Safety Research Institute, Ichige (Japan)

    2014-08-15

    Independent analyses have been performed of the core melt behavior of the Unit 1, Unit 2 and Unit 3 reactors of Fukushima Daiichi Nuclear Power Station on 11-15 March 2011. The analyses are based on a phenomenological methodology with measured data investigation and a simple physical model calculation. Estimated are time variation of core water level, core material temperature and hydrogen generation rate. The analyses have revealed characteristics of accident process of each reactor. In the case of Unit 2 reactor, the calculated result suggests little hydrogen generation because of no steam generation in the core for zirconium-steam reaction during fuel damage process. It could be the reason of no hydrogen explosion in the Unit 2 reactor building. Analyses have been performed also on the core material behavior in another chaotic period of 19-31 March 2011, and it resulted in a re-melt hypothesis that core material in each reactor should have melted again due to shortage of cooling water. The hypothesis is consistent with many observed features of radioactive materials dispersion into the environment.

  18. Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery

    DEFF Research Database (Denmark)

    Poulsen, Michael; Oh, Dong-Chan; Clardy, Jon

    2011-01-01

    and solitary Hymenoptera. Here we test this possibility by examining two species of solitary mud dauber wasps, Sceliphron caementarium and Chalybion californicum. We performed enrichment isolations from 33 wasps and obtained more than 200 isolates of Streptomyces Actinobacteria. Chemical analyses of 15...... and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding...... phylogenetically diverse and chemically prolific Actinobacteria from solitary wasps suggests that insect-associated Actinobacteria can provide a valuable source of novel natural products of pharmaceutical interest....

  19. Risk analysis for decision support in electricity distribution system asset management: methods and frameworks for analysing intangible risks

    Energy Technology Data Exchange (ETDEWEB)

    Nordgaard, Dag Eirik

    2010-04-15

    During the last 10 to 15 years electricity distribution companies throughout the world have been ever more focused on asset management as the guiding principle for their activities. Within asset management, risk is a key issue for distribution companies, together with handling of cost and performance. There is now an increased awareness of the need to include risk analyses into the companies' decision making processes. Much of the work on risk in electricity distribution systems has focused on aspects of reliability. This is understandable, since it is surely an important feature of the product delivered by the electricity distribution infrastructure, and it is high on the agenda for regulatory authorities in many countries. However, electricity distribution companies are also concerned with other risks relevant for their decision making. This typically involves intangible risks, such as safety, environmental impacts and company reputation. In contrast to the numerous methodologies developed for reliability risk analysis, there are relatively few applications of structured analyses to support decisions concerning intangible risks, even though they represent an important motivation for decisions taken in electricity distribution companies. The overall objective of this PhD work has been to explore risk analysis methods that can be used to improve and support decision making in electricity distribution system asset management, with an emphasis on the analysis of intangible risks. The main contributions of this thesis can be summarised as: An exploration and testing of quantitative risk analysis (QRA) methods to support decisions concerning intangible risks; The development of a procedure for using life curve models to provide input to QRA models; The development of a framework for risk-informed decision making where QRA are used to analyse selected problems; In addition, the results contribute to clarify the basic concepts of risk, and highlight challenges

  20. Conducting qualitative research in mental health: Thematic and content analyses.

    Science.gov (United States)

    Crowe, Marie; Inder, Maree; Porter, Richard

    2015-07-01

    The objective of this paper is to describe two methods of qualitative analysis - thematic analysis and content analysis - and to examine their use in a mental health context. A description of the processes of thematic analysis and content analysis is provided. These processes are then illustrated by conducting two analyses of the same qualitative data. Transcripts of qualitative interviews are analysed using each method to illustrate these processes. The illustration of the processes highlights the different outcomes from the same set of data. Thematic and content analyses are qualitative methods that serve different research purposes. Thematic analysis provides an interpretation of participants' meanings, while content analysis is a direct representation of participants' responses. These methods provide two ways of understanding meanings and experiences and provide important knowledge in a mental health context. © The Royal Australian and New Zealand College of Psychiatrists 2015.

  1. Combined genomic and structural analyses of a cultured magnetotactic bacterium reveals its niche adaptation to a dynamic environment

    Directory of Open Access Journals (Sweden)

    Ana Carolina Vieira Araujo

    2016-10-01

    Full Text Available Abstract Background Magnetotactic bacteria (MTB are a unique group of prokaryotes that have a potentially high impact on global geochemical cycling of significant primary elements because of their metabolic plasticity and the ability to biomineralize iron-rich magnetic particles called magnetosomes. Understanding the genetic composition of the few cultivated MTB along with the unique morphological features of this group of bacteria may provide an important framework for discerning their potential biogeochemical roles in natural environments. Results Genomic and ultrastructural analyses were combined to characterize the cultivated magnetotactic coccus Magnetofaba australis strain IT-1. Cells of this species synthesize a single chain of elongated, cuboctahedral magnetite (Fe3O4 magnetosomes that cause them to align along magnetic field lines while they swim being propelled by two bundles of flagella at velocities up to 300 μm s−1. High-speed microscopy imaging showed the cells move in a straight line rather than in the helical trajectory described for other magnetotactic cocci. Specific genes within the genome of Mf. australis strain IT-1 suggest the strain is capable of nitrogen fixation, sulfur reduction and oxidation, synthesis of intracellular polyphosphate granules and transporting iron with low and high affinity. Mf. australis strain IT-1 and Magnetococcus marinus strain MC-1 are closely related phylogenetically although similarity values between their homologous proteins are not very high. Conclusion Mf. australis strain IT-1 inhabits a constantly changing environment and its complete genome sequence reveals a great metabolic plasticity to deal with these changes. Aside from its chemoautotrophic and chemoheterotrophic metabolism, genomic data indicate the cells are capable of nitrogen fixation, possess high and low affinity iron transporters, and might be capable of reducing and oxidizing a number of sulfur compounds. The relatively

  2. Temporal Fluctuation in North East Baltic Sea Region Cattle Population Revealed by Mitochondrial and Y-Chromosomal DNA Analyses

    Science.gov (United States)

    Niemi, Marianna; Bläuer, Auli; Iso-Touru, Terhi; Harjula, Janne; Nyström Edmark, Veronica; Rannamäe, Eve; Lõugas, Lembi; Sajantila, Antti; Lidén, Kerstin; Taavitsainen, Jussi-Pekka

    2015-01-01

    Background Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies. Results Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples). Conclusions The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle. PMID:25992976

  3. Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells

    DEFF Research Database (Denmark)

    Ding, Li; Paszkowski-Rogacz, Maciej; Winzi, Maria

    2015-01-01

    We combine a genome-scale RNAi screen in mouse epiblast stem cells (EpiSCs) with genetic interaction, protein localization, and "protein-level dependency" studies-a systematic technique that uncovers post-transcriptional regulation-to delineate the network of factors that control the expression...... of Oct4, a key regulator of pluripotency. Our data signify that there are similarities, but also fundamental differences in Oct4 regulation in EpiSCs versus embryonic stem cells (ESCs). Through multiparametric data analyses, we predict that Tox4 is associating with the Paf1C complex, which maintains cell...... identity in both cell types, and validate that this protein-protein interaction exists in ESCs and EpiSCs. We also identify numerous knockdowns that increase Oct4 expression in EpiSCs, indicating that, in stark contrast to ESCs, Oct4 is under active repressive control in EpiSCs. These studies provide...

  4. Systems reliability analyses and risk analyses for the licencing procedure under atomic law

    International Nuclear Information System (INIS)

    Berning, A.; Spindler, H.

    1983-01-01

    For the licencing procedure under atomic law in accordance with Article 7 AtG, the nuclear power plant as a whole needs to be assessed, plus the reliability of systems and plant components that are essential to safety are to be determined with probabilistic methods. This requirement is the consequence of safety criteria for nuclear power plants issued by the Home Department (BMI). Systems reliability studies and risk analyses used in licencing procedures under atomic law are identified. The stress is on licencing decisions, mainly for PWR-type reactors. Reactor Safety Commission (RSK) guidelines, examples of reasoning in legal proceedings and arguments put forth by objectors are also dealt with. Correlations are shown between reliability analyses made by experts and licencing decisions by means of examples. (orig./HP) [de

  5. The genetic diversity of genus Bacillus and the related genera revealed by 16S rRNA gene sequences and ardra analyses isolated from geothermal regions of turkey

    Directory of Open Access Journals (Sweden)

    Arzu Coleri Cihan

    2012-03-01

    Full Text Available Previously isolated 115 endospore-forming bacilli were basically grouped according to their temperature requirements for growth: the thermophiles (74%, the facultative thermophiles (14% and the mesophiles (12%. These isolates were taken into 16S rRNA gene sequence analyses, and they were clustered among the 7 genera: Anoxybacillus, Aeribacillus, Bacillus, Brevibacillus, Geobacillus, Paenibacillus, and Thermoactinomycetes. Of these bacilli, only the thirty two isolates belonging to genera Bacillus (16, Brevibacillus (13, Paenibacillus (1 and Thermoactinomycetes (2 were selected and presented in this paper. The comparative sequence analyses revealed that the similarity values were ranged as 91.4-100 %, 91.8- 99.2 %, 92.6- 99.8 % and 90.7 - 99.8 % between the isolates and the related type strains from these four genera, respectively. Twenty nine of them were found to be related with the validly published type strains. The most abundant species was B. thermoruber with 9 isolates followed by B. pumilus (6, B. lichenformis (3, B. subtilis (3, B. agri (3, B. smithii (2, T. vulgaris (2 and finally P. barengoltzii (1. In addition, isolates of A391a, B51a and D295 were proposed as novel species as their 16S rRNA gene sequences displayed similarities ≤ 97% to their closely related type strains. The AluI-, HaeIII- and TaqI-ARDRA results were in congruence with the 16S rRNA gene sequence analyses. The ARDRA results allowed us to differentiate these isolates, and their discriminative restriction fragments were able to be determined. Some of their phenotypic characters and their amylase, chitinase and protease production were also studied and biotechnologically valuable enzyme producing isolates were introduced in order to use in further studies.

  6. Towards equitable access to medicines for the rural poor: analyses of insurance claims reveal rural pharmacy initiative triggers price competition in Kyrgyzstan

    Directory of Open Access Journals (Sweden)

    Leufkens Hubert GM

    2009-12-01

    Full Text Available Abstract Background A rural pharmacy initiative (RPI designed to increase access to medicines in rural Kyrgyzstan created a network of 12 pharmacies using a revolving drug fund mechanism in 12 villages where no pharmacies previously existed. The objective of this study was to determine if the establishment of the RPI resulted in the unforeseen benefit of triggering medicine price competition in pre-existing (non-RPI private pharmacies located in the region. Methods We conducted descriptive and multivariate analyses on medicine insurance claims data from Kyrgyzstan's Mandatory Health Insurance Fund for the Jumgal District of Naryn Province from October 2003 to December 2007. We compared average quarterly medicine prices in competitor pharmacies before and after the introduction of the rural pharmacy initiative in October 2004 to determine the RPI impact on price competition. Results Descriptive analyses suggest competitors reacted to RPI prices for 21 of 30 (70% medicines. Competitor medicine prices from the quarter before RPI introduction to the end of the study period decreased for 17 of 30 (57% medicines, increased for 4 of 30 (13% medicines, and remained unchanged for 9 of 30 (30% medicines. Among the 9 competitor medicines with unchanged prices, five initially decreased in price but later reverted back to baseline prices. Multivariate analyses on 19 medicines that met sample size criteria confirm these findings. Fourteen of these 19 (74% competitor medicines changed significantly in price from the quarter before RPI introduction to the quarter after RPI introduction, with 9 of 19 (47% decreasing in price and 5 of 19 (26% increasing in price. Conclusions The RPI served as a market driver, spurring competition in medicine prices in competitor pharmacies, even when they were located in different villages. Initiatives designed to increase equitable access to medicines in rural regions of developing and transitional countries should consider the

  7. Impact analyses after pipe rupture

    International Nuclear Information System (INIS)

    Chun, R.C.; Chuang, T.Y.

    1983-01-01

    Two of the French pipe whip experiments are reproduced with the computer code WIPS. The WIPS results are in good agreement with the experimental data and the French computer code TEDEL. This justifies the use of its pipe element in conjunction with its U-bar element in a simplified method of impact analyses

  8. Determination of S_1_7 from systematic analyses on "8B Coulomb breakup with the Eikonal-CDCC method

    International Nuclear Information System (INIS)

    Ogata, K.; Matsumoto, T.; Yamashita, N.; Kamimura, M.; Yahiro, M.; Iseri, Y.

    2003-01-01

    Systematic analysis of "8B Coulomb dissociation with the Asymptotic Normalization Coefficient (ANC) method is proposed to determine the astrophysical factor S_1_7(0) accurately. An important advantage of the analysis is that uncertainties of the extracted S_1_7(0) coming from the use of the ANC method can quantitatively be evaluated, in contrast to previous analyses using the Virtual Photon Theory (VPT). Calculation of measured spectra in dissociation experiments is done by means of the method of Continuum-Discretized Coupled-Channels (CDCC). From the analysis of "5"8Ni("8B,"7Be+p) "5"8Ni at 25.8 MeV, S_1_7(0) = 22.83 ± 0.51(theo) ± 2.28(expt) (eVb) is obtained; the ANC method turned out to work in this case within 1% of error. Preceding systematic analysis of experimental data at intermediate energies, we propose hybrid (HY) Coupled-Channels (CC) calculation of "8B Coulomb dissociation, which makes numerical calculation much simple, retaining its accuracy. The validity of the HY calculation is tested for "5"8Ni("8B,"7Be+p) "5"8Ni at 240 MeV. The ANC method combined with the HY CC calculation is shown to be a powerful technique to obtain a reliable S_1_7(0).

  9. Phylogenomic analyses data of the avian phylogenomics project

    DEFF Research Database (Denmark)

    Jarvis, Erich D; Mirarab, Siavash; Aberer, Andre J

    2015-01-01

    BACKGROUND: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae...... and two of the five Palaeognathae orders. We used these genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomic analyses. FINDINGS: Here we present the datasets associated with the phylogenomic analyses, which include sequence alignment files consisting of nucleotides......ML algorithm or when using statistical binning with the coalescence-based MP-EST algorithm (which we refer to as MP-EST*). Other data sets, such as the coding sequence of some exons, revealed other properties of genome evolution, namely convergence. CONCLUSIONS: The Avian Phylogenomics Project is the largest...

  10. Methodological challenges in carbohydrate analyses

    Directory of Open Access Journals (Sweden)

    Mary Beth Hall

    2007-07-01

    Full Text Available Carbohydrates can provide up to 80% of the dry matter in animal diets, yet their specific evaluation for research and diet formulation is only now becoming a focus in the animal sciences. Partitioning of dietary carbohydrates for nutritional purposes should reflect differences in digestion and fermentation characteristics and effects on animal performance. Key challenges to designating nutritionally important carbohydrate fractions include classifying the carbohydrates in terms of nutritional characteristics, and selecting analytical methods that describe the desired fraction. The relative lack of information on digestion characteristics of various carbohydrates and their interactions with other fractions in diets means that fractions will not soon be perfectly established. Developing a system of carbohydrate analysis that could be used across animal species could enhance the utility of analyses and amount of data we can obtain on dietary effects of carbohydrates. Based on quantities present in diets and apparent effects on animal performance, some nutritionally important classes of carbohydrates that may be valuable to measure include sugars, starch, fructans, insoluble fiber, and soluble fiber. Essential to selection of methods for these fractions is agreement on precisely what carbohydrates should be included in each. Each of these fractions has analyses that could potentially be used to measure them, but most of the available methods have weaknesses that must be evaluated to see if they are fatal and the assay is unusable, or if the assay still may be made workable. Factors we must consider as we seek to analyze carbohydrates to describe diets: Does the assay accurately measure the desired fraction? Is the assay for research, regulatory, or field use (affects considerations of acceptable costs and throughput? What are acceptable accuracy and variability of measures? Is the assay robust (enhances accuracy of values? For some carbohydrates, we

  11. Reactor internals vibration monitoring by neutron noise methods in PWRs

    International Nuclear Information System (INIS)

    Pazsit, I.; Por, G.; Lux, I.

    1983-01-01

    Certain elements of PWR cores such as control/fuel rods or cassettes, or other parts of reactor internals, often represent a vibration problem. Early analyses at operating PWR plant revealed that these vibrations can be detected by in-core neutron detectors, opening up the possibility of vibration monitoring and diagnostics by noise methods. Theoretical methods of calculating vibration induced neutron noise and its application to vibration diagnostics are summarized. Experiments to check theoretical conclusions are under way at the Central Research Institute for Physics, Budapest. (author)

  12. Propensity-score matching in economic analyses: comparison with regression models, instrumental variables, residual inclusion, differences-in-differences, and decomposition methods.

    Science.gov (United States)

    Crown, William H

    2014-02-01

    This paper examines the use of propensity score matching in economic analyses of observational data. Several excellent papers have previously reviewed practical aspects of propensity score estimation and other aspects of the propensity score literature. The purpose of this paper is to compare the conceptual foundation of propensity score models with alternative estimators of treatment effects. References are provided to empirical comparisons among methods that have appeared in the literature. These comparisons are available for a subset of the methods considered in this paper. However, in some cases, no pairwise comparisons of particular methods are yet available, and there are no examples of comparisons across all of the methods surveyed here. Irrespective of the availability of empirical comparisons, the goal of this paper is to provide some intuition about the relative merits of alternative estimators in health economic evaluations where nonlinearity, sample size, availability of pre/post data, heterogeneity, and missing variables can have important implications for choice of methodology. Also considered is the potential combination of propensity score matching with alternative methods such as differences-in-differences and decomposition methods that have not yet appeared in the empirical literature.

  13. Comparative live-cell imaging analyses of SPA-2, BUD-6 and BNI-1 in Neurospora crassa reveal novel features of the filamentous fungal polarisome.

    Directory of Open Access Journals (Sweden)

    Alexander Lichius

    Full Text Available A key multiprotein complex involved in regulating the actin cytoskeleton and secretory machinery required for polarized growth in fungi, is the polarisome. Recognized core constituents in budding yeast are the proteins Spa2, Pea2, Aip3/Bud6, and the key effector Bni1. Multicellular fungi display a more complex polarized morphogenesis than yeasts, suggesting that the filamentous fungal polarisome might fulfill additional functions. In this study, we compared the subcellular organization and dynamics of the putative polarisome components BUD-6 and BNI-1 with those of the bona fide polarisome marker SPA-2 at various developmental stages of Neurospora crassa. All three proteins exhibited a yeast-like polarisome configuration during polarized germ tube growth, cell fusion, septal pore plugging and tip repolarization. However, the localization patterns of all three proteins showed spatiotemporally distinct characteristics during the establishment of new polar axes, septum formation and cytokinesis, and maintained hyphal tip growth. Most notably, in vegetative hyphal tips BUD-6 accumulated as a subapical cloud excluded from the Spitzenkörper (Spk, whereas BNI-1 and SPA-2 partially colocalized with the Spk and the tip apex. Novel roles during septal plugging and cytokinesis, connected to the reinitiation of tip growth upon physical injury and conidial maturation, were identified for BUD-6 and BNI-1, respectively. Phenotypic analyses of gene deletion mutants revealed additional functions for BUD-6 and BNI-1 in cell fusion regulation, and the maintenance of Spk integrity. Considered together, our findings reveal novel polarisome-independent functions of BUD-6 and BNI-1 in Neurospora, but also suggest that all three proteins cooperate at plugged septal pores, and their complex arrangement within the apical dome of mature hypha might represent a novel aspect of filamentous fungal polarisome architecture.

  14. Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna.

    Science.gov (United States)

    Rosauer, Dan F; Catullo, Renee A; VanDerWal, Jeremy; Moussalli, Adnan; Moritz, Craig

    2015-01-01

    Areas of suitable habitat for species and communities have arisen, shifted, and disappeared with Pleistocene climate cycles, and through this shifting landscape, current biodiversity has found paths to the present. Evolutionary refugia, areas of relative habitat stability in this shifting landscape, support persistence of lineages through time, and are thus crucial to the accumulation and maintenance of biodiversity. Areas of endemism are indicative of refugial areas where diversity has persisted, and endemism of intraspecific lineages in particular is strongly associated with late-Pleistocene habitat stability. However, it remains a challenge to consistently estimate the geographic ranges of intraspecific lineages and thus infer phylogeographic endemism, because spatial sampling for genetic analyses is typically sparse relative to species records. We present a novel technique to model the geographic distribution of intraspecific lineages, which is informed by the ecological niche of a species and known locations of its constituent lineages. Our approach allows for the effects of isolation by unsuitable habitat, and captures uncertainty in the extent of lineage ranges. Applying this method to the arc of rainforest areas spanning 3500 km in eastern Australia, we estimated lineage endemism for 53 species of rainforest dependent herpetofauna with available phylogeographic data. We related endemism to the stability of rainforest habitat over the past 120,000 years and identified distinct concentrations of lineage endemism that can be considered putative refugia. These areas of lineage endemism are strongly related to historical stability of rainforest habitat, after controlling for the effects of current environment. In fact, a dynamic stability model that allows movement to track suitable habitat over time was the most important factor in explaining current patterns of endemism. The techniques presented here provide an objective, practical method for estimating

  15. Analysing Discursive Practices in Legal Research: How a Single Remark Implies a Paradigm

    Directory of Open Access Journals (Sweden)

    Paul van den Hoven

    2017-12-01

    Full Text Available Different linguistic theories of meaning (semantic theories imply different methods to discuss meaning. Discussing meaning is what legal practitioners frequently do to decide legal issues and, subsequently, legal scholars analyse in their studies these discursive practices of parties, judges and legal experts. Such scholarly analysis reveals a methodical choice on how to discuss meaning and therefore implies positioning oneself towards a semantic theory of meaning, whether the scholar is aware of this or not. Legal practitioners may not be bound to be consistent in their commitment to semantic theories, as their task is to decide legal issues. Legal scholars, however, should be consistent because commitment to a semantic theory implies a distinct position towards important legal theoretical doctrines. In this paper three examples are discussed that require an articulated position of the legal scholar because the discursive practices of legal practitioners show inconsistencies. For each of these examples it can be shown that a scholar’s methodic choice implies commitment to a specific semantic theory, and that adopting such a theory implies a distinct position towards the meaning of the Rule of Law, the separation of powers doctrine and the institutional position of the judge.

  16. Calculating ellipse area by the Monte Carlo method and analysing dice poker with Excel at high school

    Science.gov (United States)

    Benacka, Jan

    2016-08-01

    This paper reports on lessons in which 18-19 years old high school students modelled random processes with Excel. In the first lesson, 26 students formulated a hypothesis on the area of ellipse by using the analogy between the areas of circle, square and rectangle. They verified the hypothesis by the Monte Carlo method with a spreadsheet model developed in the lesson. In the second lesson, 27 students analysed the dice poker game. First, they calculated the probability of the hands by combinatorial formulae. Then, they verified the result with a spreadsheet model developed in the lesson. The students were given a questionnaire to find out if they found the lesson interesting and contributing to their mathematical and technological knowledge.

  17. Analysing Access Control Specifications

    DEFF Research Database (Denmark)

    Probst, Christian W.; Hansen, René Rydhof

    2009-01-01

    When prosecuting crimes, the main question to answer is often who had a motive and the possibility to commit the crime. When investigating cyber crimes, the question of possibility is often hard to answer, as in a networked system almost any location can be accessed from almost anywhere. The most...... common tool to answer this question, analysis of log files, faces the problem that the amount of logged data may be overwhelming. This problems gets even worse in the case of insider attacks, where the attacker’s actions usually will be logged as permissible, standard actions—if they are logged at all....... Recent events have revealed intimate knowledge of surveillance and control systems on the side of the attacker, making it often impossible to deduce the identity of an inside attacker from logged data. In this work we present an approach that analyses the access control configuration to identify the set...

  18. A Filtering Method to Reveal Crystalline Patterns from Atom Probe Microscopy Desorption Maps

    Science.gov (United States)

    2016-03-26

    reveal crystalline patterns from atom probe microscopy desorption maps Lan Yao Department of Materials Science and Engineering, University of Michigan, Ann...reveal the crystallographic information present in Atom Probe Microscopy (APM) data is presented. Themethod filters atoms based on the time difference...between their evaporation and the evaporation of the previous atom . Since this time difference correlates with the location and the local structure of

  19. Statistical universals reveal the structures and functions of human music.

    Science.gov (United States)

    Savage, Patrick E; Brown, Steven; Sakai, Emi; Currie, Thomas E

    2015-07-21

    Music has been called "the universal language of mankind." Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation.

  20. Direct Analyses of Secondary Metabolites by Mass Spectrometry Imaging (MSI) from Sunflower (Helianthus annuus L.) Trichomes.

    Science.gov (United States)

    Brentan Silva, Denise; Aschenbrenner, Anna-Katharina; Lopes, Norberto Peporine; Spring, Otmar

    2017-05-10

    Helianthus annuus (sunflower) displays non-glandular trichomes (NGT), capitate glandular trichomes (CGT), and linear glandular trichomes (LGT), which reveal different chemical compositions and locations in different plant tissues. With matrix-assisted laser desorption/ionization (MALDI) and laser desorption/ionization (LDI) mass spectrometry imaging (MSI) techniques, efficient methods were developed to analyze the tissue distribution of secondary metabolites (flavonoids and sesquiterpenes) and proteins inside of trichomes. Herein, we analyzed sesquiterpene lactones, present in CGT, from leaf transversal sections using the matrix 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA) (mixture 1:1) with sodium ions added to increase the ionization in positive ion mode. The results observed for sesquiterpenes and polymethoxylated flavones from LGT were similar. However, upon desiccation, LGT changed their shape in the ionization source, complicating analyses by MSI mainly after matrix application. An alternative method could be applied to LGT regions by employing LDI (without matrix) in negative ion mode. The polymethoxylated flavones were easily ionized by LDI, producing images with higher resolution, but the sesquiterpenes were not observed in spectra. Thus, the application and viability of MALDI imaging for the analyses of protein and secondary metabolites inside trichomes were confirmed, highlighting the importance of optimization parameters.

  1. Discrete ordinates transport methods for problems with highly forward-peaked scattering

    International Nuclear Information System (INIS)

    Pautz, S.D.

    1998-04-01

    The author examines the solutions of the discrete ordinates (S N ) method for problems with highly forward-peaked scattering kernels. He derives conditions necessary to obtain reasonable solutions in a certain forward-peaked limit, the Fokker-Planck (FP) limit. He also analyzes the acceleration of the iterative solution of such problems and offer improvements to it. He extends the analytic Fokker-Planck limit analysis to the S N equations. This analysis shows that in this asymptotic limit the S N solution satisfies a pseudospectral discretization of the FP equation, provided that the scattering term is handled in a certain way (which he describes) and that the analytic transport solution satisfies an analytic FP equation. Similar analyses of various spatially discretized S N equations reveal that they too produce solutions that satisfy discrete FP equations, given the same provisions. Numerical results agree with these theoretical predictions. He defines a multidimensional angular multigrid (ANMG) method to accelerate the iterative solution of highly forward-peaked problems. The analyses show that a straightforward application of this scheme is subject to high-frequency instabilities. However, by applying a diffusive filter to the ANMG corrections he is able to stabilize this method. Fourier analyses of model problems show that the resulting method is effective at accelerating the convergence rate when the scattering is forward-peaked. The numerical results demonstrate that these analyses are good predictors of the actual performance of the ANMG method

  2. A new method for analysing socio-ecological patterns of vulnerability

    OpenAIRE

    Kok, M.; Lüdeke, M.; Lucas, P.; Sterzel, T.; Walther, C.; Janssen, P.; Sietz, D.; de Soysa, I.

    2016-01-01

    This paper presents a method for the analysis of socio-ecological patterns of vulnerability of people being at risk of losing their livelihoods as a consequence of global environmental change. This method fills a gap in methodologies for vulnerability analysis by providing generalizations of the factors that shape vulnerability in specific socio-ecological systems and showing their spatial occurrence. The proposed method consists of four steps that include both quantitative and qualitative an...

  3. Een kwantitatieve analyse van Nederlandse bijdragen aan internationaal arbeids- en organisatiepsychologisch onderzoek

    NARCIS (Netherlands)

    de Dreu, C.K.W.

    2010-01-01

    The author reports a quantitative analysis of the absolute and relative numbers of publications in six high-ranking journals on work and organisational psychology, (co-)authored by scientists with a Dutch, German, or British affiliation. In contrast to Germany and Great Britain, analyses reveal a

  4. Comprehensive genetic analyses reveal evolutionary distinction of a mouse (Zapus hudsonius preblei) proposed for delisting from the US Endangered Species Act.

    Science.gov (United States)

    King, Tim L; Switzer, John F; Morrison, Cheryl L; Eackles, Michael S; Young, Colleen C; Lubinski, Barbara A; Cryan, Paul

    2006-12-01

    Zapus hudsonius preblei, listed as threatened under the US Endangered Species Act (ESA), is one of 12 recognized subspecies of meadow jumping mice found in North America. Recent morphometric and phylogenetic comparisons among Z. h. preblei and neighbouring conspecifics questioned the taxonomic status of selected subspecies, resulting in a proposal to delist the Z. h. preblei from the ESA. We present additional analyses of the phylogeographic structure within Z. hudsonius that calls into question previously published data (and conclusions) and confirms the original taxonomic designations. A survey of 21 microsatellite DNA loci and 1380 base pairs from two mitochondrial DNA (mtDNA) regions (control region and cytochrome b) revealed that each Z. hudsonius subspecies is genetically distinct. These data do not support the null hypothesis of a homogeneous gene pool among the five subspecies found within the southwestern portion of the species' range. The magnitude of the observed differentiation was considerable and supported by significant findings for nearly every statistical comparison made, regardless of the genome or the taxa under consideration. Structuring of nuclear multilocus genotypes and subspecies-specific mtDNA haplotypes corresponded directly with the disjunct distributions of the subspecies investigated. Given the level of correspondence between the observed genetic population structure and previously proposed taxonomic classification of subspecies (based on the geographic separation and surveys of morphological variation), we conclude that the nominal subspecies surveyed in this study do not warrant synonymy, as has been proposed for Z. h. preblei, Z. h. campestris, and Z. h. intermedius.

  5. Discontinuous Galerkin methods and a posteriori error analysis for heterogenous diffusion problems; Methodes de Galerkine discontinues et analyse d'erreur a posteriori pour les problemes de diffusion heterogene

    Energy Technology Data Exchange (ETDEWEB)

    Stephansen, A.F

    2007-12-15

    In this thesis we analyse a discontinuous Galerkin (DG) method and two computable a posteriori error estimators for the linear and stationary advection-diffusion-reaction equation with heterogeneous diffusion. The DG method considered, the SWIP method, is a variation of the Symmetric Interior Penalty Galerkin method. The difference is that the SWIP method uses weighted averages with weights that depend on the diffusion. The a priori analysis shows optimal convergence with respect to mesh-size and robustness with respect to heterogeneous diffusion, which is confirmed by numerical tests. Both a posteriori error estimators are of the residual type and control the energy (semi-)norm of the error. Local lower bounds are obtained showing that almost all indicators are independent of heterogeneities. The exception is for the non-conforming part of the error, which has been evaluated using the Oswald interpolator. The second error estimator is sharper in its estimate with respect to the first one, but it is slightly more costly. This estimator is based on the construction of an H(div)-conforming Raviart-Thomas-Nedelec flux using the conservativeness of DG methods. Numerical results show that both estimators can be used for mesh-adaptation. (author)

  6. Testing of the Defense Waste Processing Facility Cold Chemical Dissolution Method in Sludge Batch 9 Qualification

    Energy Technology Data Exchange (ETDEWEB)

    Edwards, T. [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); Coleman, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Young, J. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Brown, L. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-05-10

    For each sludge batch that is processed in the Defense Waste Processing Facility (DWPF), the Savannah River National Laboratory (SRNL) tests the applicability of the digestion methods used by the DWPF Laboratory for elemental analysis of Sludge Receipt and Adjustment Tank (SRAT) Receipt samples and SRAT Product process control samples. DWPF SRAT samples are typically dissolved using a method referred to as the DWPF Cold Chemical or Cold Chem Method (CC), (see DWPF Procedure SW4- 15.201). Testing indicates that the CC method produced mixed results. The CC method did not result in complete dissolution of either the SRAT Receipt or SRAT Product with some fine, dark solids remaining. However, elemental analyses did not reveal extreme biases for the major elements in the sludge when compared with analyses obtained following dissolution by hot aqua regia (AR) or sodium peroxide fusion (PF) methods. The CC elemental analyses agreed with the AR and PF methods well enough that it should be adequate for routine process control analyses in the DWPF after much more extensive side-by-side tests of the CC method and the PF method are performed on the first 10 SRAT cycles of the Sludge Batch 9 (SB9) campaign. The DWPF Laboratory should continue with their plans for further tests of the CC method during these 10 SRAT cycles.

  7. Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

    Science.gov (United States)

    Stukenbrock, Eva H; Dutheil, Julien Y

    2018-03-01

    Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. Copyright © 2018 Stukenbrock and Dutheil.

  8. Biomass feedstock analyses

    Energy Technology Data Exchange (ETDEWEB)

    Wilen, C.; Moilanen, A.; Kurkela, E. [VTT Energy, Espoo (Finland). Energy Production Technologies

    1996-12-31

    The overall objectives of the project `Feasibility of electricity production from biomass by pressurized gasification systems` within the EC Research Programme JOULE II were to evaluate the potential of advanced power production systems based on biomass gasification and to study the technical and economic feasibility of these new processes with different type of biomass feed stocks. This report was prepared as part of this R and D project. The objectives of this task were to perform fuel analyses of potential woody and herbaceous biomasses with specific regard to the gasification properties of the selected feed stocks. The analyses of 15 Scandinavian and European biomass feed stock included density, proximate and ultimate analyses, trace compounds, ash composition and fusion behaviour in oxidizing and reducing atmospheres. The wood-derived fuels, such as whole-tree chips, forest residues, bark and to some extent willow, can be expected to have good gasification properties. Difficulties caused by ash fusion and sintering in straw combustion and gasification are generally known. The ash and alkali metal contents of the European biomasses harvested in Italy resembled those of the Nordic straws, and it is expected that they behave to a great extent as straw in gasification. Any direct relation between the ash fusion behavior (determined according to the standard method) and, for instance, the alkali metal content was not found in the laboratory determinations. A more profound characterisation of the fuels would require gasification experiments in a thermobalance and a PDU (Process development Unit) rig. (orig.) (10 refs.)

  9. Quantitative DNA methylation analyses reveal stage dependent DNA methylation and association to clinico-pathological factors in breast tumors

    International Nuclear Information System (INIS)

    Klajic, Jovana; Tost, Jörg; Kristensen, Vessela N; Fleischer, Thomas; Dejeux, Emelyne; Edvardsen, Hege; Warnberg, Fredrik; Bukholm, Ida; Lønning, Per Eystein; Solvang, Hiroko; Børresen-Dale, Anne-Lise

    2013-01-01

    Aberrant DNA methylation of regulatory genes has frequently been found in human breast cancers and correlated to clinical outcome. In the present study we investigate stage specific changes in the DNA methylation patterns in order to identify valuable markers to understand how these changes affect breast cancer progression. Quantitative DNA methylation analyses of 12 candidate genes ABCB1, BRCCA1, CDKN2A, ESR1, GSTP1, IGF2, MGMT, HMLH1, PPP2R2B, PTEN, RASSF1A and FOXC1 was performed by pyrosequencing a series of 238 breast cancer tissue samples from DCIS to invasive tumors stage I to IV. Significant differences in methylation levels between the DCIS and invasive stage II tumors were observed for six genes RASSF1A, CDKN2A, MGMT, ABCB1, GSTP1 and FOXC1. RASSF1A, ABCB1 and GSTP1 showed significantly higher methylation levels in late stage compared to the early stage breast carcinoma. Z-score analysis revealed significantly lower methylation levels in DCIS and stage I tumors compared with stage II, III and IV tumors. Methylation levels of PTEN, PPP2R2B, FOXC1, ABCB1 and BRCA1 were lower in tumors harboring TP53 mutations then in tumors with wild type TP53. Z-score analysis showed that TP53 mutated tumors had significantly lower overall methylation levels compared to tumors with wild type TP53. Methylation levels of RASSF1A, PPP2R2B, GSTP1 and FOXC1 were higher in ER positive vs. ER negative tumors and methylation levels of PTEN and CDKN2A were higher in HER2 positive vs. HER2 negative tumors. Z-score analysis also showed that HER2 positive tumors had significantly higher z-scores of methylation compared to the HER2 negative tumors. Univariate survival analysis identifies methylation status of PPP2R2B as significant predictor of overall survival and breast cancer specific survival. In the present study we report that the level of aberrant DNA methylation is higher in late stage compared with early stage of invasive breast cancers and DCIS for genes mentioned above

  10. Salpeterzuurdestructie en ICP-MS analyse van biotisch materiaal en voeding

    NARCIS (Netherlands)

    Velde-Koerts T van der; LAC

    2000-01-01

    Voor de bepaling van elementen in voeding en biotisch materiaal werd een analytische methode ontwikkeld, bestaande uit een salpeterzuurdestructie en een ICP-MS-analyse. De destructie werd geoptimaliseerd op basis van de salpeterzuurconcentratie en de destructietijd. De ICP-MS-analyse werd

  11. Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus.

    Directory of Open Access Journals (Sweden)

    Melissa Dsouza

    Full Text Available Antarctic soils represent a unique environment characterised by extremes of temperature, salinity, elevated UV radiation, low nutrient and low water content. Despite the harshness of this environment, members of 15 bacterial phyla have been identified in soils of the Ross Sea Region (RSR. However, the survival mechanisms and ecological roles of these phyla are largely unknown. The aim of this study was to investigate whether strains of Paenibacillus darwinianus owe their resilience to substantial genomic changes. For this, genome-based comparative analyses were performed on three P. darwinianus strains, isolated from gamma-irradiated RSR soils, together with nine temperate, soil-dwelling Paenibacillus spp. The genome of each strain was sequenced to over 1,000-fold coverage, then assembled into contigs totalling approximately 3 Mbp per genome. Based on the occurrence of essential, single-copy genes, genome completeness was estimated at approximately 88%. Genome analysis revealed between 3,043-3,091 protein-coding sequences (CDSs, primarily associated with two-component systems, sigma factors, transporters, sporulation and genes induced by cold-shock, oxidative and osmotic stresses. These comparative analyses provide an insight into the metabolic potential of P. darwinianus, revealing potential adaptive mechanisms for survival in Antarctic soils. However, a large proportion of these mechanisms were also identified in temperate Paenibacillus spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. These analyses have also revealed that the P. darwinianus genomes contain significantly fewer CDSs and have a lower paralogous content. Notwithstanding the incompleteness of the assemblies, the large differences in genome sizes, determined by the number of genes in paralogous clusters and the CDS content, are indicative of genome content scaling. Finally, these sequences are a resource for further

  12. Molecular analyses reveal two geographic and genetic lineages for tapeworms, Taenia solium and Taenia saginata, from Ecuador using mitochondrial DNA.

    Science.gov (United States)

    Solano, Danilo; Navarro, Juan Carlos; León-Reyes, Antonio; Benítez-Ortiz, Washington; Rodríguez-Hidalgo, Richar

    2016-12-01

    Tapeworms Taenia solium and Taenia saginata are the causative agents of taeniasis/cysticercosis. These are diseases with high medical and veterinary importance due to their impact on public health and rural economy in tropical countries. The re-emergence of T. solium as a result of human migration, the economic burden affecting livestock industry, and the large variability of symptoms in several human cysticercosis, encourage studies on genetic diversity, and the identification of these parasites with molecular phylogenetic tools. Samples collected from the Ecuadorian provinces: Loja, Guayas, Manabí, Tungurahua (South), and Imbabura, Pichincha (North) from 2000 to 2012 were performed under Maximum Parsimony analyses and haplotype networks using partial sequences of mitochondrial DNA, cytochrome oxidase subunit I (COI) and NADH subunit I (NDI), from Genbank and own sequences of Taenia solium and Taenia saginata from Ecuador. Both species have shown reciprocal monophyly, which confirms its molecular taxonomic identity. The COI and NDI genes results suggest phylogenetic structure for both parasite species from south and north of Ecuador. In T. solium, both genes gene revealed greater geographic structure, whereas in T. saginata, the variability for both genes was low. In conclusion, COI haplotype networks of T. solium suggest two geographical events in the introduction of this species in Ecuador (African and Asian lineages) and occurring sympatric, probably through the most common routes of maritime trade between the XV-XIX centuries. Moreover, the evidence of two NDI geographical lineages in T. solium from the north (province of Imbabura) and the south (province of Loja) of Ecuador derivate from a common Indian ancestor open new approaches for studies on genetic populations and eco-epidemiology. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Proteomic analyses reveal the key roles of BrlA and AbaA in biogenesis of gliotoxin in Aspergillus fumigatus

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Kwang-Soo, E-mail: shinks@dju.kr [Division of Life Science, Daejeon University, Daejeon, 300-716 (Korea, Republic of); Kim, Young Hwan [Biomedical Omics Team, Korea Basic Science Institute (KBSI), Ohcang, 368-883 (Korea, Republic of); Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 305-764 (Korea, Republic of); Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 305-333 (Korea, Republic of); Yu, Jae-Hyuk, E-mail: jyu1@wisc.edu [Departments of Bacteriology and Genetics, The University of Wisconsin–Madison, Madison, WI, 53706 (United States)

    2015-07-31

    The opportunistic human pathogenic fungus Aspergillus fumigatus primarily reproduces by forming a large number of asexual spores (conidia). Sequential activation of the central regulators BrlA, AbaA and WetA is necessary for the fungus to undergo asexual development. In this study, to address the presumed roles of these key developmental regulators during proliferation of the fungus, we analyzed and compared the proteomes of vegetative cells of wild type (WT) and individual mutant strains. Approximately 1300 protein spots were detectable from 2-D electrophoresis gels. Among these, 13 proteins exhibiting significantly altered accumulation levels were further identified by ESI-MS/MS. Markedly, we found that the GliM and GliT proteins associated with gliotoxin (GT) biosynthesis and self-protection of the fungus from GT were significantly down-regulated in the ΔabaA and ΔbrlA mutants. Moreover, mRNA levels of other GT biosynthetic genes including gliM, gliP, gliT, and gliZ were significantly reduced in both mutant strains, and no and low levels of GT were detectable in the ΔbrlA and ΔabaA mutant strains, respectively. As GliT is required for the protection of the fungus from GT, growth of the ΔbrlA mutant with reduced levels of GliT was severely impaired by exogenous GT. Our studies demonstrate that AbaA and BrlA positively regulate expression of the GT biosynthetic gene cluster in actively growing vegetative cells, and likely bridge morphological and chemical development during the life-cycle of A. fumigatus. - Highlights: • Proteome analyses of WT and mutants reveal 13 differentially expressed proteins. • The GliT and GliM proteins are significantly down-regulated by ΔabaA and ΔbrlA. • Expression of other gliotoxin biosynthetic genes is lowered by ΔabaA and ΔbrlA. • Growth of ΔbrlA strain lacking GliT is completely inhibited by exogenous gliotoxin. • BrlA and AbaA play key roles in biogenesis of gliotoxin in Aspergillus fumigatus.

  14. Proteomic analyses reveal the key roles of BrlA and AbaA in biogenesis of gliotoxin in Aspergillus fumigatus

    International Nuclear Information System (INIS)

    Shin, Kwang-Soo; Kim, Young Hwan; Yu, Jae-Hyuk

    2015-01-01

    The opportunistic human pathogenic fungus Aspergillus fumigatus primarily reproduces by forming a large number of asexual spores (conidia). Sequential activation of the central regulators BrlA, AbaA and WetA is necessary for the fungus to undergo asexual development. In this study, to address the presumed roles of these key developmental regulators during proliferation of the fungus, we analyzed and compared the proteomes of vegetative cells of wild type (WT) and individual mutant strains. Approximately 1300 protein spots were detectable from 2-D electrophoresis gels. Among these, 13 proteins exhibiting significantly altered accumulation levels were further identified by ESI-MS/MS. Markedly, we found that the GliM and GliT proteins associated with gliotoxin (GT) biosynthesis and self-protection of the fungus from GT were significantly down-regulated in the ΔabaA and ΔbrlA mutants. Moreover, mRNA levels of other GT biosynthetic genes including gliM, gliP, gliT, and gliZ were significantly reduced in both mutant strains, and no and low levels of GT were detectable in the ΔbrlA and ΔabaA mutant strains, respectively. As GliT is required for the protection of the fungus from GT, growth of the ΔbrlA mutant with reduced levels of GliT was severely impaired by exogenous GT. Our studies demonstrate that AbaA and BrlA positively regulate expression of the GT biosynthetic gene cluster in actively growing vegetative cells, and likely bridge morphological and chemical development during the life-cycle of A. fumigatus. - Highlights: • Proteome analyses of WT and mutants reveal 13 differentially expressed proteins. • The GliT and GliM proteins are significantly down-regulated by ΔabaA and ΔbrlA. • Expression of other gliotoxin biosynthetic genes is lowered by ΔabaA and ΔbrlA. • Growth of ΔbrlA strain lacking GliT is completely inhibited by exogenous gliotoxin. • BrlA and AbaA play key roles in biogenesis of gliotoxin in Aspergillus fumigatus

  15. Analysis methods used by the geochemistry department; Methodes d'analyses utilisees par la section de geochimie

    Energy Technology Data Exchange (ETDEWEB)

    Berthollet, P.

    1958-06-15

    This note presents various analytical techniques which are respectively used for the dosing of uranium in soils (fluorescence method, chromatographic method), for the dosing of uranium in natural waters (ion exchange method, evaporation method), and for the dosing of uranium in plants. Principles, equipment and products, reactant preparation, operation mode, sample preparation and measurements, expression of results and calculations) are indicated for each of these methods.

  16. Analyser-based phase contrast image reconstruction using geometrical optics.

    Science.gov (United States)

    Kitchen, M J; Pavlov, K M; Siu, K K W; Menk, R H; Tromba, G; Lewis, R A

    2007-07-21

    Analyser-based phase contrast imaging can provide radiographs of exceptional contrast at high resolution (geometrical optics are satisfied. Analytical phase retrieval can be performed by fitting the analyser rocking curve with a symmetric Pearson type VII function. The Pearson VII function provided at least a 10% better fit to experimentally measured rocking curves than linear or Gaussian functions. A test phantom, a hollow nylon cylinder, was imaged at 20 keV using a Si(1 1 1) analyser at the ELETTRA synchrotron radiation facility. Our phase retrieval method yielded a more accurate object reconstruction than methods based on a linear fit to the rocking curve. Where reconstructions failed to map expected values, calculations of the Takagi number permitted distinction between the violation of the geometrical optics conditions and the failure of curve fitting procedures. The need for synchronized object/detector translation stages was removed by using a large, divergent beam and imaging the object in segments. Our image acquisition and reconstruction procedure enables quantitative phase retrieval for systems with a divergent source and accounts for imperfections in the analyser.

  17. Assessing Commercial and Alternative Poultry Processing Methods using Microbiome Analyses

    Science.gov (United States)

    Assessing poultry processing methods/strategies has historically used culture-based methods to assess bacterial changes or reductions, both in terms of general microbial communities (e.g. total aerobic bacteria) or zoonotic pathogens of interest (e.g. Salmonella, Campylobacter). The advent of next ...

  18. Radiochemical methods and spectroscopical analyses for investigating the catalytic effects of 2-methyltetrahydro-anthraquinone and phenanthraquinone in wood pulp production using the soda additive method

    International Nuclear Information System (INIS)

    Besser, R. v.

    1982-01-01

    The studies were to show whether 2-methyltetrahydroanthraquinone or phenanthraquinone, two additives obtainable at low cost, will have a suitable catalytic effect on the delignification using the soda additive pulping method. For this purpose, soda cookings have been made in a 7 l rotary autoclave. The results have shown that 2-MeTHAQ is by far the better catalytic agent. Further experiments have been made to investigate the mode of action of the redox additives, intended to reveal further characteristics which can be correlated with the knowledge obtained from the preceding soda cookings. The analysis shows that there is a connection between the analytical lignin characteristics and the effectiveness of quinoid additives. (orig./PW) [de

  19. Pathway-based outlier method reveals heterogeneous genomic structure of autism in blood transcriptome.

    Science.gov (United States)

    Campbell, Malcolm G; Kohane, Isaac S; Kong, Sek Won

    2013-09-24

    Decades of research strongly suggest that the genetic etiology of autism spectrum disorders (ASDs) is heterogeneous. However, most published studies focus on group differences between cases and controls. In contrast, we hypothesized that the heterogeneity of the disorder could be characterized by identifying pathways for which individuals are outliers rather than pathways representative of shared group differences of the ASD diagnosis. Two previously published blood gene expression data sets--the Translational Genetics Research Institute (TGen) dataset (70 cases and 60 unrelated controls) and the Simons Simplex Consortium (Simons) dataset (221 probands and 191 unaffected family members)--were analyzed. All individuals of each dataset were projected to biological pathways, and each sample's Mahalanobis distance from a pooled centroid was calculated to compare the number of case and control outliers for each pathway. Analysis of a set of blood gene expression profiles from 70 ASD and 60 unrelated controls revealed three pathways whose outliers were significantly overrepresented in the ASD cases: neuron development including axonogenesis and neurite development (29% of ASD, 3% of control), nitric oxide signaling (29%, 3%), and skeletal development (27%, 3%). Overall, 50% of cases and 8% of controls were outliers in one of these three pathways, which could not be identified using group comparison or gene-level outlier methods. In an independently collected data set consisting of 221 ASD and 191 unaffected family members, outliers in the neurogenesis pathway were heavily biased towards cases (20.8% of ASD, 12.0% of control). Interestingly, neurogenesis outliers were more common among unaffected family members (Simons) than unrelated controls (TGen), but the statistical significance of this effect was marginal (Chi squared P < 0.09). Unlike group difference approaches, our analysis identified the samples within the case and control groups that manifested each expression

  20. A new method for analysing socio-ecological patterns of vulnerability

    NARCIS (Netherlands)

    Kok, M.; Lüdeke, M.; Lucas, P.; Sterzel, T.; Walther, C.; Janssen, P.; Sietz, D.; Soysa, de I.

    2016-01-01

    This paper presents a method for the analysis of socio-ecological patterns of vulnerability of people being at risk of losing their livelihoods as a consequence of global environmental change. This method fills a gap in methodologies for vulnerability analysis by providing generalizations of the

  1. Four novel prosthodontic methods for managing upper airway resistance syndrome: An investigative analysis revealing the efficacy of the new nasopharyngeal aperture guard appliance

    Directory of Open Access Journals (Sweden)

    Venkat R

    2010-01-01

    Full Text Available Statement of Problem: Obstructive sleep apnea is the most frequent cause for insomnia in the populace. Snoring is mulled over as the potential factor that can lead the sequel to obstructive sleep apnea. Although the etiology and deterrence measures for snoring are yet to be undoubtedly clarified by our scientific sorority, various means of surgical corrections have been affirmed and put into practice, with a substantial degree of success. Despite this, it is implicit that a noninvasive method of managing obstructive sleep apnea is more relevant for overcoming this condition. Purpose: This manuscript intends to establish how snoring can be controlled prosthodontically by different modalities of scientifically defensible approaches. The most effective among the modalities was affirmed as the investigative analyses of the treatment outcomes with each modality. Novel Methods: Four new methods of managing obstructive sleep apnea - uvula lift appliance, uvula and velopharynx lift appliance, nasopharyngeal aperture guard, and soft palate lift appliance were demonstrated through this article. Clinical Reports: The four new modalities stated and one conventional modality of mandibular advancement appliance for managing obstructive sleep apnea, a total of five types of appliance therapies, were described with case reports for each. Investigation: Five individuals undergoing the appliance therapy were chosen for each modality. The treatment outcome with each modality was examined by analysis of clinical predictors and also by means of standard investigation, with nasal and oral endoscopic analyses. Result: Among the five types of appliance therapies, the nasopharyngeal aperture guard provided the best treatment outcome in terms of clinical predictors and endoscopic analyses. Conclusion: Nasopharyngeal aperture guard, the novel method stated in this article is the better modality for managing obstructive sleep apnea, among the five different appliance

  2. Analysing harmonic motions with an iPhone’s magnetometer

    Science.gov (United States)

    Yavuz, Ahmet; Kağan Temiz, Burak

    2016-05-01

    In this paper, we propose an experiment for analysing harmonic motion using an iPhone’s (or iPad’s) magnetometer. This experiment consists of the detection of magnetic field variations obtained from an iPhone’s magnetometer sensor. A graph of harmonic motion is directly displayed on the iPhone’s screen using the Sensor Kinetics application. Data from this application was analysed with Eureqa software to establish the equation of the harmonic motion. Analyses show that the use of an iPhone’s magnetometer to analyse harmonic motion is a practical and effective method for small oscillations and frequencies less than 15-20 Hz.

  3. Revealing the uncultivated majority: combining DNA stable-isotope probing, multiple displacement amplification and metagenomic analyses of uncultivated Methylocystis in acidic peatlands.

    Science.gov (United States)

    Chen, Yin; Dumont, Marc G; Neufeld, Josh D; Bodrossy, Levente; Stralis-Pavese, Nancy; McNamara, Niall P; Ostle, Nick; Briones, Maria J I; Murrell, J Colin

    2008-10-01

    Peatlands represent an enormous carbon reservoir and have a potential impact on the global climate because of the active methanogenesis and methanotrophy in these soils. Uncultivated methanotrophs from seven European peatlands were studied using a combination of molecular methods. Screening for methanotroph diversity using a particulate methane monooxygenase-based diagnostic gene array revealed that Methylocystis-related species were dominant in six of the seven peatlands studied. The abundance and methane oxidation activity of Methylocystis spp. were further confirmed by DNA stable-isotope probing analysis of a sample taken from the Moor House peatland (England). After ultracentrifugation, (13)C-labelled DNA, containing genomic DNA of these Methylocystis spp., was separated from (12)C DNA and subjected to multiple displacement amplification (MDA) to generate sufficient DNA for the preparation of a fosmid metagenomic library. Potential bias of MDA was detected by fingerprint analysis of 16S rRNA using denaturing gradient gel electrophoresis for low-template amplification (0.01 ng template). Sufficient template (1-5 ng) was used in MDA to circumvent this bias and chimeric artefacts were minimized by using an enzymatic treatment of MDA-generated DNA with S1 nuclease and DNA polymerase I. Screening of the metagenomic library revealed one fosmid containing methanol dehydrogenase and two fosmids containing 16S rRNA genes from these Methylocystis-related species as well as one fosmid containing a 16S rRNA gene related to that of Methylocella/Methylocapsa. Sequencing of the 14 kb methanol dehydrogenase-containing fosmid allowed the assembly of a gene cluster encoding polypeptides involved in bacterial methanol utilization (mxaFJGIRSAC). This combination of DNA stable-isotope probing, MDA and metagenomics provided access to genomic information of a relatively large DNA fragment of these thus far uncultivated, predominant and active methanotrophs in peatland soil.

  4. Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements

    Science.gov (United States)

    Egan, Jan B.; Barrett, Michael T.; Champion, Mia D.; Middha, Sumit; Lenkiewicz, Elizabeth; Evers, Lisa; Francis, Princy; Schmidt, Jessica; Shi, Chang-Xin; Van Wier, Scott; Badar, Sandra; Ahmann, Gregory; Kortuem, K. Martin; Boczek, Nicole J.; Fonseca, Rafael; Craig, David W.; Carpten, John D.; Borad, Mitesh J.; Stewart, A. Keith

    2014-01-01

    Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR) where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2. PMID:24505276

  5. Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements.

    Directory of Open Access Journals (Sweden)

    Jan B Egan

    Full Text Available Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2.

  6. VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

    Directory of Open Access Journals (Sweden)

    Andrew E. Webb

    2017-06-01

    Full Text Available Background Large-scale molecular evolutionary analyses of protein coding sequences requires a number of preparatory inter-related steps from finding gene families, to generating alignments and phylogenetic trees and assessing selective pressure variation. Each phase of these analyses can represent significant challenges, particularly when working with entire proteomes (all protein coding sequences in a genome from a large number of species. Methods We present VESPA, software capable of automating a selective pressure analysis using codeML in addition to the preparatory analyses and summary statistics. VESPA is written in python and Perl and is designed to run within a UNIX environment. Results We have benchmarked VESPA and our results show that the method is consistent, performs well on both large scale and smaller scale datasets, and produces results in line with previously published datasets. Discussion Large-scale gene family identification, sequence alignment, and phylogeny reconstruction are all important aspects of large-scale molecular evolutionary analyses. VESPA provides flexible software for simplifying these processes along with downstream selective pressure variation analyses. The software automatically interprets results from codeML and produces simplified summary files to assist the user in better understanding the results. VESPA may be found at the following website: http://www.mol-evol.org/VESPA.

  7. Handbook of methods for risk-based analyses of technical specifications

    International Nuclear Information System (INIS)

    Samanta, P.K.; Kim, I.S.; Mankamo, T.; Vesely, W.E.

    1994-12-01

    Technical Specifications (TS) requirements for nuclear power plants define the Limiting Conditions for Operation (LCOs) and Surveillance Requirements (SRs) to assure safety during operation. In general, these requirements are based on deterministic analysis and engineering judgments. Experiences with plant operation indicate that some elements of the requirements are unnecessarily restrictive, while a few may not be conducive to safety. The US Nuclear Regulatory Commission (USNRC) Office of Research has sponsored research to develop systematic risk-based methods to improve various aspects of TS requirements. This handbook summarizes these risk-based methods. The scope of the handbook includes reliability and risk-based methods for evaluating allowed outage times (AOTs), scheduled or preventive maintenance, action statements requiring shutdown where shutdown risk may be substantial, surveillance test intervals (STIs), and management of plant configurations resulting from outages of systems, or components. For each topic, the handbook summarizes analytic methods with data needs, outlines the insights to be gained, lists additional references, and gives examples of evaluations

  8. Handbook of methods for risk-based analyses of technical specifications

    Energy Technology Data Exchange (ETDEWEB)

    Samanta, P.K.; Kim, I.S. [Brookhaven National Lab., Upton, NY (United States); Mankamo, T. [Avaplan Oy, Espoo (Finland); Vesely, W.E. [Science Applications International Corp., Dublin, OH (United States)

    1994-12-01

    Technical Specifications (TS) requirements for nuclear power plants define the Limiting Conditions for Operation (LCOs) and Surveillance Requirements (SRs) to assure safety during operation. In general, these requirements are based on deterministic analysis and engineering judgments. Experiences with plant operation indicate that some elements of the requirements are unnecessarily restrictive, while a few may not be conducive to safety. The US Nuclear Regulatory Commission (USNRC) Office of Research has sponsored research to develop systematic risk-based methods to improve various aspects of TS requirements. This handbook summarizes these risk-based methods. The scope of the handbook includes reliability and risk-based methods for evaluating allowed outage times (AOTs), scheduled or preventive maintenance, action statements requiring shutdown where shutdown risk may be substantial, surveillance test intervals (STIs), and management of plant configurations resulting from outages of systems, or components. For each topic, the handbook summarizes analytic methods with data needs, outlines the insights to be gained, lists additional references, and gives examples of evaluations.

  9. Relating system-to-CFD coupled code analyses to theoretical framework of a multi-scale method

    International Nuclear Information System (INIS)

    Cadinu, F.; Kozlowski, T.; Dinh, T.N.

    2007-01-01

    Over past decades, analyses of transient processes and accidents in a nuclear power plant have been performed, to a significant extent and with a great success, by means of so called system codes, e.g. RELAP5, CATHARE, ATHLET codes. These computer codes, based on a multi-fluid model of two-phase flow, provide an effective, one-dimensional description of the coolant thermal-hydraulics in the reactor system. For some components in the system, wherever needed, the effect of multi-dimensional flow is accounted for through approximate models. The later are derived from scaled experiments conducted for selected accident scenarios. Increasingly, however, we have to deal with newer and ever more complex accident scenarios. In some such cases the system codes fail to serve as simulation vehicle, largely due to its deficient treatment of multi-dimensional flow (in e.g. downcomer, lower plenum). A possible way of improvement is to use the techniques of Computational Fluid Dynamics (CFD). Based on solving Navier-Stokes equations, CFD codes have been developed and used, broadly, to perform analysis of multi-dimensional flow, dominantly in non-nuclear industry and for single-phase flow applications. It is clear that CFD simulations can not substitute system codes but just complement them. Given the intrinsic multi-scale nature of this problem, we propose to relate it to the more general field of research on multi-scale simulations. Even though multi-scale methods are developed on case-by-case basis, the need for a unified framework brought to the development of the heterogeneous multi-scale method (HMM)

  10. Development of digital image correlation method to analyse crack ...

    Indian Academy of Sciences (India)

    samples were performed to verify the performance of the digital image correlation method. ... development cannot be measured accurately. ..... Mendelson A 1983 Plasticity: Theory and application (USA: Krieger Publishing company Malabar,.

  11. Bayesian uncertainty analyses of probabilistic risk models

    International Nuclear Information System (INIS)

    Pulkkinen, U.

    1989-01-01

    Applications of Bayesian principles to the uncertainty analyses are discussed in the paper. A short review of the most important uncertainties and their causes is provided. An application of the principle of maximum entropy to the determination of Bayesian prior distributions is described. An approach based on so called probabilistic structures is presented in order to develop a method of quantitative evaluation of modelling uncertainties. The method is applied to a small example case. Ideas for application areas for the proposed method are discussed

  12. Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution.

    Science.gov (United States)

    Alsop, Eric B; Boyd, Eric S; Raymond, Jason

    2014-05-28

    The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity. By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition. Clustering based on the frequency in which orthologous proteins occur among metagenomes

  13. Self-disclosure on Facebook: How much do we really reveal?

    Directory of Open Access Journals (Sweden)

    Stephanie Day

    Full Text Available This paper investigates the use of the social networking site Facebook to self-disclose and analyses the responses of a small group of Facebook users surveyed about their own willingness to self-disclose. An online survey was used to ask Facebook users about their level of Facebook use, what types of personal information they are willing to reveal and the frequency of these personal revelations. The survey also asked the participants to take a look at their publicly viewable profile and the types of information revealed there. Results indicated that overall, most people tended to be cautious about the types of information they revealed, posted mainly positive statements about themselves and were aware of personal privacy issues.

  14. Periodic safety analyses; Les essais periodiques

    Energy Technology Data Exchange (ETDEWEB)

    Gouffon, A; Zermizoglou, R

    1990-12-01

    The IAEA Safety Guide 50-SG-S8 devoted to 'Safety Aspects of Foundations of Nuclear Power Plants' indicates that operator of a NPP should establish a program for inspection of safe operation during construction, start-up and service life of the plant for obtaining data needed for estimating the life time of structures and components. At the same time the program should ensure that the safety margins are appropriate. Periodic safety analysis are an important part of the safety inspection program. Periodic safety reports is a method for testing the whole system or a part of the safety system following the precise criteria. Periodic safety analyses are not meant for qualification of the plant components. Separate analyses are devoted to: start-up, qualification of components and materials, and aging. All these analyses are described in this presentation. The last chapter describes the experience obtained for PWR-900 and PWR-1300 units from 1986-1989.

  15. Development of the computer code system for the analyses of PWR core

    International Nuclear Information System (INIS)

    Tsujimoto, Iwao; Naito, Yoshitaka.

    1992-11-01

    This report is one of the materials for the work titled 'Development of the computer code system for the analyses of PWR core phenomena', which is performed under contracts between Shikoku Electric Power Company and JAERI. In this report, the numerical method adopted in our computer code system are described, that is, 'The basic course and the summary of the analysing method', 'Numerical method for solving the Boltzmann equation', 'Numerical method for solving the thermo-hydraulic equations' and 'Description on the computer code system'. (author)

  16. A review of multivariate analyses in imaging genetics

    Directory of Open Access Journals (Sweden)

    Jingyu eLiu

    2014-03-01

    Full Text Available Recent advances in neuroimaging technology and molecular genetics provide the unique opportunity to investigate genetic influence on the variation of brain attributes. Since the year 2000, when the initial publication on brain imaging and genetics was released, imaging genetics has been a rapidly growing research approach with increasing publications every year. Several reviews have been offered to the research community focusing on various study designs. In addition to study design, analytic tools and their proper implementation are also critical to the success of a study. In this review, we survey recent publications using data from neuroimaging and genetics, focusing on methods capturing multivariate effects accommodating the large number of variables from both imaging data and genetic data. We group the analyses of genetic or genomic data into either a prior driven or data driven approach, including gene-set enrichment analysis, multifactor dimensionality reduction, principal component analysis, independent component analysis (ICA, and clustering. For the analyses of imaging data, ICA and extensions of ICA are the most widely used multivariate methods. Given detailed reviews of multivariate analyses of imaging data available elsewhere, we provide a brief summary here that includes a recently proposed method known as independent vector analysis. Finally, we review methods focused on bridging the imaging and genetic data by establishing multivariate and multiple genotype-phenotype associations, including sparse partial least squares, sparse canonical correlation analysis, sparse reduced rank regression and parallel ICA. These methods are designed to extract latent variables from both genetic and imaging data, which become new genotypes and phenotypes, and the links between the new genotype-phenotype pairs are maximized using different cost functions. The relationship between these methods along with their assumptions, advantages, and

  17. Academic Procrastination and the Performance of Graduate-Level Cooperative Groups in Research Methods Courses

    Science.gov (United States)

    Jiao, Qun G.; DaRos-Voseles, Denise A.; Collins, Kathleen M. T.; Onwuegbuzie, Anthony J.

    2011-01-01

    This study examined the extent to which academic procrastination predicted the performance of cooperative groups in graduate-level research methods courses. A total of 28 groups was examined (n = 83 students), ranging in size from 2 to 5 (M = 2.96, SD = 1.10). Multiple regression analyses revealed that neither within-group mean nor within-group…

  18. Statistical methods for analysing responses of wildlife to human disturbance.

    Science.gov (United States)

    Haiganoush K. Preisler; Alan A. Ager; Michael J. Wisdom

    2006-01-01

    1. Off-road recreation is increasing rapidly in many areas of the world, and effects on wildlife can be highly detrimental. Consequently, we have developed methods for studying wildlife responses to off-road recreation with the use of new technologies that allow frequent and accurate monitoring of human-wildlife interactions. To illustrate these methods, we studied the...

  19. Determination of oxygen to metal ratio for varying UO2 content in sintered (U,Th)O2 pellet by oxidation-reduction method using thermo-gravimetric analyser

    International Nuclear Information System (INIS)

    Mahanty, B.N.; Khan, F.A.; Karande, A.P.; Prakash, A.; Afzal, Md.; Panakkal, J.P.

    2009-01-01

    Experiments were carried out to determine oxygen to metal ratio in 4%, 6%, 10%, 20%, 50% and 80% UO 2 in sintered (U, Th) O 2 pellets by oxidation-reduction method using thermo gravimetric analyser. (author)

  20. Categorizing words using 'frequent frames': what cross-linguistic analyses reveal about distributional acquisition strategies.

    Science.gov (United States)

    Chemla, Emmanuel; Mintz, Toben H; Bernal, Savita; Christophe, Anne

    2009-04-01

    Mintz (2003) described a distributional environment called a frame, defined as the co-occurrence of two context words with one intervening target word. Analyses of English child-directed speech showed that words that fell within any frequently occurring frame consistently belonged to the same grammatical category (e.g. noun, verb, adjective, etc.). In this paper, we first generalize this result to French, a language in which the function word system allows patterns that are potentially detrimental to a frame-based analysis procedure. Second, we show that the discontinuity of the chosen environments (i.e. the fact that target words are framed by the context words) is crucial for the mechanism to be efficient. This property might be relevant for any computational approach to grammatical categorization. Finally, we investigate a recursive application of the procedure and observe that the categorization is paradoxically worse when context elements are categories rather than actual lexical items. Item-specificity is thus also a core computational principle for this type of algorithm. Our analysis, along with results from behavioural studies (Gómez, 2002; Gómez and Maye, 2005; Mintz, 2006), provides strong support for frames as a basis for the acquisition of grammatical categories by infants. Discontinuity and item-specificity appear to be crucial features.

  1. Finite element analyses for RF photoinjector gun cavities

    International Nuclear Information System (INIS)

    Marhauser, F.

    2006-01-01

    This paper details electromagnetical, thermal and structural 3D Finite Element Analyses (FEA) for normal conducting RF photoinjector gun cavities. The simulation methods are described extensively. Achieved results are presented. (orig.)

  2. Finite element analyses for RF photoinjector gun cavities

    Energy Technology Data Exchange (ETDEWEB)

    Marhauser, F. [Berliner Elektronenspeicherring-Gesellschaft fuer Synchrotronstrahlung mbH (BESSY), Berlin (Germany)

    2006-07-01

    This paper details electromagnetical, thermal and structural 3D Finite Element Analyses (FEA) for normal conducting RF photoinjector gun cavities. The simulation methods are described extensively. Achieved results are presented. (orig.)

  3. Transcriptome-wide analyses indicate mitochondrial responses to particulate air pollution exposure

    DEFF Research Database (Denmark)

    Winckelmans, Ellen; Nawrot, Tim S.; Tsamou, Maria

    2017-01-01

    validation cohort (n = 169, 55.6% women). Results: Overrepresentation analyses revealed significant pathways (p-value transport chain (ETC) for medium-term exposure in women. For men, medium-term PM10....... Conclusions: In this exploratory study, we identified mitochondrial genes and pathways associated with particulate air pollution indicating upregulation of energy producing pathways as a potential mechanism to compensate for PM-induced mitochondrial damage....

  4. Improvement of spectrographic analyses by the use of a mechanical packer in the arc distillation technique; Amelioration de l'analyse spectrograpique par l'utilisation d'un tasseur mecanique dans la methode de distillation dans l'arc

    Energy Technology Data Exchange (ETDEWEB)

    Buffereau, M; Deniaud, S; Pichotin, B; Violet, R [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1965-07-01

    One studies improvement of spectrographic analysis by the 'carrier distillation' method with the help of a mechanical device. Experiments and advantages of such an apparatus are given (precision and reproducibility improvement, operator factor suppression). A routine apparatus (French patent no 976.493) is described. (authors) [French] On etudie l'amelioration des analyses spectrographiques par la methode de distillation avec entra eur dans l'arc au moyen d'un tasseur mecanique. On indique les experiences realisees et les avantages de l'emploi d'un tel appareil (amelioration de la precision et de la reproductibilite, suppression du facteur operateur). On decrit l'appareil de routine objet du brevet no 976.493 du 29 mai 1964. (auteurs)

  5. Quality of meta-analyses in major leading gastroenterology and hepatology journals: A systematic review.

    Science.gov (United States)

    Liu, Pengfei; Qiu, Yuanyu; Qian, Yuting; Chen, Xiao; Wang, Yiran; Cui, Jin; Zhai, Xiao

    2017-01-01

    To appraise the current reporting methodological quality of meta-analyses in five leading gastroenterology and hepatology journals, and to identify the variables associated with the reporting quality. We systematically searched the literature of meta-analyses in Gastroenterology, Gut, Hepatology, Journal of Hepatology (J HEPATOL) and American Journal of Gastroenterology (AM J GASTROENTEROL) from 2006 to 2008 and from 2012 to 2014. Characteristics were extracted based on the PRISMA statement and the AMSTAR tool. Country, number of patients, funding source were also revealed and descriptively reported. A total of 127 meta-analyses were enrolled in this study and were compared among journals, study years, and other characters. Compliances with the PRISMA statement and the AMSTAR checklist were 20.8 ± 4.2 out of a maximum of 27 and 7.6 ± 2.4 out of a maximum of 11, respectively. Some domains were poorly reported including describing a protocol and/or registration (item 5, 0.0%), describing methods, and giving results of additional analyses (item 16, 45.7% and item 23, 48.0%) for PRISMA and duplicating study selection and data extraction (item 2, 53.5%), and providing a list of included and excluded studies (item 5, 14.2%) for AMSTAR. Publication in recent years showed a significantly better methodological quality than those published in previous years. This study shows that methodological reporting quality of MAs in the major gastroenterology and hepatology journals has improved in recent years after the publication of the developed PRISMA statement, and it can be further improved. © 2016 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

  6. Analyser-based phase contrast image reconstruction using geometrical optics

    International Nuclear Information System (INIS)

    Kitchen, M J; Pavlov, K M; Siu, K K W; Menk, R H; Tromba, G; Lewis, R A

    2007-01-01

    Analyser-based phase contrast imaging can provide radiographs of exceptional contrast at high resolution (<100 μm), whilst quantitative phase and attenuation information can be extracted using just two images when the approximations of geometrical optics are satisfied. Analytical phase retrieval can be performed by fitting the analyser rocking curve with a symmetric Pearson type VII function. The Pearson VII function provided at least a 10% better fit to experimentally measured rocking curves than linear or Gaussian functions. A test phantom, a hollow nylon cylinder, was imaged at 20 keV using a Si(1 1 1) analyser at the ELETTRA synchrotron radiation facility. Our phase retrieval method yielded a more accurate object reconstruction than methods based on a linear fit to the rocking curve. Where reconstructions failed to map expected values, calculations of the Takagi number permitted distinction between the violation of the geometrical optics conditions and the failure of curve fitting procedures. The need for synchronized object/detector translation stages was removed by using a large, divergent beam and imaging the object in segments. Our image acquisition and reconstruction procedure enables quantitative phase retrieval for systems with a divergent source and accounts for imperfections in the analyser

  7. Pancreatic Adenocarcinoma Therapeutic Targets Revealed by Tumor-Stroma Cross-Talk Analyses in Patient-Derived Xenografts

    Directory of Open Access Journals (Sweden)

    Rémy Nicolle

    2017-11-01

    Full Text Available Preclinical models based on patient-derived xenografts have remarkable specificity in distinguishing transformed human tumor cells from non-transformed murine stromal cells computationally. We obtained 29 pancreatic ductal adenocarcinoma (PDAC xenografts from either resectable or non-resectable patients (surgery and endoscopic ultrasound-guided fine-needle aspirate, respectively. Extensive multiomic profiling revealed two subtypes with distinct clinical outcomes. These subtypes uncovered specific alterations in DNA methylation and transcription as well as in signaling pathways involved in tumor-stromal cross-talk. The analysis of these pathways indicates therapeutic opportunities for targeting both compartments and their interactions. In particular, we show that inhibiting NPC1L1 with Ezetimibe, a clinically available drug, might be an efficient approach for treating pancreatic cancers. These findings uncover the complex and diverse interplay between PDAC tumors and the stroma and demonstrate the pivotal role of xenografts for drug discovery and relevance to PDAC.

  8. Functional proteomic analyses of Bothrops atrox venom reveals phenotypes associated with habitat variation in the Amazon.

    Science.gov (United States)

    Sousa, Leijiane F; Portes-Junior, José A; Nicolau, Carolina A; Bernardoni, Juliana L; Nishiyama, Milton Y; Amazonas, Diana R; Freitas-de-Sousa, Luciana A; Mourão, Rosa Hv; Chalkidis, Hipócrates M; Valente, Richard H; Moura-da-Silva, Ana M

    2017-04-21

    Venom variability is commonly reported for venomous snakes including Bothrops atrox. Here, we compared the composition of venoms from B. atrox snakes collected at Amazonian conserved habitats (terra-firme upland forest and várzea) and human modified areas (pasture and degraded areas). Venom samples were submitted to shotgun proteomic analysis as a whole or compared after fractionation by reversed-phase chromatography. Whole venom proteomes revealed a similar composition among the venoms with predominance of SVMPs, CTLs, and SVSPs and intermediate amounts of PLA 2 s and LAAOs. However, when distribution of particular isoforms was analyzed by either method, the venom from várzea snakes showed a decrease in hemorrhagic SVMPs and an increase in SVSPs, and procoagulant SVMPs and PLA 2 s. These differences were validated by experimental approaches including both enzymatic and in vivo assays, and indicated restrictions in respect to antivenom efficacy to variable components. Thus, proteomic analysis at the isoform level combined to in silico prediction of functional properties may indicate venom biological activity. These results also suggest that the prevalence of functionally distinct isoforms contributes to the variability of the venoms and could reflect the adaptation of B. atrox to distinct prey communities in different Amazon habitats. In this report, we compared isoforms present in venoms from snakes collected at different Amazonian habitats. By means of a species venom gland transcriptome and the in silico functional prediction of each isoform, we were able to predict the principal venom activities in vitro and in animal models. We also showed remarkable differences in the venom pools from snakes collected at the floodplain (várzea habitat) compared to other habitats. Not only was this venom less hemorrhagic and more procoagulant, when compared to the venom pools from the other three habitats studied, but also this enhanced procoagulant activity was not

  9. Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus.

    Science.gov (United States)

    Chen, Juan; Zeng, Xu; Yang, Yan Long; Xing, Yong Mei; Zhang, Qi; Li, Jia Mei; Ma, Ke; Liu, Hong Wei; Guo, Shun Xing

    2017-08-31

    The lion's mane mushroom Hericium erinaceus is a famous traditional medicinal fungus credited with anti-dementia activity and a producer of cyathane diterpenoid natural products (erinacines) useful against nervous system diseases. To date, few studies have explored the biosynthesis of these compounds, although their chemical synthesis is known. Here, we report the first genome and tanscriptome sequence of the medicinal fungus H. erinaceus. The size of the genome is 39.35 Mb, containing 9895 gene models. The genome of H. erinaceus reveals diverse enzymes and a large family of cytochrome P450 (CYP) proteins involved in the biosynthesis of terpenoid backbones, diterpenoids, sesquiterpenes and polyketides. Three gene clusters related to terpene biosynthesis and one gene cluster for polyketides biosynthesis (PKS) were predicted. Genes involved in terpenoid biosynthesis were generally upregulated in mycelia, while the PKS gene was upregulated in the fruiting body. Comparative genome analysis of 42 fungal species of Basidiomycota revealed that most edible and medicinal mushroom show many more gene clusters involved in terpenoid and polyketide biosynthesis compared to the pathogenic fungi. None of the gene clusters for terpenoid or polyketide biosynthesis were predicted in the poisonous mushroom Amanita muscaria. Our findings may facilitate future discovery and biosynthesis of bioactive secondary metabolites from H. erinaceus and provide fundamental information for exploring the secondary metabolites in other Basidiomycetes.

  10. Differential co-expression and regulation analyses reveal different mechanisms underlying major depressive disorder and subsyndromal symptomatic depression.

    Science.gov (United States)

    Xu, Fan; Yang, Jing; Chen, Jin; Wu, Qingyuan; Gong, Wei; Zhang, Jianguo; Shao, Weihua; Mu, Jun; Yang, Deyu; Yang, Yongtao; Li, Zhiwei; Xie, Peng

    2015-04-03

    Recent depression research has revealed a growing awareness of how to best classify depression into depressive subtypes. Appropriately subtyping depression can lead to identification of subtypes that are more responsive to current pharmacological treatment and aid in separating out depressed patients in which current antidepressants are not particularly effective. Differential co-expression analysis (DCEA) and differential regulation analysis (DRA) were applied to compare the transcriptomic profiles of peripheral blood lymphocytes from patients with two depressive subtypes: major depressive disorder (MDD) and subsyndromal symptomatic depression (SSD). Six differentially regulated genes (DRGs) (FOSL1, SRF, JUN, TFAP4, SOX9, and HLF) and 16 transcription factor-to-target differentially co-expressed gene links or pairs (TF2target DCLs) appear to be the key differential factors in MDD; in contrast, one DRG (PATZ1) and eight TF2target DCLs appear to be the key differential factors in SSD. There was no overlap between the MDD target genes and SSD target genes. Venlafaxine (Efexor™, Effexor™) appears to have a significant effect on the gene expression profile of MDD patients but no significant effect on the gene expression profile of SSD patients. DCEA and DRA revealed no apparent similarities between the differential regulatory processes underlying MDD and SSD. This bioinformatic analysis may provide novel insights that can support future antidepressant R&D efforts.

  11. Fourier Transform Mass Spectrometry: The Transformation of Modern Environmental Analyses

    Science.gov (United States)

    Lim, Lucy; Yan, Fangzhi; Bach, Stephen; Pihakari, Katianna; Klein, David

    2016-01-01

    Unknown compounds in environmental samples are difficult to identify using standard mass spectrometric methods. Fourier transform mass spectrometry (FTMS) has revolutionized how environmental analyses are performed. With its unsurpassed mass accuracy, high resolution and sensitivity, researchers now have a tool for difficult and complex environmental analyses. Two features of FTMS are responsible for changing the face of how complex analyses are accomplished. First is the ability to quickly and with high mass accuracy determine the presence of unknown chemical residues in samples. For years, the field has been limited by mass spectrometric methods that were based on knowing what compounds of interest were. Secondly, by utilizing the high resolution capabilities coupled with the low detection limits of FTMS, analysts also could dilute the sample sufficiently to minimize the ionization changes from varied matrices. PMID:26784175

  12. Phylogeny of haemosporidian blood parasites revealed by a multi-gene approach.

    Science.gov (United States)

    Borner, Janus; Pick, Christian; Thiede, Jenny; Kolawole, Olatunji Matthew; Kingsley, Manchang Tanyi; Schulze, Jana; Cottontail, Veronika M; Wellinghausen, Nele; Schmidt-Chanasit, Jonas; Bruchhaus, Iris; Burmester, Thorsten

    2016-01-01

    The apicomplexan order Haemosporida is a clade of unicellular blood parasites that infect a variety of reptilian, avian and mammalian hosts. Among them are the agents of human malaria, parasites of the genus Plasmodium, which pose a major threat to human health. Illuminating the evolutionary history of Haemosporida may help us in understanding their enormous biological diversity, as well as tracing the multiple host switches and associated acquisitions of novel life-history traits. However, the deep-level phylogenetic relationships among major haemosporidian clades have remained enigmatic because the datasets employed in phylogenetic analyses were severely limited in either gene coverage or taxon sampling. Using a PCR-based approach that employs a novel set of primers, we sequenced fragments of 21 nuclear genes from seven haemosporidian parasites of the genera Leucocytozoon, Haemoproteus, Parahaemoproteus, Polychromophilus and Plasmodium. After addition of genomic data from 25 apicomplexan species, the unreduced alignment comprised 20,580 bp from 32 species. Phylogenetic analyses were performed based on nucleotide, codon and amino acid data employing Bayesian inference, maximum likelihood and maximum parsimony. All analyses resulted in highly congruent topologies. We found consistent support for a basal position of Leucocytozoon within Haemosporida. In contrast to all previous studies, we recovered a sister group relationship between the genera Polychromophilus and Plasmodium. Within Plasmodium, the sauropsid and mammal-infecting lineages were recovered as sister clades. Support for these relationships was high in nearly all trees, revealing a novel phylogeny of Haemosporida, which is robust to the choice of the outgroup and the method of tree inference. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Power System Oscillatory Behaviors: Sources, Characteristics, & Analyses

    Energy Technology Data Exchange (ETDEWEB)

    Follum, James D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Tuffner, Francis K. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dosiek, Luke A. [Union College, Schenectady, NY (United States); Pierre, John W. [Univ. of Wyoming, Laramie, WY (United States)

    2017-05-17

    This document is intended to provide a broad overview of the sources, characteristics, and analyses of natural and forced oscillatory behaviors in power systems. These aspects are necessarily linked. Oscillations appear in measurements with distinguishing characteristics derived from the oscillation’s source. These characteristics determine which analysis methods can be appropriately applied, and the results from these analyses can only be interpreted correctly with an understanding of the oscillation’s origin. To describe oscillations both at their source within a physical power system and within measurements, a perspective from the boundary between power system and signal processing theory has been adopted.

  14. A QUANTITATIVE METHOD FOR ANALYSING 3-D BRANCHING IN EMBRYONIC KIDNEYS: DEVELOPMENT OF A TECHNIQUE AND PRELIMINARY DATA

    Directory of Open Access Journals (Sweden)

    Gabriel Fricout

    2011-05-01

    Full Text Available The normal human adult kidney contains between 300,000 and 1 million nephrons (the functional units of the kidney. Nephrons develop at the tips of the branching ureteric duct, and therefore ureteric duct branching morphogenesis is critical for normal kidney development. Current methods for analysing ureteric branching are mostly qualitative and those quantitative methods that do exist do not account for the 3- dimensional (3D shape of the ureteric "tree". We have developed a method for measuring the total length of the ureteric tree in 3D. This method is described and preliminary data are presented. The algorithm allows for performing a semi-automatic segmentation of a set of grey level confocal images and an automatic skeletonisation of the resulting binary object. Measurements of length are automatically obtained, and numbers of branch points are manually counted. The final representation can be reconstructed by means of 3D volume rendering software, providing a fully rotating 3D perspective of the skeletonised tree, making it possible to identify and accurately measure branch lengths. Preliminary data shows the total length estimates obtained with the technique to be highly reproducible. Repeat estimates of total tree length vary by just 1-2%. We will now use this technique to further define the growth of the ureteric tree in vitro, under both normal culture conditions, and in the presence of various levels of specific molecules suspected of regulating ureteric growth. The data obtained will provide fundamental information on the development of renal architecture, as well as the regulation of nephron number.

  15. Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses.

    Science.gov (United States)

    Rutter, William B; Salcedo, Andres; Akhunova, Alina; He, Fei; Wang, Shichen; Liang, Hanquan; Bowden, Robert L; Akhunov, Eduard

    2017-04-12

    Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining a compatible interaction with the plant host. To better understand how the diversified arsenals of fungal genes promote interaction with the same compatible wheat line, we performed a comparative genomic analysis of two North American isolates of Puccinia graminis f. sp. tritici (Pgt). The patterns of inter-isolate divergence in the secreted candidate effector genes were compared with the levels of conservation and divergence of plant-pathogen gene co-expression networks (GCN) developed for each isolate. Comprative genomic analyses revealed substantial level of interisolate divergence in effector gene complement and sequence divergence. Gene Ontology (GO) analyses of the conserved and unique parts of the isolate-specific GCNs identified a number of conserved host pathways targeted by both isolates. Interestingly, the degree of inter-isolate sub-network conservation varied widely for the different host pathways and was positively associated with the proportion of conserved effector candidates associated with each sub-network. While different Pgt isolates tended to exploit similar wheat pathways for infection, the mode of plant-pathogen interaction varied for different pathways with some pathways being associated with the conserved set of effectors and others being linked with the diverged or isolate-specific effectors. Our data suggest that at the intra-species level pathogen populations likely maintain divergent sets of effectors capable of targeting the same plant host pathways. This functional redundancy may play an important role in the dynamic of the "arms-race" between host and pathogen serving as the basis for diverse virulence strategies and creating conditions where mutations in certain effector groups will not have a major effect on the pathogen

  16. Advanced toroidal facility vaccuum vessel stress analyses

    International Nuclear Information System (INIS)

    Hammonds, C.J.; Mayhall, J.A.

    1987-01-01

    The complex geometry of the Advance Toroidal Facility (ATF) vacuum vessel required special analysis techniques in investigating the structural behavior of the design. The response of a large-scale finite element model was found for transportation and operational loading. Several computer codes and systems, including the National Magnetic Fusion Energy Computer Center Cray machines, were implemented in accomplishing these analyses. The work combined complex methods that taxed the limits of both the codes and the computer systems involved. Using MSC/NASTRAN cyclic-symmetry solutions permitted using only 1/12 of the vessel geometry to mathematically analyze the entire vessel. This allowed the greater detail and accuracy demanded by the complex geometry of the vessel. Critical buckling-pressure analyses were performed with the same model. The development, results, and problems encountered in performing these analyses are described. 5 refs., 3 figs

  17. Analysing coupling architecture in the cortical EEG of a patient with unilateral cerebral palsy

    Science.gov (United States)

    Kornilov, Maksim V.; Baas, C. Marjolein; van Rijn, Clementina M.; Sysoev, Ilya V.

    2016-04-01

    The detection of coupling presence and direction between cortical areas from the EEG is a popular approach in neuroscience. Granger causality method is promising for this task, since it allows to operate with short time series and to detect nonlinear coupling or coupling between nonlinear systems. In this study EEG multichannel data from adolescent children, suffering from unilateral cerebral palsy were investigated. Signals, obtained in rest and during motor activity of affected and less affected hand, were analysed. The changes in inter-hemispheric and intra-hemispheric interactions were studied over time with an interval of two months. The obtained results of coupling were tested for significance using surrogate times series. In the present proceeding paper we report the data of one patient. The modified nonlinear Granger causality is indeed able to reveal couplings within the human brain.

  18. A model for analysing factors which may influence quality management procedures in higher education

    Directory of Open Access Journals (Sweden)

    Cătălin MAICAN

    2015-12-01

    Full Text Available In all universities, the Office for Quality Assurance defines the procedure for assessing the performance of the teaching staff, with a view to establishing students’ perception as regards the teachers’ activity from the point of view of the quality of the teaching process, of the relationship with the students and of the assistance provided for learning. The present paper aims at creating a combined model for evaluation, based on Data Mining statistical methods: starting from the findings revealed by the evaluations teachers performed to students, using the cluster analysis and the discriminant analysis, we identified the subjects which produced significant differences between students’ grades, subjects which were subsequently subjected to an evaluation by students. The results of these analyses allowed the formulation of certain measures for enhancing the quality of the evaluation process.

  19. CADDIS Volume 4. Data Analysis: Advanced Analyses - Controlling for Natural Variability

    Science.gov (United States)

    Methods for controlling natural variability, predicting environmental conditions from biological observations method, biological trait data, species sensitivity distributions, propensity scores, Advanced Analyses of Data Analysis references.

  20. Analysing public relations education through international standards: The Portuguese case

    OpenAIRE

    Gonçalves, Gisela Marques Pereira; Spínola, Susana de Carvalho; Padamo, Celma

    2013-01-01

    By using international reports on PR education as a benchmark we analyse the status of PR higher education in Portugal. Despite differences among the study programs, the findings reveal that the standard five courses recommendation by the Commission on Public Relations Education (CPRE) are a part of Portuguese undergraduate curriculum. This includes 12 of the 14 content field guidelines needed to achieve the ideal master's program. Data shows, however, the difficulty of positioning public rel...

  1. Ultrastructural and Molecular Analyses Reveal Enhanced Nucleolar Activity in Medicago truncatula Cells Overexpressing the MtTdp2α Gene

    Science.gov (United States)

    Macovei, Anca; Faè, Matteo; Biggiogera, Marco; de Sousa Araújo, Susana; Carbonera, Daniela; Balestrazzi, Alma

    2018-01-01

    The role of tyrosyl-DNA phosphodiesterase 2 (Tdp2) involved in the repair of 5′-end-blocking DNA lesions is still poorly explored in plants. To gain novel insights, Medicago truncatula suspension cultures overexpressing the MtTdp2α gene (Tdp2α-13C and Tdp2α-28 lines, respectively) and a control (CTRL) line carrying the empty vector were investigated. Transmission electron microscopy (TEM) revealed enlarged nucleoli (up to 44% expansion of the area, compared to CTRL), the presence of nucleolar vacuoles, increased frequency of multinucleolate cells (up to 4.3-fold compared to CTRL) and reduced number of ring-shaped nucleoli in Tdp2α-13C and Tdp2α-28 lines. Ultrastructural data suggesting for enhanced nucleolar activity in MtTdp2α-overexpressing lines were integrated with results from bromouridine incorporation. The latter revealed an increase of labeled transcripts in both Tdp2α-13C and Tdp2α-28 cells, within the nucleolus and in the extra-nucleolar region. MtTdp2α-overexpressing cells showed tolerance to etoposide, a selective inhibitor of DNA topoisomerase II, as evidenced by DNA diffusion assay. TEM analysis revealed etoposide-induced rearrangements within the nucleolus, resembling the nucleolar caps observed in animal cells under transcription impairment. Based on these findings it is evident that MtTdp2α-overexpression enhances nucleolar activity in plant cells. PMID:29868059

  2. Ultrastructural and Molecular Analyses Reveal Enhanced Nucleolar Activity in Medicago truncatula Cells Overexpressing the MtTdp2α Gene

    Directory of Open Access Journals (Sweden)

    Anca Macovei

    2018-05-01

    Full Text Available The role of tyrosyl-DNA phosphodiesterase 2 (Tdp2 involved in the repair of 5′-end-blocking DNA lesions is still poorly explored in plants. To gain novel insights, Medicago truncatula suspension cultures overexpressing the MtTdp2α gene (Tdp2α-13C and Tdp2α-28 lines, respectively and a control (CTRL line carrying the empty vector were investigated. Transmission electron microscopy (TEM revealed enlarged nucleoli (up to 44% expansion of the area, compared to CTRL, the presence of nucleolar vacuoles, increased frequency of multinucleolate cells (up to 4.3-fold compared to CTRL and reduced number of ring-shaped nucleoli in Tdp2α-13C and Tdp2α-28 lines. Ultrastructural data suggesting for enhanced nucleolar activity in MtTdp2α-overexpressing lines were integrated with results from bromouridine incorporation. The latter revealed an increase of labeled transcripts in both Tdp2α-13C and Tdp2α-28 cells, within the nucleolus and in the extra-nucleolar region. MtTdp2α-overexpressing cells showed tolerance to etoposide, a selective inhibitor of DNA topoisomerase II, as evidenced by DNA diffusion assay. TEM analysis revealed etoposide-induced rearrangements within the nucleolus, resembling the nucleolar caps observed in animal cells under transcription impairment. Based on these findings it is evident that MtTdp2α-overexpression enhances nucleolar activity in plant cells.

  3. Does Male Circumcision Protect against Sexually Transmitted Infections? Arguments and Meta-Analyses to the Contrary Fail to Withstand Scrutiny.

    Science.gov (United States)

    Morris, Brian J; Hankins, Catherine A; Tobian, Aaron A R; Krieger, John N; Klausner, Jeffrey D

    2014-01-01

    We critically evaluate a recent article by Van Howe involving 12 meta-analyses that concludes, contrary to current evidence, that male circumcision increases the risk of various common sexually transmitted infections (STIs). Our detailed scrutiny reveals that these meta-analyses (1) failed to include results of all relevant studies, especially data from randomized controlled trials, (2) introduced bias through use of inappropriate control groups, (3) altered original data, in the case of human papillomavirus (HPV), by questionable adjustments for "sampling bias," (4) failed to control for confounders through use of crude odds ratios, and (5) used unnecessarily complicated methods without adequate explanation, so impeding replication by others. Interventions that can reduce the prevalence of STIs are important to international health. Of major concern is the global epidemic of oncogenic types of HPV that contribute to the burden of genital cancers. Meta-analyses, when well conducted, can better inform public health policy and medical practice, but when seriously flawed can have detrimental consequences. Our critical evaluation leads us to reject the findings and conclusions of Van Howe on multiple grounds. Our timely analysis thus reaffirms the medical evidence supporting male circumcision as a desirable intervention for STI prevention.

  4. Genes but not genomes reveal bacterial domestication of Lactococcus lactis.

    Directory of Open Access Journals (Sweden)

    Delphine Passerini

    Full Text Available BACKGROUND: The population structure and diversity of Lactococcus lactis subsp. lactis, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE. METHODOLOGY/PRINCIPAL FINDINGS: The MLST analysis revealed that L. lactis subsp. lactis is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST differing by up to 230 kb in genome size. CONCLUSION/SIGNIFICANCE: The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between "environmental" strains, the main contributors to the genetic diversity within the subspecies, and "domesticated" strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the "domesticated" strains essentially arose through substantial genomic flux within the dispensable

  5. A case study of discordant overlapping meta-analyses: vitamin d supplements and fracture.

    Directory of Open Access Journals (Sweden)

    Mark J Bolland

    Full Text Available BACKGROUND: Overlapping meta-analyses on the same topic are now very common, and discordant results often occur. To explore why discordant results arise, we examined a common topic for overlapping meta-analyses- vitamin D supplements and fracture. METHODS AND FINDINGS: We identified 24 meta-analyses of vitamin D (with or without calcium and fracture in a PubMed search in October 2013, and analysed a sample of 7 meta-analyses in the highest ranking general medicine journals. We used the AMSTAR tool to assess the quality of the meta-analyses, and compared their methodologies, analytic techniques and results. Applying the AMSTAR tool suggested the meta-analyses were generally of high quality. Despite this, there were important differences in trial selection, data extraction, and analytical methods that were only apparent after detailed assessment. 25 trials were included in at least one meta-analysis. Four meta-analyses included all eligible trials according to the stated inclusion and exclusion criteria, but the other 3 meta-analyses "missed" between 3 and 8 trials, and 2 meta-analyses included apparently ineligible trials. The relative risks used for individual trials differed between meta-analyses for total fracture in 10 of 15 trials, and for hip fracture in 6 of 12 trials, because of different outcome definitions and analytic approaches. The majority of differences (11/16 led to more favourable estimates of vitamin D efficacy compared to estimates derived from unadjusted intention-to-treat analyses using all randomised participants. The conclusions of the meta-analyses were discordant, ranging from strong statements that vitamin D prevents fractures to equally strong statements that vitamin D without calcium does not prevent fractures. CONCLUSIONS: Substantial differences in trial selection, outcome definition and analytic methods between overlapping meta-analyses led to discordant estimates of the efficacy of vitamin D for fracture prevention

  6. Method-Based Higher Education in Sustainability: The Potential of the Scenario Method

    Directory of Open Access Journals (Sweden)

    Richard Beecroft

    2014-05-01

    Full Text Available Both sustainability and education are challenging process-oriented objectives. When the aim is to combine both notions, as in Higher Education in Sustainability (HES, it is indispensable to first establish a common ground between them. In this paper, we characterise this common ground in terms of four aspects: future orientation, normativity, global perspective, and theory engaged in practice. Based on an analysis of the common ground, one method that is well-established in a wide range of sustainability sciences shows high potential for use in HES because it covers all four aspects in detail: the scenario method. We argue that a didactical reconstruction of the scenario method is necessary to utilise its potential and develop adequate forms of teaching in higher education. The scenario method is used to construct and analyse a set of alternative future developments to support decisions that have to be made in the present. Didactical reconstruction reveals a spectrum of objectives for which the scenario method can be employed: (1 projection; (2 teleological planning and (3 an explorative search for possibilities not yet considered. By studying and experimenting with this spectrum of objectives, students in HES can develop fundamental reflexive competencies in addressing the future in different ways that are relevant for both sustainability and education.

  7. Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

    Science.gov (United States)

    Yin, Wei; Wang, Zong-ji; Li, Qi-ye; Lian, Jin-ming; Zhou, Yang; Lu, Bing-zheng; Jin, Li-jun; Qiu, Peng-xin; Zhang, Pei; Zhu, Wen-bo; Wen, Bo; Huang, Yi-jun; Lin, Zhi-long; Qiu, Bi-tao; Su, Xing-wen; Yang, Huan-ming; Zhang, Guo-jie; Yan, Guang-mei; Zhou, Qi

    2016-01-01

    Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution. PMID:27708285

  8. Protein fraction heterogeneity in donkey’s milk analysed by proteomic methods

    Directory of Open Access Journals (Sweden)

    G. D'Urso

    2010-04-01

    Full Text Available Donkey’s milk is often well tolerate by patients affected by cow’s milk protein allergy, probably thanks to its protein composition. This empiric evidence, confirmed by some clinical trials, needs to be better investigated. A preliminary survey on the protein fraction of donkey’s milk was carried out: fifty-six individual milk samples have been collected and analysed by IEF and SDS-PAGE. Five different IEF patterns have been identified, showing a marked heterogeneity both in casein and whey protein fractions. A single IEF pattern showed an apparent reduced amount of casein fraction highlighted by SDS. Three of the five IEF patterns have been further investigated by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS.

  9. Dynamic regulation of GDP binding to G proteins revealed by magnetic field-dependent NMR relaxation analyses.

    Science.gov (United States)

    Toyama, Yuki; Kano, Hanaho; Mase, Yoko; Yokogawa, Mariko; Osawa, Masanori; Shimada, Ichio

    2017-02-22

    Heterotrimeric guanine-nucleotide-binding proteins (G proteins) serve as molecular switches in signalling pathways, by coupling the activation of cell surface receptors to intracellular responses. Mutations in the G protein α-subunit (Gα) that accelerate guanosine diphosphate (GDP) dissociation cause hyperactivation of the downstream effector proteins, leading to oncogenesis. However, the structural mechanism of the accelerated GDP dissociation has remained unclear. Here, we use magnetic field-dependent nuclear magnetic resonance relaxation analyses to investigate the structural and dynamic properties of GDP bound Gα on a microsecond timescale. We show that Gα rapidly exchanges between a ground-state conformation, which tightly binds to GDP and an excited conformation with reduced GDP affinity. The oncogenic D150N mutation accelerates GDP dissociation by shifting the equilibrium towards the excited conformation.

  10. Iron interference in arsenic absorption by different plant species, analysed by neutron activation, k0-method

    International Nuclear Information System (INIS)

    Uemura, George; Matos, Ludmila Vieira da Silva; Silva, Maria Aparecida da; Menezes, Maria Angela de Barros Correia

    2009-01-01

    Natural arsenic contamination is a cause for concern in many countries of the world including Argentina, Bangladesh, Chile, China, India, Mexico, Thailand, United States of America and also in Brazil, specially in the Iron Quadrangle area, where mining activities have been contributing to aggravate natural contamination. Among other elements, iron is capable to interfere with the arsenic absorption by plants; iron ore has been proposed to remediate areas contaminated by the mentioned metalloid. In order to verify if iron can interfere with arsenic absorption by different taxa of plants, specimens of Brassicacea and Equisetaceae were kept in a 1/4 Murashige and Skoog basal salt solution (M and S), with 10 μgL -1 of arsenic acid. And varying concentrations of iron. The specimens were analysed by neutron activation analysis, k 0 -method, a routine technique in CDTN, and also very appropriate for arsenic studies. The preliminary results were quite surprising, showing that iron can interfere with arsenic absorption by plants, but in different ways, according to the species studied. (author)

  11. Validation of an UHPLC-MS/MS Method for Screening of Antimicrobial Residues in Eggs and Their Application to Analyses of Eggs from Laying Hens Subjected to Pharmacological Treatment

    Directory of Open Access Journals (Sweden)

    Letícia Gomes Magnago Caldeira

    2017-01-01

    Full Text Available A multiresidue method by UHPLC/MS-MS was optimized and validated for the screening and semiquantitative detection of antimicrobials residues from tetracyclines, aminoglycosides, quinolones, lincosamides, β-lactams, sulfonamides, and macrolides families in eggs. A qualitative approach was used to ensure adequate sensitivity to detect residues at the level of interest, defined as maximum residue limit (MRL, or less. The applicability of the methods was assessed by analyzing egg samples from hens that had been subjected to pharmacological treatment with neomycin, enrofloxacin, lincomycin, oxytetracycline, and doxycycline during five days and after discontinuation of medication (10 days. The method was adequate for screening all studied analytes in eggs, since the performance parameters ensured a false-compliant rate below or equal to 5%, except for flumequine. In the analyses of eggs from laying hens subjected to pharmacological treatment, all antimicrobial residues were detected throughout the experimental period, even after discontinuation of medication, except for neomycin, demonstrating the applicability of the method for analyses of antimicrobial residues in eggs.

  12. Divergent Significance of Bone Mineral Density Changes in Aging Depending on Sites and Sex Revealed through Separate Analyses of Bone Mineral Content and Area

    Directory of Open Access Journals (Sweden)

    Yasumoto Matsui

    2012-01-01

    Full Text Available Bone mineral density (aBMD is equivalent to bone mineral content (BMC divided by area. We rechecked the significance of aBMD changes in aging by examining BMC and area separately. Subjects were 1167 community-dwelling Japanese men and women, aged 40–79 years. ABMDs of femoral neck and lumbar spine were assessed by DXA twice, at 6-year intervals. The change rates of BMC and area, as well as aBMD, were calculated and described separately by the age stratum and by sex. In the femoral neck region, aBMDs were significantly decreased in all age strata by an increase in area as well as BMC loss in the same pattern in both sexes. In the lumbar spine region, aBMDs decreased until the age of 60 in women, caused by the significant BMC decrease accompanying the small area change. Very differently in men, aBMDs increased after their 50s due to BMC increase, accompanied by an area increase. Separate analyses of BMC and area change revealed that the significance of aBMD changes in aging was very divergent among sites and between sexes. This may explain in part the dissociation of aBMD change and bone strength, suggesting that we should be more cautious when interpreting the meaning of aBMD change.

  13. How to take environmental samples for stable isotope analyses

    International Nuclear Information System (INIS)

    Rogers, K.M.

    2009-01-01

    It is possible to analyse a diverse range of samples for environmental investigations. The main types are soil/sediments, vegetation, fauna, shellfish, waste and water. Each type of samples requires different storage and collection methods. Outlined here are the preferred methods of collection to ensure maximum sample integrity and reliability. (author).

  14. How to take environmental samples for stable isotope analyses

    International Nuclear Information System (INIS)

    Rogers, K.M.

    2013-01-01

    It is possible to analyse a diverse range of samples for environmental investigations. The main types are soil/sediments, vegetation, fauna, shellfish, waste and water. Each type of samples requires different storage and collection methods. Outlined here are the preferred methods of collection to ensure maximum sample integrity and reliability. (author).

  15. How to take environmental samples for stable isotope analyses

    International Nuclear Information System (INIS)

    Rogers, K.M.

    2012-01-01

    It is possible to analyse a diverse range of samples for environmental investigations. The main types are soil/sediments, vegetation, fauna, shellfish, waste and water. Each type of samples requires different storage and collection methods. Outlined here are the preferred methods of collection to ensure maximum sample integrity and reliability. (author).

  16. How to take environmental samples for stable isotope analyses

    International Nuclear Information System (INIS)

    Rogers, K.M.

    2009-01-01

    It is possible to analyse a diverse range of samples for environmental investigations. The main types are soil/sediments, vegetation, fauna, shellfish, waste and water. Each type of samples requires different storage and collection methods. Outlined here are the preferred methods of collection to ensure maximum sample integrity and reliability. (author)

  17. Forensic application of phylogenetic analyses - Exploration of suspected HIV-1 transmission case.

    Science.gov (United States)

    Siljic, Marina; Salemovic, Dubravka; Cirkovic, Valentina; Pesic-Pavlovic, Ivana; Ranin, Jovan; Todorovic, Marija; Nikolic, Slobodan; Jevtovic, Djordje; Stanojevic, Maja

    2017-03-01

    Transmission of human immunodeficiency virus (HIV) between individuals may have important legal implications and therefore may come to require forensic investigation based upon phylogenetic analysis. In criminal trials results of phylogenetic analyses have been used as evidence of responsibility for HIV transmission. In Serbia, as in many countries worldwide, exposure and deliberate transmission of HIV are criminalized. We present the results of applying state of the art phylogenetic analyses, based on pol and env genetic sequences, in exploration of suspected HIV transmission among three subjects: a man and two women, with presumed assumption of transmission direction from one woman to a man. Phylogenetic methods included relevant neighbor-joining (NJ), maximum likelihood (ML) and Bayesian methods of phylogenetic trees reconstruction and hypothesis testing, that has been shown to be the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals. End-point limiting-dilution PCR (EPLD-PCR) assay, generating the minimum of 10 sequences per genetic region per subject, was performed to assess HIV quasispecies distribution and to explore the direction of HIV transmission between three subjects. Phylogenetic analysis revealed that the viral sequences from the three subjects were more genetically related to each other than to other strains circulating in the same area with the similar epidemiological profile, forming strongly supported transmission chain, which could be in favour of a priori hypothesis of one of the women infecting the man. However, in the EPLD based phylogenetic trees for both pol and env genetic region, viral sequences of one subject (man) were paraphyletic to those of two other subjects (women), implying the direction of transmission opposite to the a priori assumption. The dated tree in our analysis confirmed the clustering pattern of query sequences. Still, in the context of unsampled sequences and

  18. Fourier Transform Mass Spectrometry: The Transformation of Modern Environmental Analyses

    Directory of Open Access Journals (Sweden)

    Lucy Lim

    2016-01-01

    Full Text Available Unknown compounds in environmental samples are difficult to identify using standard mass spectrometric methods. Fourier transform mass spectrometry (FTMS has revolutionized how environmental analyses are performed. With its unsurpassed mass accuracy, high resolution and sensitivity, researchers now have a tool for difficult and complex environmental analyses. Two features of FTMS are responsible for changing the face of how complex analyses are accomplished. First is the ability to quickly and with high mass accuracy determine the presence of unknown chemical residues in samples. For years, the field has been limited by mass spectrometric methods that were based on knowing what compounds of interest were. Secondly, by utilizing the high resolution capabilities coupled with the low detection limits of FTMS, analysts also could dilute the sample sufficiently to minimize the ionization changes from varied matrices.

  19. Analysing the Improper Pronunciation of Diphthongs by Iraqi EFL learners

    Directory of Open Access Journals (Sweden)

    Mukhalad Malik Almutalabi

    2018-04-01

    Full Text Available The current study aims at analysing the improper pronunciation of Iraqi EFL learners concerning the pronunciation of diphthongs in words of various syllables. It describes and identifies thoroughly the mispronunciations of such important sounds in English language. The study attempts at analysing such mispronunciations by clarifying and assigning the phonetic deviations of Iraqi EFL learners when they pronounce diphthongs. So the main objective of the study is to analyse the errors committed by Iraqi learners in the pronunciation of diphthongs grouping each error into its specific category. To verify the objective of the paper, 25 Iraqi EFL learners from the department of English at Cihan University/ Slemani are chosen to be the main participants of the study. The test which was conducted in the laboratory of the Department of English contained 10 words comprising various diphthongs. The results clearly revealed that mispronouncing English diphthongs by Iraqi EFL were mostly observed by replacing the required diphthong with another improper one and they also tended to use simple vowels instead of the correct required diphthongs.

  20. Financial relationships in economic analyses of targeted therapies in oncology.

    Science.gov (United States)

    Valachis, Antonis; Polyzos, Nikolaos P; Nearchou, Andreas; Lind, Pehr; Mauri, Davide

    2012-04-20

    A potential financial relationship between investigators and pharmaceutical manufacturers has been associated with an increased likelihood of reporting favorable conclusions about a sponsor's proprietary agent in pharmacoeconomic studies. The purpose of this study is to investigate whether there is an association between financial relationships and outcome in economic analyses of new targeted therapies in oncology. We searched PubMed (last update June 2011) for economic analyses of targeted therapies (including monoclonal antibodies, tyrosine-kinase inhibitors, and mammalian target of rapamycin inhibitors) in oncology. The trials were qualitatively rated regarding the cost assessment as favorable, neutral, or unfavorable on the basis of prespecified criteria. Overall, 81 eligible studies were identified. Economic analyses that were funded by pharmaceutical companies were more likely to report favorable qualitative cost estimates (28 [82%] of 34 v 21 [45%] of 47; P = .003). The presence of an author affiliated with manufacturer was not associated with study outcome. Furthermore, if only studies including a conflict of interest statement were included (66 of 81), studies that reported any financial relationship with manufacturers (author affiliation and/or funding and/or other financial relationship) were more likely to report favorable results of targeted therapies compared with studies without financial relationship (32 [71%] of 45 v nine [43%] of 21; P = .025). Our study reveals a potential threat for industry-related bias in economic analyses of targeted therapies in oncology in favor of analyses with financial relationships between authors and manufacturers. A more balanced funding of economic analyses from other sources may allow greater confidence in the interpretation of their results.

  1. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids.

    Science.gov (United States)

    Jansen, Robert K; Kaittanis, Charalambos; Saski, Christopher; Lee, Seung-Bum; Tomkins, Jeffrey; Alverson, Andrew J; Daniell, Henry

    2006-04-09

    The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids. The Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade. However, maximum likelihood analyses place

  2. Phylogenetic analyses of Vitis (Vitaceae based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids

    Directory of Open Access Journals (Sweden)

    Alverson Andrew J

    2006-04-01

    Full Text Available Abstract Background The Vitaceae (grape is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several alternative placements of this family, including sister to Caryophyllales, asterids, Saxifragales, Dilleniaceae or to rest of rosids, though support for these different results has been weak. There has been a recent interest in using complete chloroplast genome sequences for resolving phylogenetic relationships among angiosperms. These studies have clarified relationships among several major lineages but they have also emphasized the importance of taxon sampling and the effects of different phylogenetic methods for obtaining accurate phylogenies. We sequenced the complete chloroplast genome of Vitis vinifera and used these data to assess relationships among 27 angiosperms, including nine taxa of rosids. Results The Vitis vinifera chloroplast genome is 160,928 bp in length, including a pair of inverted repeats of 26,358 bp that are separated by small and large single copy regions of 19,065 bp and 89,147 bp, respectively. The gene content and order of Vitis is identical to many other unrearranged angiosperm chloroplast genomes, including tobacco. Phylogenetic analyses using maximum parsimony and maximum likelihood were performed on DNA sequences of 61 protein-coding genes for two datasets with 28 or 29 taxa, including eight or nine taxa from four of the seven currently recognized major clades of rosids. Parsimony and likelihood phylogenies of both data sets provide strong support for the placement of Vitaceae as sister to the remaining rosids. However, the position of the Myrtales and support for the monophyly of the eurosid I clade differs between the two data sets and the two methods of analysis. In parsimony analyses, the inclusion of Gossypium is necessary to obtain trees that support the monophyly of the eurosid I clade

  3. Indirect questioning method reveals hidden support for female genital cutting in South Central Ethiopia.

    Science.gov (United States)

    Gibson, Mhairi A; Gurmu, Eshetu; Cobo, Beatriz; Rueda, María M; Scott, Isabel M

    2018-01-01

    Female genital cutting (FGC) has major implications for women's physical, sexual and psychological health, and eliminating the practice is a key target for public health policy-makers. To date one of the main barriers to achieving this has been an inability to infer privately-held views on FGC within communities where it is prevalent. As a sensitive (and often illegal) topic, people are anticipated to hide their true support for the practice when questioned directly. Here we use an indirect questioning method (unmatched count technique) to identify hidden support for FGC in a rural South Central Ethiopian community where the practice is common, but thought to be in decline. Employing a socio-demographic household survey of 1620 Arsi Oromo adults, which incorporated both direct and indirect direct response (unmatched count) techniques we compare directly-stated versus privately-held views in support of FGC, and individual variation in responses by age, gender and education and target female (daughters versus daughters-in-law). Both genders express low support for FGC when questioned directly, while indirect methods reveal substantially higher acceptance (of cutting both daughters and daughters-in-law). Educated adults (those who have attended school) are privately more supportive of the practice than they are prepared to admit openly to an interviewer, indicating that education may heighten secrecy rather than decrease support for FGC. Older individuals hold the strongest views in favour of FGC (particularly educated older males), but they are also more inclined to conceal their support for FGC when questioned directly. As these elders represent the most influential members of society, their hidden support for FGC may constitute a pivotal barrier to eliminating the practice in this community. Our results demonstrate the great potential for indirect questioning methods to advance knowledge and inform policy on culturally-sensitive topics like FGC; providing more

  4. Thermal and stress analyses with ANSYS program

    International Nuclear Information System (INIS)

    Kanoo, Iwao; Kawaguchi, Osamu; Asakura, Junichi.

    1975-03-01

    Some analyses of the heat conduction and elastic/inelastic stresses, carried out in Power Reactor and Nuclear Fuel Development Corporation (PNC) in fiscal 1973 using ANSYS (Engineering Analysis System) program, are summarized. In chapter I, the present state of structural analysis programs available for a FBR (fast breeder reactor) in PNC is explained. Chapter II is a brief description of the ANSYS current status. In chapter III are presented 8 examples of the steady-state and transient thermal analyses for fast-reactor plant components, and in chapter IV 5 examples of the inelastic structural analysis. With the advance in the field of finite element method, its applications in design study should extend progressively in the future. The present report, it is hoped, will contribute as references in similar analyses and at the same time help to understand the deformation and strain behaviors of structures. (Mori, K.)

  5. Surface analytical methods in nuclear technology

    International Nuclear Information System (INIS)

    Baumgaertner, F.

    1985-06-01

    Application of SEM-EDX, AES, XPS are exemplarily demonstrated for highly radioactive materials with ionizing dose rates of about 1 Sv near the surface. The samples studied are aerosols from the high level waste vitrification process, postprecipitation in a pretreated fuel solution and emulsifying sludge from a solvent extraction process. The results of the chemical composition differentiated down to microscopic level reveal much more information about the history of a sample than those available from the integral macro-methods analysing. Elucidication of chemical composition and body structure in micrometer level may give insight into the origin and generation processes of samples under investigation. (orig.)

  6. RAPD and Internal Transcribed Spacer Sequence Analyses Reveal Zea nicaraguensis as a Section Luxuriantes Species Close to Zea luxurians

    Science.gov (United States)

    Wang, Pei; Lu, Yanli; Zheng, Mingmin; Rong, Tingzhao; Tang, Qilin

    2011-01-01

    Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species. PMID:21525982

  7. Accuracy of the hypothetical sky-polarimetric Viking navigation versus sky conditions: revealing solar elevations and cloudinesses favourable for this navigation method

    Science.gov (United States)

    Száz, Dénes; Farkas, Alexandra; Barta, András; Kretzer, Balázs; Blahó, Miklós; Egri, Ádám; Szabó, Gyula; Horváth, Gábor

    2017-09-01

    According to Thorkild Ramskou's theory proposed in 1967, under overcast and foggy skies, Viking seafarers might have used skylight polarization analysed with special crystals called sunstones to determine the position of the invisible Sun. After finding the occluded Sun with sunstones, its elevation angle had to be measured and its shadow had to be projected onto the horizontal surface of a sun compass. According to Ramskou's theory, these sunstones might have been birefringent calcite or dichroic cordierite or tourmaline crystals working as polarizers. It has frequently been claimed that this method might have been suitable for navigation even in cloudy weather. This hypothesis has been accepted and frequently cited for decades without any experimental support. In this work, we determined the accuracy of this hypothetical sky-polarimetric Viking navigation for 1080 different sky situations characterized by solar elevation θ and cloudiness ρ, the sky polarization patterns of which were measured by full-sky imaging polarimetry. We used the earlier measured uncertainty functions of the navigation steps 1, 2 and 3 for calcite, cordierite and tourmaline sunstone crystals, respectively, and the newly measured uncertainty function of step 4 presented here. As a result, we revealed the meteorological conditions under which Vikings could have used this hypothetical navigation method. We determined the solar elevations at which the navigation uncertainties are minimal at summer solstice and spring equinox for all three sunstone types. On average, calcite sunstone ensures a more accurate sky-polarimetric navigation than tourmaline and cordierite. However, in some special cases (generally at 35° ≤ θ ≤ 40°, 1 okta ≤ ρ ≤ 6 oktas for summer solstice, and at 20° ≤ θ ≤ 25°, 0 okta ≤ ρ ≤ 4 oktas for spring equinox), the use of tourmaline and cordierite results in smaller navigation uncertainties than that of calcite. Generally, under clear or less cloudy

  8. Floral reversion mechanism in longan (Dimocarpus longan Lour.) revealed by proteomic and anatomic analyses.

    Science.gov (United States)

    You, Xiangrong; Wang, Lingxia; Liang, Wenyu; Gai, Yonghong; Wang, Xiaoyan; Chen, Wei

    2012-02-02

    Two-dimensional gel electrophoresis (2-DE) was used to analyze the proteins related to floral reversion in Dimocarpus longan Lour. Proteins were extracted from buds undergoing the normal process of flowering and from those undergoing floral reversion in three developing stages in D. longan. Differentially expressed proteins were identified from the gels after 2-DE analysis, which were confirmed using matrix-assisted laser desorption/ionization-time of flying-mass spectroscopy and protein database search. A total of 39 proteins, including 18 up-regulated and 21 down-regulated proteins, were classified into different categories, such as energy and substance metabolism, protein translation, secondary metabolism, phytohormone, cytoskeleton structure, regulation, and stress tolerance. Among these, the largest functional class was associated with primary metabolism. Down-regulated proteins were involved in photosynthesis, transcription, and translation, whereas up-regulated proteins were involved in respiration. Decreased flavonoid synthesis and up-regulated GA20ox might be involved in the floral reversion process. Up-regulated 14-3-3 proteins played a role in the regulation of floral reversion in D. longan by responding to abiotic stress. Observations via transmission electron microscopy revealed the ultrastructure changes in shedding buds undergoing floral reversion. Overall, the results provided insights into the molecular basis for the floral reversion mechanism in D. longan. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses.

    Science.gov (United States)

    Yan, Liying; Huang, Lei; Xu, Liya; Huang, Jin; Ma, Fei; Zhu, Xiaohui; Tang, Yaqiong; Liu, Mingshan; Lian, Ying; Liu, Ping; Li, Rong; Lu, Sijia; Tang, Fuchou; Qiao, Jie; Xie, X Sunney

    2015-12-29

    In vitro fertilization (IVF), preimplantation genetic diagnosis (PGD), and preimplantation genetic screening (PGS) help patients to select embryos free of monogenic diseases and aneuploidy (chromosome abnormality). Next-generation sequencing (NGS) methods, while experiencing a rapid cost reduction, have improved the precision of PGD/PGS. However, the precision of PGD has been limited by the false-positive and false-negative single-nucleotide variations (SNVs), which are not acceptable in IVF and can be circumvented by linkage analyses, such as short tandem repeats or karyomapping. It is noteworthy that existing methods of detecting SNV/copy number variation (CNV) and linkage analysis often require separate procedures for the same embryo. Here we report an NGS-based PGD/PGS procedure that can simultaneously detect a single-gene disorder and aneuploidy and is capable of linkage analysis in a cost-effective way. This method, called "mutated allele revealed by sequencing with aneuploidy and linkage analyses" (MARSALA), involves multiple annealing and looping-based amplification cycles (MALBAC) for single-cell whole-genome amplification. Aneuploidy is determined by CNVs, whereas SNVs associated with the monogenic diseases are detected by PCR amplification of the MALBAC product. The false-positive and -negative SNVs are avoided by an NGS-based linkage analysis. Two healthy babies, free of the monogenic diseases of their parents, were born after such embryo selection. The monogenic diseases originated from a single base mutation on the autosome and the X-chromosome of the disease-carrying father and mother, respectively.

  10. Comparison of a point-of-care analyser for the determination of HbA1c with HPLC method.

    Science.gov (United States)

    Grant, D A; Dunseath, G J; Churm, R; Luzio, S D

    2017-08-01

    As the use of Point of Care Testing (POCT) devices for measurement of glycated haemoglobin (HbA1c) increases, it is imperative to determine how their performance compares to laboratory methods. This study compared the performance of the automated Quo-Test POCT device (EKF Diagnostics), which uses boronate fluorescence quenching technology, with a laboratory based High Performance Liquid Chromatography (HPLC) method (Biorad D10) for measurement of HbA1c. Whole blood EDTA samples from subjects (n=100) with and without diabetes were assayed using a BioRad D10 and a Quo-Test analyser. Intra-assay variation was determined by measuring six HbA1c samples in triplicate and inter-assay variation was determined by assaying four samples on 4 days. Stability was determined by assaying three samples stored at -20 °C for 14 and 28 days post collection. Median (IQR) HbA1c was 60 (44.0-71.2) mmol/mol (7.6 (6.17-8.66) %) and 62 (45.0-69.0) mmol/mol (7.8 (6.27-8.46) %) for D10 and Quo-Test, respectively, with very good agreement (R 2 =0.969, Pglucose intolerance (IGT and T2DM) and 100% for diagnosis of T2DM. Good agreement between the D10 and Quo-Test was seen across a wide HbA1c range. The Quo-Test POCT device provided similar performance to a laboratory based HPLC method.

  11. ACCURATE 3D SCANNING OF DAMAGED ANCIENT GREEK INSCRIPTIONS FOR REVEALING WEATHERED LETTERS

    Directory of Open Access Journals (Sweden)

    A. I. Papadaki

    2015-02-01

    Full Text Available In this paper two non-invasive non-destructive alternative techniques to the traditional and invasive technique of squeezes are presented alongside with specialized developed processing methods, aiming to help the epigraphists to reveal and analyse weathered letters in ancient Greek inscriptions carved in masonry or marble. The resulting 3D model would serve as a detailed basis for the epigraphists to try to decipher the inscription. The data were collected by using a Structured Light scanner. The creation of the final accurate three dimensional model is a complicated procedure requiring large computation cost and human effort. It includes the collection of geometric data in limited space and time, the creation of the surface, the noise filtering and the merging of individual surfaces. The use of structured light scanners is time consuming and requires costly hardware and software. Therefore an alternative methodology for collecting 3D data of the inscriptions was also implemented for reasons of comparison. Hence, image sequences from varying distances were collected using a calibrated DSLR camera aiming to reconstruct the 3D scene through SfM techniques in order to evaluate the efficiency and the level of precision and detail of the obtained reconstructed inscriptions. Problems in the acquisition processes as well as difficulties in the alignment step and mesh optimization are also encountered. A meta-processing framework is proposed and analysed. Finally, the results of processing and analysis and the different 3D models are critically inspected and then evaluated by a specialist in terms of accuracy, quality and detail of the model and the capability of revealing damaged and ”hidden” letters.

  12. Accurate 3d Scanning of Damaged Ancient Greek Inscriptions for Revealing Weathered Letters

    Science.gov (United States)

    Papadaki, A. I.; Agrafiotis, P.; Georgopoulos, A.; Prignitz, S.

    2015-02-01

    In this paper two non-invasive non-destructive alternative techniques to the traditional and invasive technique of squeezes are presented alongside with specialized developed processing methods, aiming to help the epigraphists to reveal and analyse weathered letters in ancient Greek inscriptions carved in masonry or marble. The resulting 3D model would serve as a detailed basis for the epigraphists to try to decipher the inscription. The data were collected by using a Structured Light scanner. The creation of the final accurate three dimensional model is a complicated procedure requiring large computation cost and human effort. It includes the collection of geometric data in limited space and time, the creation of the surface, the noise filtering and the merging of individual surfaces. The use of structured light scanners is time consuming and requires costly hardware and software. Therefore an alternative methodology for collecting 3D data of the inscriptions was also implemented for reasons of comparison. Hence, image sequences from varying distances were collected using a calibrated DSLR camera aiming to reconstruct the 3D scene through SfM techniques in order to evaluate the efficiency and the level of precision and detail of the obtained reconstructed inscriptions. Problems in the acquisition processes as well as difficulties in the alignment step and mesh optimization are also encountered. A meta-processing framework is proposed and analysed. Finally, the results of processing and analysis and the different 3D models are critically inspected and then evaluated by a specialist in terms of accuracy, quality and detail of the model and the capability of revealing damaged and "hidden" letters.

  13. MutSpec: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes.

    Science.gov (United States)

    Ardin, Maude; Cahais, Vincent; Castells, Xavier; Bouaoun, Liacine; Byrnes, Graham; Herceg, Zdenko; Zavadil, Jiri; Olivier, Magali

    2016-04-18

    The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called MutSpec. MutSpec includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the COSMIC database and other sources. MutSpec offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. MutSpec may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. MutSpec offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. MutSpec can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.

  14. Flux decay during thermonuclear X-ray bursts analysed with the dynamic power-law index method

    Science.gov (United States)

    Kuuttila, J.; Kajava, J. J. E.; Nättilä, J.; Motta, S. E.; Sánchez-Fernández, C.; Kuulkers, E.; Cumming, A.; Poutanen, J.

    2017-08-01

    The cooling of type-I X-ray bursts can be used to probe the nuclear burning conditions in neutron star envelopes. The flux decay of the bursts has been traditionally modelled with an exponential, even if theoretical considerations predict power-law-like decays. We have analysed a total of 540 type-I X-ray bursts from five low-mass X-ray binaries observed with the Rossi X-ray Timing Explorer. We grouped the bursts according to the source spectral state during which they were observed (hard or soft), flagging those bursts that showed signs of photospheric radius expansion (PRE). The decay phase of all the bursts were then fitted with a dynamic power-law index method. This method provides a new way of probing the chemical composition of the accreted material. Our results show that in the hydrogen-rich sources the power-law decay index is variable during the burst tails and that simple cooling models qualitatively describe the cooling of presumably helium-rich sources 4U 1728-34 and 3A 1820-303. The cooling in the hydrogen-rich sources 4U 1608-52, 4U 1636-536, and GS 1826-24, instead, is clearly different and depends on the spectral states and whether PRE occurred or not. Especially the hard state bursts behave differently than the models predict, exhibiting a peculiar rise in the cooling index at low burst fluxes, which suggests that the cooling in the tail is much faster than expected. Our results indicate that the drivers of the bursting behaviour are not only the accretion rate and chemical composition of the accreted material, but also the cooling that is somehow linked to the spectral states. The latter suggests that the properties of the burning layers deep in the neutron star envelope might be impacted differently depending on the spectral state.

  15. Effectiveness of various transport synthetic acceleration methods with and without GMRES

    International Nuclear Information System (INIS)

    Chang, J.H.; Adams, M.L.

    2005-01-01

    We explore the effectiveness of three types of transport synthetic acceleration (TSA) methods as stand-alone methods and as pre-conditioners within the GMRES Krylov solver. The three types are β TSA, 'stretched' TSA, and 'stretched and filtered' (SF) TSA. We analyzed the effectiveness of these algorithms using Fourier mode analysis of model two-dimensional problems with periodic boundary conditions, including problems with alternating layers of different materials. The analyses revealed that both β-TSA and stretched TSA can diverge for fairly weak heterogeneities. Performance of SF TSA, even with the optimum filtering parameter, degrades with heterogeneity. However, with GMRES, all TSA methods are convergent. SF TSA with the optimum filtering parameter was the most effective method. Numerical results support our Fourier mode analysis. (authors)

  16. Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes

    NARCIS (Netherlands)

    Revuelta, M.V.; Kan, van J.A.L.; Kay, J.; Have, ten A.

    2014-01-01

    The A1 family of eukaryotic aspartic proteinases (APs) forms one of the 16 AP families. Although one of the best characterized families, the recent increase in genome sequence data has revealed many fungal AP homologs with novel sequence characteristics. This study was performed to explore the

  17. Sensitivity analyses of the peach bottom turbine trip 2 experiment

    International Nuclear Information System (INIS)

    Bousbia Salah, A.; D'Auria, F.

    2003-01-01

    In the light of the sustained development in computer technology, the possibilities for code calculations in predicting more realistic transient scenarios in nuclear power plants have been enlarged substantially. Therefore, it becomes feasible to perform 'Best-estimate' simulations through the incorporation of three-dimensional modeling of reactor core into system codes. This method is particularly suited for complex transients that involve strong feedback effects between thermal-hydraulics and kinetics as well as to transient involving local asymmetric effects. The Peach bottom turbine trip test is characterized by a prompt core power excursion followed by a self limiting power behavior. To emphasize and understand the feedback mechanisms involved during this transient, a series of sensitivity analyses were carried out. This should allow the characterization of discrepancies between measured and calculated trends and assess the impact of the thermal-hydraulic and kinetic response of the used models. On the whole, the data comparison revealed a close dependency of the power excursion with the core feedback mechanisms. Thus for a better best estimate simulation of the transient, both of the thermal-hydraulic and the kinetic models should be made more accurate. (author)

  18. Analysing the Experience of Motherhood Among Adolescents Living With HIV

    Directory of Open Access Journals (Sweden)

    Gabriela Cássia Ritt

    2017-05-01

    Full Text Available AimAdolescent motherhood is considered a condition of vulnerability that can be further complicated by the presence of HIV infection, but little is known about how adolescent mothers experience this process. The aim of this study was to analyse the experience of motherhood among adolescents living with HIV.MethodSeven mothers (15-21 years recruited in specialized services in Porto Alegre/Brazil, whose babies’ ages ranged from four to six months, were interviewed. Interviews were tape-recorded and transcribed verbatim.ResultsThe qualitative content analysis of the interviews revealed a positive vision of motherhood, related to satisfaction with the maternal role and personal fulfilment. Pregnancy and motherhood served to these adolescents as an encouragement for self-care. The mothers’ difficulties were related to HIV and to the repercussions of this clinical condition, especially feelings of frustration and incompleteness of motherhood on the impossibility of breastfeeding, as well as fear facing the risk of MTCT.ConclusionFuture research of longitudinal design and with larger samples will be important to extend the knowledge of the specificities of this experience over time for young people of different ages and social backgrounds.

  19. The development of an on-line gold analyser

    International Nuclear Information System (INIS)

    Robert, R.V.D.; Ormrod, G.T.W.

    1982-01-01

    An on-line analyser to monitor the gold in solutions from the carbon-in-pulp process is described. The automatic system is based on the delivery of filtered samples of the solutions to a distribution valve for measurement by flameless atomic-absorption spectrophotometry. The samples is introduced by the aerosol-deposition method. Operation of the analyser on a pilot plant and on a full-scale carbon-in-pulp plant has shown that the system is economically feasible and capable of providing a continuous indication of the efficiency of the extraction process

  20. Synthesis, Hirshfeld surface analyses and magnetism of a 1D Mn(II ...

    African Journals Online (AJOL)

    A new Mn-based complex of {[Mn(L)2(mi)]·H2O}n (1) (HL = p-hydroxy phenylacetic acid; mi = 1,1'-(1,4-butanediyl)bis(imidazole)), has been synthesized and structurally characterized. Single-crystal X-ray analyses reveal that compound 1 has a dinuclear Mn(II) unit linking by four carboxylate groups. The bridging N-donor ...

  1. How Genes Modulate Patterns of Aging-Related Changes on the Way to 100: Biodemographic Models and Methods in Genetic Analyses of Longitudinal Data

    Science.gov (United States)

    Yashin, Anatoliy I.; Arbeev, Konstantin G.; Wu, Deqing; Arbeeva, Liubov; Kulminski, Alexander; Kulminskaya, Irina; Akushevich, Igor; Ukraintseva, Svetlana V.

    2016-01-01

    Background and Objective To clarify mechanisms of genetic regulation of human aging and longevity traits, a number of genome-wide association studies (GWAS) of these traits have been performed. However, the results of these analyses did not meet expectations of the researchers. Most detected genetic associations have not reached a genome-wide level of statistical significance, and suffered from the lack of replication in the studies of independent populations. The reasons for slow progress in this research area include low efficiency of statistical methods used in data analyses, genetic heterogeneity of aging and longevity related traits, possibility of pleiotropic (e.g., age dependent) effects of genetic variants on such traits, underestimation of the effects of (i) mortality selection in genetically heterogeneous cohorts, (ii) external factors and differences in genetic backgrounds of individuals in the populations under study, the weakness of conceptual biological framework that does not fully account for above mentioned factors. One more limitation of conducted studies is that they did not fully realize the potential of longitudinal data that allow for evaluating how genetic influences on life span are mediated by physiological variables and other biomarkers during the life course. The objective of this paper is to address these issues. Data and Methods We performed GWAS of human life span using different subsets of data from the original Framingham Heart Study cohort corresponding to different quality control (QC) procedures and used one subset of selected genetic variants for further analyses. We used simulation study to show that approach to combining data improves the quality of GWAS. We used FHS longitudinal data to compare average age trajectories of physiological variables in carriers and non-carriers of selected genetic variants. We used stochastic process model of human mortality and aging to investigate genetic influence on hidden biomarkers of aging

  2. Preliminary investigation of fuel cycle in fast reactors by the correlations method and sensitivity analyses of nuclear characteristics

    International Nuclear Information System (INIS)

    Amorim, E.S. do; Castro Lobo, P.D. de.

    1980-11-01

    A reduction of computing effort was achieved as a result of the application of space - independent continuous slowing down theory in the spectrum averaged cross sections and further expressing then in a quadratic corelation whith the temperature and the composition. The decoupling between variables that express some of the important nuclear characteristics allowed to introduce a sensitivity analyses treatment for the full prediction of the behavior, over the fuel cycle, of the LMFBR considered. As a potential application of the method here in developed is to predict the nuclear characteristics of another reactor, face some reference reactor of the family considered. Excellent agreement with exact calculation is observed only when perturbations occur in nuclear data and/or fuel isotopic characteristics, but fair results are obtained whith variations in system components other than the fuel. (Author) [pt

  3. Pathway analyses implicate glial cells in schizophrenia.

    Directory of Open Access Journals (Sweden)

    Laramie E Duncan

    Full Text Available The quest to understand the neurobiology of schizophrenia and bipolar disorder is ongoing with multiple lines of evidence indicating abnormalities of glia, mitochondria, and glutamate in both disorders. Despite high heritability estimates of 81% for schizophrenia and 75% for bipolar disorder, compelling links between findings from neurobiological studies, and findings from large-scale genetic analyses, are only beginning to emerge.Ten publically available gene sets (pathways related to glia, mitochondria, and glutamate were tested for association to schizophrenia and bipolar disorder using MAGENTA as the primary analysis method. To determine the robustness of associations, secondary analyses were performed with: ALIGATOR, INRICH, and Set Screen. Data from the Psychiatric Genomics Consortium (PGC were used for all analyses. There were 1,068,286 SNP-level p-values for schizophrenia (9,394 cases/12,462 controls, and 2,088,878 SNP-level p-values for bipolar disorder (7,481 cases/9,250 controls.The Glia-Oligodendrocyte pathway was associated with schizophrenia, after correction for multiple tests, according to primary analysis (MAGENTA p = 0.0005, 75% requirement for individual gene significance and also achieved nominal levels of significance with INRICH (p = 0.0057 and ALIGATOR (p = 0.022. For bipolar disorder, Set Screen yielded nominally and method-wide significant associations to all three glial pathways, with strongest association to the Glia-Astrocyte pathway (p = 0.002.Consistent with findings of white matter abnormalities in schizophrenia by other methods of study, the Glia-Oligodendrocyte pathway was associated with schizophrenia in our genomic study. These findings suggest that the abnormalities of myelination observed in schizophrenia are at least in part due to inherited factors, contrasted with the alternative of purely environmental causes (e.g. medication effects or lifestyle. While not the primary purpose of our study

  4. Bearing Capacity Analyses for the Great Belt East Bridge Anchor Blocks

    DEFF Research Database (Denmark)

    Sørensen, Carsten Steen; Clausen, Carl J. Frimann; Andersen, Henrik

    1993-01-01

    This paper presents a comparison between different methods of bearing capacity analyses: Upper Bound Method. Limit Equilibrium Analysis and Finite Element Analysis. For the Great Belt East Bridge anchor blocks it was concluded that these methods of calculation agree within 5%. However, for cases ...

  5. Chemical analyses of wasp-associated streptomyces bacteria reveal a prolific potential for natural products discovery.

    Directory of Open Access Journals (Sweden)

    Michael Poulsen

    2011-02-01

    Full Text Available Identifying new sources for small molecule discovery is necessary to help mitigate the continuous emergence of antibiotic-resistance in pathogenic microbes. Recent studies indicate that one potentially rich source of novel natural products is Actinobacterial symbionts associated with social and solitary Hymenoptera. Here we test this possibility by examining two species of solitary mud dauber wasps, Sceliphron caementarium and Chalybion californicum. We performed enrichment isolations from 33 wasps and obtained more than 200 isolates of Streptomyces Actinobacteria. Chemical analyses of 15 of these isolates identified 11 distinct and structurally diverse secondary metabolites, including a novel polyunsaturated and polyoxygenated macrocyclic lactam, which we name sceliphrolactam. By pairing the 15 Streptomyces strains against a collection of fungi and bacteria, we document their antifungal and antibacterial activity. The prevalence and anti-microbial properties of Actinobacteria associated with these two solitary wasp species suggest the potential role of these Streptomyces as antibiotic-producing symbionts, potentially helping defend their wasp hosts from pathogenic microbes. Finding phylogenetically diverse and chemically prolific Actinobacteria from solitary wasps suggests that insect-associated Actinobacteria can provide a valuable source of novel natural products of pharmaceutical interest.

  6. Indian Point 2 steam generator tube rupture analyses

    International Nuclear Information System (INIS)

    Dayan, A.

    1985-01-01

    Analyses were conducted with RETRAN-02 to study consequences of steam generator tube rupture (SGTR) events. The Indian Point, Unit 2, power plant (IP2, PWR) was modeled as a two asymmetric loops, consisting of 27 volumes and 37 junctions. The break section was modeled once, conservatively, as a 150% flow area opening at the wall of the steam generator cold leg plenum, and once as a 200% double-ended tube break. Results revealed 60% overprediction of breakflow rates by the traditional conservative model. Two SGTR transients were studied, one with low-pressure reactor trip and one with an earlier reactor trip via over temperature ΔT. The former is more typical to a plant with low reactor average temperature such as IP2. Transient analyses for a single tube break event over 500 seconds indicated continued primary subcooling and no need for steam line pressure relief. In addition, SGTR transients with reactor trip while the pressurizer still contains water were found to favorably reduce depressurization rates. Comparison of the conservative results with independent LOFTRAN predictions showed good agreement

  7. Species-delimitation and phylogenetic analyses of some cosmopolitan species of Hypnea (Rhodophyta) reveal synonyms and misapplied names to H. cervicornis, including a new species from Brazil.

    Science.gov (United States)

    de Jesus, Priscila Barreto; Nauer, Fabio; Lyra, Goia de Mattos; Cassano, Valéria; Oliveira, Mariana Cabral; Nunes, José Marcos de Castro; Schnadelbach, Alessandra Selbach

    2016-10-01

    Hypnea has an intricate nomenclatural history due to a wide pantropical distribution and considerable morphological variation. Recent molecular studies have provided further clarification on the systematics of the genus; however, species of uncertain affinities remain due to flawed taxonomic identification. Detailed analyses coupled with literature review indicated a strong relationship among H. aspera, H. cervicornis, H. flexicaulis, and H. tenuis, suggesting a need for further taxonomic studies. Here, we analyzed sequences from two molecular markers (COI-5P and rbcL) and performed several DNA-based delimitation methods (mBGD, ABGD, SPN, PTP and GMYC). These molecular approaches were contrasted with morphological and phylogenetic evidence from type specimens and/or topotype collections of related species under a conservative approach. Our results demonstrate that H. aspera and H. flexicaulis represent heterotypic synonyms of H. cervicornis and indicate the existence of a misidentified Hypnea species, widely distributed on the Brazilian coast, described here as a new species: H. brasiliensis. Finally, inconsistencies observed among our results based on six different species delimitation methods evidence the need for adequate sampling and marker choice for different methods. © 2016 Phycological Society of America.

  8. Medieval land use management and geochemistry - spatial analyses on scales from households properties to whole fields systems

    Science.gov (United States)

    Horák, Jan; Janovský, Martin; Klír, Tomáš; Šmejda, Ladislav; Legut-Pintal, Maria

    2017-04-01

    We present the final or preliminary results of our researches of five villages: Spindelbach (Ore Mountains, North-Western Bohemia), Hol (near Prague, Central Bohemia), Lovětín and Regenholz (near Třešť, Czech-Moravian Upland) and Goschwitz (near Wroclaw, Poland). Our research is methodically based on broad spatial sampling of soil samples and mapping of basic soil conditions. We use XRF spectrometry as a main tool for multi-elemental analyses and as a tool for first step screening of large areas. The crucial factor of our methods is also a design of sampling based on a respect to historical land and land use features like parts of village field system or possesions of the households. Also macroscopic visual method of getting data and knowledge of the site is crucial. It was revealed that generally used and acknowledged human indicator - Phosphorus - can be present at only very low levels of concentration, or undetectable, even in the nearness of households. The natural conditions cannot be the causing factor at all cases. This situation is caused also by last human activity intensity and by its spatial manifestation. In such cases, multi-elemental analysis is very useful. Zinc is usually correlated with Phosphorus, which is also connected to Lead. The past human activity indicators are spatially usually connected to modern pollution indicators. These two inputs can be sometimes distinguished by statistical analyses and by spatial visualisation of data. Working with just concentrations can be misleading. Past land use management and its strategies were important for spatial distribution of soil geochemical indicators. Therefore, we can use them not only as quantifiers of human impact on nature, but we can also detect different management or knowledge and experience. As it was revealed e. g. by analyses of households` possessions differences. For example, generally presumed decreasing gradient of management intensity (e.g. manuring) along the distance from

  9. Entropy resistance minimization: An alternative method for heat exchanger analyses

    International Nuclear Information System (INIS)

    Cheng, XueTao

    2013-01-01

    In this paper, the concept of entropy resistance is proposed based on the entropy generation analyses of heat transfer processes. It is shown that smaller entropy resistance leads to larger heat transfer rate with fixed thermodynamic force difference and smaller thermodynamic force difference with fixed heat transfer rate, respectively. For the discussed two-stream heat exchangers in which the heat transfer rates are not given and the three-stream heat exchanger with prescribed heat capacity flow rates and inlet temperatures of the streams, smaller entropy resistance leads to larger heat transfer rate. For the two-stream heat exchangers with fixed heat transfer rate, smaller entropy resistance leads to larger effectiveness. Furthermore, it is shown that smaller values of the concepts of entropy generation numbers and modified entropy generation number do not always correspond to better performance of the discussed heat exchangers. - Highlights: • The concept of entropy resistance is defined for heat exchangers. • The concepts based on entropy generation are used to analyze heat exchangers. • Smaller entropy resistance leads to better performance of heat exchangers. • The applicability of entropy generation minimization is conditional

  10. Non-invasive PGAA, PIXE and ToF-ND analyses on Hungarian Bronze Age defensive armour

    International Nuclear Information System (INIS)

    Marianne Moedlinger; Imre Kovacs; Zoltan Szoekefalvi-Nagy; Ziad El Morr

    2014-01-01

    Non-invasive, archaeometric analyses on selected Hungarian Bronze Age defensive armour is presented here: three greaves, three helmets two shields as well as one vessel fragment were analysed with PIXE, PGAA and TOF-ND. The detected alloy elemental and phase composition as well as its intergranular or spatial concentration distribution reveals important insights into the alloys used and the manufacturing techniques applied c. 1200-950 BC, and allows to reconstruct the production techniques used during the Late Bronze Age. (author)

  11. A Review of Sparsity-Based Methods for Analysing Radar Returns from Helicopter Rotor Blades

    Science.gov (United States)

    2016-09-01

    performance study of these algorithms in the particular problem of analysing backscatter signals from rotating blades. The report is organised as follows...provide further insight into the behaviour of the techniques. Here, the algorithms for MP, OMP, CGP, gOMP and ROMP terminate when 10 atoms are

  12. Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

    Science.gov (United States)

    Reynaud, Yann; Millet, Julie; Rastogi, Nalin

    2015-01-01

    Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family. PMID:26517715

  13. Argon activation analysis, application to dating by the potassium-argon method; Analyse par activation de l'argon. Application a la datation par la methode potassium-argon

    Energy Technology Data Exchange (ETDEWEB)

    Dumesnil, P [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1967-07-01

    Activation analysis using radiogenic argon-40 has been applied to rock-dating by the K-Ar method. The argon is extracted from the sample, purified, activated to saturation in a flux of 2 X 10{sup 13} neutrons/cm{sup 2} sec{sup -1} and measured by gamma spectroscopy. The sensitivity obtained is such that it is possible to measure amounts of argon corresponding to age of a few thousand years only. However since it has not been possible to measure the amount of pollution of radiogenic argon by atmospheric argon with any accuracy, the measurable age limit is in fact of the order of MY. The method has been applied to basalts from the Mont-Dore region. The results obtained are in fairly good agreement with geological, stratigraphic and paleomagnetic data. (author) [French] L'analyse par activation de l'argon 40 radiogenique a ete appliquee a la datation des roches par la methode K-Ar. L'argon est extrait de l'echantillon, purifie, active a saturation dans un flux de 2.10{sup 13} neutrons.cm{sup -2}.s{sup -1} et mesure en spectrometrie gamma. La sensibilite obtenue est telle qu'il est possible de mesurer des quantites d'argon correspondant a des ages de quelques milliers d'annees seulement. Cependant la correction de pollution de l'argon radiogenique par l'argon atmospherique n'ayant pu etre etablie avec precision, la limite d'age mesurable pratique est de l'ordre de 1 Ma. La methode a ete appliquee aux basaltes de la region du Mont-Dore. Les ages obtenus sont en assez bon accord avec les donnees geologiques, stratigraphiques et paleomagnetiques. (auteur)

  14. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit.

    Science.gov (United States)

    Ashoori, Maryam; Burns, Catherine M; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamwork and leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams.

  15. Using team cognitive work analysis to reveal healthcare team interactions in a birthing unit

    Science.gov (United States)

    Ashoori, Maryam; Burns, Catherine M.; d'Entremont, Barbara; Momtahan, Kathryn

    2014-01-01

    Cognitive work analysis (CWA) as an analytical approach for examining complex sociotechnical systems has shown success in modelling the work of single operators. The CWA approach incorporates social and team interactions, but a more explicit analysis of team aspects can reveal more information for systems design. In this paper, Team CWA is explored to understand teamwork within a birthing unit at a hospital. Team CWA models are derived from theories and models of teamworkand leverage the existing CWA approaches to analyse team interactions. Team CWA is explained and contrasted with prior approaches to CWA. Team CWA does not replace CWA, but supplements traditional CWA to more easily reveal team information. As a result, Team CWA may be a useful approach to enhance CWA in complex environments where effective teamwork is required. Practitioner Summary: This paper looks at ways of analysing cognitive work in healthcare teams. Team Cognitive Work Analysis, when used to supplement traditional Cognitive Work Analysis, revealed more team information than traditional Cognitive Work Analysis. Team Cognitive Work Analysis should be considered when studying teams PMID:24837514

  16. SCIENTIFIC METHODOLOGY FOR THE APPLIED SOCIAL SCIENCES: CRITICAL ANALYSES ABOUT RESEARCH METHODS, TYPOLOGIES AND CONTRIBUTIONS FROM MARX, WEBER AND DURKHEIM

    Directory of Open Access Journals (Sweden)

    Mauricio Corrêa da Silva

    2015-06-01

    Full Text Available This study aims to discuss the importance of the scientific method to conduct and advertise research in applied social sciences and research typologies, as well as to highlight contributions from Marx, Weber and Durkheim to the scientific methodology. To reach this objective, we conducted a review of the literature on the term research, the scientific method,the research techniques and the scientific methodologies. The results of the investigation revealed that it is fundamental that the academic investigator uses a scientific method to conduct and advertise his/her academic works in applied social sciences in comparison with the biochemical or computer sciences and in the indicated literature. Regarding the contributions to the scientific methodology, we have Marx, dialogued, the dialectical, striking analysis, explicative of social phenomenon, the need to understand the phenomena as historical and concrete totalities; Weber, the distinction between “facts” and “value judgments” to provide objectivity to the social sciences and Durkheim, the need to conceptualize very well its object of study, reject sensible data and imbue with the spirit of discovery and of being surprised with the results.

  17. Exploratory study on a statistical method to analyse time resolved data obtained during nanomaterial exposure measurements

    International Nuclear Information System (INIS)

    Clerc, F; Njiki-Menga, G-H; Witschger, O

    2013-01-01

    Most of the measurement strategies that are suggested at the international level to assess workplace exposure to nanomaterials rely on devices measuring, in real time, airborne particles concentrations (according different metrics). Since none of the instruments to measure aerosols can distinguish a particle of interest to the background aerosol, the statistical analysis of time resolved data requires special attention. So far, very few approaches have been used for statistical analysis in the literature. This ranges from simple qualitative analysis of graphs to the implementation of more complex statistical models. To date, there is still no consensus on a particular approach and the current period is always looking for an appropriate and robust method. In this context, this exploratory study investigates a statistical method to analyse time resolved data based on a Bayesian probabilistic approach. To investigate and illustrate the use of the this statistical method, particle number concentration data from a workplace study that investigated the potential for exposure via inhalation from cleanout operations by sandpapering of a reactor producing nanocomposite thin films have been used. In this workplace study, the background issue has been addressed through the near-field and far-field approaches and several size integrated and time resolved devices have been used. The analysis of the results presented here focuses only on data obtained with two handheld condensation particle counters. While one was measuring at the source of the released particles, the other one was measuring in parallel far-field. The Bayesian probabilistic approach allows a probabilistic modelling of data series, and the observed task is modelled in the form of probability distributions. The probability distributions issuing from time resolved data obtained at the source can be compared with the probability distributions issuing from the time resolved data obtained far-field, leading in a

  18. Sensitivity and uncertainty analyses for performance assessment modeling

    International Nuclear Information System (INIS)

    Doctor, P.G.

    1988-08-01

    Sensitivity and uncertainty analyses methods for computer models are being applied in performance assessment modeling in the geologic high level radioactive waste repository program. The models used in performance assessment tend to be complex physical/chemical models with large numbers of input variables. There are two basic approaches to sensitivity and uncertainty analyses: deterministic and statistical. The deterministic approach to sensitivity analysis involves numerical calculation or employs the adjoint form of a partial differential equation to compute partial derivatives; the uncertainty analysis is based on Taylor series expansions of the input variables propagated through the model to compute means and variances of the output variable. The statistical approach to sensitivity analysis involves a response surface approximation to the model with the sensitivity coefficients calculated from the response surface parameters; the uncertainty analysis is based on simulation. The methods each have strengths and weaknesses. 44 refs

  19. Sequencing of the Chlamydophila psittaci ompA Gene Reveals a New Genotype, E/B, and the Need for a Rapid Discriminatory Genotyping Method

    Science.gov (United States)

    Geens, Tom; Desplanques, Ann; Van Loock, Marnix; Bönner, Brigitte M.; Kaleta, Erhard F.; Magnino, Simone; Andersen, Arthur A.; Everett, Karin D. E.; Vanrompay, Daisy

    2005-01-01

    Twenty-one avian Chlamydophila psittaci isolates from different European countries were characterized using ompA restriction fragment length polymorphism, ompA sequencing, and major outer membrane protein serotyping. Results reveal the presence of a new genotype, E/B, in several European countries and stress the need for a discriminatory rapid genotyping method. PMID:15872282

  20. The postglacial recolonization of Northern Europe by Rana arvalis as revealed by microsatellite and mitochondrial DNA analyses.

    Science.gov (United States)

    Knopp, T; Merilä, J

    2009-02-01

    The postglacial history of the moor frog (Rana arvalis) in Northern Europe was investigated with the aid of eight variable microsatellite loci and a 661 bp sequence of the mitochondrial cytochrome b gene. A division between eastern and western mitochondrial lineages was discovered, supporting two recolonization routes to Fennoscandia since the last glacial maximum. This result was corroborated by the microsatellite data, which revealed a contact zone between the two lineages in Northern Sweden. These findings add to the increasing evidence that an intraspecific genetic biodiversity founded on the existence of eastern and western clades is a common element in Fennoscandian fauna and flora.

  1. Network methods to support user involvement in qualitative data analyses: an introduction to Participatory Theme Elicitation.

    Science.gov (United States)

    Best, Paul; Badham, Jennifer; Corepal, Rekesh; O'Neill, Roisin F; Tully, Mark A; Kee, Frank; Hunter, Ruth F

    2017-11-23

    While Patient and Public Involvement (PPI) is encouraged throughout the research process, engagement is typically limited to intervention design and post-analysis stages. There are few approaches to participatory data analyses within complex health interventions. Using qualitative data from a feasibility randomised controlled trial (RCT), this proof-of-concept study tests the value of a new approach to participatory data analysis called Participatory Theme Elicitation (PTE). Forty excerpts were given to eight members of a youth advisory PPI panel to sort into piles based on their perception of related thematic content. Using algorithms to detect communities in networks, excerpts were then assigned to a thematic cluster that combined the panel members' perspectives. Network analysis techniques were also used to identify key excerpts in each grouping that were then further explored qualitatively. While PTE analysis was, for the most part, consistent with the researcher-led analysis, young people also identified new emerging thematic content. PTE appears promising for encouraging user led identification of themes arising from qualitative data collected during complex interventions. Further work is required to validate and extend this method. ClinicalTrials.gov, ID: NCT02455986 . Retrospectively Registered on 21 May 2015.

  2. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses.

    Science.gov (United States)

    Montefusco, David J; Chen, Lujia; Matmati, Nabil; Lu, Songjian; Newcomb, Benjamin; Cooper, Gregory F; Hannun, Yusuf A; Lu, Xinghua

    2013-10-29

    Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule that participates in various cellular regulatory events and that has been implicated in disease. Deciphering ceramide signaling is challenging because multiple ceramide species exist, and many of them may have distinct functions. We applied systems biology and molecular approaches to perturb ceramide metabolism in the yeast Saccharomyces cerevisiae and inferred causal relationships between ceramide species and their potential targets by combining lipidomic, genomic, and transcriptomic analyses. We found that during heat stress, distinct metabolic mechanisms controlled the abundance of different groups of ceramide species and provided experimental support for the importance of the dihydroceramidase Ydc1 in mediating the decrease in dihydroceramides during heat stress. Additionally, distinct groups of ceramide species, with different N-acyl chains and hydroxylations, regulated different sets of functionally related genes, indicating that the structural complexity of these lipids produces functional diversity. The transcriptional modules that we identified provide a resource to begin to dissect the specific functions of ceramides.

  3. Precursor analyses - The use of deterministic and PSA based methods in the event investigation process at nuclear power plants

    International Nuclear Information System (INIS)

    2004-09-01

    The efficient feedback of operating experience (OE) is a valuable source of information for improving the safety and reliability of nuclear power plants (NPPs). It is therefore essential to collect information on abnormal events from both internal and external sources. Internal operating experience is analysed to obtain a complete understanding of an event and of its safety implications. Corrective or improvement measures may then be developed, prioritized and implemented in the plant if considered appropriate. Information from external events may also be analysed in order to learn lessons from others' experience and prevent similar occurrences at our own plant. The traditional ways of investigating operational events have been predominantly qualitative. In recent years, a PSA-based method called probabilistic precursor event analysis has been developed, used and applied on a significant scale in many places for a number of plants. The method enables a quantitative estimation of the safety significance of operational events to be incorporated. The purpose of this report is to outline a synergistic process that makes more effective use of operating experience event information by combining the insights and knowledge gained from both approaches, traditional deterministic event investigation and PSA-based event analysis. The PSA-based view on operational events and PSA-based event analysis can support the process of operational event analysis at the following stages of the operational event investigation: (1) Initial screening stage. (It introduces an element of quantitative analysis into the selection process. Quantitative analysis of the safety significance of nuclear plant events can be a very useful measure when it comes to selecting internal and external operating experience information for its relevance.) (2) In-depth analysis. (PSA based event evaluation provides a quantitative measure for judging the significance of operational events, contributors to

  4. Identification of magnetic particulates in road dust accumulated on roadside snow using magnetic, geochemical and micro-morphological analyses

    International Nuclear Information System (INIS)

    Bucko, Michal S.; Magiera, Tadeusz; Johanson, Bo; Petrovsky, Eduard; Pesonen, Lauri J.

    2011-01-01

    The aim of this study is to test the applicability of snow surveying in the collection and detailed characterization of vehicle-derived magnetic particles. Road dust extracted from snow, collected near a busy urban highway and a low traffic road in a rural environment (southern Finland), was studied using magnetic, geochemical and micro-morphological analyses. Significant differences in horizontal distribution of mass specific magnetic susceptibility (χ) were noticed for both roads. Multi-domain (MD) magnetite was identified as the primary magnetic mineral. Scanning electron microscope (SEM) analyses of road dust from both roads revealed: (1) angular-shaped particles (diameter ∼1-300 μm) mostly composed of Fe, Cr and Ni, derived from circulation of motor vehicles and (2) iron-rich spherules (d ∼ 2-70 μm). Tungsten-rich particles (d < 2 μm), derived from tyre stud abrasion were also identified. Additionally, a decreasing trend in χ and selected trace elements was observed with increasing distance from the road edge. - Highlights: → Snow surveying is an effective method in studies of vehicle-derived particles. → Multi-domain (MD) magnetite was identified as the primary magnetic mineral. → Particles mostly composed of Fe, Cr and Ni were identified in the roadside snow. → Snow located near the road is contaminated by heavy metals. - Snow surveying is an effective method in detailed studies of vehicle-derived magnetic particles.

  5. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

    Science.gov (United States)

    Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

    2015-01-01

    Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

  6. Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

    Directory of Open Access Journals (Sweden)

    Fagen Li

    Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

  7. Optimized methods to measure acetoacetate, 3-hydroxybutyrate, glycerol, alanine, pyruvate, lactate and glucose in human blood using a centrifugal analyser with a fluorimetric attachment.

    Science.gov (United States)

    Stappenbeck, R; Hodson, A W; Skillen, A W; Agius, L; Alberti, K G

    1990-01-01

    Optimized methods are described for the analysis of glucose, lactate, pyruvate, alanine, glycerol, D-3-hydroxybutyrate and acetoacetate in perchloric acid extracts of human blood using the Cobas Bio centrifugal analyser. Glucose and lactate are measured using the photometric mode and other metabolites using the fluorimetric mode. The intra-assay coefficients of variation ranged from 0.7 to 4.1%, except with very low levels of pyruvate and acetoacetate where the coefficients of variation were 7.1 and 12% respectively. All seven metabolites can be measured in a perchloric acid extract of 20 mul of blood. The methods have been optimized with regard to variation in the perchloric acid content of the samples. These variations arise from the method of sample preparation used to minimize changes occurring in metabolite concentration after venepuncture.

  8. Quantitative metagenomic analyses based on average genome size normalization

    DEFF Research Database (Denmark)

    Frank, Jeremy Alexander; Sørensen, Søren Johannes

    2011-01-01

    provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data...... marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how......). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis....

  9. Job Demands, Burnout, and Teamwork in Healthcare Professionals Working in a General Hospital that Was Analysed At Two Points in Time

    Science.gov (United States)

    Mijakoski, Dragan; Karadzhinska-Bislimovska, Jovanka; Stoleski, Sasho; Minov, Jordan; Atanasovska, Aneta; Bihorac, Elida

    2018-01-01

    AIM: The purpose of the paper was to assess job demands, burnout, and teamwork in healthcare professionals (HPs) working in a general hospital that was analysed at two points in time with a time lag of three years. METHODS: Time 1 respondents (N = 325) were HPs who participated during the first wave of data collection (2011). Time 2 respondents (N = 197) were HPs from the same hospital who responded at Time 2 (2014). Job demands, burnout, and teamwork were measured with Hospital Experience Scale, Maslach Burnout Inventory, and Hospital Survey on Patient Safety Culture, respectively. RESULTS: Significantly higher scores of emotional exhaustion (21.03 vs. 15.37, t = 5.1, p Teamwork levels were similar at both points in time (Time 1 = 3.84 vs. Time 2 = 3.84, t = 0.043, p = 0.97). CONCLUSION: Actual longitudinal study revealed significantly higher mean values of emotional exhaustion and depersonalization in 2014 that could be explained by significantly increased job demands between analysed points in time. PMID:29731948

  10. A method of mounting multiple otoliths for beam-based microchemical analyses

    Science.gov (United States)

    Donohoe, C.J.; Zimmerman, C.E.

    2010-01-01

    Beam-based analytical methods are widely used to measure the concentrations of elements and isotopes in otoliths. These methods usually require that otoliths be individually mounted and prepared to properly expose the desired growth region to the analytical beam. Most analytical instruments, such as LA-ICPMS and ion and electron microprobes, have sample holders that will accept only one to six slides or mounts at a time. We describe a method of mounting otoliths that allows for easy transfer of many otoliths to a single mount after they have been prepared. Such an approach increases the number of otoliths that can be analyzed in a single session by reducing the need open the sample chamber to exchange slides-a particularly time consuming step on instruments that operate under vacuum. For ion and electron microprobes, the method also greatly reduces the number of slides that must be coated with an electrical conductor prior to analysis. In this method, a narrow strip of cover glass is first glued at one end to a standard microscope slide. The otolith is then mounted in thermoplastic resin on the opposite, free end of the strip. The otolith can then be ground and flipped, if needed, by reheating the mounting medium. After otolith preparation is complete, the cover glass is cut with a scribe to free the otolith and up to 20 small otoliths can be arranged on a single petrographic slide. ?? 2010 The Author(s).

  11. DNA sequence analyses reveal co-occurrence of novel haplotypes of Fasciola gigantica with F. hepatica in South Africa and Zimbabwe.

    Science.gov (United States)

    Mucheka, Vimbai T; Lamb, Jennifer M; Pfukenyi, Davies M; Mukaratirwa, Samson

    2015-11-30

    The aim of this study was to identify and determine the genetic diversity of Fasciola species in cattle from Zimbabwe, the KwaZulu-Natal and Mpumalanga provinces of South Africa and selected wildlife hosts from Zimbabwe. This was based on analysis of DNA sequences of the nuclear ribosomal internal transcribed spacer (ITS1 and 2) and mitochondrial cytochrome oxidase 1 (CO1) regions. The sample of 120 flukes was collected from livers of 57 cattle at 4 abattoirs in Zimbabwe and 47 cattle at 6 abattoirs in South Africa; it also included three alcohol-preserved duiker, antelope and eland samples from Zimbabwe. Aligned sequences (ITS 506 base pairs and CO1 381 base pairs) were analyzed by neighbour-joining, maximum parsimony and Bayesian inference methods. Phylogenetic trees revealed the presence of Fasciola gigantica in cattle from Zimbabwe and F. gigantica and Fasciola hepatica in the samples from South Africa. F. hepatica was more prevalent (64%) in South Africa than F. gigantica. In Zimbabwe, F. gigantica was present in 99% of the samples; F. hepatica was found in only one cattle sample, an antelope (Hippotragus niger) and a duiker (Sylvicapra grimmia). This is the first molecular confirmation of the identity Fasciola species in Zimbabwe and South Africa. Knowledge on the identity and distribution of these liver flukes at molecular level will allow disease surveillance and control in the studied areas. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Performance and Vibration Analyses of Lift-Offset Helicopters

    Directory of Open Access Journals (Sweden)

    Jeong-In Go

    2017-01-01

    Full Text Available A validation study on the performance and vibration analyses of the XH-59A compound helicopter is conducted to establish techniques for the comprehensive analysis of lift-offset compound helicopters. This study considers the XH-59A lift-offset compound helicopter using a rigid coaxial rotor system as a verification model. CAMRAD II (Comprehensive Analytical Method of Rotorcraft Aerodynamics and Dynamics II, a comprehensive analysis code, is used as a tool for the performance, vibration, and loads analyses. A general free wake model, which is a more sophisticated wake model than other wake models, is used to obtain good results for the comprehensive analysis. Performance analyses of the XH-59A helicopter with and without auxiliary propulsion are conducted in various flight conditions. In addition, vibration analyses of the XH-59A compound helicopter configuration are conducted in the forward flight condition. The present comprehensive analysis results are in good agreement with the flight test and previous analyses. Therefore, techniques for the comprehensive analysis of lift-offset compound helicopters are appropriately established. Furthermore, the rotor lifts are calculated for the XH-59A lift-offset compound helicopter in the forward flight condition to investigate the airloads characteristics of the ABC™ (Advancing Blade Concept rotor.

  13. Medulloblastoma in China: clinicopathologic analyses of SHH, WNT, and non-SHH/WNT molecular subgroups reveal different therapeutic responses to adjuvant chemotherapy.

    Directory of Open Access Journals (Sweden)

    Zhen-Yu Zhang

    Full Text Available Medulloblastoma (MB is one of the most common primary central nervous system tumors in children. Data is lacking of a large cohort of medulloblastoma patients in China. Also, our knowledge on the sensitivity of different molecular subgroups of MB to adjuvant radiation therapy (RT or chemotherapy (CHT is still limited. The authors performed a retrospective study of 173 medulloblastoma patients treated at two institutions from 2002 to 2011. Formalin-fixed paraffin embedded (FFPE tissues were available in all the cases and sections were stained to classify histological and molecular subgroups. Univariate and multivariate analyses were used to investigate prognostic factors. Of 173 patients, there were 118 children and 55 adults, 112 males and 61 females. Estimated 5-year overall survival (OS rates for all patients, children and adults were 52%, 48% and 63%, respectively. After multivariate analysis, postoperative primary radiation therapy (RT and chemotherapy (CHT were revealed as favorable prognostic factors influencing OS and EFS. Postoperative primary chemotherapy (CHT was found significantly improving the survival of children (p<0.001 while it was not a significant prognostic factor for adult patients. Moreover, patients in WNT subtype had better OS (p = 0.028 than others (SHH and Non-SHH/WNT subtypes given postoperative adjuvant therapies. Postoperative primary RT was found to be a strong prognostic factor influencing the survival in all histological and molecular subgroups (p<0.001. Postoperative primary CHT was found significantly to influence the survival of classic medulloblastoma (CMB (OS p<0.001, EFS p<0.001, SHH subgroup (OS p = 0.020, EFS p = 0.049 and WNT subgroup (OS p = 0.003, EFS p = 0.016 but not in desmoplastic/nodular medulloblastoma (DMB (OS p = 0.361, EFS p = 0.834 and Non-SHH/WNT subgroup (OS p = 0.127, EFS p = 0.055. Our study showed postoperative primary CHT significantly influence the

  14. Network class superposition analyses.

    Directory of Open Access Journals (Sweden)

    Carl A B Pearson

    Full Text Available Networks are often used to understand a whole system by modeling the interactions among its pieces. Examples include biomolecules in a cell interacting to provide some primary function, or species in an environment forming a stable community. However, these interactions are often unknown; instead, the pieces' dynamic states are known, and network structure must be inferred. Because observed function may be explained by many different networks (e.g., ≈ 10(30 for the yeast cell cycle process, considering dynamics beyond this primary function means picking a single network or suitable sample: measuring over all networks exhibiting the primary function is computationally infeasible. We circumvent that obstacle by calculating the network class ensemble. We represent the ensemble by a stochastic matrix T, which is a transition-by-transition superposition of the system dynamics for each member of the class. We present concrete results for T derived from boolean time series dynamics on networks obeying the Strong Inhibition rule, by applying T to several traditional questions about network dynamics. We show that the distribution of the number of point attractors can be accurately estimated with T. We show how to generate Derrida plots based on T. We show that T-based Shannon entropy outperforms other methods at selecting experiments to further narrow the network structure. We also outline an experimental test of predictions based on T. We motivate all of these results in terms of a popular molecular biology boolean network model for the yeast cell cycle, but the methods and analyses we introduce are general. We conclude with open questions for T, for example, application to other models, computational considerations when scaling up to larger systems, and other potential analyses.

  15. Comparison of transfer entropy methods for financial time series

    Science.gov (United States)

    He, Jiayi; Shang, Pengjian

    2017-09-01

    There is a certain relationship between the global financial markets, which creates an interactive network of global finance. Transfer entropy, a measurement for information transfer, offered a good way to analyse the relationship. In this paper, we analysed the relationship between 9 stock indices from the U.S., Europe and China (from 1995 to 2015) by using transfer entropy (TE), effective transfer entropy (ETE), Rényi transfer entropy (RTE) and effective Rényi transfer entropy (ERTE). We compared the four methods in the sense of the effectiveness for identification of the relationship between stock markets. In this paper, two kinds of information flows are given. One reveals that the U.S. took the leading position when in terms of lagged-current cases, but when it comes to the same date, China is the most influential. And ERTE could provide superior results.

  16. Heavy water standards. Qualitative analyses, sample treating, stocking and manipulation

    International Nuclear Information System (INIS)

    Pavelescu, M.; Steflea, D.; Mihancea, I.; Varlam, M.; Irimescu, R.

    1995-01-01

    This paper presents methods and procedures for measuring heavy water concentration, and also sampling, stocking and handling of samples to be analysed. The main concentration analysis methods are: mass spectrometry, for concentrations less then 1%, densitometry, for concentrations within the range 1% - 99% and infrared spectrometry for concentrations above 99%. Procedures of sampling, processing and purification appropriate to these measuring methods were established. 1 Tab

  17. Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network

    Directory of Open Access Journals (Sweden)

    Chamovitz Daniel A

    2009-09-01

    Full Text Available Abstract Background Analyses of gene expression data from microarray experiments has become a central tool for identifying co-regulated, functional gene modules. A crucial aspect of such analysis is the integration of data from different experiments and different laboratories. How to weigh the contribution of different experiments is an important point influencing the final outcomes. We have developed a novel method for this integration, and applied it to genome-wide data from multiple Arabidopsis microarray experiments performed under a variety of experimental conditions. The goal of this study is to identify functional globally co-regulated gene modules in the Arabidopsis genome. Results Following the analysis of 21,000 Arabidopsis genes in 43 datasets and about 2 × 108 gene pairs, we identified a globally co-expressed gene network. We found clusters of globally co-expressed Arabidopsis genes that are enriched for known Gene Ontology annotations. Two types of modules were identified in the regulatory network that differed in their sensitivity to the node-scoring parameter; we further showed these two pertain to general and specialized modules. Some of these modules were further investigated using the Genevestigator compendium of microarray experiments. Analyses of smaller subsets of data lead to the identification of condition-specific modules. Conclusion Our method for identification of gene clusters allows the integration of diverse microarray experiments from many sources. The analysis reveals that part of the Arabidopsis transcriptome is globally co-expressed, and can be further divided into known as well as novel functional gene modules. Our methodology is general enough to apply to any set of microarray experiments, using any scoring function.

  18. Polyploidy in the Olive Complex (Olea europaea): Evidence from Flow Cytometry and Nuclear Microsatellite Analyses

    Science.gov (United States)

    Besnard, G.; Garcia-Verdugo, C.; Rubio De Casas, R.; Treier, U. A.; Galland, N.; Vargas, P.

    2008-01-01

    Background Phylogenetic and phylogeographic investigations have been previously performed to study the evolution of the olive tree complex (Olea europaea). A particularly high genomic diversity has been found in north-west Africa. However, to date no exhaustive study has been addressed to infer putative polyploidization events and their evolutionary significance in the diversification of the olive tree and its relatives. Methods Representatives of the six olive subspecies were investigated using (a) flow cytometry to estimate genome content, and (b) six highly variable nuclear microsatellites to assess the presence of multiple alleles at co-dominant loci. In addition, nine individuals from a controlled cross between two individuals of O. europaea subsp. maroccana were characterized with microsatellites to check for chromosome inheritance. Key Results Based on flow cytometry and genetic analyses, strong evidence for polyploidy was obtained in subspp. cerasiformis (tetraploid) and maroccana (hexaploid), whereas the other subspecies appeared to be diploids. Agreement between flow cytometry and genetic analyses gives an alternative approach to chromosome counting to determine ploidy level of trees. Lastly, abnormalities in chromosomes inheritance leading to aneuploid formation were revealed using microsatellite analyses in the offspring from the controlled cross in subsp. maroccana. Conclusions This study constitutes the first report for multiple polyploidy in olive tree relatives. Formation of tetraploids and hexaploids may have played a major role in the diversification of the olive complex in north-west Africa. The fact that polyploidy is found in narrow endemic subspecies from Madeira (subsp. cerasiformis) and the Agadir Mountains (subsp. maroccana) suggests that polyploidization has been favoured to overcome inbreeding depression. Lastly, based on previous phylogenetic analyses, we hypothesize that subsp. cerasiformis resulted from hybridization between ancestors

  19. The paradox of HBV evolution as revealed from a 16th century mummy.

    Directory of Open Access Journals (Sweden)

    Zoe Patterson Ross

    2018-01-01

    Full Text Available Hepatitis B virus (HBV is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox, showed no DNA reads for VARV yet did for hepatitis B virus (HBV. Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles. We attempted to enrich and sequence for both VARV and HBV DNA. Although we did not recover any reads identified as VARV, we were successful in reconstructing an HBV genome at 163.8X coverage. Strikingly, both the HBV sequence and that of the associated host mitochondrial DNA displayed a nearly identical cytosine deamination pattern near the termini of DNA fragments, characteristic of an ancient origin. In contrast, phylogenetic analyses revealed a close relationship between the putative ancient virus and contemporary HBV strains (of genotype D, at first suggesting contamination. In addressing this paradox we demonstrate that HBV evolution is characterized by a marked lack of temporal structure. This confounds attempts to use molecular clock-based methods to date the origin of this virus over the time-frame sampled so far, and means that phylogenetic measures alone cannot yet be used to determine HBV sequence authenticity. If genuine, this phylogenetic pattern indicates that the genotypes of HBV diversified long before the 16th century, and enables comparison of potential pathogenic similarities between modern and ancient HBV. These results have important implications for our understanding of the emergence and evolution of this common viral pathogen.

  20. Growth of Bi doped cadmium zinc telluride single crystals by Bridgman oscillation method and its structural, optical, and electrical analyses

    International Nuclear Information System (INIS)

    Carcelen, V.; Rodriguez-Fernandez, J.; Dieguez, E.; Hidalgo, P.

    2010-01-01

    The II-VI compound semiconductor cadmium zinc telluride (CZT) is very useful for room temperature radiation detection applications. In the present research, we have successfully grown Bi doped CZT single crystals with two different zinc concentrations (8 and 14 at. %) by the Bridgman oscillation method, in which one experiment has been carried out with a platinum (Pt) tube as the ampoule support. Pt also acts as a cold finger and reduces the growth velocity and enhances crystalline perfection. The grown single crystals have been studied with different analysis methods. The stoichiometry was confirmed by energy dispersive by x-ray and inductively coupled plasma mass spectroscopy analyses and it was found there is no incorporation of impurities in the grown crystal. The presence of Cd and Te vacancies was determined by cathodoluminescence studies. Electrical properties were assessed by I-V analysis and indicated higher resistive value (8.53x10 8 Ω cm) for the crystal grown with higher zinc concentration (with Cd excess) compare to the other (3.71x10 5 Ω cm).

  1. Comparison of elastic and inelastic analyses

    International Nuclear Information System (INIS)

    Ammerman, D.J.; Heinstein, M.W.; Wellman, G.W.

    1992-01-01

    The use of inelastic analysis methods instead of the traditional elastic analysis methods in the design of radioactive material (RAM) transport packagings leads to a better understanding of the response of the package to mechanical loadings. Thus, better assessment of the containment, thermal protection, and shielding integrity of the package after a structure accident event can be made. A more accurate prediction of the package response can lead to enhanced safety and also allow for a more efficient use of materials, possibly leading to a package with higher capacity or lower weight. This paper discusses the advantages and disadvantages of using inelastic analysis in the design of RAM shipping packages. The use of inelastic analysis presents several problems to the package designer. When using inelastic analysis the entire nonlinear response of the material must be known, including the effects of temperature changes and strain rate. Another problem is that there currently is not an acceptance criteria for this type of analysis that is approved by regulatory agencies. Inelastic analysis acceptance criteria based on failure stress, failure strain , or plastic energy density could be developed. For both elastic and inelastic analyses it is also important to include other sources of stress in the analyses, such as fabrication stresses, thermal stresses, stresses from bolt preloading, and contact stresses at material interfaces. Offsetting these added difficulties is the improved knowledge of the package behavior. This allows for incorporation of a more uniform margin of safety, which can result in weight savings and a higher level of confidence in the post-accident configuration of the package. In this paper, comparisons between elastic and inelastic analyses are made for a simple ring structure and for a package to transport a large quantity of RAM by rail (rail cask) with lead gamma shielding to illustrate the differences in the two analysis techniques

  2. Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida.

    Science.gov (United States)

    Wu, Fengnian; Kumagai, Luci; Cen, Yijing; Chen, Jianchi; Wallis, Christopher M; Polek, MaryLou; Jiang, Hongyan; Zheng, Zheng; Liang, Guangwen; Deng, Xiaoling

    2017-08-31

    Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) transmits "Candidatus Liberibacter asiaticus" (CLas), an unculturable alpha-proteobacterium associated with citrus Huanglongbing (HLB). CLas has recently been found in California. Understanding ACP population diversity is necessary for HLB regulatory practices aimed at reducing CLas spread. In this study, two circular ACP mitogenome sequences from California (mt-CApsy, ~15,027 bp) and Florida (mt-FLpsy, ~15,012 bp), USA, were acquired. Each mitogenome contained 13 protein coding genes, 2 ribosomal RNA and 22 transfer RNA genes, and a control region varying in sizes. The Californian mt-CApsy was identical to the Floridian mt-FLpsy, but different from the mitogenome (mt-GDpsy) of Guangdong, China, in 50 single nucleotide polymorphisms (SNPs). Further analyses were performed on sequences in cox1 and trnAsn regions with 100 ACPs, SNPs in nad1-nad4-nad5 locus through PCR with 252 ACP samples. All results showed the presence of a Chinese ACP cluster (CAC) and an American ACP cluster (AAC). We proposed that ACP in California was likely not introduced from China based on our current ACP collection but somewhere in America. However, more studies with ACP samples from around the world are needed. ACP mitogenome sequence analyses will facilitate ACP population research.

  3. A method for calorimetric analysis in variable conditions heating; Methode d'analyse calorimetrique en regime variable

    Energy Technology Data Exchange (ETDEWEB)

    Berthier, G [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1965-07-01

    By the analysis of the thermal transition conditions given by the quenching of a sample in a furnace maintained at a high temperature, it is possible to study the thermal diffusivity of some materials and those of solid state structure transformation on a qualitative as well as a quantitative standpoint. For instance the transformation energy of {alpha}-quartz into {beta}-quartz and the Wigner energy stored within neutron-irradiated beryllium oxide have been measured. (author) [French] L'analyse du regime thermique transitoire, obtenu par la trempe d'un echantillon dans l'enceinte d'un four maintenu a tres haute temperature, peut permettre l'etude de la diffusivite thermique de certains materiaux et celle des transformations structurales en phase solide, tant du point de vue qualitatif que du point de vue quantitatif (mesure de l'energie de transformation du quartz {alpha} en quartz {beta} et determination de l'energie Wigner emmagasinee par l'oxyde de beryllium irradie aux neutrons). (auteur)

  4. Combined Analyses of Chloroplast DNA Haplotypes and Microsatellite Markers Reveal New Insights Into the Origin and Dissemination Route of Cultivated Pears Native to East Asia

    Directory of Open Access Journals (Sweden)

    Xiaoyan Yue

    2018-05-01

    Full Text Available Asian pear plays an important role in the world pear industry, accounting for over 70% of world total production volume. Commercial Asian pear production relies on four major pear cultivar groups, Japanese pear (JP, Chinese white pear (CWP, Chinese sand pear (CSP, and Ussurian pear (UP, but their origins remain controversial. We estimated the genetic diversity levels and structures in a large sample of existing local cultivars to investigate the origins of Asian pears using twenty-five genome-covering nuclear microsatellite (simple sequence repeats, nSSR markers and two non-coding chloroplast DNA (cpDNA regions (trnL-trnF and accD-psaI. High levels of genetic diversity were detected for both nSSRs (HE = 0.744 and cpDNAs (Hd = 0.792. The major variation was found within geographic populations of cultivated pear groups, demonstrating a close relationship among cultivar groups. CSPs showed a greater genetic diversity than CWPs and JPs, and lowest levels of genetic differentiation were detected among them. Phylogeographical analyses indicated that the CSP, CWP, and JP were derived from the same progenitor of Pyrus pyrifolia in China. A dissemination route of cultivated P. pyrifolia estimated by approximate Bayesian computation suggested that cultivated P. pyrifolia from the Middle Yangtze River Valley area contributed the major genetic resources to the cultivars, excluding those of southwestern China. Three major genetic groups of cultivated Pyrus pyrifolia were revealed using nSSRs and a Bayesian statistical inference: (a JPs; (b cultivars from South-Central China northward to northeastern China, covering the main pear production area in China; (c cultivars from southwestern China to southeastern China, including Yunnan, Guizhou, Guangdong, Guangxi, and Fujian Provinces. This reflected the synergistic effects of ecogeographical factors and human selection during cultivar spread and improvement. The analyses indicated that UP cultivars might be

  5. Phase analysis in duplex stainless steel: comparison of EBSD and quantitative metallography methods

    International Nuclear Information System (INIS)

    Michalska, J; Chmiela, B

    2014-01-01

    The purpose of the research was to work out the qualitative and quantitative analysis of phases in DSS in as-received state and after thermal aging. For quantitative purposes, SEM observations, EDS analyses and electron backscattered diffraction (EBSD) methods were employed. Qualitative analysis of phases was performed by two methods: EBSD and classical quantitative metallography. A juxtaposition of different etchants for the revealing of microstructure and brief review of sample preparation methods for EBSD studies were presented. Different ways of sample preparation were tested and based on these results a detailed methodology of DSS phase analysis was developed including: surface finishing, selective etching methods and image acquisition. The advantages and disadvantages of applied methods were pointed out and compared the accuracy of the analysis phase performed by both methods

  6. Graphite analyser upgrade for the IRIS spectrometer at ISIS

    International Nuclear Information System (INIS)

    Campbell, S.I.; Telling, M.T.F.; Carlile, C.J.

    1999-01-01

    Complete text of publication follows. The pyrolytic graphite (PG) analyser bank on the IRIS high resolution inelastic spectrometer [1] at ISIS is to be upgraded. At present the analyser consists of 1350 graphite pieces (6 rows by 225 columns) cooled to 25K [2]. The new analyser array, however, will provide a three-fold increase in area and employ 4212 crystal pieces (18 rows by 234 columns). In addition, the graphite crystals will be cooled close to liquid helium temperature to further reduce thermal diffuse scattering (TDS) and improve the sensitivity of the spectrometer [2]. For an instrument such as IRIS, with its analyser in near back-scattering geometry, optical aberration and variation in the time-of-flight of the analysed neutrons is introduced as one moves out from the horizontal scattering plane. To minimise such effects, the profile of the analyser array has been redesigned. The concept behind the design of the new analyser bank and factors that effect the overall resolution of the instrument are discussed. Results of Monte Carlo simulations of the expected resolution and intensity of the complete instrument are presented and compared to the current instrument performance. (author) [1] C.J. Carlile et al, Physica B 182 (1992) 431-440.; [2] C.J. Carlile et al, Nuclear Instruments and Methods In Physics Research A 338 (1994) 78-82

  7. Physical characterization of biomass-based pyrolysis liquids. Application of standard fuel oil analyses

    Energy Technology Data Exchange (ETDEWEB)

    Oasmaa, A; Leppaemaeki, E; Koponen, P; Levander, J; Tapola, E [VTT Energy, Espoo (Finland). Energy Production Technologies

    1998-12-31

    The main purpose of the study was to test the applicability of standard fuel oil methods developed for petroleum-based fuels to pyrolysis liquids. In addition, research on sampling, homogeneity, stability, miscibility and corrosivity was carried out. The standard methods have been tested for several different pyrolysis liquids. Recommendations on sampling, sample size and small modifications of standard methods are presented. In general, most of the methods can be used as such but the accuracy of the analysis can be improved by minor modifications. Fuel oil analyses not suitable for pyrolysis liquids have been identified. Homogeneity of the liquids is the most critical factor in accurate analysis. The presence of air bubbles may disturb in several analyses. Sample preheating and prefiltration should be avoided when possible. The former may cause changes in the composition and structure of the pyrolysis liquid. The latter may remove part of organic material with particles. The size of the sample should be determined on the basis of the homogeneity and the water content of the liquid. The basic analyses of the Technical Research Centre of Finland (VTT) include water, pH, solids, ash, Conradson carbon residue, heating value, CHN, density, viscosity, pourpoint, flash point, and stability. Additional analyses are carried out when needed. (orig.) 53 refs.

  8. In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence.

    Science.gov (United States)

    Laing, Chad R; Buchanan, Cody; Taboada, Eduardo N; Zhang, Yongxiang; Karmali, Mohamed A; Thomas, James E; Gannon, Victor Pj

    2009-06-29

    Many approaches have been used to study the evolution, population structure and genetic diversity of Escherichia coli O157:H7; however, observations made with different genotyping systems are not easily relatable to each other. Three genetic lineages of E. coli O157:H7 designated I, II and I/II have been identified using octamer-based genome scanning and microarray comparative genomic hybridization (mCGH). Each lineage contains significant phenotypic differences, with lineage I strains being the most commonly associated with human infections. Similarly, a clade of hyper-virulent O157:H7 strains implicated in the 2006 spinach and lettuce outbreaks has been defined using single-nucleotide polymorphism (SNP) typing. In this study an in silico comparison of six different genotyping approaches was performed on 19 E. coli genome sequences from 17 O157:H7 strains and single O145:NM and K12 MG1655 strains to provide an overall picture of diversity of the E. coli O157:H7 population, and to compare genotyping methods for O157:H7 strains. In silico determination of lineage, Shiga-toxin bacteriophage integration site, comparative genomic fingerprint, mCGH profile, novel region distribution profile, SNP type and multi-locus variable number tandem repeat analysis type was performed and a supernetwork based on the combination of these methods was produced. This supernetwork showed three distinct clusters of strains that were O157:H7 lineage-specific, with the SNP-based hyper-virulent clade 8 synonymous with O157:H7 lineage I/II. Lineage I/II/clade 8 strains clustered closest on the supernetwork to E. coli K12 and E. coli O55:H7, O145:NM and sorbitol-fermenting O157 strains. The results of this study highlight the similarities in relationships derived from multi-locus genome sampling methods and suggest a "common genotyping language" may be devised for population genetics and epidemiological studies. Future genotyping methods should provide data that can be stored centrally and

  9. In silico genomic analyses reveal three distinct lineages of Escherichia coli O157:H7, one of which is associated with hyper-virulence

    Directory of Open Access Journals (Sweden)

    Karmali Mohamed A

    2009-06-01

    methods should provide data that can be stored centrally and accessed locally in an easily transferable, informative and extensible format based on comparative genomic analyses.

  10. Mitochondrial DNA analyses and ecological niche modeling reveal post-LGM expansion of the Assam macaque (Macaca assamensis) in the foothills of Nepal Himalaya.

    Science.gov (United States)

    Khanal, Laxman; Chalise, Mukesh K; He, Kai; Acharya, Bipin K; Kawamoto, Yoshi; Jiang, Xuelong

    2018-03-01

    Genetic diversity of a species is influenced by multiple factors, including the Quaternary glacial-interglacial cycles and geophysical barriers. Such factors are not yet well documented for fauna from the southern border of the Himalayan region. This study used mitochondrial DNA (mtDNA) sequences and ecological niche modeling (ENM) to explore how the late Pleistocene climatic fluctuations and complex geography of the Himalayan region have shaped genetic diversity, population genetic structure, and demographic history of the Nepalese population of Assam macaques (Macaca assamensis) in the Himalayan foothills. A total of 277 fecal samples were collected from 39 wild troops over almost the entire distribution of the species in Nepal. The mtDNA fragment encompassing the complete control region (1121 bp) was recovered from 208 samples, thus defining 54 haplotypes. Results showed low nucleotide diversity (0.0075 ± SD 0.0001) but high haplotype diversity (0.965 ± SD 0.004). The mtDNA sequences revealed a shallow population genetic structure with a moderate but statistically significant effect of isolation by distance. Demographic history analyses using mtDNA sequences suggested a post-pleistocene population expansion. Paleodistribution reconstruction projected that the potential habitat of the Assam macaque was confined to the lower elevations of central Nepal during the Last Glacial Maximum. With the onset of the Holocene climatic optimum, the glacial refugia population experienced eastward range expansion to higher elevations. We conclude that the low genetic diversity and shallow population genetic structure of the Assam macaque population in the Nepal Himalaya region are the consequence of recent demographic and spatial expansion. © 2018 Wiley Periodicals, Inc.

  11. Efficacy of pharmacotherapy and psychotherapy for adult psychiatric disorders: a systematic overview of meta-analyses.

    Science.gov (United States)

    Huhn, Maximilian; Tardy, Magdolna; Spineli, Loukia Maria; Kissling, Werner; Förstl, Hans; Pitschel-Walz, Gabriele; Leucht, Claudia; Samara, Myrto; Dold, Markus; Davis, John M; Leucht, Stefan

    2014-06-01

    There is debate about the effectiveness of psychiatric treatments and whether pharmacotherapy or psychotherapy should be primarily used. To perform a systematic overview on the efficacy of pharmacotherapies and psychotherapies for major psychiatric disorders and to compare the quality of pharmacotherapy and psychotherapy trials. We searched MEDLINE, EMBASE, PsycINFO, and the Cochrane Library (April 2012, with no time or language limit) for systematic reviews on pharmacotherapy or psychotherapy vs placebo, pharmacotherapy vs psychotherapy, and their combination vs either modality alone. Two reviewers independently selected the meta-analyses and extracted efficacy effect sizes. We assessed the quality of the individual trials included in the pharmacotherapy and psychotherapy meta-analyses with the Cochrane risk of bias tool. The search yielded 45,233 results. We included 61 meta-analyses on 21 psychiatric disorders, which contained 852 individual trials and 137,126 participants. The mean effect size of the meta-analyses was medium (mean, 0.50; 95% CI, 0.41-0.59). Effect sizes of psychotherapies vs placebo tended to be higher than those of medication, but direct comparisons, albeit usually based on few trials, did not reveal consistent differences. Individual pharmacotherapy trials were more likely to have large sample sizes, blinding, control groups, and intention-to-treat analyses. In contrast, psychotherapy trials had lower dropout rates and provided follow-up data. In psychotherapy studies, wait-list designs showed larger effects than did comparisons with placebo. Many pharmacotherapies and psychotherapies are effective, but there is a lot of room for improvement. Because of the multiple differences in the methods used in pharmacotherapy and psychotherapy trials, indirect comparisons of their effect sizes compared with placebo or no treatment are problematic. Well-designed direct comparisons, which are scarce, need public funding. Because patients often benefit

  12. The reliability of radiochemical and chemical trace analyses in environmental materials

    International Nuclear Information System (INIS)

    Heinonen, Jorma.

    1977-12-01

    After theoretically exploring the factors which influence the quality of analytical data as well as the means by which a sufficient quality can be assured and controlled, schemes of different kinds have been developed and applied in order to demonstrate the analytical quality assurance and control in practice. Methods have been developed for the determination of cesium, bromine and arsenic by neutron activation analysis at the natural ''background'' concentration level in environmental materials. The calibration of methods is described. The methods were also applied on practical routine analysis, the results of which are briefly reviewed. In the case of Ce the precision of a comprehensive calibration was found to vary between 5.2-9.2% as a relative standard deviation, which agrees well with the calculated statistical random error 5.7-8.7%. In the case of Br the method showed a reasonable precision, about 11% on the average, and accuracy. In employing the method to analyze died samples containing Br from 3 to 12 ppm a continuous control of precison was performed. The analysis of As demonstrates the many problems and difficulties associated with environmental analysis. In developing the final method four former intercomparison materials of IAEA were utilized in the calibration. The tests performed revealed a systematic error. In this case a scheme was developed for the continuous control of both precision and accuracy. The results of radiochemical analyses in environmental materials show a reliability somewhat better than that occuring in the determination of stable trace elements. According to a rough classification, 15% of the results of radiochemical analysis show excellent reliability, whereas 60% show a reliability adequate for certain purposes. The remaining 15% are excellent, 60% adequate for some purposes and 30% good-for-nothing. The reasons for often insufficient reliability of results are both organizational and technical. With reasonable effort and

  13. Temporal analyses of Salmonellae in a headwater spring ecosystem reveals the effects of precipitation and runoff events.

    Science.gov (United States)

    Gaertner, James P; Garres, Tiffany; Becker, Jesse C; Jimenez, Maria L; Forstner, Michael R J; Hahn, Dittmar

    2009-03-01

    Sediments and water from the spring and slough arm of Spring Lake, the pristine headwaters of the San Marcos River, Texas, were analyzed for Salmonellae by culture and molecular techniques before and after three major precipitation events, each with intermediate dry periods. Polymerase chain reaction (PCR)-assisted analyses of enrichment cultures detected Salmonellae in samples after all three precipitation events, but failed to detect them immediately prior to the rainfall events. Detection among individual locations differed with respect to the precipitation event analyzed, and strains isolated were highly variable with respect to serovars. These results demonstrate that rainwater associated effects, most likely surface runoff, provide an avenue for short-term pollution of aquatic systems with Salmonellae that do not, however, appear to establish for the long-term in water nor sediments.

  14. Optimized methods to measure acetoacetate, 3-hydroxybutyrate, glycerol, alanine, pyruvate, lactate and glucose in human blood using a centrifugal analyser with a fluorimetric attachment

    OpenAIRE

    Stappenbeck, R.; Hodson, A. W.; Skillen, A. W.; Agius, L.; Alberti, K. G. M. M.

    1990-01-01

    Optimized methods are described for the analysis of glucose, lactate, pyruvate, alanine, glycerol, D-3-hydroxybutyrate and acetoacetate in perchloric acid extracts of human blood using the Cobas Bio centrifugal analyser. Glucose and lactate are measured using the photometric mode and other metabolites using the fluorimetric mode. The intra-assay coefficients of variation ranged from 0.7 to 4.1%, except with very low levels of pyruvate and acetoacetate where the coefficients of variation were ...

  15. Applications of neural network to numerical analyses

    International Nuclear Information System (INIS)

    Takeda, Tatsuoki; Fukuhara, Makoto; Ma, Xiao-Feng; Liaqat, Ali

    1999-01-01

    Applications of a multi-layer neural network to numerical analyses are described. We are mainly concerned with the computed tomography and the solution of differential equations. In both cases as the objective functions for the training process of the neural network we employed residuals of the integral equation or the differential equations. This is different from the conventional neural network training where sum of the squared errors of the output values is adopted as the objective function. For model problems both the methods gave satisfactory results and the methods are considered promising for some kind of problems. (author)

  16. Integrative analyses of leprosy susceptibility genes indicate a common autoimmune profile.

    Science.gov (United States)

    Zhang, Deng-Feng; Wang, Dong; Li, Yu-Ye; Yao, Yong-Gang

    2016-04-01

    Leprosy is an ancient chronic infection in the skin and peripheral nerves caused by Mycobacterium leprae. The development of leprosy depends on genetic background and the immune status of the host. However, there is no systematic view focusing on the biological pathways, interaction networks and overall expression pattern of leprosy-related immune and genetic factors. To identify the hub genes in the center of leprosy genetic network and to provide an insight into immune and genetic factors contributing to leprosy. We retrieved all reported leprosy-related genes and performed integrative analyses covering gene expression profiling, pathway analysis, protein-protein interaction network, and evolutionary analyses. A list of 123 differentially expressed leprosy related genes, which were enriched in activation and regulation of immune response, was obtained in our analyses. Cross-disorder analysis showed that the list of leprosy susceptibility genes was largely shared by typical autoimmune diseases such as lupus erythematosus and arthritis, suggesting that similar pathways might be affected in leprosy and autoimmune diseases. Protein-protein interaction (PPI) and positive selection analyses revealed a co-evolution network of leprosy risk genes. Our analyses showed that leprosy associated genes constituted a co-evolution network and might undergo positive selection driven by M. leprae. We suggested that leprosy may be a kind of autoimmune disease and the development of leprosy is a matter of defect or over-activation of body immunity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  17. Comparison of genome-wide association methods in analyses of admixed populations with complex familial relationships.

    Directory of Open Access Journals (Sweden)

    Naveen K Kadri

    Full Text Available Population structure is known to cause false-positive detection in association studies. We compared the power, precision, and type-I error rates of various association models in analyses of a simulated dataset with structure at the population (admixture from two populations; P and family (K levels. We also compared type-I error rates among models in analyses of publicly available human and dog datasets. The models corrected for none, one, or both structure levels. Correction for K was performed with linear mixed models incorporating familial relationships estimated from pedigrees or genetic markers. Linear models that ignored K were also tested. Correction for P was performed using principal component or structured association analysis. In analyses of simulated and real data, linear mixed models that corrected for K were able to control for type-I error, regardless of whether they also corrected for P. In contrast, correction for P alone in linear models was insufficient. The power and precision of linear mixed models with and without correction for P were similar. Furthermore, power, precision, and type-I error rate were comparable in linear mixed models incorporating pedigree and genomic relationships. In summary, in association studies using samples with both P and K, ancestries estimated using principal components or structured assignment were not sufficient to correct type-I errors. In such cases type-I errors may be controlled by use of linear mixed models with relationships derived from either pedigree or from genetic markers.

  18. Modelling and analysing oriented fibrous structures

    International Nuclear Information System (INIS)

    Rantala, M; Lassas, M; Siltanen, S; Sampo, J; Takalo, J; Timonen, J

    2014-01-01

    A mathematical model for fibrous structures using a direction dependent scaling law is presented. The orientation of fibrous nets (e.g. paper) is analysed with a method based on the curvelet transform. The curvelet-based orientation analysis has been tested successfully on real data from paper samples: the major directions of fibrefibre orientation can apparently be recovered. Similar results are achieved in tests on data simulated by the new model, allowing a comparison with ground truth

  19. Seismic risk analyses in the German Risk Study, phase B

    International Nuclear Information System (INIS)

    Hosser, D.; Liemersdorf, H.

    1991-01-01

    The paper discusses some aspects of the seismic risk part of the German Risk Study for Nuclear Power Plants, Phase B. First simplified analyses in Phase A of the study allowed only a rough classification of structures and systems of the PWR reference plant according to their seismic risk contribution. These studies were extended in Phase B using improved models for the dynamic analyses of buildings, structures and components as well as for the probabilistic analyses of seismic loading, failure probabilities and event trees. The methodology of deriving probabilistic seismic load descriptions is explained and compared with the methods in Phase A of the study and in other studies. Some details of the linear and nonlinear dynamic analyses of structures are reported in order to demonstrate the influence of different assumptions for material behaviour and failure criteria. The probabilistic structural and event tree analyses are discussed with respect to distribution assumptions, acceptable simplifications and model uncertainties. Some results for the PWR reference plant are given. (orig.)

  20. Comparison of Genome-Wide Association Methods in Analyses of Admixed Populations with Complex Familial Relationships

    DEFF Research Database (Denmark)

    Kadri, Naveen; Guldbrandtsen, Bernt; Sørensen, Peter

    2014-01-01

    Population structure is known to cause false-positive detection in association studies. We compared the power, precision, and type-I error rates of various association models in analyses of a simulated dataset with structure at the population (admixture from two populations; P) and family (K......) levels. We also compared type-I error rates among models in analyses of publicly available human and dog datasets. The models corrected for none, one, or both structure levels. Correction for K was performed with linear mixed models incorporating familial relationships estimated from pedigrees or genetic...... corrected for P. In contrast, correction for P alone in linear models was insufficient. The power and precision of linear mixed models with and without correction for P were similar. Furthermore, power, precision, and type-I error rate were comparable in linear mixed models incorporating pedigree...

  1. Numerical analyses for efficient photoionization by nonmonochromatic fields

    International Nuclear Information System (INIS)

    Hasegawa, Shuichi; Suzuki, Atsuyuki

    2000-01-01

    Numerical analyses on excitation and ionization probabilities of atoms with hyperfine structures were performed in order to compare two different excitation methods, adiabatic excitation and broadband excitation. The lifetime of the intermediate states was considered in order to investigate the effect of the absorption line broadening. The dependences of the two excitation methods on the lifetime were found to be quite different. The ionization probability by the adiabatic excitation is higher than that by the broadband excitation for identical excitation laser intensity. (author)

  2. Experimental technique of stress analyses by neutron diffraction

    International Nuclear Information System (INIS)

    Sun, Guangai; Chen, Bo; Huang, Chaoqiang

    2009-09-01

    The structures and main components of neutron diffraction stress analyses spectrometer, SALSA, as well as functions and parameters of each components are presented. The technical characteristic and structure parameters of SALSA are described. Based on these aspects, the choice of gauge volume, method of positioning sample, determination of diffraction plane and measurement of zero stress do are discussed. Combined with the practical experiments, the basic experimental measurement and the related settings are introduced, including the adjustments of components, pattern scattering, data recording and checking etc. The above can be an instruction for stress analyses experiments by neutron diffraction and neutron stress spectrometer construction. (authors)

  3. Analysing spatially extended high-dimensional dynamics by recurrence plots

    Energy Technology Data Exchange (ETDEWEB)

    Marwan, Norbert, E-mail: marwan@pik-potsdam.de [Potsdam Institute for Climate Impact Research, 14412 Potsdam (Germany); Kurths, Jürgen [Potsdam Institute for Climate Impact Research, 14412 Potsdam (Germany); Humboldt Universität zu Berlin, Institut für Physik (Germany); Nizhny Novgorod State University, Department of Control Theory, Nizhny Novgorod (Russian Federation); Foerster, Saskia [GFZ German Research Centre for Geosciences, Section 1.4 Remote Sensing, Telegrafenberg, 14473 Potsdam (Germany)

    2015-05-08

    Recurrence plot based measures of complexity are capable tools for characterizing complex dynamics. In this letter we show the potential of selected recurrence plot measures for the investigation of even high-dimensional dynamics. We apply this method on spatially extended chaos, such as derived from the Lorenz96 model and show that the recurrence plot based measures can qualitatively characterize typical dynamical properties such as chaotic or periodic dynamics. Moreover, we demonstrate its power by analysing satellite image time series of vegetation cover with contrasting dynamics as a spatially extended and potentially high-dimensional example from the real world. - Highlights: • We use recurrence plots for analysing partially extended dynamics. • We investigate the high-dimensional chaos of the Lorenz96 model. • The approach distinguishes different spatio-temporal dynamics. • We use the method for studying vegetation cover time series.

  4. Mathematical methods for B0 anti B0 oscillation analyses

    International Nuclear Information System (INIS)

    Moser, H.G.; Roussarie, A.

    1996-01-01

    The measurement of the B 0 s anti B 0 s mixing frequency Δm s requires the search for a periodic pattern in the time distribution of the data. Using Fourier analysis the consequences of vertex and boost resolution, mistag and statistical fluctuations are treated analytically and a general expression to estimate the significance of a B 0 anti B 0 mixing analysis is derived. With the help of Fourier analysis the behaviour of a classical maximum likelihood analysis in time space is studied, too. It can be shown that a naive maximum likelihood fit fails in general to give correct confidence levels. This is especially important if limits are calculated. Alternative methods, based on the likelihood, which give correct limits are discussed. A new method, the amplitude fit, is introduced which combines the advantages of a Fourier analysis with the power and simplicity of a maximum likelihood fit. (orig.)

  5. Reactor Section standard analytical methods. Part 1

    Energy Technology Data Exchange (ETDEWEB)

    Sowden, D.

    1954-07-01

    the Standard Analytical Methods manual was prepared for the purpose of consolidating and standardizing all current analytical methods and procedures used in the Reactor Section for routine chemical analyses. All procedures are established in accordance with accepted practice and the general analytical methods specified by the Engineering Department. These procedures are specifically adapted to the requirements of the water treatment process and related operations. The methods included in this manual are organized alphabetically within the following five sections which correspond to the various phases of the analytical control program in which these analyses are to be used: water analyses, essential material analyses, cotton plug analyses boiler water analyses, and miscellaneous control analyses.

  6. Designing and recasting LHC analyses with MadAnalysis 5

    CERN Document Server

    Conte, Eric; Fuks, Benjamin; Wymant, Chris

    2014-01-01

    We present an extension of the expert mode of the MadAnalysis 5 program dedicated to the design or reinterpretation of high-energy physics collider analyses. We detail the predefined classes, functions and methods available to the user and emphasize the most recent developments. The latter include the possible definition of multiple sub-analyses and a novel user-friendly treatment for the selection criteria. We illustrate this approach by two concrete examples: a CMS search for supersymmetric partners of the top quark and a phenomenological analysis targeting hadronically decaying monotop systems.

  7. Correlating tephras and cryptotephras using glass compositional analyses and numerical and statistical methods: Review and evaluation

    Science.gov (United States)

    Lowe, David J.; Pearce, Nicholas J. G.; Jorgensen, Murray A.; Kuehn, Stephen C.; Tryon, Christian A.; Hayward, Chris L.

    2017-11-01

    We define tephras and cryptotephras and their components (mainly ash-sized particles of glass ± crystals in distal deposits) and summarize the basis of tephrochronology as a chronostratigraphic correlational and dating tool for palaeoenvironmental, geological, and archaeological research. We then document and appraise recent advances in analytical methods used to determine the major, minor, and trace elements of individual glass shards from tephra or cryptotephra deposits to aid their correlation and application. Protocols developed recently for the electron probe microanalysis of major elements in individual glass shards help to improve data quality and standardize reporting procedures. A narrow electron beam (diameter ∼3-5 μm) can now be used to analyze smaller glass shards than previously attainable. Reliable analyses of 'microshards' (defined here as glass shards T2 test). Randomization tests can be used where distributional assumptions such as multivariate normality underlying parametric tests are doubtful. Compositional data may be transformed and scaled before being subjected to multivariate statistical procedures including calculation of distance matrices, hierarchical cluster analysis, and PCA. Such transformations may make the assumption of multivariate normality more appropriate. A sequential procedure using Mahalanobis distance and the Hotelling two-sample T2 test is illustrated using glass major element data from trachytic to phonolitic Kenyan tephras. All these methods require a broad range of high-quality compositional data which can be used to compare 'unknowns' with reference (training) sets that are sufficiently complete to account for all possible correlatives, including tephras with heterogeneous glasses that contain multiple compositional groups. Currently, incomplete databases are tending to limit correlation efficacy. The development of an open, online global database to facilitate progress towards integrated, high

  8. Application of digital-image-correlation techniques in analysing ...

    Indian Academy of Sciences (India)

    Basis theory of strain analysis using the digital image correlation method .... Type 304N Stainless Steel (Modulus of Elasticity = 193 MPa, Tensile Yield .... also proves the accuracy of the qualitative analyses by using the DIC ... We thank the National Science Council of Taiwan for supporting this research through grant. No.

  9. Interspecific introgression in cetaceans: DNA markers reveal post-F1 status of a pilot whale.

    Directory of Open Access Journals (Sweden)

    Laura Miralles

    Full Text Available Visual species identification of cetacean strandings is difficult, especially when dead specimens are degraded and/or species are morphologically similar. The two recognised pilot whale species (Globicephala melas and Globicephala macrorhynchus are sympatric in the North Atlantic Ocean. These species are very similar in external appearance and their morphometric characteristics partially overlap; thus visual identification is not always reliable. Genetic species identification ensures correct identification of specimens. Here we have employed one mitochondrial (D-Loop region and eight nuclear loci (microsatellites as genetic markers to identify six stranded pilot whales found in Galicia (Northwest Spain, one of them of ambiguous phenotype. DNA analyses yielded positive amplification of all loci and enabled species identification. Nuclear microsatellite DNA genotypes revealed mixed ancestry for one individual, identified as a post-F1 interspecific hybrid employing two different Bayesian methods. From the mitochondrial sequence the maternal species was Globicephala melas. This is the first hybrid documented between Globicephala melas and G. macrorhynchus, and the first post-F1 hybrid genetically identified between cetaceans, revealing interspecific genetic introgression in marine mammals. We propose to add nuclear loci to genetic databases for cetacean species identification in order to detect hybrid individuals.

  10. Numerical analyses of flashing jet structure and droplet size characteristics

    International Nuclear Information System (INIS)

    Duan Riqiang; Jiang Shengyao; Koshizuka, Seiichi; Oka, Yoshiaki; Yamaguchi, Akira; Takata, Takashi

    2006-01-01

    In this paper, flashing jets are numerically simulated using the MPS method. The boiling mode for flashing is identified as surface boiling mode, based on the postulation of jets from a short nozzle under high depressurization. The Homogeneous Non-equilibrium Relaxation Model (HRM) is used for calculating the evaporation rate of flashing. The numerical simulation results show that flashing jets comprise an inner intact core which is surrounded by two-phase droplet flow. The effect of degree of superheat on the jet topological geometry is investigated. With increasing degree of superheat, the topological shape of flashing jets evolves from cylindrical core for low degree of superheat to cone-shaped core for high degree of superheat, and meanwhile the extinction length comes to decrease and tends asymptotically constant as the injection temperature approaches the saturation temperature corresponding to the injection pressure. The analyses of the droplet size distribution engendered from primary breakup of flashing jets show that: two peaks exist for droplet size distribution at lower degree of superheat; however, merely one peak for higher degree of superheat. From droplet size distribution, it is revealed that the primary breakup mechanism of flashing jets can be attributed to dominant mechanical breakup mode plus enhancement via surface evaporation. (author)

  11. Differential metabolism of Mycoplasma species as revealed by their genomes

    Directory of Open Access Journals (Sweden)

    Fabricio B.M. Arraes

    2007-01-01

    Full Text Available The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall, has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take up a variety of carbohydrates via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS. Our data showed that these two organisms are unable to synthesize purine and pyrimidine de novo, since they only possess the sequences which encode salvage pathway enzymes. Comparative analyses of M. synoviae and M. hyopneumoniae with other Mollicutes have revealed differential genes in the former two genomes coding for enzymes that participate in carbohydrate, amino acid and nucleotide metabolism and host-pathogen interaction. The identification of these metabolic pathways will provide a better understanding of the biology and pathogenicity of these organisms.

  12. Proteomic Analyses Reveal the Mechanism of Dunaliella salina Ds-26-16 Gene Enhancing Salt Tolerance in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Yanlong Wang

    Full Text Available We previously screened the novel gene Ds-26-16 from a 4 M salt-stressed Dunaliella salina cDNA library and discovered that this gene conferred salt tolerance to broad-spectrum organisms, including E. coli (Escherichia coli, Haematococcus pluvialis and tobacco. To determine the mechanism of this gene conferring salt tolerance, we studied the proteome of E. coli overexpressing the full-length cDNA of Ds-26-16 using the iTRAQ (isobaric tags for relative and absolute quantification approach. A total of 1,610 proteins were identified, which comprised 39.4% of the whole proteome. Of the 559 differential proteins, 259 were up-regulated and 300 were down-regulated. GO (gene ontology and KEGG (Kyoto encyclopedia of genes and genomes enrichment analyses identified 202 major proteins, including those involved in amino acid and organic acid metabolism, energy metabolism, carbon metabolism, ROS (reactive oxygen species scavenging, membrane proteins and ABC (ATP binding cassette transporters, and peptidoglycan synthesis, as well as 5 up-regulated transcription factors. Our iTRAQ data suggest that Ds-26-16 up-regulates the transcription factors in E. coli to enhance salt resistance through osmotic balance, energy metabolism, and oxidative stress protection. Changes in the proteome were also observed in E. coli overexpressing the ORF (open reading frame of Ds-26-16. Furthermore, pH, nitric oxide and glycerol content analyses indicated that Ds-26-16 overexpression increases nitric oxide content but has no effect on glycerol content, thus confirming that enhanced nitric oxide synthesis via lower intercellular pH was one of the mechanisms by which Ds-26-16 confers salt tolerance to E. coli.

  13. N-Nitrosodiethanolamine (NDELA) in cosmetica methode ontwikkeling en monster analyse

    NARCIS (Netherlands)

    Rijst EC van; Schothorst RC; ARO

    1997-01-01

    In 1995 is op verzoek van de Inspectie Gezondheids Bescherming de N-nitrosamine problematiek in cosmetische producten in kaart gebracht. Voor het bepalen van NDELA in cosmetica is de GC-TEA methode ontwikkeld en gevalideerd. De terugwinning voor NDELA is gemiddeld 99% (N=4) en de

  14. Studying the properties of photonic quasi-crystals by the scaling convergence method

    International Nuclear Information System (INIS)

    Ho, I-Lin; Ng, Ming-Yaw; Mai, Chien Chin; Ko, Peng Yu; Chang, Yia-Chung

    2013-01-01

    This work introduces the iterative scaling (or inflation) method to systematically approach and analyse the infinite structure of quasi-crystals. The resulting structures preserve local geometric orderings in order to prevent artificial disclination across the boundaries of super-cells, with realistic quasi-crystals coming out under high iteration (infinite super-cell). The method provides an easy way for decorations of quasi-crystalline lattices, and for compact reliefs with a quasi-periodic arrangement to underlying applications. Numerical examples for in-plane and off-plane properties of square-triangle quasi-crystals show fast convergence during iteratively geometric scaling, revealing characteristics that do not appear on regular crystals. (paper)

  15. Antarctic Temperature Extremes from MODIS Land Surface Temperatures: New Processing Methods Reveal Data Quality Puzzles

    Science.gov (United States)

    Grant, G.; Gallaher, D. W.

    2017-12-01

    New methods for processing massive remotely sensed datasets are used to evaluate Antarctic land surface temperature (LST) extremes. Data from the MODIS/Terra sensor (Collection 6) provides a twice-daily look at Antarctic LSTs over a 17 year period, at a higher spatiotemporal resolution than past studies. Using a data condensation process that creates databases of anomalous values, our processes create statistical images of Antarctic LSTs. In general, the results find few significant trends in extremes; however, they do reveal a puzzling picture of inconsistent cloud detection and possible systemic errors, perhaps due to viewing geometry. Cloud discrimination shows a distinct jump in clear-sky detections starting in 2011, and LSTs around the South Pole exhibit a circular cooling pattern, which may also be related to cloud contamination. Possible root causes are discussed. Ongoing investigations seek to determine whether the results are a natural phenomenon or, as seems likely, the results of sensor degradation or processing artefacts. If the unusual LST patterns or cloud detection discontinuities are natural, they point to new, interesting processes on the Antarctic continent. If the data artefacts are artificial, MODIS LST users should be alerted to the potential issues.

  16. Prey-capture success revealed by echolocation signals in pipistrelle bats (Pipistrellus pygmaeus)

    DEFF Research Database (Denmark)

    Surlykke, Annemarie; Futtrup, Vibeke; Tougaard, Jakob

    2003-01-01

    Three Pipistrellus pygmaeus bats were trained to capture prey on the wing while flying in the laboratory. The bats' capture behaviour and capture success were determined and correlated with acoustic analyses of post-buzz echolocation signals. Three acoustic parameters revealed capture success: in...

  17. USE OF BOUNDING ANALYSES TO ESTIMATE THE PREFORMANCE OF A SEISMICALLY ISOLATED STRUCTURE

    Directory of Open Access Journals (Sweden)

    Gökhan ÖZDEMİR

    2017-03-01

    Full Text Available Current design approach for seismic isolated structures is to perform bounding analyses. These analyses provide an envelope for the response of the seismic isolated structure rather than focusing on the actual performance. In this study, the success of bounding analyses to estimate performance of a seismic isolated structure, in which the isolation is provided by means of lead rubber bearings (LRBs, is evaluated in a comparative manner. For this purpose, nonlinear response history analyses were performed under the effect of bidirectional ground motion excitations. In bounding analyses, non-deteriorating hysteretic representations were used to model the hysteretic behavior of LRBs. On the other hand, to estimate the actual performance of both the superstructure and isolator units, deteriorating hysteretic idealizations were employed. The deterioration in strength of LRBs was defined as a function of temperature rise in the lead core. The analyzed structure is an existing seismically isolated hospital building and analytically modeled in accordance with its reported design properties for both isolation units and superstructure. Results obtained from analyses where LRBs are idealized by both deteriorating and non-deteriorating hysteretic representations are used in the comparisons. The response quantities used in the comparisons are maximum isolator displacement, maximum isolator force, maximum absolute floor acceleration, and maximum relative story displacements. In an average sense, bounding analyses is found to provide conservative estimates for the selected response quantities and fulfills its intended purpose. However, it is revealed that there may be individual cases where bounding analyses fails to provide a safe envelope.

  18. Comparisons and Analyses of Gifted Students' Characteristics and Learning Methods

    Science.gov (United States)

    Lu, Jiamei; Li, Daqi; Stevens, Carla; Ye, Renmin

    2017-01-01

    Using PISA 2009, an international education database, this study compares gifted and talented (GT) students in three groups with normal (non-GT) students by examining student characteristics, reading, schooling, learning methods, and use of strategies for understanding and memorizing. Results indicate that the GT and non-GT gender distributions…

  19. A revised method of presenting wavenumber-frequency power spectrum diagrams that reveals the asymmetric nature of tropical large-scale waves

    Energy Technology Data Exchange (ETDEWEB)

    Chao, Winston C. [NASA/Goddard Space Flight Center, Global Modeling and Assimilation Office, Mail Code 610.1, Greenbelt, MD (United States); Yang, Bo; Fu, Xiouhua [University of Hawaii at Manoa, School of Ocean and Earth Science and Technology, International Pacific Research Center, Honolulu, HI (United States)

    2009-11-15

    The popular method of presenting wavenumber-frequency power spectrum diagrams for studying tropical large-scale waves in the literature is shown to give an incomplete presentation of these waves. The so-called ''convectively coupled Kelvin (mixed Rossby-gravity) waves'' are presented as existing only in the symmetric (anti-symmetric) component of the diagrams. This is obviously not consistent with the published composite/regression studies of ''convectively coupled Kelvin waves,'' which illustrate the asymmetric nature of these waves. The cause of this inconsistency is revealed in this note and a revised method of presenting the power spectrum diagrams is proposed. When this revised method is used, ''convectively coupled Kelvin waves'' do show anti-symmetric components, and ''convectively coupled mixed Rossby-gravity waves (also known as Yanai waves)'' do show a hint of symmetric components. These results bolster a published proposal that these waves should be called ''chimeric Kelvin waves,'' ''chimeric mixed Rossby-gravity waves,'' etc. This revised method of presenting power spectrum diagrams offers an additional means of comparing the GCM output with observations by calling attention to the capability of GCMs to correctly simulate the asymmetric characteristics of equatorial waves. (orig.)

  20. Angular analyses in relativistic quantum mechanics; Analyses angulaires en mecanique quantique relativiste

    Energy Technology Data Exchange (ETDEWEB)

    Moussa, P [Commissariat a l' Energie Atomique, 91 - Saclay (France). Centre d' Etudes Nucleaires

    1968-06-01

    This work describes the angular analysis of reactions between particles with spin in a fully relativistic fashion. One particle states are introduced, following Wigner's method, as representations of the inhomogeneous Lorentz group. In order to perform the angular analyses, the reduction of the product of two representations of the inhomogeneous Lorentz group is studied. Clebsch-Gordan coefficients are computed for the following couplings: l-s coupling, helicity coupling, multipolar coupling, and symmetric coupling for more than two particles. Massless and massive particles are handled simultaneously. On the way we construct spinorial amplitudes and free fields; we recall how to establish convergence theorems for angular expansions from analyticity hypothesis. Finally we substitute these hypotheses to the idea of 'potential radius', which gives at low energy the usual 'centrifugal barrier' factors. The presence of such factors had never been deduced from hypotheses compatible with relativistic invariance. (author) [French] On decrit un formalisme permettant de tenir compte de l'invariance relativiste, dans l'analyse angulaire des amplitudes de reaction entre particules de spin quelconque. Suivant Wigner, les etats a une particule sont introduits a l'aide des representations du groupe de Lorentz inhomogene. Pour effectuer les analyses angulaires, on etudie la reduction du produit de deux representations du groupe de Lorentz inhomogene. Les coefficients de Clebsch-Gordan correspondants sont calcules dans les couplages suivants: couplage l-s couplage d'helicite, couplage multipolaire, couplage symetrique pour plus de deux particules. Les particules de masse nulle et de masse non nulle sont traitees simultanement. Au passage, on introduit les amplitudes spinorielles et on construit les champs libres, on rappelle comment des hypotheses d'analyticite permettent d'etablir des theoremes de convergence pour les developpements angulaires. Enfin on fournit un substitut a la

  1. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    Science.gov (United States)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  2. Coalescent-based genome analyses resolve the early branches of the euarchontoglires.

    Directory of Open Access Journals (Sweden)

    Vikas Kumar

    Full Text Available Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides from all orders except Dermoptera (flying lemurs. Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.

  3. Sequence and expression analyses of porcine ISG15 and ISG43 genes.

    Science.gov (United States)

    Huang, Jiangnan; Zhao, Shuhong; Zhu, Mengjin; Wu, Zhenfang; Yu, Mei

    2009-08-01

    The coding sequences of porcine interferon-stimulated gene 15 (ISG15) and the interferon-stimulated gene (ISG43) were cloned from swine spleen mRNA. The amino acid sequences deduced from porcine ISG15 and ISG43 genes coding sequence shared 24-75% and 29-83% similarity with ISG15s and ISG43s from other vertebrates, respectively. Structural analyses revealed that porcine ISG15 comprises two ubiquitin homologues motifs (UBQ) domain and a conserved C-terminal LRLRGG conjugating motif. Porcine ISG43 contains an ubiquitin-processing proteases-like domain. Phylogenetic analyses showed that porcine ISG15 and ISG43 were mostly related to rat ISG15 and cattle ISG43, respectively. Using quantitative real-time PCR assay, significant increased expression levels of porcine ISG15 and ISG43 genes were detected in porcine kidney endothelial cells (PK15) cells treated with poly I:C. We also observed the enhanced mRNA expression of three members of dsRNA pattern-recognition receptors (PRR), TLR3, DDX58 and IFIH1, which have been reported to act as critical receptors in inducing the mRNA expression of ISG15 and ISG43 genes. However, we did not detect any induced mRNA expression of IFNalpha and IFNbeta, suggesting that transcriptional activations of ISG15 and ISG43 were mediated through IFN-independent signaling pathway in the poly I:C treated PK15 cells. Association analyses in a Landrace pig population revealed that ISG15 c.347T>C (BstUI) polymorphism and the ISG43 c.953T>G (BccI) polymorphism were significantly associated with hematological parameters and immune-related traits.

  4. Argon activation analysis, application to dating by the potassium-argon method; Analyse par activation de l'argon. Application a la datation par la methode potassium-argon

    Energy Technology Data Exchange (ETDEWEB)

    Dumesnil, P. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1967-07-01

    Activation analysis using radiogenic argon-40 has been applied to rock-dating by the K-Ar method. The argon is extracted from the sample, purified, activated to saturation in a flux of 2 X 10{sup 13} neutrons/cm{sup 2} sec{sup -1} and measured by gamma spectroscopy. The sensitivity obtained is such that it is possible to measure amounts of argon corresponding to age of a few thousand years only. However since it has not been possible to measure the amount of pollution of radiogenic argon by atmospheric argon with any accuracy, the measurable age limit is in fact of the order of MY. The method has been applied to basalts from the Mont-Dore region. The results obtained are in fairly good agreement with geological, stratigraphic and paleomagnetic data. (author) [French] L'analyse par activation de l'argon 40 radiogenique a ete appliquee a la datation des roches par la methode K-Ar. L'argon est extrait de l'echantillon, purifie, active a saturation dans un flux de 2.10{sup 13} neutrons.cm{sup -2}.s{sup -1} et mesure en spectrometrie gamma. La sensibilite obtenue est telle qu'il est possible de mesurer des quantites d'argon correspondant a des ages de quelques milliers d'annees seulement. Cependant la correction de pollution de l'argon radiogenique par l'argon atmospherique n'ayant pu etre etablie avec precision, la limite d'age mesurable pratique est de l'ordre de 1 Ma. La methode a ete appliquee aux basaltes de la region du Mont-Dore. Les ages obtenus sont en assez bon accord avec les donnees geologiques, stratigraphiques et paleomagnetiques. (auteur)

  5. Nuclear analyses in biology and medical science. Measuring on nucleii in stead of atoms

    International Nuclear Information System (INIS)

    De Goeij, J.J.M.

    1996-01-01

    A brief overview is given of the use of nuclear analyses in life sciences. Features of nuclear analytical methods (NAMs) are grouped into four categories: physical basis, isotopic analyses rather than elemental analyses, no interference of electronic and molecular structure, and penetrating character of nuclear radiation. Obstacles in applying NAMs in the life sciences are outlined. 1 tab

  6. The Need for Speed in Rodent Locomotion Analyses

    Science.gov (United States)

    Batka, Richard J.; Brown, Todd J.; Mcmillan, Kathryn P.; Meadows, Rena M.; Jones, Kathryn J.; Haulcomb, Melissa M.

    2016-01-01

    Locomotion analysis is now widely used across many animal species to understand the motor defects in disease, functional recovery following neural injury, and the effectiveness of various treatments. More recently, rodent locomotion analysis has become an increasingly popular method in a diverse range of research. Speed is an inseparable aspect of locomotion that is still not fully understood, and its effects are often not properly incorporated while analyzing data. In this hybrid manuscript, we accomplish three things: (1) review the interaction between speed and locomotion variables in rodent studies, (2) comprehensively analyze the relationship between speed and 162 locomotion variables in a group of 16 wild-type mice using the CatWalk gait analysis system, and (3) develop and test a statistical method in which locomotion variables are analyzed and reported in the context of speed. Notable results include the following: (1) over 90% of variables, reported by CatWalk, were dependent on speed with an average R2 value of 0.624, (2) most variables were related to speed in a nonlinear manner, (3) current methods of controlling for speed are insufficient, and (4) the linear mixed model is an appropriate and effective statistical method for locomotion analyses that is inclusive of speed-dependent relationships. Given the pervasive dependency of locomotion variables on speed, we maintain that valid conclusions from locomotion analyses cannot be made unless they are analyzed and reported within the context of speed. PMID:24890845

  7. Genome-wide DNA polymorphism analyses using VariScan

    Directory of Open Access Journals (Sweden)

    Vilella Albert J

    2006-09-01

    Full Text Available Abstract Background DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis. Results We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i exhaustive population-genetic analyses including those based on the coalescent theory; ii analysis adapted to the shallow data generated by the high-throughput genome projects; iii use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v visualization of the results integrated with current genome annotations in commonly available genome browsers. Conclusion VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

  8. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    Science.gov (United States)

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses

    Science.gov (United States)

    Lanfear, Robert; Hua, Xia; Warren, Dan L.

    2016-01-01

    Bayesian phylogenetic analyses estimate posterior distributions of phylogenetic tree topologies and other parameters using Markov chain Monte Carlo (MCMC) methods. Before making inferences from these distributions, it is important to assess their adequacy. To this end, the effective sample size (ESS) estimates how many truly independent samples of a given parameter the output of the MCMC represents. The ESS of a parameter is frequently much lower than the number of samples taken from the MCMC because sequential samples from the chain can be non-independent due to autocorrelation. Typically, phylogeneticists use a rule of thumb that the ESS of all parameters should be greater than 200. However, we have no method to calculate an ESS of tree topology samples, despite the fact that the tree topology is often the parameter of primary interest and is almost always central to the estimation of other parameters. That is, we lack a method to determine whether we have adequately sampled one of the most important parameters in our analyses. In this study, we address this problem by developing methods to estimate the ESS for tree topologies. We combine these methods with two new diagnostic plots for assessing posterior samples of tree topologies, and compare their performance on simulated and empirical data sets. Combined, the methods we present provide new ways to assess the mixing and convergence of phylogenetic tree topologies in Bayesian MCMC analyses. PMID:27435794

  10. Audio-visual perception of 3D cinematography: an fMRI study using condition-based and computation-based analyses.

    Directory of Open Access Journals (Sweden)

    Akitoshi Ogawa

    Full Text Available The use of naturalistic stimuli to probe sensory functions in the human brain is gaining increasing interest. Previous imaging studies examined brain activity associated with the processing of cinematographic material using both standard "condition-based" designs, as well as "computational" methods based on the extraction of time-varying features of the stimuli (e.g. motion. Here, we exploited both approaches to investigate the neural correlates of complex visual and auditory spatial signals in cinematography. In the first experiment, the participants watched a piece of a commercial movie presented in four blocked conditions: 3D vision with surround sounds (3D-Surround, 3D with monaural sound (3D-Mono, 2D-Surround, and 2D-Mono. In the second experiment, they watched two different segments of the movie both presented continuously in 3D-Surround. The blocked presentation served for standard condition-based analyses, while all datasets were submitted to computation-based analyses. The latter assessed where activity co-varied with visual disparity signals and the complexity of auditory multi-sources signals. The blocked analyses associated 3D viewing with the activation of the dorsal and lateral occipital cortex and superior parietal lobule, while the surround sounds activated the superior and middle temporal gyri (S/MTG. The computation-based analyses revealed the effects of absolute disparity in dorsal occipital and posterior parietal cortices and of disparity gradients in the posterior middle temporal gyrus plus the inferior frontal gyrus. The complexity of the surround sounds was associated with activity in specific sub-regions of S/MTG, even after accounting for changes of sound intensity. These results demonstrate that the processing of naturalistic audio-visual signals entails an extensive set of visual and auditory areas, and that computation-based analyses can track the contribution of complex spatial aspects characterizing such life

  11. Audio-visual perception of 3D cinematography: an fMRI study using condition-based and computation-based analyses.

    Science.gov (United States)

    Ogawa, Akitoshi; Bordier, Cecile; Macaluso, Emiliano

    2013-01-01

    The use of naturalistic stimuli to probe sensory functions in the human brain is gaining increasing interest. Previous imaging studies examined brain activity associated with the processing of cinematographic material using both standard "condition-based" designs, as well as "computational" methods based on the extraction of time-varying features of the stimuli (e.g. motion). Here, we exploited both approaches to investigate the neural correlates of complex visual and auditory spatial signals in cinematography. In the first experiment, the participants watched a piece of a commercial movie presented in four blocked conditions: 3D vision with surround sounds (3D-Surround), 3D with monaural sound (3D-Mono), 2D-Surround, and 2D-Mono. In the second experiment, they watched two different segments of the movie both presented continuously in 3D-Surround. The blocked presentation served for standard condition-based analyses, while all datasets were submitted to computation-based analyses. The latter assessed where activity co-varied with visual disparity signals and the complexity of auditory multi-sources signals. The blocked analyses associated 3D viewing with the activation of the dorsal and lateral occipital cortex and superior parietal lobule, while the surround sounds activated the superior and middle temporal gyri (S/MTG). The computation-based analyses revealed the effects of absolute disparity in dorsal occipital and posterior parietal cortices and of disparity gradients in the posterior middle temporal gyrus plus the inferior frontal gyrus. The complexity of the surround sounds was associated with activity in specific sub-regions of S/MTG, even after accounting for changes of sound intensity. These results demonstrate that the processing of naturalistic audio-visual signals entails an extensive set of visual and auditory areas, and that computation-based analyses can track the contribution of complex spatial aspects characterizing such life-like stimuli.

  12. Eddy Heat Conduction and Nonlinear Stability of a Darcy Lapwood System Analysed by the Finite Spectral Method

    Directory of Open Access Journals (Sweden)

    Jónas Elíasson

    2014-01-01

    Full Text Available A finite Fourier transform is used to perform both linear and nonlinear stability analyses of a Darcy-Lapwood system of convective rolls. The method shows how many modes are unstable, the wave number instability band within each mode, the maximum growth rate (most critical wave numbers on each mode, and the nonlinear growth rates for each amplitude as a function of the porous Rayleigh number. Single amplitude controls the nonlinear growth rates and thereby the physical flow rate and fluid velocity, on each mode. They are called the flak amplitudes. A discrete Fourier transform is used for numerical simulations and here frequency combinations appear that the traditional cut-off infinite transforms do not have. The discrete show a stationary solution in the weak instability phase, but when carried past 2 unstable modes they show fluctuating motion where all amplitudes except the flak may be zero on the average. This leads to a flak amplitude scaling process of the heat conduction, producing an eddy heat conduction coefficient where a Nu-RaL relationship is found. It fits better to experiments than previously found solutions but is lower than experiments.

  13. A method that reveals the multi-level ultrametric tree hidden in p -spin-glass-like systems

    International Nuclear Information System (INIS)

    Baviera, R; Virasoro, M A

    2015-01-01

    In the study of disordered models like spin glasses the key object of interest is the rugged energy hypersurface defined in configuration space. The statistical mechanics calculation of the Gibbs–Boltzmann partition function gives the information necessary to understand the equilibrium behavior of the system as a function of the temperature but is not enough if we are interested in the more general aspects of the hypersurface: it does not give us, for instance, the different degrees of ruggedness at different scales. In the context of the replica symmetry breaking (RSB) approach we discuss here a rather simple extension that can provide a much more detailed picture. The attractiveness of the method relies on the fact that it is conceptually transparent and the additional calculations are rather straightforward. We think that this approach reveals an ultrametric organisation with many levels in models like p-spin glasses when we include saddle points. In this first paper we present detailed calculations for the spherical p-spin glass model where we discover that the corresponding decreasing Parisi function q(x) codes this hidden ultrametric organisation. (paper)

  14. Study of the production mechanism of the η meson in proton-proton collisions by means of analysing power measurements

    International Nuclear Information System (INIS)

    Czyzykiewicz, R.

    2007-02-01

    The analysing power measurements for the #vector#pp→ppη reaction studied in this dissertation are used in the determination of the reaction mechanism of the η meson production in nucleon-nucleon collisions. Measurements have been performed in the close-to-threshold energy region at beam momenta of p beam =2.010 and 2.085 GeV/c, corresponding to the excess energies of Q=10 and 36 MeV, respectively. The experiments were realised by means of a cooler synchrotron and storage ring COSY along with a cluster jet target. For registration of the reaction products the COSY-11 facility has been used. The identification of the η meson has been performed with the missing mass method. The results for the angular dependence of the analysing power combined with the hitherto determined isospin dependence of the total cross section for the η meson production in the nucleon-nucleon collisions, reveal a statistically significant indication that the excitation of the nucleon to the S 11 resonance, the process which intermediates the production of the η meson, is predominantly due to the exchange of a π meson between the colliding nucleons. The determined values of the analysing power at both excess energies are consistent with zero implying that the η meson is produced predominantly in the s-wave at both excess energies. (orig.)

  15. Ultrasonic partial discharge monitoring method on instrument transformers

    Directory of Open Access Journals (Sweden)

    Kartalović Nenad

    2012-01-01

    Full Text Available Sonic and ultrasonic partial discharge monitoring have been applied since the early days of these phenomena monitoring. Modern measurement and partial discharge acoustic (ultrasonic and sonic monitoring method has been rapidly evolving as a result of new electronic component design, information technology and updated software solutions as well as the development of knowledge in the partial discharge diagnosis. Electrical discharges in the insulation system generate voltage-current pulses in the network and ultrasonic waves that propagate through the insulation system and structure. Amplitude-phase-frequency analysis of these signals reveals information about the intensity, type and location of partial discharges. The paper discusses the possibility of ultrasonic method selectivity improvement and the increase of diagnosis reliability in the field. Measurements were performed in the laboratory and in the field while a number of transformers were analysed for dissolved gases in the oil. A comparative review of methods for the partial discharge detection is also presented in this paper.

  16. Techniques for Scaling Up Analyses Based on Pre-interpretations

    DEFF Research Database (Denmark)

    Gallagher, John Patrick; Henriksen, Kim Steen; Banda, Gourinath

    2005-01-01

    a variety of analyses, both generic (such as mode analysis) and program-specific (with respect to a type describing some particular property of interest). Previous work demonstrated the approach using pre-interpretations over small domains. In this paper we present techniques that allow the method...

  17. Systematic approaches to data analysis from the Critical Decision Method

    Directory of Open Access Journals (Sweden)

    Martin Sedlár

    2015-01-01

    Full Text Available The aim of the present paper is to introduce how to analyse the qualitative data from the Critical Decision Method. At first, characterizing the method provides the meaningful introduction into the issue. This method used in naturalistic decision making research is one of the cognitive task analysis methods, it is based on the retrospective semistructured interview about critical incident from the work and it may be applied in various domains such as emergency services, military, transport, sport or industry. Researchers can make two types of methodological adaptation. Within-method adaptations modify the way of conducting the interviews and cross-method adaptations combine this method with other related methods. There are many decsriptions of conducting the interview, but the descriptions how the data should be analysed are rare. Some researchers use conventional approaches like content analysis, grounded theory or individual procedures with reference to the objectives of research project. Wong (2004 describes two approaches to data analysis proposed for this method of data collection, which are described and reviewed in the details. They enable systematic work with a large amount of data. The structured approach organizes the data according to an a priori analysis framework and it is suitable for clearly defined object of research. Each incident is studied separately. At first, the decision chart showing the main decision points and then the incident summary are made. These decision points are used to identify the relevant statements from the transcript, which are analysed in terms of the Recognition-Primed Decision Model. Finally, the results from all the analysed incidents are integrated. The limitation of the structured approach is it may not reveal some interesting concepts. The emergent themes approach helps to identify these concepts while maintaining a systematic framework for analysis and it is used for exploratory research design. It

  18. Anti-schistosomal intervention targets identified by lifecycle transcriptomic analyses.

    Directory of Open Access Journals (Sweden)

    Jennifer M Fitzpatrick

    2009-11-01

    Full Text Available Novel methods to identify anthelmintic drug and vaccine targets are urgently needed, especially for those parasite species currently being controlled by singular, often limited strategies. A clearer understanding of the transcriptional components underpinning helminth development will enable identification of exploitable molecules essential for successful parasite/host interactions. Towards this end, we present a combinatorial, bioinformatics-led approach, employing both statistical and network analyses of transcriptomic data, for identifying new immunoprophylactic and therapeutic lead targets to combat schistosomiasis.Utilisation of a Schistosoma mansoni oligonucleotide DNA microarray consisting of 37,632 elements enabled gene expression profiling from 15 distinct parasite lifecycle stages, spanning three unique ecological niches. Statistical approaches of data analysis revealed differential expression of 973 gene products that minimally describe the three major characteristics of schistosome development: asexual processes within intermediate snail hosts, sexual maturation within definitive vertebrate hosts and sexual dimorphism amongst adult male and female worms. Furthermore, we identified a group of 338 constitutively expressed schistosome gene products (including 41 transcripts sharing no sequence similarity outside the Platyhelminthes, which are likely to be essential for schistosome lifecycle progression. While highly informative, statistics-led bioinformatics mining of the transcriptional dataset has limitations, including the inability to identify higher order relationships between differentially expressed transcripts and lifecycle stages. Network analysis, coupled to Gene Ontology enrichment investigations, facilitated a re-examination of the dataset and identified 387 clusters (containing 12,132 gene products displaying novel examples of developmentally regulated classes (including 294 schistosomula and/or adult transcripts with no

  19. Probabilistic and Nonprobabilistic Sensitivity Analyses of Uncertain Parameters

    Directory of Open Access Journals (Sweden)

    Sheng-En Fang

    2014-01-01

    Full Text Available Parameter sensitivity analyses have been widely applied to industrial problems for evaluating parameter significance, effects on responses, uncertainty influence, and so forth. In the interest of simple implementation and computational efficiency, this study has developed two sensitivity analysis methods corresponding to the situations with or without sufficient probability information. The probabilistic method is established with the aid of the stochastic response surface and the mathematical derivation proves that the coefficients of first-order items embody the parameter main effects on the response. Simultaneously, a nonprobabilistic interval analysis based method is brought forward for the circumstance when the parameter probability distributions are unknown. The two methods have been verified against a numerical beam example with their accuracy compared to that of a traditional variance-based method. The analysis results have demonstrated the reliability and accuracy of the developed methods. And their suitability for different situations has also been discussed.

  20. Biochemical and full genome sequence analyses of clinical Vibrio cholerae isolates in Mexico reveals the presence of novel V. cholerae strains.

    Science.gov (United States)

    Díaz-Quiñonez, José Alberto; Hernández-Monroy, Irma; Montes-Colima, Norma Angélica; Moreno-Pérez, María Asunción; Galicia-Nicolás, Adriana Guadalupe; López-Martínez, Irma; Ruiz-Matus, Cuitláhuac; Kuri-Morales, Pablo; Ortíz-Alcántara, Joanna María; Garcés-Ayala, Fabiola; Ramírez-González, José Ernesto

    2016-05-01

    The first week of September 2013, the National Epidemiological Surveillance System identified two cases of cholera in Mexico City. The cultures of both samples were confirmed as Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Initial analyses by PFGE and by PCR-amplification of the virulence genes, suggested that both strains were similar, but different from those previously reported in Mexico. The following week, four more cases were identified in a community in the state of Hidalgo, located 121 km northeast of Mexico City. Thereafter a cholera outbreak started in the region of La Huasteca. Genomic analyses of the four strains obtained in this study confirmed the presence of Pathogenicity Islands VPI-1 and -2, VSP-1 and -2, and of the integrative element SXT. The genomic structure of the 4 isolates was similar to that of V. cholerae strain 2010 EL-1786, identified during the epidemic in Haiti in 2010. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  1. Voxel-based morphometry analyses of in-vivo MRI in the aging mouse lemur primate

    Directory of Open Access Journals (Sweden)

    Stephen John Sawiak

    2014-05-01

    Full Text Available Cerebral atrophy is one of the most widely brain alterations associated to aging. A clear relationship has been established between age-associated cognitive impairments and cerebral atrophy. The mouse lemur (Microcebus murinus is a small primate used as a model of age-related neurodegenerative processes. It is the first nonhuman primate in which cerebral atrophy has been correlated with cognitive deficits. Previous studies of cerebral atrophy in this model were based on time consuming manual delineation or measurement of selected brain regions from magnetic resonance images (MRI. These measures could not be used to analyse regions that cannot be easily outlined such as the nucleus basalis of Meynert or the subiculum. In humans, morphometric assessment of structural changes with age is generally performed with automated procedures such as voxel-based morphometry (VBM. The objective of our work was to perform user-independent assessment of age-related morphological changes in the whole brain of large mouse lemur populations thanks to VBM. The study was based on the SPMMouse toolbox of SPM 8 and involved thirty mouse lemurs aged from 1.9 to 11.3 years. The automatic method revealed for the first time atrophy in regions where manual delineation is prohibitive (nucleus basalis of Meynert, subiculum, prepiriform cortex, Brodmann areas 13-16, hypothalamus, putamen, thalamus, corpus callosum. Some of these regions are described as particularly sensitive to age-associated alterations in humans. The method revealed also age-associated atrophy in cortical regions (cingulate, occipital, parietal, nucleus septalis, and the caudate. Manual measures performed in some of these regions were in good agreement with results from automatic measures. The templates generated in this study as well as the toolbox for SPM8 can be downloaded. These tools will be valuable for future evaluation of various treatments that are tested to modulate cerebral aging in lemurs.

  2. Japanese standard method for safety evaluation using best estimate code based on uncertainty and scaling analyses with statistical approach

    International Nuclear Information System (INIS)

    Mizokami, Shinya; Hotta, Akitoshi; Kudo, Yoshiro; Yonehara, Tadashi; Watada, Masayuki; Sakaba, Hiroshi

    2009-01-01

    Current licensing practice in Japan consists of using conservative boundary and initial conditions(BIC), assumptions and analytical codes. The safety analyses for licensing purpose are inherently deterministic. Therefore, conservative BIC and assumptions, such as single failure, must be employed for the analyses. However, using conservative analytical codes are not considered essential. The standard committee of Atomic Energy Society of Japan(AESJ) has drawn up the standard for using best estimate codes for safety analyses in 2008 after three-years of discussions reflecting domestic and international recent findings. (author)

  3. Determining the sensitivity of Data Envelopment Analysis method used in airport benchmarking

    Directory of Open Access Journals (Sweden)

    Mircea BOSCOIANU

    2013-03-01

    Full Text Available In the last decade there were some important changes in the airport industry, caused by the liberalization of the air transportation market. Until recently airports were considered infrastructure elements, and they were evaluated only by traffic values or their maximum capacity. Gradual orientation towards commercial led to the need of finding another ways of evaluation, more efficiency oriented. The existing methods for assessing efficiency used for other production units were not suitable to be used in case of airports due to specific features and high complexity of airport operations. In the last years there were some papers that proposed the Data Envelopment Analysis as a method for assessing the operational efficiency in order to conduct the benchmarking. This method offers the possibility of dealing with a large number of variables of different types, which represents the main advantage of this method and also recommends it as a good benchmarking tool for the airports management. This paper goal is to determine the sensitivity of this method in relation with its inputs and outputs. A Data Envelopment Analysis is conducted for 128 airports worldwide, in both input- and output-oriented measures, and the results are analysed against some inputs and outputs variations. Possible weaknesses of using DEA for assessing airports performance are revealed and analysed against this method advantages.

  4. Robustness assessments are needed to reduce bias in meta-analyses that include zero-event randomized trials

    DEFF Research Database (Denmark)

    Keus, F; Wetterslev, J; Gluud, C

    2009-01-01

    of statistical method on inference. RESULTS: In seven meta-analyses of seven outcomes from 15 trials, there were zero-event trials in 0 to 71.4% of the trials. We found inconsistency in significance in one of seven outcomes (14%; 95% confidence limit 0.4%-57.9%). There was also considerable variability......OBJECTIVES: Meta-analysis of randomized trials with binary data can use a variety of statistical methods. Zero-event trials may create analytic problems. We explored how different methods may impact inferences from meta-analyses containing zero-event trials. METHODS: Five levels of statistical...... methods are identified for meta-analysis with zero-event trials, leading to numerous data analyses. We used the binary outcomes from our Cochrane review of randomized trials of laparoscopic vs. small-incision cholecystectomy for patients with symptomatic cholecystolithiasis to illustrate the influence...

  5. A novel RNA sequencing data analysis method for cell line authentication.

    Directory of Open Access Journals (Sweden)

    Erik Fasterius

    Full Text Available We have developed a novel analysis method that can interrogate the authenticity of biological samples used for generation of transcriptome profiles in public data repositories. The method uses RNA sequencing information to reveal mutations in expressed transcripts and subsequently confirms the identity of analysed cells by comparison with publicly available cell-specific mutational profiles. Cell lines constitute key model systems widely used within cancer research, but their identity needs to be confirmed in order to minimise the influence of cell contaminations and genetic drift on the analysis. Using both public and novel data, we demonstrate the use of RNA-sequencing data analysis for cell line authentication by examining the validity of COLO205, DLD1, HCT15, HCT116, HKE3, HT29 and RKO colorectal cancer cell lines. We successfully authenticate the studied cell lines and validate previous reports indicating that DLD1 and HCT15 are synonymous. We also show that the analysed HKE3 cells harbour an unexpected KRAS-G13D mutation and confirm that this cell line is a genuine KRAS dosage mutant, rather than a true isogenic derivative of HCT116 expressing only the wild type KRAS. This authentication method could be used to revisit the numerous cell line based RNA sequencing experiments available in public data repositories, analyse new experiments where whole genome sequencing is not available, as well as facilitate comparisons of data from different experiments, platforms and laboratories.

  6. Sequencing, Characterization, and Comparative Analyses of the Plastome of Caragana rosea var. rosea

    Directory of Open Access Journals (Sweden)

    Mei Jiang

    2018-05-01

    Full Text Available To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea, C. microphylla, C. kozlowii, and C. Korshinskii. The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C. rosea, C. microphylla, C. kozlowii, and C. korshinskii, respectively. Analyses of sequence divergence found two intergenic regions: trnI-CAU-ycf2 and trnN-GUU-ycf1, exhibiting a high degree of variations. Phylogenetic analyses showed that the four Caragana species belong to a monophyletic clade. Analyses of Ka/Ks ratios revealed that five genes: rpl16, rpl20, rps11, rps7, and ycf1 and several sites having undergone strong positive selection in the Caragana branch. The results lay the foundation for the development of molecular markers and the understanding of the evolutionary process for drought-resistant characteristics.

  7. Direct synthesis of L1 type Fe-Pt nanoparticles using microwave-polyol method

    International Nuclear Information System (INIS)

    Minami, Rumiko; Kitamoto, Yoshitaka; Chikata, Tsukasa; Kato, Shunsaku

    2005-01-01

    We report the synthesis of Fe-Pt nanoparticles with microwave irradiation during polyol-reduction reaction. Chemically ordered Fe-Pt nanoparticles with L1 structure are fabricated at 250 deg. C using a microwave-polyol method without any post-synthesis treatments. Moessbauer analyses reveal the nanoparticles have partially ordered L1 structure. The partially ordered Fe-Pt nanoparticles exhibit coercivity of 3.4 kOe, saturation magnetization of 49 emu/g, and anisotropy field of 83 kOe at room temperature

  8. Magnetotomography—a new method for analysing fuel cell performance and quality

    Science.gov (United States)

    Hauer, Karl-Heinz; Potthast, Roland; Wüster, Thorsten; Stolten, Detlef

    Magnetotomography is a new method for the measurement and analysis of the current density distribution of fuel cells. The method is based on the measurement of the magnetic flux surrounding the fuel cell stack caused by the current inside the stack. As it is non-invasive, magnetotomography overcomes the shortcomings of traditional methods for the determination of current density in fuel cells [J. Stumper, S.A. Campell, D.P. Wilkinson, M.C. Johnson, M. Davis, In situ methods for the determination of current distributions in PEM fuel cells, Electrochem. Acta 43 (1998) 3773; S.J.C. Cleghorn, C.R. Derouin, M.S. Wilson, S. Gottesfeld, A printed circuit board approach to measuring current distribution in a fuel cell, J. Appl. Electrochem. 28 (1998) 663; Ch. Wieser, A. Helmbold, E. Gülzow, A new technique for two-dimensional current distribution measurements in electro-chemical cells, J. Appl. Electrochem. 30 (2000) 803; Grinzinger, Methoden zur Ortsaufgelösten Strommessung in Polymer Elektrolyt Brennstoffzellen, Diploma thesis, TU-München, 2003; Y.-G. Yoon, W.-Y. Lee, T.-H. Yang, G.-G. Park, C.-S. Kim, Current distribution in a single cell of PEMFC, J. Power Sources 118 (2003) 193-199; M.M. Mench, C.Y. Wang, An in situ method for determination of current distribution in PEM fuel cells applied to a direct methanol fuel cell, J. Electrochem. Soc. 150 (2003) A79-A85; S. Schönbauer, T. Kaz, H. Sander, E. Gülzow, Segmented bipolar plate for the determination of current distribution in polymer electrolyte fuel cells, in: Proceedings of the Second European PEMFC Forum, vol. 1, Lucerne/Switzerland, 2003, pp. 231-237; G. Bender, S.W. Mahlon, T.A. Zawodzinski, Further refinements in the segmented cell approach to diagnosing performance in polymer electrolyte fuel cells, J. Power Sources 123 (2003) 163-171]. After several years of research a complete prototype system is now available for research on single cells and stacks. This paper describes the basic system (fundamentals

  9. A test method for analysing disturbed ethernet data streams

    Science.gov (United States)

    Kreitlow, M.; Sabath, F.; Garbe, H.

    2015-11-01

    Ethernet connections, which are widely used in many computer networks, can suffer from electromagnetic interference. Typically, a degradation of the data transmission rate can be perceived as electromagnetic disturbances lead to corruption of data frames on the network media. In this paper a software-based measuring method is presented, which allows a direct assessment of the effects on the link layer. The results can directly be linked to the physical interaction without the influence of software related effects on higher protocol layers. This gives a simple tool for a quantitative analysis of the disturbance of an Ethernet connection based on time domain data. An example is shown, how the data can be used for further investigation of mechanisms and detection of intentional electromagnetic attacks.

  10. Bacterial diversity associated with the rotifer Brachionus plicatilis sp. complex determined by culture-dependent and -independent methods.

    Science.gov (United States)

    Ishino, Ryota; Iehata, Shunpei; Nakano, Miyo; Tanaka, Reiji; Yoshimatsu, Takao; Maeda, Hiroto

    2012-03-01

    The bacterial communities associated with rotifers (Brachionus plicatilis sp. complex) and their culture water were determined using culture-dependent and -independent methods (16S rRNA gene clone library). The bacterial communities determined by the culture-independent method were more diverse than those determined by the culture-dependent method. Although the culture-dependent method indicated the bacterial community of rotifers was relatively similar to that of the culture water, 16S rRNA gene clone library analyses revealed a great difference between the two microbiotas. Our results suggest that most bacteria associated with rotifers are not easily cultured using conventional methods, and that the microbiota of rotifers do not correspond with that of the culture water completely.

  11. Whole brain white matter changes revealed by multiple diffusion metrics in multiple sclerosis: A TBSS study

    International Nuclear Information System (INIS)

    Liu, Yaou; Duan, Yunyun; He, Yong; Yu, Chunshui; Wang, Jun; Huang, Jing; Ye, Jing; Parizel, Paul M.; Li, Kuncheng; Shu, Ni

    2012-01-01

    Objective: To investigate whole brain white matter changes in multiple sclerosis (MS) by multiple diffusion indices, we examined patients with diffusion tensor imaging and utilized tract-based spatial statistics (TBSS) method to analyze the data. Methods: Forty-one relapsing-remitting multiple sclerosis (RRMS) patients and 41 age- and gender-matched normal controls were included in this study. Diffusion weighted images were acquired by employing a single-shot echo planar imaging sequence on a 1.5 T MR scanner. Voxel-wise analyses of multiple diffusion metrics, including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD) were performed with TBSS. Results: The MS patients had significantly decreased FA (9.11%), increased MD (8.26%), AD (3.48%) and RD (13.17%) in their white matter skeletons compared with the controls. Through TBSS analyses, we found abnormal diffusion changes in widespread white matter regions in MS patients. Specifically, decreased FA, increased MD and increased RD were involved in whole-brain white matter, while several regions exhibited increased AD. Furthermore, white matter regions with significant correlations between the diffusion metrics and the clinical variables (the EDSS scores, disease durations and white matter lesion loads) in MS patients were identified. Conclusion: Widespread white matter abnormalities were observed in MS patients revealed by multiple diffusion metrics. The diffusion changes and correlations with clinical variables were mainly attributed to increased RD, implying the predominant role of RD in reflecting the subtle pathological changes in MS

  12. Whole brain white matter changes revealed by multiple diffusion metrics in multiple sclerosis: A TBSS study

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yaou, E-mail: asiaeurope80@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Duan, Yunyun, E-mail: xiaoyun81.love@163.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); He, Yong, E-mail: yong.h.he@gmail.com [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China); Yu, Chunshui, E-mail: csyuster@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Wang, Jun, E-mail: jun_wang@bnu.edu.cn [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China); Huang, Jing, E-mail: sainthj@126.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Ye, Jing, E-mail: jingye.2007@yahoo.com.cn [Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Parizel, Paul M., E-mail: paul.parizel@ua.ac.be [Department of Radiology, Antwerp University Hospital and University of Antwerp, Wilrijkstraat 10, 2650 Edegem, 8 Belgium (Belgium); Li, Kuncheng, E-mail: kunchengli55@gmail.com [Department of Radiology, Xuanwu Hospital, Capital Medical University, Beijing 100053 (China); Shu, Ni, E-mail: nshu55@gmail.com [State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875 (China)

    2012-10-15

    Objective: To investigate whole brain white matter changes in multiple sclerosis (MS) by multiple diffusion indices, we examined patients with diffusion tensor imaging and utilized tract-based spatial statistics (TBSS) method to analyze the data. Methods: Forty-one relapsing-remitting multiple sclerosis (RRMS) patients and 41 age- and gender-matched normal controls were included in this study. Diffusion weighted images were acquired by employing a single-shot echo planar imaging sequence on a 1.5 T MR scanner. Voxel-wise analyses of multiple diffusion metrics, including fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD) and radial diffusivity (RD) were performed with TBSS. Results: The MS patients had significantly decreased FA (9.11%), increased MD (8.26%), AD (3.48%) and RD (13.17%) in their white matter skeletons compared with the controls. Through TBSS analyses, we found abnormal diffusion changes in widespread white matter regions in MS patients. Specifically, decreased FA, increased MD and increased RD were involved in whole-brain white matter, while several regions exhibited increased AD. Furthermore, white matter regions with significant correlations between the diffusion metrics and the clinical variables (the EDSS scores, disease durations and white matter lesion loads) in MS patients were identified. Conclusion: Widespread white matter abnormalities were observed in MS patients revealed by multiple diffusion metrics. The diffusion changes and correlations with clinical variables were mainly attributed to increased RD, implying the predominant role of RD in reflecting the subtle pathological changes in MS.

  13. Freefem++ in THM analyses of KBS-3 deposition hole

    International Nuclear Information System (INIS)

    Lempinen, A.

    2006-12-01

    The applicability of Freefem++ as a software for thermo-hydro-mechanical analysis of KBS-3V deposition hole was evaluated. Freefem++ is software for multiphysical simulations with finite element method. A set of previously performed analyses were successfully repeated with Freefem++. The only significant problem was to impose unique values for variables at the canister surface. This problem can be circumvented with an iterative method, and it can possibly be solved later, since Freefem++ is opensource software. (orig.)

  14. Accuracy of the hypothetical sky-polarimetric Viking navigation versus sky conditions: revealing solar elevations and cloudinesses favourable for this navigation method.

    Science.gov (United States)

    Száz, Dénes; Farkas, Alexandra; Barta, András; Kretzer, Balázs; Blahó, Miklós; Egri, Ádám; Szabó, Gyula; Horváth, Gábor

    2017-09-01

    According to Thorkild Ramskou's theory proposed in 1967, under overcast and foggy skies, Viking seafarers might have used skylight polarization analysed with special crystals called sunstones to determine the position of the invisible Sun. After finding the occluded Sun with sunstones, its elevation angle had to be measured and its shadow had to be projected onto the horizontal surface of a sun compass. According to Ramskou's theory, these sunstones might have been birefringent calcite or dichroic cordierite or tourmaline crystals working as polarizers. It has frequently been claimed that this method might have been suitable for navigation even in cloudy weather. This hypothesis has been accepted and frequently cited for decades without any experimental support. In this work, we determined the accuracy of this hypothetical sky-polarimetric Viking navigation for 1080 different sky situations characterized by solar elevation θ and cloudiness ρ , the sky polarization patterns of which were measured by full-sky imaging polarimetry. We used the earlier measured uncertainty functions of the navigation steps 1, 2 and 3 for calcite, cordierite and tourmaline sunstone crystals, respectively, and the newly measured uncertainty function of step 4 presented here. As a result, we revealed the meteorological conditions under which Vikings could have used this hypothetical navigation method. We determined the solar elevations at which the navigation uncertainties are minimal at summer solstice and spring equinox for all three sunstone types. On average, calcite sunstone ensures a more accurate sky-polarimetric navigation than tourmaline and cordierite. However, in some special cases (generally at 35° ≤  θ  ≤ 40°, 1 okta ≤  ρ  ≤ 6 oktas for summer solstice, and at 20° ≤  θ  ≤ 25°, 0 okta ≤  ρ  ≤ 4 oktas for spring equinox), the use of tourmaline and cordierite results in smaller navigation uncertainties than that of calcite

  15. Coupled 230Th/234U-ESR analyses for corals: A new method to assess sealevel change

    International Nuclear Information System (INIS)

    Blackwell, Bonnie A.B.; Teng, Steve J.T.; Lundberg, Joyce A.; Blickstein, Joel I.B.; Skinner, Anne R.

    2007-01-01

    Although coupled 230 Th/ 234 U-ESR analyses have become routine for dating teeth, they have never been used for corals. While the ESR age depends on, and requires assumptions about, the time-averaged cosmic dose rate, D-bar cos (t), 230 Th/ 234 U dates do not. Since D-bar cos (t) received by corals depends on the attenuation by any intervening material, D-bar cos (t) response reflects changing water depths and sediment cover. By coupling the two methods, one can determine the age and a unique D-bar cos,coupled (t) simultaneously. From a coral's water depth and sedimentary history as predicted by a given sealevel curve, one can predict D-bar cos,sealevel (t). If D-bar cos,coupled (t) agrees well with D-bar cos,sealevel (t), this provides independent validation for the curve used to build D-bar cos,sealevel (t). For six corals dated at 7-128 ka from Florida Platform reef crests, the sealevel curve by Waelbroeck et al. [2002. Sea-level and deep water temperature changes derived from benthonic foraminifera isotopic records. Quat. Sci. Rev. 21, 295-305] predicted their D-bar cos,coupled (t) values as well as, or better than, the SPECMAP sealevel curve. Where a whole reef can be sampled over a transect, a precise test for sealevel curves could be developed

  16. Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells.

    Science.gov (United States)

    Yamamuro, Ayaka; Kouzuma, Atsushi; Abe, Takashi; Watanabe, Kazuya

    2014-01-01

    Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs) have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2) (based on the projected area of the anode). In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

  17. Lagrangian Coherent Structure Analysis of Terminal Winds: Three-Dimensionality, Intramodel Variations, and Flight Analyses

    Directory of Open Access Journals (Sweden)

    Brent Knutson

    2015-01-01

    Full Text Available We present a study of three-dimensional Lagrangian coherent structures (LCS near the Hong Kong International Airport and relate to previous developments of two-dimensional (2D LCS analyses. The LCS are contrasted among three independent models and against 2D coherent Doppler light detection and ranging (LIDAR data. Addition of the velocity information perpendicular to the LIDAR scanning cone helps solidify flow structures inferred from previous studies; contrast among models reveals the intramodel variability; and comparison with flight data evaluates the performance among models in terms of Lagrangian analyses. We find that, while the three models and the LIDAR do recover similar features of the windshear experienced by a landing aircraft (along the landing trajectory, their Lagrangian signatures over the entire domain are quite different—a portion of each numerical model captures certain features resembling those LCS extracted from independent 2D LIDAR analyses based on observations.

  18. Evaluating public involvement in research design and grant development: Using a qualitative document analysis method to analyse an award scheme for researchers.

    Science.gov (United States)

    Baxter, Susan; Muir, Delia; Brereton, Louise; Allmark, Christine; Barber, Rosemary; Harris, Lydia; Hodges, Brian; Khan, Samaira; Baird, Wendy

    2016-01-01

    money was used, including a description of the aims and outcomes of the public involvement activities. The purpose of this study was to analyse the content of these reports. We aimed to find out what researcher views and experiences of public involvement activities were, and what lessons might be learned. Methods We used an innovative method of data analysis, drawing on group participatory approaches, qualitative content analysis, and Framework Analysis to sort and label the content of the reports. We developed a framework of categories and sub-categories (or themes and sub-themes) from this process. Results Twenty five documents were analysed. Four main themes were identified in the data: the added value of public involvement; planning and designing involvement; the role of public members; and valuing public member contributions. Within these themes, sub-themes related to the timing of involvement (prior to the research study/intended during the research study), and also specific benefits of public involvement such as: validating ideas; ensuring appropriate outcomes; ensuring the acceptability of data collection methods/tools and advice regarding research processes. Other sub-themes related to: finding and approaching public members; timing of events; training/support; the format of sessions; setting up public involvement panels: use of public contributors in analysis and interpretation of data; and using public members to assist with dissemination and translation into practice. Conclusions The analysis of reports submitted by researchers following involvement events provides evidence of the value of public involvement during the development of applications for research funding, and details a method for involving members of the public in data analysis which could be of value to other researchers The findings of the analysis indicate recognition amongst researchers of the variety in potential roles for public members in research, and also an acknowledgement of how

  19. Transcriptomic and Functional Analyses Reveal That PpGLK1 Regulates Chloroplast Development in Peach (Prunus persica

    Directory of Open Access Journals (Sweden)

    Min Chen

    2018-01-01

    Full Text Available Peach is an ideal species for fruit tree research because of its small, fully sequenced genome. Chloroplast development is dependent on the tight cooperation between the nuclear and plastid genomes, and is regulated by GLK transcription factors. In this work, the pigment content was monitored and the chloroplast-to-chromoplast conversion during the fruit ripening was visualized by transmission electron microscopy. Localization and expression analyses showed that PpGLK1 was located in the nucleus and expressed mainly in the leaves and fruit skin. A transcriptome analysis showed that PpGLK1 and its target genes were significantly differentially expressed in ripening peach fruit skin. PpGLK1 silencing affected chlorophyll accumulation in peach leaves and fruits. Overexpression of PpGLK1 rescued the phenotypes of the Arabidopsis Atglk1Atglk2 double mutant and the tomato uniform ripening mutant. The results of a yeast two-hybrid analysis showed that PpGLK1 is autoactivated and that PpGLK1 (301-542 a.a. interacted with PpARF5. Together, our results indicate that PpGLK1 regulates chloroplast development in green tissues in peach. Therefore, it may be a promising target gene for improving the production and quality of peach by genetic engineering and breeding approaches.

  20. Thermal and structural study of guava (Psidium guajava L powders obtained by two dehydration methods

    Directory of Open Access Journals (Sweden)

    Coralia Osorio

    2011-01-01

    Full Text Available Two food products (powders were obtained by hot-air drying or lyophilisation methods on the whole guava fruits. The powders were characterised by sensory and thermal analyses (TGA-DSC, infrared spectroscopy (IR, X-ray diffraction (XRD and scanning electron microscopy (SEM. Thermal, morphological and structural characterisations showed a similar behaviour for the two solids. TGA-DSC and IR showed the presence of pectin as the main constituent of solids. A semi-crystalline profile was evidenced by XRD, and lamellar/spherical morphologies were observed by SEM. Sensory analyses revealed an aroma highly related to guava. These value-added food products are an alternative to process guava and avoid loss during postharvest handling.