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Sample records for resequencing highly variable

  1. Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data.

    Science.gov (United States)

    Chiara, Matteo; Pavesi, Giulio

    2017-01-01

    Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human "variome," through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science. Bioinformatic analysis of human resequencing data is one of the main factors limiting the effectiveness and general applicability of NGS for clinical studies. The requirement for multiple tools, to be combined in dedicated protocols in order to accommodate different types of data (gene panels, exomes, or whole genomes) and the high variability of the data makes difficult the establishment of a ultimate strategy of general use. While there already exist several studies comparing sensitivity and accuracy of bioinformatic pipelines for the identification of single nucleotide variants from resequencing data, little is known about the impact of quality assessment and reads pre-processing strategies. In this work we discuss major strengths and limitations of the various genome resequencing protocols are currently used in molecular diagnostics and for the discovery of novel disease-causing mutations. By taking advantage of publicly available data we devise and suggest a series of best practices for the pre-processing of the data that consistently improve the outcome of genotyping with minimal impacts on computational costs.

  2. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  3. High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.

    Science.gov (United States)

    Majoros, William H; Campbell, Michael S; Holt, Carson; DeNardo, Erin K; Ware, Doreen; Allen, Andrew S; Yandell, Mark; Reddy, Timothy E

    2017-05-15

    The accurate interpretation of genetic variants is critical for characterizing genotype-phenotype associations. Because the effects of genetic variants can depend strongly on their local genomic context, accurate genome annotations are essential. Furthermore, as some variants have the potential to disrupt or alter gene structure, variant interpretation efforts stand to gain from the use of individualized annotations that account for differences in gene structure between individuals or strains. We describe a suite of software tools for identifying possible functional changes in gene structure that may result from sequence variants. ACE ('Assessing Changes to Exons') converts phased genotype calls to a collection of explicit haplotype sequences, maps transcript annotations onto them, detects gene-structure changes and their possible repercussions, and identifies several classes of possible loss of function. Novel transcripts predicted by ACE are commonly supported by spliced RNA-seq reads, and can be used to improve read alignment and transcript quantification when an individual-specific genome sequence is available. Using publicly available RNA-seq data, we show that ACE predictions confirm earlier results regarding the quantitative effects of nonsense-mediated decay, and we show that predicted loss-of-function events are highly concordant with patterns of intolerance to mutations across the human population. ACE can be readily applied to diverse species including animals and plants, making it a broadly useful tool for use in eukaryotic population-based resequencing projects, particularly for assessing the joint impact of all variants at a locus. ACE is written in open-source C ++ and Perl and is available from geneprediction.org/ACE. myandell@genetics.utah.edu or tim.reddy@duke.edu. Supplementary information is available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e

  4. RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing

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    Jinfeng Chen

    2017-01-01

    Full Text Available Background Transposable element (TE polymorphisms are important components of population genetic variation. The functional impacts of TEs in gene regulation and generating genetic diversity have been observed in multiple species, but the frequency and magnitude of TE variation is under appreciated. Inexpensive and deep sequencing technology has made it affordable to apply population genetic methods to whole genomes with methods that identify single nucleotide and insertion/deletion polymorphisms. However, identifying TE polymorphisms, particularly transposition events or non-reference insertion sites can be challenging due to the repetitive nature of these sequences, which hamper both the sensitivity and specificity of analysis tools. Methods We have developed the tool RelocaTE2 for identification of TE insertion sites at high sensitivity and specificity. RelocaTE2 searches for known TE sequences in whole genome sequencing reads from second generation sequencing platforms such as Illumina. These sequence reads are used as seeds to pinpoint chromosome locations where TEs have transposed. RelocaTE2 detects target site duplication (TSD of TE insertions allowing it to report TE polymorphism loci with single base pair precision. Results and Discussion The performance of RelocaTE2 is evaluated using both simulated and real sequence data. RelocaTE2 demonstrate high level of sensitivity and specificity, particularly when the sequence coverage is not shallow. In comparison to other tools tested, RelocaTE2 achieves the best balance between sensitivity and specificity. In particular, RelocaTE2 performs best in prediction of TSDs for TE insertions. Even in highly repetitive regions, such as those tested on rice chromosome 4, RelocaTE2 is able to report up to 95% of simulated TE insertions with less than 0.1% false positive rate using 10-fold genome coverage resequencing data. RelocaTE2 provides a robust solution to identify TE insertion sites and can be

  5. Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

    Directory of Open Access Journals (Sweden)

    Zdepski Anna

    2011-05-01

    Full Text Available Abstract Background High throughput sequencing (HTS technologies have revolutionized the field of genomics by drastically reducing the cost of sequencing, making it feasible for individual labs to sequence or resequence plant genomes. Obtaining high quality, high molecular weight DNA from plants poses significant challenges due to the high copy number of chloroplast and mitochondrial DNA, as well as high levels of phenolic compounds and polysaccharides. Multiple methods have been used to isolate DNA from plants; the CTAB method is commonly used to isolate total cellular DNA from plants that contain nuclear DNA, as well as chloroplast and mitochondrial DNA. Alternatively, DNA can be isolated from nuclei to minimize chloroplast and mitochondrial DNA contamination. Results We describe optimized protocols for isolation of nuclear DNA from eight different plant species encompassing both monocot and eudicot species. These protocols use nuclei isolation to minimize chloroplast and mitochondrial DNA contamination. We also developed a protocol to determine the number of chloroplast and mitochondrial DNA copies relative to the nuclear DNA using quantitative real time PCR (qPCR. We compared DNA isolated from nuclei to total cellular DNA isolated with the CTAB method. As expected, DNA isolated from nuclei consistently yielded nuclear DNA with fewer chloroplast and mitochondrial DNA copies, as compared to the total cellular DNA prepared with the CTAB method. This protocol will allow for analysis of the quality and quantity of nuclear DNA before starting a plant whole genome sequencing or resequencing experiment. Conclusions Extracting high quality, high molecular weight nuclear DNA in plants has the potential to be a bottleneck in the era of whole genome sequencing and resequencing. The methods that are described here provide a framework for researchers to extract and quantify nuclear DNA in multiple types of plants.

  6. Global assessment of genomic variation in cattle by genome resequencing and high-throughput genotyping

    DEFF Research Database (Denmark)

    Zhan, Bujie; Fadista, João; Thomsen, Bo

    2011-01-01

    Background Integration of genomic variation with phenotypic information is an effective approach for uncovering genotype-phenotype associations. This requires an accurate identification of the different types of variation in individual genomes. Results We report the integration of the whole genome...... of split-read and read-pair approaches proved to be complementary in finding different signatures. CNVs were identified on the basis of the depth of sequenced reads, and by using SNP and CGH arrays. Conclusions Our results provide high resolution mapping of diverse classes of genomic variation...

  7. Reliable Detection of Herpes Simplex Virus Sequence Variation by High-Throughput Resequencing.

    Science.gov (United States)

    Morse, Alison M; Calabro, Kaitlyn R; Fear, Justin M; Bloom, David C; McIntyre, Lauren M

    2017-08-16

    High-throughput sequencing (HTS) has resulted in data for a number of herpes simplex virus (HSV) laboratory strains and clinical isolates. The knowledge of these sequences has been critical for investigating viral pathogenicity. However, the assembly of complete herpesviral genomes, including HSV, is complicated due to the existence of large repeat regions and arrays of smaller reiterated sequences that are commonly found in these genomes. In addition, the inherent genetic variation in populations of isolates for viruses and other microorganisms presents an additional challenge to many existing HTS sequence assembly pipelines. Here, we evaluate two approaches for the identification of genetic variants in HSV1 strains using Illumina short read sequencing data. The first, a reference-based approach, identifies variants from reads aligned to a reference sequence and the second, a de novo assembly approach, identifies variants from reads aligned to de novo assembled consensus sequences. Of critical importance for both approaches is the reduction in the number of low complexity regions through the construction of a non-redundant reference genome. We compared variants identified in the two methods. Our results indicate that approximately 85% of variants are identified regardless of the approach. The reference-based approach to variant discovery captures an additional 15% representing variants divergent from the HSV1 reference possibly due to viral passage. Reference-based approaches are significantly less labor-intensive and identify variants across the genome where de novo assembly-based approaches are limited to regions where contigs have been successfully assembled. In addition, regions of poor quality assembly can lead to false variant identification in de novo consensus sequences. For viruses with a well-assembled reference genome, a reference-based approach is recommended.

  8. Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.

    Directory of Open Access Journals (Sweden)

    Mayumi Kamada

    Full Text Available De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food "natto." The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome.

  9. Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle

    DEFF Research Database (Denmark)

    Vilkki, Johanna; Iso-Touru, Terhi; Schulman, Nina F

    Mastitis is the most common disease of dairy cattle, causing high economic losses each year. Studies to locate QTL affecting clinical mastitis and milk somatic cell counts have been carried out to increase our understanding of the disease. As part of the EU FP7 Quantomics project, we have used most...... recent genomic tools to characterize QTL affecting mastitis incidence in the Finnish Ayrshire cattle. Clinical mastitis diagnoses from -15 to 50 days and 51 to 300 days of first lactation and SCC (geometric mean of SCS observations between 5 to 170 days of first lactation) were included. In total, 1920...... progeny tested bulls were genotyped with the Illumina BovineSNP50 chip. After quality control, 38473 SNPs were analyzed using a mixed linear model (software package DMU). Associations (5% Bonferroni threshold) were detected in 9 peaks on 5 chromosomes. A set of 238 of the bulls were re...

  10. High-throughput multiplex cpDNA resequencing clarifies the genetic diversity and genetic relationships among Brassica napus, Brassica rapa and Brassica oleracea.

    Science.gov (United States)

    Qiao, Jiangwei; Cai, Mengxian; Yan, Guixin; Wang, Nian; Li, Feng; Chen, Binyun; Gao, Guizhen; Xu, Kun; Li, Jun; Wu, Xiaoming

    2016-01-01

    Brassica napus (rapeseed) is a recent allotetraploid plant and the second most important oilseed crop worldwide. The origin of B. napus and the genetic relationships with its diploid ancestor species remain largely unresolved. Here, chloroplast DNA (cpDNA) from 488 B. napus accessions of global origin, 139 B. rapa accessions and 49 B. oleracea accessions were populationally resequenced using Illumina Solexa sequencing technologies. The intraspecific cpDNA variants and their allelic frequencies were called genomewide and further validated via EcoTILLING analyses of the rpo region. The cpDNA of the current global B. napus population comprises more than 400 variants (SNPs and short InDels) and maintains one predominant haplotype (Bncp1). Whole-genome resequencing of the cpDNA of Bncp1 haplotype eliminated its direct inheritance from any accession of the B. rapa or B. oleracea species. The distribution of the polymorphism information content (PIC) values for each variant demonstrated that B. napus has much lower cpDNA diversity than B. rapa; however, a vast majority of the wild and cultivated B. oleracea specimens appeared to share one same distinct cpDNA haplotype, in contrast to its wild C-genome relatives. This finding suggests that the cpDNA of the three Brassica species is well differentiated. The predominant B. napus cpDNA haplotype may have originated from uninvestigated relatives or from interactions between cpDNA mutations and natural/artificial selection during speciation and evolution. These exhaustive data on variation in cpDNA would provide fundamental data for research on cpDNA and chloroplasts. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  11. SNP detection for massively parallel whole-genome resequencing

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Li, Yingrui; Fang, Xiaodong

    2009-01-01

    -genome or target region resequencing. Here, we have developed a consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology. We designed this method by carefully considering the data quality, alignment, and experimental errors common to this technology. All...... of this information was integrated into a single quality score for each base under Bayesian theory to measure the accuracy of consensus calling. We tested this methodology using a large-scale human resequencing data set of 36x coverage and assembled a high-quality nonrepetitive consensus sequence for 92.......25% of the diploid autosomes and 88.07% of the haploid X chromosome. Comparison of the consensus sequence with Illumina human 1M BeadChip genotyped alleles from the same DNA sample showed that 98.6% of the 37,933 genotyped alleles on the X chromosome and 98% of 999,981 genotyped alleles on autosomes were covered...

  12. A targeted resequencing gene panel for focal epilepsy.

    Science.gov (United States)

    Hildebrand, Michael S; Myers, Candace T; Carvill, Gemma L; Regan, Brigid M; Damiano, John A; Mullen, Saul A; Newton, Mark R; Nair, Umesh; Gazina, Elena V; Milligan, Carol J; Reid, Christopher A; Petrou, Steven; Scheffer, Ingrid E; Berkovic, Samuel F; Mefford, Heather C

    2016-04-26

    We report development of a targeted resequencing gene panel for focal epilepsy, the most prevalent phenotypic group of the epilepsies. The targeted resequencing gene panel was designed using molecular inversion probe (MIP) capture technology and sequenced using massively parallel Illumina sequencing. We demonstrated proof of principle that mutations can be detected in 4 previously genotyped focal epilepsy cases. We searched for both germline and somatic mutations in 251 patients with unsolved sporadic or familial focal epilepsy and identified 11 novel or very rare missense variants in 5 different genes: CHRNA4, GRIN2B, KCNT1, PCDH19, and SCN1A. Of these, 2 were predicted to be pathogenic or likely pathogenic, explaining ∼0.8% of the cohort, and 8 were of uncertain significance based on available data. We have developed and validated a targeted resequencing panel for focal epilepsies, the most important clinical class of epilepsies, accounting for about 60% of all cases. Our application of MIP technology is an innovative approach that will be advantageous in the clinical setting because it is highly sensitive, efficient, and cost-effective for screening large patient cohorts. Our findings indicate that mutations in known genes likely explain only a small proportion of focal epilepsy cases. This is not surprising given the established clinical and genetic heterogeneity of these disorders and underscores the importance of further gene discovery studies in this complex syndrome. © 2016 American Academy of Neurology.

  13. High-density genetic map using whole-genome re-sequencing for fine mapping and candidate gene discovery for disease resistance in peanut

    Science.gov (United States)

    High-density genetic linkage maps are essential for fine mapping QTLs controlling disease resistance traits, such as early leaf spot (ELS), late leaf spot (LLS), and Tomato spotted wilt virus (TSWV). With completion of the genome sequences of two diploid ancestors of cultivated peanut, we could use ...

  14. MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.

    Directory of Open Access Journals (Sweden)

    Mikhail Shugay

    2017-05-01

    Full Text Available Unique molecular identifiers (UMIs show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats of UMI-based analysis to obtain high-fidelity mutation profiles and call ultra-rare variants. Using an extensive set of benchmark datasets including gold-standard biological samples with known variant frequencies, cell-free DNA from tumor patient blood samples and publicly available UMI-encoded datasets we demonstrate that our method is both robust and efficient in calling rare variants. The versatility of our software is supported by accurate results obtained for both tumor DNA and viral RNA samples in datasets prepared using three different UMI-based protocols.

  15. Universal Detection and Identification of Avian Influenza Virus by Use of Resequencing Microarrays

    Science.gov (United States)

    2009-04-01

    Recent outbreaks of Nipah virus , severe acute respiratory syndrome virus , and avian influenza virus reiterate the impor- tance of zoonotic microbes as...Society for Microbiology. All Rights Reserved. Universal Detection and Identification of Avian Influenza Virus by Use of Resequencing Microarrays...been, and continue to emerge as, threats to human health. The recent outbreaks of highly pathogenic avian influenza virus in bird populations and the

  16. Conspicuous plumage colours are highly variable

    OpenAIRE

    Delhey, Kaspar; Szecsenyi, Beatrice; Nakagawa, Shinichi; Peters, Anne

    2017-01-01

    Elaborate ornamental traits are often under directional selection for greater elaboration, which in theory should deplete underlying genetic variation. Despite this, many ornamental traits appear to remain highly variable and how this essential variation is maintained is a key question in evolutionary biology. One way to address this question is to compare differences in intraspecific variability across different types of traits to determine whether high levels of variation are associated wit...

  17. Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses.

    Science.gov (United States)

    Dacheux, Laurent; Berthet, Nicolas; Dissard, Gabriel; Holmes, Edward C; Delmas, Olivier; Larrous, Florence; Guigon, Ghislaine; Dickinson, Philip; Faye, Ousmane; Sall, Amadou A; Old, Iain G; Kong, Katherine; Kennedy, Giulia C; Manuguerra, Jean-Claude; Cole, Stewart T; Caro, Valérie; Gessain, Antoine; Bourhy, Hervé

    2010-09-01

    The rapid and accurate identification of pathogens is critical in the control of infectious disease. To this end, we analyzed the capacity for viral detection and identification of a newly described high-density resequencing microarray (RMA), termed PathogenID, which was designed for multiple pathogen detection using database similarity searching. We focused on one of the largest and most diverse viral families described to date, the family Rhabdoviridae. We demonstrate that this approach has the potential to identify both known and related viruses for which precise sequence information is unavailable. In particular, we demonstrate that a strategy based on consensus sequence determination for analysis of RMA output data enabled successful detection of viruses exhibiting up to 26% nucleotide divergence with the closest sequence tiled on the array. Using clinical specimens obtained from rabid patients and animals, this method also shows a high species level concordance with standard reference assays, indicating that it is amenable for the development of diagnostic assays. Finally, 12 animal rhabdoviruses which were currently unclassified, unassigned, or assigned as tentative species within the family Rhabdoviridae were successfully detected. These new data allowed an unprecedented phylogenetic analysis of 106 rhabdoviruses and further suggest that the principles and methodology developed here may be used for the broad-spectrum surveillance and the broader-scale investigation of biodiversity in the viral world.

  18. Application of Broad-Spectrum Resequencing Microarray for Genotyping Rhabdoviruses▿

    Science.gov (United States)

    Dacheux, Laurent; Berthet, Nicolas; Dissard, Gabriel; Holmes, Edward C.; Delmas, Olivier; Larrous, Florence; Guigon, Ghislaine; Dickinson, Philip; Faye, Ousmane; Sall, Amadou A.; Old, Iain G.; Kong, Katherine; Kennedy, Giulia C.; Manuguerra, Jean-Claude; Cole, Stewart T.; Caro, Valérie; Gessain, Antoine; Bourhy, Hervé

    2010-01-01

    The rapid and accurate identification of pathogens is critical in the control of infectious disease. To this end, we analyzed the capacity for viral detection and identification of a newly described high-density resequencing microarray (RMA), termed PathogenID, which was designed for multiple pathogen detection using database similarity searching. We focused on one of the largest and most diverse viral families described to date, the family Rhabdoviridae. We demonstrate that this approach has the potential to identify both known and related viruses for which precise sequence information is unavailable. In particular, we demonstrate that a strategy based on consensus sequence determination for analysis of RMA output data enabled successful detection of viruses exhibiting up to 26% nucleotide divergence with the closest sequence tiled on the array. Using clinical specimens obtained from rabid patients and animals, this method also shows a high species level concordance with standard reference assays, indicating that it is amenable for the development of diagnostic assays. Finally, 12 animal rhabdoviruses which were currently unclassified, unassigned, or assigned as tentative species within the family Rhabdoviridae were successfully detected. These new data allowed an unprecedented phylogenetic analysis of 106 rhabdoviruses and further suggest that the principles and methodology developed here may be used for the broad-spectrum surveillance and the broader-scale investigation of biodiversity in the viral world. PMID:20610710

  19. Conspicuous plumage colours are highly variable.

    Science.gov (United States)

    Delhey, Kaspar; Szecsenyi, Beatrice; Nakagawa, Shinichi; Peters, Anne

    2017-01-25

    Elaborate ornamental traits are often under directional selection for greater elaboration, which in theory should deplete underlying genetic variation. Despite this, many ornamental traits appear to remain highly variable and how this essential variation is maintained is a key question in evolutionary biology. One way to address this question is to compare differences in intraspecific variability across different types of traits to determine whether high levels of variation are associated with specific trait characteristics. Here we assess intraspecific variation in more than 100 plumage colours across 55 bird species to test whether colour variability is linked to their level of elaboration (indicated by degree of sexual dichromatism and conspicuousness) or their condition dependence (indicated by mechanism of colour production). Conspicuous colours had the highest levels of variation and conspicuousness was the strongest predictor of variability, with high explanatory power. After accounting for this, there were no significant effects of sexual dichromatism or mechanisms of colour production. Conspicuous colours may entail higher production costs or may be more sensitive to disruptions during production. Alternatively, high variability could also be related to increased perceptual difficulties inherent to discriminating highly elaborate colours. Such psychophysical effects may constrain the exaggeration of animal colours. © 2017 The Author(s).

  20. High efficiency, variable geometry, centrifugal cryogenic pump

    International Nuclear Information System (INIS)

    Forsha, M.D.; Nichols, K.E.; Beale, C.A.

    1994-01-01

    A centrifugal cryogenic pump has been developed which has a basic design that is rugged and reliable with variable speed and variable geometry features that achieve high pump efficiency over a wide range of head-flow conditions. The pump uses a sealless design and rolling element bearings to achieve high reliability and the ruggedness to withstand liquid-vapor slugging. The pump can meet a wide range of variable head, off-design flow requirements and maintain design point efficiency by adjusting the pump speed. The pump also has features that allow the impeller and diffuser blade heights to be adjusted. The adjustable height blades were intended to enhance the pump efficiency when it is operating at constant head, off-design flow rates. For small pumps, the adjustable height blades are not recommended. For larger pumps, they could provide off-design efficiency improvements. This pump was developed for supercritical helium service, but the design is well suited to any cryogenic application where high efficiency is required over a wide range of head-flow conditions

  1. BFAST: an alignment tool for large scale genome resequencing.

    Directory of Open Access Journals (Sweden)

    Nils Homer

    2009-11-01

    Full Text Available The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25-100 base range, in the presence of errors and true biological variation.We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels.We compare BFAST to a selection of large-scale alignment tools -- BLAT, MAQ, SHRiMP, and SOAP -- in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at (http://bfast.sourceforge.net.

  2. Quantification of differential gene expression by multiplexed targeted resequencing of cDNA

    Science.gov (United States)

    Arts, Peer; van der Raadt, Jori; van Gestel, Sebastianus H.C.; Steehouwer, Marloes; Shendure, Jay; Hoischen, Alexander; Albers, Cornelis A.

    2017-01-01

    Whole-transcriptome or RNA sequencing (RNA-Seq) is a powerful and versatile tool for functional analysis of different types of RNA molecules, but sample reagent and sequencing cost can be prohibitive for hypothesis-driven studies where the aim is to quantify differential expression of a limited number of genes. Here we present an approach for quantification of differential mRNA expression by targeted resequencing of complementary DNA using single-molecule molecular inversion probes (cDNA-smMIPs) that enable highly multiplexed resequencing of cDNA target regions of ∼100 nucleotides and counting of individual molecules. We show that accurate estimates of differential expression can be obtained from molecule counts for hundreds of smMIPs per reaction and that smMIPs are also suitable for quantification of relative gene expression and allele-specific expression. Compared with low-coverage RNA-Seq and a hybridization-based targeted RNA-Seq method, cDNA-smMIPs are a cost-effective high-throughput tool for hypothesis-driven expression analysis in large numbers of genes (10 to 500) and samples (hundreds to thousands). PMID:28474677

  3. Integration of transcriptome and whole genomic resequencing data to identify key genes affecting swine fat deposition.

    Directory of Open Access Journals (Sweden)

    Kai Xing

    Full Text Available Fat deposition is highly correlated with the growth, meat quality, reproductive performance and immunity of pigs. Fatty acid synthesis takes place mainly in the adipose tissue of pigs; therefore, in this study, a high-throughput massively parallel sequencing approach was used to generate adipose tissue transcriptomes from two groups of Songliao black pigs that had opposite backfat thickness phenotypes. The total number of paired-end reads produced for each sample was in the range of 39.29-49.36 millions. Approximately 188 genes were differentially expressed in adipose tissue and were enriched for metabolic processes, such as fatty acid biosynthesis, lipid synthesis, metabolism of fatty acids, etinol, caffeine and arachidonic acid and immunity. Additionally, many genetic variations were detected between the two groups through pooled whole-genome resequencing. Integration of transcriptome and whole-genome resequencing data revealed important genomic variations among the differentially expressed genes for fat deposition, for example, the lipogenic genes. Further studies are required to investigate the roles of candidate genes in fat deposition to improve pig breeding programs.

  4. Variable high gradient permanent magnet quadrupole (QUAPEVA)

    Science.gov (United States)

    Marteau, F.; Ghaith, A.; N'Gotta, P.; Benabderrahmane, C.; Valléau, M.; Kitegi, C.; Loulergue, A.; Vétéran, J.; Sebdaoui, M.; André, T.; Le Bec, G.; Chavanne, J.; Vallerand, C.; Oumbarek, D.; Cosson, O.; Forest, F.; Jivkov, P.; Lancelot, J. L.; Couprie, M. E.

    2017-12-01

    Different applications such as laser plasma acceleration, colliders, and diffraction limited light sources require high gradient quadrupoles, with strength that can reach up to 200 T/m for a typical 10 mm bore diameter. We present here a permanent magnet based quadrupole (so-called QUAPEVA) composed of a Halbach ring and surrounded by four permanent magnet cylinders. Its design including magnetic simulation modeling enabling us to reach 201 T/m with a gradient variability of 45% and mechanical issues are reported. Magnetic measurements of seven systems of different lengths are presented and confirmed the theoretical expectations. The variation of the magnetic center while changing the gradient strength is ±10 μm. A triplet of QUAPEVA magnets is used to efficiently focus a beam with large energy spread and high divergence that is generated by a Laser Plasma Acceleration source for a free electron laser demonstration and has enabled us to perform beam based alignment and control the dispersion of the beam.

  5. Efficient alignment of pyrosequencing reads for re-sequencing applications

    Directory of Open Access Journals (Sweden)

    Russo Luis MS

    2011-05-01

    Full Text Available Abstract Background Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these techniques also raise important computational difficulties mostly due to the huge volume of data produced, but also because of some of their specific characteristics such as read length and sequencing errors. Among the most critical problems is that of efficiently and accurately mapping reads to a reference genome in the context of re-sequencing projects. Results We present an efficient method for the local alignment of pyrosequencing reads produced by the GS FLX (454 system against a reference sequence. Our approach explores the characteristics of the data in these re-sequencing applications and uses state of the art indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. An evaluation performed using real and simulated data shows that our proposed method outperforms a number of mainstream tools on the quantity and quality of successful alignments, as well as on the execution time. Conclusions The proposed methodology was implemented in a software tool called TAPyR--Tool for the Alignment of Pyrosequencing Reads--which is publicly available from http://www.tapyr.net.

  6. Selective whole genome amplification for resequencing target microbial species from complex natural samples.

    Science.gov (United States)

    Leichty, Aaron R; Brisson, Dustin

    2014-10-01

    Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. Copyright © 2014 by the Genetics Society of America.

  7. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

    DEFF Research Database (Denmark)

    Xu, Xun; Liu, Xin; Ge, Song

    2012-01-01

    Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 x...... diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable...... raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower...

  8. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions.

    Science.gov (United States)

    Guo, Shaogui; Zhang, Jianguo; Sun, Honghe; Salse, Jerome; Lucas, William J; Zhang, Haiying; Zheng, Yi; Mao, Linyong; Ren, Yi; Wang, Zhiwen; Min, Jiumeng; Guo, Xiaosen; Murat, Florent; Ham, Byung-Kook; Zhang, Zhaoliang; Gao, Shan; Huang, Mingyun; Xu, Yimin; Zhong, Silin; Bombarely, Aureliano; Mueller, Lukas A; Zhao, Hong; He, Hongju; Zhang, Yan; Zhang, Zhonghua; Huang, Sanwen; Tan, Tao; Pang, Erli; Lin, Kui; Hu, Qun; Kuang, Hanhui; Ni, Peixiang; Wang, Bo; Liu, Jingan; Kou, Qinghe; Hou, Wenju; Zou, Xiaohua; Jiang, Jiao; Gong, Guoyi; Klee, Kathrin; Schoof, Heiko; Huang, Ying; Hu, Xuesong; Dong, Shanshan; Liang, Dequan; Wang, Juan; Wu, Kui; Xia, Yang; Zhao, Xiang; Zheng, Zequn; Xing, Miao; Liang, Xinming; Huang, Bangqing; Lv, Tian; Wang, Junyi; Yin, Ye; Yi, Hongping; Li, Ruiqiang; Wu, Mingzhu; Levi, Amnon; Zhang, Xingping; Giovannoni, James J; Wang, Jun; Li, Yunfu; Fei, Zhangjun; Xu, Yong

    2013-01-01

    Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolutionary scenario for the origin of the 11 watermelon chromosomes derived from a 7-chromosome paleohexaploid eudicot ancestor. Resequencing of 20 watermelon accessions representing three different C. lanatus subspecies produced numerous haplotypes and identified the extent of genetic diversity and population structure of watermelon germplasm. Genomic regions that were preferentially selected during domestication were identified. Many disease-resistance genes were also found to be lost during domestication. In addition, integrative genomic and transcriptomic analyses yielded important insights into aspects of phloem-based vascular signaling in common between watermelon and cucumber and identified genes crucial to valuable fruit-quality traits, including sugar accumulation and citrulline metabolism.

  9. Air temperature variability in a high-elevation Himalayan catchment

    NARCIS (Netherlands)

    Heynen, Martin; Miles, Evan; Ragettli, Silvan; Buri, Pascal; Immerzeel, Walter W.; Pellicciotti, Francesca

    2016-01-01

    Air temperature is a key control of processes affecting snow and glaciers in high-elevation catchments, including melt, snowfall and sublimation. It is therefore a key input variable to models of land-surface-atmosphere interaction. Despite this importance, its spatial variability is poorly

  10. Variable kernel density estimation in high-dimensional feature spaces

    CSIR Research Space (South Africa)

    Van der Walt, Christiaan M

    2017-02-01

    Full Text Available Estimating the joint probability density function of a dataset is a central task in many machine learning applications. In this work we address the fundamental problem of kernel bandwidth estimation for variable kernel density estimation in high...

  11. An evolutionary framework for association testing in resequencing studies.

    Directory of Open Access Journals (Sweden)

    C Ryan King

    2010-11-01

    Full Text Available Sequencing technologies are becoming cheap enough to apply to large numbers of study participants and promise to provide new insights into human phenotypes by bringing to light rare and previously unknown genetic variants. We develop a new framework for the analysis of sequence data that incorporates all of the major features of previously proposed approaches, including those focused on allele counts and allele burden, but is both more general and more powerful. We harness population genetic theory to provide prior information on effect sizes and to create a pooling strategy for information from rare variants. Our method, EMMPAT (Evolutionary Mixed Model for Pooled Association Testing, generates a single test per gene (substantially reducing multiple testing concerns, facilitates graphical summaries, and improves the interpretation of results by allowing calculation of attributable variance. Simulations show that, relative to previously used approaches, our method increases the power to detect genes that affect phenotype when natural selection has kept alleles with large effect sizes rare. We demonstrate our approach on a population-based re-sequencing study of association between serum triglycerides and variation in ANGPTL4.

  12. Quantitative genome re-sequencing defines multiple mutations conferring chloroquine resistance in rodent malaria

    Science.gov (United States)

    2012-01-01

    Background Drug resistance in the malaria parasite Plasmodium falciparum severely compromises the treatment and control of malaria. A knowledge of the critical mutations conferring resistance to particular drugs is important in understanding modes of drug action and mechanisms of resistances. They are required to design better therapies and limit drug resistance. A mutation in the gene (pfcrt) encoding a membrane transporter has been identified as a principal determinant of chloroquine resistance in P. falciparum, but we lack a full account of higher level chloroquine resistance. Furthermore, the determinants of resistance in the other major human malaria parasite, P. vivax, are not known. To address these questions, we investigated the genetic basis of chloroquine resistance in an isogenic lineage of rodent malaria parasite P. chabaudi in which high level resistance to chloroquine has been progressively selected under laboratory conditions. Results Loci containing the critical genes were mapped by Linkage Group Selection, using a genetic cross between the high-level chloroquine-resistant mutant and a genetically distinct sensitive strain. A novel high-resolution quantitative whole-genome re-sequencing approach was used to reveal three regions of selection on chr11, chr03 and chr02 that appear progressively at increasing drug doses on three chromosomes. Whole-genome sequencing of the chloroquine-resistant parent identified just four point mutations in different genes on these chromosomes. Three mutations are located at the foci of the selection valleys and are therefore predicted to confer different levels of chloroquine resistance. The critical mutation conferring the first level of chloroquine resistance is found in aat1, a putative aminoacid transporter. Conclusions Quantitative trait loci conferring selectable phenotypes, such as drug resistance, can be mapped directly using progressive genome-wide linkage group selection. Quantitative genome-wide short

  13. Market Designs for High Levels of Variable Generation: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Milligan, M.; Holttinen, H.; Kiviluoma, J.; Orths, A.; Lynch, M.; Soder, L.

    2014-10-01

    Variable renewable generation is increasing in penetration in modern power systems, leading to higher variability in the supply and price of electricity as well as lower average spot prices. This raises new challenges, particularly in ensuring sufficient capacity and flexibility from conventional technologies. Because the fixed costs and lifetimes of electricity generation investments are significant, designing markets and regulations that ensure the efficient integration of renewable generation is a significant challenge. This papers reviews the state of play of market designs for high levels of variable generation in the United States and Europe and considers new developments in both regions.

  14. LipidSeq: a next-generation clinical resequencing panel for monogenic dyslipidemias[S

    Science.gov (United States)

    Johansen, Christopher T.; Dubé, Joseph B.; Loyzer, Melissa N.; MacDonald, Austin; Carter, David E.; McIntyre, Adam D.; Cao, Henian; Wang, Jian; Robinson, John F.; Hegele, Robert A.

    2014-01-01

    We report the design of a targeted resequencing panel for monogenic dyslipidemias, LipidSeq, for the purpose of replacing Sanger sequencing in the clinical detection of dyslipidemia-causing variants. We also evaluate the performance of the LipidSeq approach versus Sanger sequencing in 84 patients with a range of phenotypes including extreme blood lipid concentrations as well as additional dyslipidemias and related metabolic disorders. The panel performs well, with high concordance (95.2%) in samples with known mutations based on Sanger sequencing and a high detection rate (57.9%) of mutations likely to be causative for disease in samples not previously sequenced. Clinical implementation of LipidSeq has the potential to aid in the molecular diagnosis of patients with monogenic dyslipidemias with a high degree of speed and accuracy and at lower cost than either Sanger sequencing or whole exome sequencing. Furthermore, LipidSeq will help to provide a more focused picture of monogenic and polygenic contributors that underlie dyslipidemia while excluding the discovery of incidental pathogenic clinically actionable variants in nonmetabolism-related genes, such as oncogenes, that would otherwise be identified by a whole exome approach, thus minimizing potential ethical issues. PMID:24503134

  15. High-Speed Photo-Polarimetry of Magnetic Cataclysmic Variables

    Directory of Open Access Journals (Sweden)

    S. B. Potter

    2015-02-01

    Full Text Available I review recent highlights of the SAAO High-speed Photo-POlarimeter (HIPPO on the study of magnetic Cataclysmic Variables. Its high-speed capabilities are demonstrated with example observations made of the intermediate polar NY Lup and the polar IGRJ14536-5522.

  16. High Suicidal Ideation and Psychosocial Variables in University Students

    Science.gov (United States)

    Sanchez-Teruel, David; Garcia-Leon, Ana; Muela-Martinez, Jose A.

    2013-01-01

    Introduction: The college students have high rates of suicidal ideation often associated with psychosocial factors. The aim of this study was to evaluate whether some of these psychosocial variables are related to the high prevalence of suicidal ideation in a College Spanish. Method: Participants (n = 40), aged between 21 and 34 years, Mean =…

  17. Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

    Directory of Open Access Journals (Sweden)

    Stothard Paul

    2011-11-01

    Full Text Available Abstract Background One of the goals of livestock genomics research is to identify the genetic differences responsible for variation in phenotypic traits, particularly those of economic importance. Characterizing the genetic variation in livestock species is an important step towards linking genes or genomic regions with phenotypes. The completion of the bovine genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of the genetic variations present in cattle. Here we describe the whole-genome resequencing of two Bos taurus bulls from distinct breeds for the purpose of identifying and annotating novel forms of genetic variation in cattle. Results The genomes of a Black Angus bull and a Holstein bull were sequenced to 22-fold and 19-fold coverage, respectively, using the ABI SOLiD system. Comparisons of the sequences with the Btau4.0 reference assembly yielded 7 million single nucleotide polymorphisms (SNPs, 24% of which were identified in both animals. Of the total SNPs found in Holstein, Black Angus, and in both animals, 81%, 81%, and 75% respectively are novel. In-depth annotations of the data identified more than 16 thousand distinct non-synonymous SNPs (85% novel between the two datasets. Alignments between the SNP-altered proteins and orthologues from numerous species indicate that many of the SNPs alter well-conserved amino acids. Several SNPs predicted to create or remove stop codons were also found. A comparison between the sequencing SNPs and genotyping results from the BovineHD high-density genotyping chip indicates a detection rate of 91% for homozygous SNPs and 81% for heterozygous SNPs. The false positive rate is estimated to be about 2% for both the Black Angus and Holstein SNP sets, based on follow-up genotyping of 422 and 427 SNPs, respectively. Comparisons of read depth between the two bulls along the reference assembly identified 790 putative copy-number variations (CNVs. Ten

  18. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Raquel S Linheiro

    Full Text Available Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes.

  19. High-voltage variable-duration pulse generator

    International Nuclear Information System (INIS)

    Anisimova, T.E.; Akkuratov, E.V.; Gromovenko, V.M.; Nikonov, Yu.P.; Malinin, A.N.

    1988-01-01

    A high-voltage generator is described that allows pulse duration tau to be varied within wide limits and has high efficiency (at least 50% for tau = 0.5 tau/sub max/) and an amplitude of up to 5 kV, a repetition frequency of up to 200 Hz,and a variable duration of 0-30 μsec. The generator is used in the controller of an electron accelerator

  20. Targeted resequencing and analysis of the Diamond-Blackfan anemia disease locus RPS19.

    Directory of Open Access Journals (Sweden)

    Alvaro Martinez Barrio

    2009-07-01

    Full Text Available The Ribosomal protein S19 gene locus (RPS19 has been linked to two kinds of red cell aplasia, Diamond-Blackfan Anemia (DBA and Transient Erythroblastopenia in Childhood (TEC. Mutations in RPS19 coding sequences have been found in 25% of DBA patients, but not in TEC patients. It has been suggested that non-coding RPS19 sequence variants contribute to the considerable clinical variability in red cell aplasia. We therefore aimed at identifying non-coding variations associated with DBA or TEC phenotypes.We targeted a region of 19'980 bp encompassing the RPS19 gene in a cohort of 89 DBA and TEC patients for resequencing. We provide here a catalog of the considerable, previously unrecognized degree of variation in this region. We identified 73 variations (65 SNPs, 8 indels that all are located outside of the RPS19 open reading frame, and of which 67.1% are classified as novel. We hypothesize that specific alleles in non-coding regions of RPS19 could alter the binding of regulatory proteins or transcription factors. Therefore, we carried out an extensive analysis to identify transcription factor binding sites (TFBS. A series of putative interaction sites coincide with detected variants. Sixteen of the corresponding transcription factors are of particular interest, as they are housekeeping genes or show a direct link to hematopoiesis, tumorigenesis or leukemia (e.g. GATA-1/2, PU.1, MZF-1.Specific alleles at predicted TFBSs may alter the expression of RPS19, modify an important interaction between transcription factors with overlapping TFBS or remove an important stimulus for hematopoiesis. We suggest that the detected interactions are of importance for hematopoiesis and could provide new insights into individual response to treatment.

  1. North Atlantic Origin of Interdecadal variability of Siberian High

    Science.gov (United States)

    Kim, Seon-Hwa; Sung, Mi-Kyung; Kim, Baek-Min

    2017-04-01

    We suggest that the changes in the mean atmospheric circulation structure in the North Atlantic Ocean upstream region of Eurasian continent play an important role in the interdecadal variability of Siberian High (SH) through the modulation of Ural blocking frequency. Previous studies suggested that the interdecadal variability of SH is partly explained by the Arctic Oscillation. However, in this study, we emphasize the role of 'Warm Arctic and Cold Eurasia (WACE)', which is the second mode of winter surface air temperature variability over Eurasia. We show that the correlation between SH and WACE is high in general compared to that between SH and AO. However, the correlation between SH and WACE does not always exhibit high constant value. It shows a distinctive interdecadal fluctuation in the correlation. We found that this fluctuation in the correlation is due to the interdecadal fluctuation of the continental trough over the North Atlantic and the resultant strengthening of in-situ atmospheric baroclinicity. This accompanies changes in the transient vorticity flux divergence which leads to the downstream wave development and anomalous anticyclonic flow near Ural region. Obviously, the existence of anticyclonic flow over Ural region helps more frequent occurrence of Ural blocking and it is shown that this condition favors positive WACE event, which links to an intensified SH.

  2. Beta activity measurements in high, variable gamma backgrounds

    International Nuclear Information System (INIS)

    Stanga, D.; Sandu, E.; Craciun, L.

    1997-01-01

    In many cases beta activity measurements must be performed in high and variable gamma backgrounds. In such instances it is necessary to use well-shielded detectors but this technique is limited to laboratory equipment and frequently insufficient. In order to perform in a simple manner beta activity measurements in high and variable backgrounds a software-aided counting technique have been developed and a counting system have been constructed. This technique combines the different counting techniques with traditional method of successive measurement of the sample and background. The counting system is based on a programmable multi-scaler which is endowed with appropriate software and allow all operations to be performed via keyboard in an interactive fashion. Two large - area proportional detectors were selected in order to have the same background and the same gamma response within 5%. A program has been developed for the counting data analysis and beta activity computing. The software-aided counting technique has been implemented for beta activity measurement in high and variable backgrounds. (authors)

  3. Seychelles Dome variability in a high resolution ocean model

    Science.gov (United States)

    Nyadjro, E. S.; Jensen, T.; Richman, J. G.; Shriver, J. F.

    2016-02-01

    The Seychelles-Chagos Thermocline Ridge (SCTR; 5ºS-10ºS, 50ºE-80ºE) in the tropical Southwest Indian Ocean (SWIO) has been recognized as a region of prominence with regards to climate variability in the Indian Ocean. Convective activities in this region have regional consequences as it affect socio-economic livelihood of the people especially in the countries along the Indian Ocean rim. The SCTR is characterized by a quasi-permanent upwelling that is often associated with thermocline shoaling. This upwelling affects sea surface temperature (SST) variability. We present results on the variability and dynamics of the SCTR as simulated by the 1/12º high resolution HYbrid Coordinate Ocean Model (HYCOM). It is observed that locally, wind stress affects SST via Ekman pumping of cooler subsurface waters, mixing and anomalous zonal advection. Remotely, wind stress curl in the eastern equatorial Indian Ocean generates westward-propagating Rossby waves that impacts the depth of the thermocline which in turn impacts SST variability in the SCTR region. The variability of the contributions of these processes, especially with regard to the Indian Ocean Dipole (IOD) are further examined. In a typical positive IOD (PIOD) year, the net vertical velocity in the SCTR is negative year-round as easterlies along the region are intensified leading to a strong positive curl. This vertical velocity is caused mainly by anomalous local Ekman downwelling (with peak during September-November), a direct opposite to the climatology scenario when local Ekman pumping is positive (upwelling favorable) year-round. The anomalous remote contribution to the vertical velocity changes is minimal especially during the developing and peak stages of PIOD events. In a typical negative IOD (NIOD) year, anomalous vertical velocity is positive almost year-round with peaks in May and October. The remote contribution is positive, in contrast to the climatology and most of the PIOD years.

  4. Massively multiplexed microbial identification using resequencing DNA microarrays for outbreak investigation

    Science.gov (United States)

    Leski, T. A.; Ansumana, R.; Jimmy, D. H.; Bangura, U.; Malanoski, A. P.; Lin, B.; Stenger, D. A.

    2011-06-01

    Multiplexed microbial diagnostic assays are a promising method for detection and identification of pathogens causing syndromes characterized by nonspecific symptoms in which traditional differential diagnosis is difficult. Also such assays can play an important role in outbreak investigations and environmental screening for intentional or accidental release of biothreat agents, which requires simultaneous testing for hundreds of potential pathogens. The resequencing pathogen microarray (RPM) is an emerging technological platform, relying on a combination of massively multiplex PCR and high-density DNA microarrays for rapid detection and high-resolution identification of hundreds of infectious agents simultaneously. The RPM diagnostic system was deployed in Sierra Leone, West Africa in collaboration with Njala University and Mercy Hospital Research Laboratory located in Bo. We used the RPM-Flu microarray designed for broad-range detection of human respiratory pathogens, to investigate a suspected outbreak of avian influenza in a number of poultry farms in which significant mortality of chickens was observed. The microarray results were additionally confirmed by influenza specific real-time PCR. The results of the study excluded the possibility that the outbreak was caused by influenza, but implicated Klebsiella pneumoniae as a possible pathogen. The outcome of this feasibility study confirms that application of broad-spectrum detection platforms for outbreak investigation in low-resource locations is possible and allows for rapid discovery of the responsible agents, even in cases when different agents are suspected. This strategy enables quick and cost effective detection of low probability events such as outbreak of a rare disease or intentional release of a biothreat agent.

  5. Discovery of Gene Sources for Economic Traits in Hanwoo by Whole-genome Resequencing

    Directory of Open Access Journals (Sweden)

    Younhee Shin

    2016-09-01

    Full Text Available Hanwoo, a Korean native cattle (Bos taurus coreana, has great economic value due to high meat quality. Also, the breed has genetic variations that are associated with production traits such as health, disease resistance, reproduction, growth as well as carcass quality. In this study, next generation sequencing technologies and the availability of an appropriate reference genome were applied to discover a large amount of single nucleotide polymorphisms (SNPs in ten Hanwoo bulls. Analysis of whole-genome resequencing generated a total of 26.5 Gb data, of which 594,716,859 and 592,990,750 reads covered 98.73% and 93.79% of the bovine reference genomes of UMD 3.1 and Btau 4.6.1, respectively. In total, 2,473,884 and 2,402,997 putative SNPs were discovered, of which 1,095,922 (44.3% and 982,674 (40.9% novel SNPs were discovered against UMD3.1 and Btau 4.6.1, respectively. Among the SNPs, the 46,301 (UMD 3.1 and 28,613 SNPs (Btau 4.6.1 that were identified as Hanwoo-specific SNPs were included in the functional genes that may be involved in the mechanisms of milk production, tenderness, juiciness, marbling of Hanwoo beef and yellow hair. Most of the Hanwoo-specific SNPs were identified in the promoter region, suggesting that the SNPs influence differential expression of the regulated genes relative to the relevant traits. In particular, the non-synonymous (ns SNPs found in CORIN, which is a negative regulator of Agouti, might be a causal variant to determine yellow hair of Hanwoo. Our results will provide abundant genetic sources of variation to characterize Hanwoo genetics and for subsequent breeding.

  6. Scales of snow depth variability in high elevation rangeland sagebrush

    Science.gov (United States)

    Tedesche, Molly E.; Fassnacht, Steven R.; Meiman, Paul J.

    2017-09-01

    In high elevation semi-arid rangelands, sagebrush and other shrubs can affect transport and deposition of wind-blown snow, enabling the formation of snowdrifts. Datasets from three field experiments were used to investigate the scales of spatial variability of snow depth around big mountain sagebrush ( Artemisia tridentata Nutt.) at a high elevation plateau rangeland in North Park, Colorado, during the winters of 2002, 2003, and 2008. Data were collected at multiple resolutions (0.05 to 25 m) and extents (2 to 1000 m). Finer scale data were collected specifically for this study to examine the correlation between snow depth, sagebrush microtopography, the ground surface, and the snow surface, as well as the temporal consistency of snow depth patterns. Variograms were used to identify the spatial structure and the Moran's I statistic was used to determine the spatial correlation. Results show some temporal consistency in snow depth at several scales. Plot scale snow depth variability is partly a function of the nature of individual shrubs, as there is some correlation between the spatial structure of snow depth and sagebrush, as well as between the ground and snow depth. The optimal sampling resolution appears to be 25-cm, but over a large area, this would require a multitude of samples, and thus a random stratified approach is recommended with a fine measurement resolution of 5-cm.

  7. High Turndown Ratio, High Delta-Emittance, Variable Emissivity Electrochromics, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Variable-emittance materials are in high demand for applications ranging from manned and unmanned space platforms (e.g. in radiators at the Moon's poles where damage...

  8. Quantitation of heteroplasmy of mtDNA sequence variants identified in a population of AD patients and controls by array-based resequencing.

    Science.gov (United States)

    Coon, Keith D; Valla, Jon; Szelinger, Szabolics; Schneider, Lonnie E; Niedzielko, Tracy L; Brown, Kevin M; Pearson, John V; Halperin, Rebecca; Dunckley, Travis; Papassotiropoulos, Andreas; Caselli, Richard J; Reiman, Eric M; Stephan, Dietrich A

    2006-08-01

    The role of mitochondrial dysfunction in the pathogenesis of Alzheimer's disease (AD) has been well documented. Though evidence for the role of mitochondria in AD seems incontrovertible, the impact of mitochondrial DNA (mtDNA) mutations in AD etiology remains controversial. Though mutations in mitochondrially encoded genes have repeatedly been implicated in the pathogenesis of AD, many of these studies have been plagued by lack of replication as well as potential contamination of nuclear-encoded mitochondrial pseudogenes. To assess the role of mtDNA mutations in the pathogenesis of AD, while avoiding the pitfalls of nuclear-encoded mitochondrial pseudogenes encountered in previous investigations and showcasing the benefits of a novel resequencing technology, we sequenced the entire coding region (15,452 bp) of mtDNA from 19 extremely well-characterized AD patients and 18 age-matched, unaffected controls utilizing a new, reliable, high-throughput array-based resequencing technique, the Human MitoChip. High-throughput, array-based DNA resequencing of the entire mtDNA coding region from platelets of 37 subjects revealed the presence of 208 loci displaying a total of 917 sequence variants. There were no statistically significant differences in overall mutational burden between cases and controls, however, 265 independent sites of statistically significant change between cases and controls were identified. Changed sites were found in genes associated with complexes I (30.2%), III (3.0%), IV (33.2%), and V (9.1%) as well as tRNA (10.6%) and rRNA (14.0%). Despite their statistical significance, the subtle nature of the observed changes makes it difficult to determine whether they represent true functional variants involved in AD etiology or merely naturally occurring dissimilarity. Regardless, this study demonstrates the tremendous value of this novel mtDNA resequencing platform, which avoids the pitfalls of erroneously amplifying nuclear-encoded mtDNA pseudogenes, and

  9. pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data.

    Science.gov (United States)

    Beyens, Matthias; Boeckx, Nele; Van Camp, Guy; Op de Beeck, Ken; Vandeweyer, Geert

    2017-12-14

    Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in subsequent data-analysis. No variant filtering rationale addressing amplicon enrichment related systematic errors, in the form of an all-in-one package, exists to our knowledge. We present pyAmpli, a platform independent parallelized Python package that implements an amplicon-based germline and somatic variant filtering strategy for Haloplex data. pyAmpli can filter variants for systematic errors by user pre-defined criteria. We show that pyAmpli significantly increases specificity, without reducing sensitivity, essential for reporting true positive clinical relevant mutations in gene panel data. pyAmpli is an easy-to-use software tool which increases the true positive variant call rate in targeted resequencing data. It specifically reduces errors related to PCR-based enrichment of targeted regions.

  10. Highly variable Pliocene sea surface conditions in the Norwegian Sea

    Directory of Open Access Journals (Sweden)

    P. E. Bachem

    2017-09-01

    Full Text Available The Pliocene was a time of global warmth with small sporadic glaciations, which transitioned towards the larger-scale Pleistocene glacial–interglacial variability. Here, we present high-resolution records of sea surface temperature (SST and ice-rafted debris (IRD in the Norwegian Sea from 5.32 to 3.14 Ma, providing evidence that the Pliocene surface conditions of the Norwegian Sea underwent a series of transitions in response to orbital forcing and gateway changes. Average SSTs are 2 °C above the regional Holocene mean, with notable variability on millennial to orbital timescales. Both gradual changes and threshold effects are proposed for the progression of regional climate towards the Late Pliocene intensification of Northern Hemisphere glaciation. Cooling from 4.5 to 4.3 Ma may be linked to the onset of poleward flow through the Bering Strait. This cooling was further intensified by a period of cool summers due to weak obliquity forcing. A 7 °C warming of the Norwegian Sea at 4.0 Ma suggests a major increase in northward heat transport from the North Atlantic, leading to an enhanced zonal SST gradient in the Nordic Seas, which may be linked to the expansion of sea ice in the Arctic and Nordic Seas. A warm Norwegian Sea and enhanced zonal temperature gradient between 4.0 and 3.6 Ma may have been a priming factor for increased glaciation around the Nordic Seas due to enhanced evaporation and precipitation at high northern latitudes.

  11. A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing

    Directory of Open Access Journals (Sweden)

    Guangtu Gao

    2018-04-01

    Full Text Available Single-nucleotide polymorphisms (SNPs are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout (Oncorhynchus mykiss, SNP discovery has been previously done through sequencing of restriction-site associated DNA (RAD libraries, reduced representation libraries (RRL and RNA sequencing. Recently we have performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University (WSU and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly (GCA_002163495.1 which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup, followed by filtering of SNPs based on quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs and multi-sequence variants (MSVs. Overall, 30,302,087 SNPs were identified on the rainbow trout genome 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25. The average SNP density on the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. Results from the phylogenetic analysis that we conducted indicate that the SNP markers contain enough population-specific polymorphisms for recovering population relationships despite the small sample size used. Intra-Population polymorphism assessment revealed high level of polymorphism and

  12. Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages.

    Directory of Open Access Journals (Sweden)

    2006-03-01

    Full Text Available Hemiascomycete yeasts cover an evolutionary span comparable to that of the entire phylum of chordates. Since this group currently contains the largest number of complete genome sequences it presents unique opportunities to understand the evolution of genome organization in eukaryotes. We inferred rates of genome instability on all branches of a phylogenetic tree for 11 species and calculated species-specific rates of genome rearrangements. We characterized all inversion events that occurred within synteny blocks between six representatives of the different lineages. We show that the rates of macro- and microrearrangements of gene order are correlated within individual lineages but are highly variable across different lineages. The most unstable genomes correspond to the pathogenic yeasts Candida albicans and Candida glabrata. Chromosomal maps have been intensively shuffled by numerous interchromosomal rearrangements, even between species that have retained a very high physical fraction of their genomes within small synteny blocks. Despite this intensive reshuffling of gene positions, essential genes, which cluster in low recombination regions in the genome of Saccharomyces cerevisiae, tend to remain syntenic during evolution. This work reveals that the high plasticity of eukaryotic genomes results from rearrangement rates that vary between lineages but also at different evolutionary times of a given lineage.

  13. FPGA implementation of high-frequency multiple PWM for variable voltage variable frequency controller

    Energy Technology Data Exchange (ETDEWEB)

    Boumaaraf, Abdelâali, E-mail: aboumaaraf@yahoo.fr [Université Abbès Laghrour, Laboratoire des capteurs, Instrumentations et procédés (LCIP), Khenchela (Algeria); University of Farhat Abbas Setif1, Sétif, 19000 (Algeria); Mohamadi, Tayeb [University of Farhat Abbas Setif1, Sétif, 19000 (Algeria); Gourmat, Laïd [Université Abbès Laghrour, Khenchela, 40000 (Algeria)

    2016-07-25

    In this paper, we present the FPGA implementation of the multiple pulse width modulation (MPWM) signal generation with repetition of data segments, applied to the variable frequency variable voltage systems and specially at to the photovoltaic water pumping system, in order to generate a signal command very easily between 10 Hz to 60 Hz with a small frequency and reduce the cost of the control system.

  14. High-p{sub T} B-tagging and top-tagging with variable-R jets in ATLAS

    Energy Technology Data Exchange (ETDEWEB)

    Behr, Katharina [Sub-department of Particle Physics, University of Oxford, Denys-Wilkinson Building, Keble Road, Oxford OX1 3RH (United Kingdom)

    2015-07-01

    Variable-R jets, whose effective size is inversely proportional to their transverse momentum, are a versatile tool for object reconstruction across the large transverse momentum regime accessible during Run 2 of the LHC. I discuss the performance of Variable-R jets in two different contexts: (1) Boosted top-tagging. The separation between the decay products of highly energetic top quarks decreases with p{sub T}{sup top} causing them to overlap and merge into a single jet. Taggers relying on large fixed-R jets overestimate the real size of the top jet in the highly boosted regime and are more susceptible to the effects of pile-up. Variable-R jets are studied as the basis for more natural taggers which may not even require grooming. (2) B-tagging. The b-tagging performance in boosted topologies suffers in the presence of close-by jets. This limits the sensitivity of many searches such as those in boosted hh → 4b final states. New b-taggers relying on track jets with smaller sizes than the traditional R=0.4 to better isolate the b-hadron decay show significant improvements in highly boosted scenarios but perform worse at low transverse momenta where they fail to capture the full b-jet. Variable-R track jets provide a unified approach to b-tagging in both p{sub T} regimes.

  15. A new Variable Resolution Associative Memory for High Energy Physics

    CERN Document Server

    Annovi, A; The ATLAS collaboration; Beretta, M; Bossini, E; Crescioli, F; Dell'Orso, M; Giannetti, P; Hoff, J; Liberali, V; Liu, T; Magalotti, D; Piendibene, M; Sacco, A; Schoening, A; Soltveit, H K; Stabile, A; Tripiccione, R; Vitillo, R; Volpi, G

    2011-01-01

    We describe an important advancement for the Associative Memory device (AM). The AM is a VLSI processor for pattern recognition based on Content Addressable Memory (CAM) architecture. The AM is optimized for on-line track finding in high-energy physics experiments. Pattern matching is carried out finding track candidates in coarse resolution “roads”. A large AM bank stores all trajectories of interest, called “patterns”, for a given detector resolution. The AM extracts roads compatible with a given event during detector read-out. Two important variables characterize the quality of the AM bank: its “coverage” and the level of “found fakes”. The coverage, which describes the geometric efficiency of a bank, is defined as the fraction of tracks that match at least a pattern in the bank. Given a certain road size, the coverage of the bank can be increased just adding patterns to the bank, while the number of found fakes unfortunately is roughly proportional to this number of patterns in the bank. M...

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

    Science.gov (United States)

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

    2016-12-05

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

  17. Input variable selection for interpolating high-resolution climate ...

    African Journals Online (AJOL)

    Although the primary input data of climate interpolations are usually meteorological data, other related (independent) variables are frequently incorporated in the interpolation process. One such variable is elevation, which is known to have a strong influence on climate. This research investigates the potential of 4 additional ...

  18. Variability Bugs in Highly Configurable Systems: A Qualitative Analysis

    DEFF Research Database (Denmark)

    Abal, Iago; Melo, Jean; Stanciulescu, Stefan

    2018-01-01

    Variability-sensitive verification pursues effective analysis of the exponentially many variants in number of features of a program family. Several variability-aware techniques have been proposed, but researchers still lack examples of concrete bugs induced by variability, occurring in real large......-scale systems. A collection of real world bugs is needed to evaluate tool implementations of variability-sensitive analyses by testing them on real bugs. We present a qualitative study of 98 diverse variability bugs collected from bug-fixing commits in the Apache, BusyBox, Linux kernel and Marlin repositories....... We analyze each of the bugs, and record the results in a database. For each bug, we create a self-contained simplified C99 version and a simplified patch, in order to help researchers who are not experts on these subject studies to understand them, so that they can use it for evaluation...

  19. Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster.

    Science.gov (United States)

    Jha, Aashish R; Miles, Cecelia M; Lippert, Nodia R; Brown, Christopher D; White, Kevin P; Kreitman, Martin

    2015-10-01

    Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  20. Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing.

    Science.gov (United States)

    Zhang, Tifu; Gu, Minfeng; Liu, Yuhe; Lv, Yuanda; Zhou, Ling; Lu, Haiyan; Liang, Shuaiqiang; Bao, Huabin; Zhao, Han

    2017-09-05

    Quinoa (Chenopodium quinoa Willd.) is a balanced nutritional crop, but its breeding improvement has been limited by the lack of information on its genetics and genomics. Therefore, it is necessary to obtain knowledge on genomic variation, population structure, and genetic diversity and to develop novel Insertion/Deletion (InDel) markers for quinoa by whole-genome re-sequencing. We re-sequenced 11 quinoa accessions and obtained a coverage depth between approximately 7× to 23× the quinoa genome. Based on the 1453-megabase (Mb) assembly from the reference accession Riobamba, 8,441,022 filtered bi-allelic single nucleotide polymorphisms (SNPs) and 842,783 filtered InDels were identified, with an estimated SNP and InDel density of 5.81 and 0.58 per kilobase (kb). From the genomic InDel variations, 85 dimorphic InDel markers were newly developed and validated. Together with the 62 simple sequence repeat (SSR) markers reported, a total of 147 markers were used for genotyping the 129 quinoa accessions. Molecular grouping analysis showed classification into two major groups, the Andean highland (composed of the northern and southern highland subgroups) and Chilean coastal, based on combined STRUCTURE, phylogenetic tree and PCA (Principle Component Analysis) analyses. Further analysis of the genetic diversity exhibited a decreasing tendency from the Chilean coast group to the Andean highland group, and the gene flow between subgroups was more frequent than that between the two subgroups and the Chilean coastal group. The majority of the variations (approximately 70%) were found through an analysis of molecular variation (AMOVA) due to the diversity between the groups. This was congruent with the observation of a highly significant F ST value (0.705) between the groups, demonstrating significant genetic differentiation between the Andean highland type of quinoa and the Chilean coastal type. Moreover, a core set of 16 quinoa germplasms that capture all 362 alleles was

  1. High Variability in Outcome Reporting Patterns in High-Impact ACL Literature.

    Science.gov (United States)

    Makhni, Eric C; Padaki, Ajay S; Petridis, Petros D; Steinhaus, Michael E; Ahmad, Christopher S; Cole, Brian J; Bach, Bernard R

    2015-09-16

    ACL (anterior cruciate ligament) reconstruction is one of the most commonly performed and studied procedures in modern sports medicine. A multitude of objective and subjective patient outcome measures exists; however, nonstandardized reporting patterns of these metrics may create challenges in objectively analyzing pooled results from different studies. The goal of this study was to document the variability in outcome reporting patterns in high-impact orthopaedic studies of ACL reconstruction. All clinical studies pertaining to ACL reconstruction in four high-impact-factor orthopaedic journals over a five-year period were reviewed. Biomechanical, basic science, and imaging studies were excluded, as were studies with fewer than fifty patients, yielding 119 studies for review. Incorporation of various objective and subjective outcomes was noted for each study. Substantial variability in reporting of both objective and subjective measures was noted in the study cohort. Although a majority of studies reported instrumented laxity findings, there was substantial variability in the type and method of laxity reporting. Most other objective outcomes, including range of motion, strength, and complications, were reported in <50% of all studies. Return to pre-injury level of activity was infrequently reported (24% of studies), as were patient satisfaction and pain assessment following surgery (8% and 13%, respectively). Of the patient-reported outcomes, the International Knee Documentation Committee (IKDC), Lysholm, and Tegner scores were most often reported (71%, 63%, and 42%, respectively). Substantial variability in outcome reporting patterns exists among high-impact studies of ACL reconstruction. Such variability may create challenges in interpreting results and pooling them across different studies. Copyright © 2015 by The Journal of Bone and Joint Surgery, Incorporated.

  2. Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1

    DEFF Research Database (Denmark)

    Carvill, Gemma L; Heavin, Sinéad B; Yendle, Simone C

    2013-01-01

    Epileptic encephalopathies are a devastating group of epilepsies with poor prognosis, of which the majority are of unknown etiology. We perform targeted massively parallel resequencing of 19 known and 46 candidate genes for epileptic encephalopathy in 500 affected individuals (cases) to identify...... CHD2 and SYNGAP1 mutations are new causes of epileptic encephalopathies, accounting for 1.2% and 1% of cases, respectively. We also expand the phenotypic spectra explained by SCN1A, SCN2A and SCN8A mutations. To our knowledge, this is the largest cohort of cases with epileptic encephalopathies...

  3. High density plasma heating in the Tokamak à configuration variable

    International Nuclear Information System (INIS)

    Curchod, L.

    2011-04-01

    The Tokamak à Configuration Variable (TCV) is a medium size magnetic confinement thermonuclear fusion experiment designed for the study of the plasma performances as a function of its shape. It is equipped with a high power and highly flexible electron cyclotron heating (ECH) and current drive (ECCD) system. Up to 3 MW of 2 nd harmonic EC power in ordinary (O 2 ) or extraordinary (X 2 ) polarization can be injected from TCV low-field side via six independently steerable launchers. In addition, up to 1.5 MW of 3 rd harmonic EC power (X 3 ) can be launched along the EC resonance from the top of TCV vacuum vessel. At high density, standard ECH and ECCD are prevented by the appearance of a cutoff layer screening the access to the EC resonance at the plasma center. As a consequence, less than 50% of TCV density operational domain is accessible to X 2 and X 3 ECH. The electron Bernstein waves (EBW) have been proposed to overcome this limitation. EBW is an electrostatic mode propagating beyond the plasma cutoff without upper density limit. Since it cannot propagate in vacuum, it has to be excited by mode conversion of EC waves in the plasma. Efficient electron Bernstein waves heating (EBH) and current drive (EBCD) were previously performed in several fusion devices, in particular in the W7-AS stellarator and in the MAST spherical tokamak. In TCV, the conditions for an efficient O-X-B mode conversion (i.e. a steep density gradient at the O 2 plasma cutoff) are met at the edge of high confinement (H-mode) plasmas characterized by the appearance of a pedestal in the electron temperature and density profiles. TCV experiments have demonstrated the first EBW coupling to overdense plasmas in a medium aspect-ratio tokamak via O-X-B mode conversion. This thesis work focuses on several aspects of ECH and EBH in low and high density plasmas. Firstly, the experimental optimum angles for the O-X-B mode conversion is successfully compared to the full-wave mode conversion calculation

  4. High-performance control of continuously variable transmissions

    NARCIS (Netherlands)

    Meulen, van der S.H.

    2010-01-01

    Nowadays, developments with respect to the pushbelt continuously variable transmission (CVT) are mainly directed towards a reduction of the fuel consumption of a vehicle. The fuel consumption of a vehicle is affected by the variator of the CVT, which transfers the torque and varies the transmission

  5. Do high fetal catecholamine levels affect heart rate variability and ...

    African Journals Online (AJOL)

    Objectives. To deternrine the relationship between Umbilical arterial catecholamine levels and fetal heart rate variability and meconium passage. Study design. A prospective descriptive study was perfonned. Umbilical artery catecholamine levels were measured in 55 newborns and correlated with fetal heart rate before ...

  6. High-resolution grids of hourly meteorological variables for Germany

    Science.gov (United States)

    Krähenmann, S.; Walter, A.; Brienen, S.; Imbery, F.; Matzarakis, A.

    2018-02-01

    We present a 1-km2 gridded German dataset of hourly surface climate variables covering the period 1995 to 2012. The dataset comprises 12 variables including temperature, dew point, cloud cover, wind speed and direction, global and direct shortwave radiation, down- and up-welling longwave radiation, sea level pressure, relative humidity and vapour pressure. This dataset was constructed statistically from station data, satellite observations and model data. It is outstanding in terms of spatial and temporal resolution and in the number of climate variables. For each variable, we employed the most suitable gridding method and combined the best of several information sources, including station records, satellite-derived data and data from a regional climate model. A module to estimate urban heat island intensity was integrated for air and dew point temperature. Owing to the low density of available synop stations, the gridded dataset does not capture all variations that may occur at a resolution of 1 km2. This applies to areas of complex terrain (all the variables), and in particular to wind speed and the radiation parameters. To achieve maximum precision, we used all observational information when it was available. This, however, leads to inhomogeneities in station network density and affects the long-term consistency of the dataset. A first climate analysis for Germany was conducted. The Rhine River Valley, for example, exhibited more than 100 summer days in 2003, whereas in 1996, the number was low everywhere in Germany. The dataset is useful for applications in various climate-related studies, hazard management and for solar or wind energy applications and it is available via doi: 10.5676/DWD_CDC/TRY_Basis_v001.

  7. Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean

    Directory of Open Access Journals (Sweden)

    Ying-hui Li

    2014-11-01

    Full Text Available As a complement to single nucleotide polymorphisms (SNPs and simple sequence repeats (SSRs, biallelic insertions and deletions (InDels represent powerful molecular markers with desirable features for filling the gap in current genetic linkage maps. In this study, 28,908 small InDel polymorphisms (1–5 base pair, bp distributed genome-wide were identified and annotated by comparison of a whole-genome resequencing data set from two soybean [ (L. Merr.] genotypes, cultivar Zhonghunag13 (ZH and line Zhongpin03-5373 (ZP. The physical distribution of InDel polymorphisms in soybean genome was uneven, and matched closely with the distribution of previously annotated genes. The average density of InDel in the arm region was significantly higher than that in the pericentromeric region. The genomic regions that were fixed between the two elites were elucidated. With this information, five InDel markers within a putative quantitative trait locus (QTL for seed weight (SW, , were developed and used to genotype 254 recombinant inbred lines (RILs derived from the cross of ZP × ZH. Adding these five InDel markers to previously used SNP and SSR markers facilitated the discovery of further recombination events allowing fine-mapping the QTL to a 0.5 Mbp region. Our study clearly underlines the high value of InDel markers for map-based cloning and marker-assisted selection in soybean.

  8. Targeted resequencing and variant validation using pxlence PCR assays

    Directory of Open Access Journals (Sweden)

    Frauke Coppieters

    2016-01-01

    Full Text Available The advent of next-generation sequencing technologies had a profound impact on molecular diagnostics. PCR is a popular method for target enrichment of disease gene panels. Using our proprietary primer-design pipeline, primerXL, we have created almost one million assays covering over 98% of the human exome. Here we describe the assay specification and both in silico and wet-lab validation of a selected set of 2294 assays using both next-generation sequencing and Sanger sequencing. Using a universal PCR protocol without optimization, these assays result in high coverage uniformity and limited non-specific coverage. In addition, data indicates a positive correlation between the predictive in silico specificity score and the amount of assay non-specific coverage.

  9. Signatures of selection in tilapia revealed by whole genome resequencing.

    Science.gov (United States)

    Xia, Jun Hong; Bai, Zhiyi; Meng, Zining; Zhang, Yong; Wang, Le; Liu, Feng; Jing, Wu; Wan, Zi Yi; Li, Jiale; Lin, Haoran; Yue, Gen Hua

    2015-09-16

    Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10-100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia.

  10. Whole-genome resequencing reveals candidate mutations for pig prolificacy.

    Science.gov (United States)

    Li, Wen-Ting; Zhang, Meng-Meng; Li, Qi-Gang; Tang, Hui; Zhang, Li-Fan; Wang, Ke-Jun; Zhu, Mu-Zhen; Lu, Yun-Feng; Bao, Hai-Gang; Zhang, Yuan-Ming; Li, Qiu-Yan; Wu, Ke-Liang; Wu, Chang-Xin

    2017-12-20

    Changes in pig fertility have occurred as a result of domestication, but are not understood at the level of genetic variation. To identify variations potentially responsible for prolificacy, we sequenced the genomes of the highly prolific Taihu pig breed and four control breeds. Genes involved in embryogenesis and morphogenesis were targeted in the Taihu pig, consistent with the morphological differences observed between the Taihu pig and others during pregnancy. Additionally, excessive functional non-coding mutations have been specifically fixed or nearly fixed in the Taihu pig. We focused attention on an oestrogen response element (ERE) within the first intron of the bone morphogenetic protein receptor type-1B gene ( BMPR1B ) that overlaps with a known quantitative trait locus (QTL) for pig fecundity. Using 242 pigs from 30 different breeds, we confirmed that the genotype of the ERE was nearly fixed in the Taihu pig. ERE function was assessed by luciferase assays, examination of histological sections, chromatin immunoprecipitation, quantitative polymerase chain reactions, and western blots. The results suggest that the ERE may control pig prolificacy via the cis-regulation of BMPR1B expression. This study provides new insight into changes in reproductive performance and highlights the role of non-coding mutations in generating phenotypic diversity between breeds. © 2017 The Author(s).

  11. [Identification of novel pathogenic gene mutations in pediatric acute myeloid leukemia by whole-exome resequencing].

    Science.gov (United States)

    Shiba, Norio

    2015-12-01

    A new class of gene mutations, identified in the pathogenesis of adult acute myeloid leukemia (AML), includes DNMT3A, IDH1/2, TET2 and EZH2. However, these mutations are rare in pediatric AML cases, indicating that pathogeneses differ between adult and pediatric forms of AML. Meanwhile, the recent development of massively parallel sequencing technologies has provided a new opportunity to discover genetic changes across entire genomes or proteincoding sequences. In order to reveal a complete registry of gene mutations, we performed whole exome resequencing of paired tumor-normal specimens from 19 pediatric AML cases using Illumina HiSeq 2000. In total, 80 somatic mutations or 4.2 mutations per sample were identified. Many of the recurrent mutations identified in this study involved previously reported targets in AML, such as FLT3, CEBPA, KIT, CBL, NRAS, WT1 and EZH2. On the other hand, several genes were newly identified in the current study, including BCORL1 and major cohesin components such as SMC3 and RAD21. Whole exome resequencing revealed a complex array of gene mutations in pediatric AML genomes. Our results indicate that a subset of pediatric AML represents a discrete entity that could be discriminated from its adult counterpart, in terms of the spectrum of gene mutations.

  12. A database and API for variation, dense genotyping and resequencing data

    Directory of Open Access Journals (Sweden)

    Flicek Paul

    2010-05-01

    Full Text Available Abstract Background Advances in sequencing and genotyping technologies are leading to the widespread availability of multi-species variation data, dense genotype data and large-scale resequencing projects. The 1000 Genomes Project and similar efforts in other species are challenging the methods previously used for storage and manipulation of such data necessitating the redesign of existing genome-wide bioinformatics resources. Results Ensembl has created a database and software library to support data storage, analysis and access to the existing and emerging variation data from large mammalian and vertebrate genomes. These tools scale to thousands of individual genome sequences and are integrated into the Ensembl infrastructure for genome annotation and visualisation. The database and software system is easily expanded to integrate both public and non-public data sources in the context of an Ensembl software installation and is already being used outside of the Ensembl project in a number of database and application environments. Conclusions Ensembl's powerful, flexible and open source infrastructure for the management of variation, genotyping and resequencing data is freely available at http://www.ensembl.org.

  13. Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes.

    Science.gov (United States)

    Liu, Wen; Ghouri, Fozia; Yu, Hang; Li, Xiang; Yu, Shuhong; Shahid, Muhammad Qasim; Liu, Xiangdong

    2017-01-01

    Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89.6% (> = 1 fold) of reference genomes. Two wild rice lines showed high SNP (single-nucleotide polymorphisms) variation rate in 12 chromosomes against the reference genomes of Nipponbare (japonica cultivar) and 93-11 (indica cultivar). InDels (insertion/deletion polymorphisms) count-length distribution exhibited normal distribution in the two lines, and most of the InDels were ranged from -5 to 5 bp. With reference to the Nipponbare genome sequence, we detected a total of 1,209,308 SNPs, 161,117 InDels and 4,192 SVs (structural variations) in Huaye 1, and 1,387,959 SNPs, 180,226 InDels and 5,305 SVs in Huaye 2. A total of 44.9% and 46.9% genes exhibited sequence variations in two wild rice lines compared to the Nipponbare and 93-11 reference genomes, respectively. Analysis of NBS-LRR mutant candidate genes showed that they were mainly distributed on chromosome 11, and NBS domain was more conserved than LRR domain in both wild rice lines. NBS genes depicted higher levels of genetic diversity in Huaye 1 than that found in Huaye 2. Furthermore, protein-protein interaction analysis showed that NBS genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region. We explored abundant NBS-LRR encoding genes in two common wild rice lines through genome wide re-sequencing

  14. High efficiency pool filtering systems utilising variable frequency drives

    Energy Technology Data Exchange (ETDEWEB)

    Hameiri, Z.; Sproul, A.B. [School of Photovoltaic and Renewable Energy Engineering, UNSW, Sydney, NSW 2052 (Australia); Spooner, T. [School of Electrical Engineering and Telecommunications, UNSW, Sydney, NSW 2052 (Australia)

    2009-02-15

    Over 1 year, private swimming pools in Australia will typically consume 1680 GWh of electricity, producing 2130 kt of CO{sub 2}. Redesigning a pool's filtration system and using it more efficiently can reduce the energy use, and hence the CO{sub 2} production, by a significant amount. This paper describes experimental measurements carried out on a new design of pool pump system. Initial experiments using a variable frequency drive (VFD) with a standard, single phase pump/motor system have achieved energy savings of 40%. Utilising a VFD and a three phase pump/motor energy savings of 61% have been achieved, without degrading the system performance. (author)

  15. Design study and performance analysis of a high-speed multistage variable-geometry fan for a variable cycle engine

    Science.gov (United States)

    Sullivan, T. J.; Parker, D. E.

    1979-01-01

    A design technology study was performed to identify a high speed, multistage, variable geometry fan configuration capable of achieving wide flow modulation with near optimum efficiency at the important operating condition. A parametric screening study of the front and rear block fans was conducted in which the influence of major fan design features on weight and efficiency was determined. Key design parameters were varied systematically to determine the fan configuration most suited for a double bypass, variable cycle engine. Two and three stage fans were considered for the front block. A single stage, core driven fan was studied for the rear block. Variable geometry concepts were evaluated to provide near optimum off design performance. A detailed aerodynamic design and a preliminary mechanical design were carried out for the selected fan configuration. Performance predictions were made for the front and rear block fans.

  16. Smallpox virus resequencing GeneChips can also rapidly ascertain species status for some zoonotic non-variola orthopoxviruses.

    Science.gov (United States)

    Sulaiman, Irshad M; Sammons, Scott A; Wohlhueter, Robert M

    2008-04-01

    We recently developed a set of seven resequencing GeneChips for the rapid sequencing of Variola virus strains in the WHO Repository of the Centers for Disease Control and Prevention. In this study, we attempted to hybridize these GeneChips with some known non-Variola orthopoxvirus isolates, including monkeypox, cowpox, and vaccinia viruses, for rapid detection.

  17. High intraspecific variability of Echinococcus granulosus sensu stricto in Chile.

    Science.gov (United States)

    Alvarez Rojas, Cristian A; Ebi, Dennis; Paredes, Rodolfo; Acosta-Jamett, Gerardo; Urriola, Nicole; Roa, Juan Carlos; Manterola, Carlos; Cortes, Sandra; Romig, Thomas; Scheerlinck, Jean-Pierre; Lightowlers, Marshall W

    2017-04-01

    Echinococcus granulosus sensu stricto is the major cause of cystic echinococcosis in most human and animal cases in the world and the most widespread species within the E. granulosus sensu lato complex. E. granulosus s.s. remains endemic in South America together with other species of the Echinococcus genus, especially in some areas in Argentina, Brazil, Chile and Peru. Except for a single human case caused by E. canadensis (G6) described in the literature, only E. granulosus s.s. has been found in the Chilean territory. In the current study 1609bp of the cox1 gene from 69 Chilean isolates of E. granulosus s.s. from humans and animals were analysed. In total, 26 cox1 haplotypes were found, including the widespread haplotype EG01 (22 isolates) and also EGp1 (5), EgRUS7 (1), EgAus02 (1) and EgAus03 (2). Twenty-one different haplotype not previously described were identified from 38 Chilean isolates designated EgCL1-EgCL21. Previous work had described low variability of E. granulosus s.s. in South America, based on isolates from Peru. Results obtained in this work challenge the previously described idea of the low diversity of the parasite in South America, and warrant future investigation on the origin and spread of the parasite in the continent after the Spanish arrival. Copyright © 2016. Published by Elsevier B.V.

  18. Atmospheric kinematics of high velocity long period variables

    International Nuclear Information System (INIS)

    Willson, L.A.

    1982-01-01

    Radial velocities of atomic absorption lines of three long period variables, RT Cyg, Z Oph and S Car, have been analysed in order to understand velocity gradients and discontinuities in their atmospheres. Phase coverage is from five days before maximum to 73 days after maximum for RT Cyg, from 17 days before to 44 days after maximum for Z Oph, and at 9 days before maximum for S Car. On a few spectrograms double lines were seen. All spectrograms were analysed by a four-parameter regression programme to yield the dependence of the radial velocity on the excitation potential, first ionization potential, wavelength and line strength, as indicators of the depth of line formation. The data were analysed to yield the velocity discontinuity across shock waves and velocity gradients between shock waves. Near maximum light the radial velocities cannot be understood by the presence of one shock only but rather require two shocks. The lower shock becomes apparent at the longer wavelengths. Consistent parameters are obtained if these stars are fundamental mode pulsators with total masses in the range of 0.5 to 1.0 solar mass and effective radii in the range of 0.85 to 1.5 x 10 13 cm. (author)

  19. Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.

    Science.gov (United States)

    Kim, Tae-Sung; He, Qiang; Kim, Kyu-Won; Yoon, Min-Young; Ra, Won-Hee; Li, Feng Peng; Tong, Wei; Yu, Jie; Oo, Win Htet; Choi, Buung; Heo, Eun-Beom; Yun, Byoung-Kook; Kwon, Soon-Jae; Kwon, Soon-Wook; Cho, Yoo-Hyun; Lee, Chang-Yong; Park, Beom-Seok; Park, Yong-Jin

    2016-05-26

    Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.

  20. Visualization of conserved structures by fusing highly variable datasets.

    Science.gov (United States)

    Silverstein, Jonathan C; Chhadia, Ankur; Dech, Fred

    2002-01-01

    Skill, effort, and time are required to identify and visualize anatomic structures in three-dimensions from radiological data. Fundamentally, automating these processes requires a technique that uses symbolic information not in the dynamic range of the voxel data. We were developing such a technique based on mutual information for automatic multi-modality image fusion (MIAMI Fuse, University of Michigan). This system previously demonstrated facility at fusing one voxel dataset with integrated symbolic structure information to a CT dataset (different scale and resolution) from the same person. The next step of development of our technique was aimed at accommodating the variability of anatomy from patient to patient by using warping to fuse our standard dataset to arbitrary patient CT datasets. A standard symbolic information dataset was created from the full color Visible Human Female by segmenting the liver parenchyma, portal veins, and hepatic veins and overwriting each set of voxels with a fixed color. Two arbitrarily selected patient CT scans of the abdomen were used for reference datasets. We used the warping functions in MIAMI Fuse to align the standard structure data to each patient scan. The key to successful fusion was the focused use of multiple warping control points that place themselves around the structure of interest automatically. The user assigns only a few initial control points to align the scans. Fusion 1 and 2 transformed the atlas with 27 points around the liver to CT1 and CT2 respectively. Fusion 3 transformed the atlas with 45 control points around the liver to CT1 and Fusion 4 transformed the atlas with 5 control points around the portal vein. The CT dataset is augmented with the transformed standard structure dataset, such that the warped structure masks are visualized in combination with the original patient dataset. This combined volume visualization is then rendered interactively in stereo on the ImmersaDesk in an immersive Virtual

  1. Analysis of key variables controlling phosphorus removal in high ...

    African Journals Online (AJOL)

    This study evaluates the influence of hydraulic retention time (HRT), solar radiation, and water temperature on phosphorus removal from two experimental high rate oxidation ponds (HROP) with clarifiers. Both HROPs were operated for a period of one year with different HRTs (3 to 10 d), but under the same environmental ...

  2. Variable high pressure processing sensitivities for GII human noroviruses

    Science.gov (United States)

    Human norovirus (HuNoV) is the leading cause of foodborne diseases worldwide. High pressure processing (HPP) is one of the most promising non-thermal technologies for decontamination of viral pathogens in foods. However, the survival of HuNoVs by HPP is poorly understood because these viruses cann...

  3. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Thudi, Mahendar; Khan, Aamir W; Kumar, Vinay; Gaur, Pooran M; Katta, Krishnamohan; Garg, Vanika; Roorkiwal, Manish; Samineni, Srinivasan; Varshney, Rajeev K

    2016-01-27

    Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach. A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads, with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome. Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively. Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for

  4. Electric Grid Expansion Planning with High Levels of Variable Generation

    Energy Technology Data Exchange (ETDEWEB)

    Hadley, Stanton W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); You, Shutang [Univ. of Tennessee, Knoxville, TN (United States); Shankar, Mallikarjun [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Liu, Yilu [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-02-01

    Renewables are taking a large proportion of generation capacity in U.S. power grids. As their randomness has increasing influence on power system operation, it is necessary to consider their impact on system expansion planning. To this end, this project studies the generation and transmission expansion co-optimization problem of the US Eastern Interconnection (EI) power grid with a high wind power penetration rate. In this project, the generation and transmission expansion problem for the EI system is modeled as a mixed-integer programming (MIP) problem. This study analyzed a time series creation method to capture the diversity of load and wind power across balancing regions in the EI system. The obtained time series can be easily introduced into the MIP co-optimization problem and then solved robustly through available MIP solvers. Simulation results show that the proposed time series generation method and the expansion co-optimization model and can improve the expansion result significantly after considering the diversity of wind and load across EI regions. The improved expansion plan that combines generation and transmission will aid system planners and policy makers to maximize the social welfare. This study shows that modelling load and wind variations and diversities across balancing regions will produce significantly different expansion result compared with former studies. For example, if wind is modeled in more details (by increasing the number of wind output levels) so that more wind blocks are considered in expansion planning, transmission expansion will be larger and the expansion timing will be earlier. Regarding generation expansion, more wind scenarios will slightly reduce wind generation expansion in the EI system and increase the expansion of other generation such as gas. Also, adopting detailed wind scenarios will reveal that it may be uneconomic to expand transmission networks for transmitting a large amount of wind power through a long distance

  5. QTL Mapping by Whole Genome Re-sequencing and Analysis of Candidate Genes for Nitrogen Use Efficiency in Rice

    Directory of Open Access Journals (Sweden)

    Xinghai Yang

    2017-09-01

    Full Text Available Nitrogen is a major nutritional element in rice production. However, excessive application of nitrogen fertilizer has caused severe environmental pollution. Therefore, development of rice varieties with improved nitrogen use efficiency (NUE is urgent for sustainable agriculture. In this study, bulked segregant analysis (BSA combined with whole genome re-sequencing (WGS technology was applied to finely map quantitative trait loci (QTL for NUE. A key QTL, designated as qNUE6 was identified on chromosome 6 and further validated by Insertion/Deletion (InDel marker-based substitutional mapping in recombinants from F2 population (NIL-13B4 × GH998. Forty-four genes were identified in this 266.5-kb region. According to detection and annotation analysis of variation sites, 39 genes with large-effect single-nucleotide polymorphisms (SNPs and large-effect InDels were selected as candidates and their expression levels were analyzed by qRT-PCR. Significant differences in the expression levels of LOC_Os06g15370 (peptide transporter PTR2 and LOC_Os06g15420 (asparagine synthetase were observed between two parents (Y11 and GH998. Phylogenetic analysis in Arabidopsis thaliana identified two closely related homologs, AT1G68570 (AtNPF3.1 and AT5G65010 (ASN2, which share 72.3 and 87.5% amino acid similarity with LOC_Os06g15370 and LOC_Os06g15420, respectively. Taken together, our results suggested that qNUE6 is a possible candidate gene for NUE in rice. The fine mapping and candidate gene analysis of qNUE6 provide the basis of molecular breeding for genetic improvement of rice varieties with high NUE, and lay the foundation for further cloning and functional analysis.

  6. Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction.

    Directory of Open Access Journals (Sweden)

    Louise V Wain

    2014-05-01

    Full Text Available Chronic obstructive pulmonary disease (COPD is a leading cause of global morbidity and mortality and, whilst smoking remains the single most important risk factor, COPD risk is heritable. Of 26 independent genomic regions showing association with lung function in genome-wide association studies, eleven have been reported to show association with airflow obstruction. Although the main risk factor for COPD is smoking, some individuals are observed to have a high forced expired volume in 1 second (FEV1 despite many years of heavy smoking. We hypothesised that these "resistant smokers" may harbour variants which protect against lung function decline caused by smoking and provide insight into the genetic determinants of lung health. We undertook whole exome re-sequencing of 100 heavy smokers who had healthy lung function given their age, sex, height and smoking history and applied three complementary approaches to explore the genetic architecture of smoking resistance. Firstly, we identified novel functional variants in the "resistant smokers" and looked for enrichment of these novel variants within biological pathways. Secondly, we undertook association testing of all exonic variants individually with two independent control sets. Thirdly, we undertook gene-based association testing of all exonic variants. Our strongest signal of association with smoking resistance for a non-synonymous SNP was for rs10859974 (P = 2.34 × 10(-4 in CCDC38, a gene which has previously been reported to show association with FEV1/FVC, and we demonstrate moderate expression of CCDC38 in bronchial epithelial cells. We identified an enrichment of novel putatively functional variants in genes related to cilia structure and function in resistant smokers. Ciliary function abnormalities are known to be associated with both smoking and reduced mucociliary clearance in patients with COPD. We suggest that genetic influences on the development or function of cilia in the bronchial

  7. The Evolution of Power System Planning with High Levels of Variable Renewable Generation

    Energy Technology Data Exchange (ETDEWEB)

    Katz, Jessica [National Renewable Energy Lab. (NREL), Golden, CO (United States); Milligan, Michael [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2016-09-01

    Greening the Grid provides technical assistance to energy system planners, regulators, and grid operators to overcome challenges associated with integrating variable renewable energy into the grid. This document, part of the Greening the Grid introduces the evolution of power system planning with high levels of variable renewable generation.

  8. Integrating High Levels of Variable Renewable Energy into Electric Power Systems

    Energy Technology Data Exchange (ETDEWEB)

    Kroposki, Benjamin D. [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-08-01

    As more variable renewable energy is integrated into electric power systems, there are a range of challenges and solutions to accommodating very high penetration levels. This presentation highlights some of the recent research in this area.

  9. Sub-Hour X-Ray Variability of High-Energy Peaked BL Lacertae Objects

    OpenAIRE

    Bidzina Kapanadze

    2018-01-01

    The study of multi-wavelength flux variability in BL Lacertae objects is very important to discern unstable processes and emission mechanisms underlying their extreme observational features. While the innermost regions of these objects are not accessible from direct observations, we may draw conclusions about their internal structure via the detection of flux variations on various timescales, based on the light-travel argument. In this paper, we review the sub-hour X-ray variability in high-e...

  10. WEATHER ON OTHER WORLDS. III. A SURVEY FOR T DWARFS WITH HIGH-AMPLITUDE OPTICAL VARIABILITY

    International Nuclear Information System (INIS)

    Heinze, Aren N.; Metchev, Stanimir; Kellogg, Kendra

    2015-01-01

    We have monitored 12 T dwarfs with the Kitt Peak 2.1 m telescope using an F814W filter (0.7-0.95 μm) to place in context the remarkable 10%-20% variability exhibited by the nearby T dwarf Luhman 16B in this wavelength regime. The motivation was the poorly known red optical behavior of T dwarfs, which have been monitored almost exclusively at infrared wavelengths, where variability amplitudes greater than 10% have been found to be very rare. We detect highly significant variability in two T dwarfs. The T2.5 dwarf 2MASS 13243559+6358284 shows consistent ∼17% variability on two consecutive nights. The T2 dwarf 2MASS J16291840+0335371 exhibits ∼10% variability that may evolve from night to night, similarly to Luhman 16B. Both objects were previously known to be variable in the infrared, but with considerably lower amplitudes. We also find evidence for variability in the T6 dwarf J162414.37+002915.6, but since it has lower significance, we conservatively refrain from claiming this object as a variable. We explore and rule out various telluric effects, demonstrating that the variations we detect are astrophysically real. We suggest that high-amplitude photometric variability for T dwarfs is likely more common in the red optical than at longer wavelengths. The two new members of the growing class of high-amplitude variable T dwarfs offer excellent prospects for further study of cloud structures and their evolution

  11. WEATHER ON OTHER WORLDS. III. A SURVEY FOR T DWARFS WITH HIGH-AMPLITUDE OPTICAL VARIABILITY

    Energy Technology Data Exchange (ETDEWEB)

    Heinze, Aren N.; Metchev, Stanimir [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794-3800 (United States); Kellogg, Kendra, E-mail: aren.heinze@stonybrook.edu, E-mail: smetchev@uwo.ca [Department of Physics and Astronomy, The University of Western Ontario, 1151 Richmond St, London, ON N6A 3K7 (Canada)

    2015-03-10

    We have monitored 12 T dwarfs with the Kitt Peak 2.1 m telescope using an F814W filter (0.7-0.95 μm) to place in context the remarkable 10%-20% variability exhibited by the nearby T dwarf Luhman 16B in this wavelength regime. The motivation was the poorly known red optical behavior of T dwarfs, which have been monitored almost exclusively at infrared wavelengths, where variability amplitudes greater than 10% have been found to be very rare. We detect highly significant variability in two T dwarfs. The T2.5 dwarf 2MASS 13243559+6358284 shows consistent ∼17% variability on two consecutive nights. The T2 dwarf 2MASS J16291840+0335371 exhibits ∼10% variability that may evolve from night to night, similarly to Luhman 16B. Both objects were previously known to be variable in the infrared, but with considerably lower amplitudes. We also find evidence for variability in the T6 dwarf J162414.37+002915.6, but since it has lower significance, we conservatively refrain from claiming this object as a variable. We explore and rule out various telluric effects, demonstrating that the variations we detect are astrophysically real. We suggest that high-amplitude photometric variability for T dwarfs is likely more common in the red optical than at longer wavelengths. The two new members of the growing class of high-amplitude variable T dwarfs offer excellent prospects for further study of cloud structures and their evolution.

  12. Characterization of GM events by insert knowledge adapted re-sequencing approaches.

    Science.gov (United States)

    Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

    2013-10-03

    Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.

  13. Bayesian Multiresolution Variable Selection for Ultra-High Dimensional Neuroimaging Data.

    Science.gov (United States)

    Zhao, Yize; Kang, Jian; Long, Qi

    2018-01-01

    Ultra-high dimensional variable selection has become increasingly important in analysis of neuroimaging data. For example, in the Autism Brain Imaging Data Exchange (ABIDE) study, neuroscientists are interested in identifying important biomarkers for early detection of the autism spectrum disorder (ASD) using high resolution brain images that include hundreds of thousands voxels. However, most existing methods are not feasible for solving this problem due to their extensive computational costs. In this work, we propose a novel multiresolution variable selection procedure under a Bayesian probit regression framework. It recursively uses posterior samples for coarser-scale variable selection to guide the posterior inference on finer-scale variable selection, leading to very efficient Markov chain Monte Carlo (MCMC) algorithms. The proposed algorithms are computationally feasible for ultra-high dimensional data. Also, our model incorporates two levels of structural information into variable selection using Ising priors: the spatial dependence between voxels and the functional connectivity between anatomical brain regions. Applied to the resting state functional magnetic resonance imaging (R-fMRI) data in the ABIDE study, our methods identify voxel-level imaging biomarkers highly predictive of the ASD, which are biologically meaningful and interpretable. Extensive simulations also show that our methods achieve better performance in variable selection compared to existing methods.

  14. Genetic variability of the equine casein genes.

    Science.gov (United States)

    Brinkmann, J; Jagannathan, V; Drögemüller, C; Rieder, S; Leeb, T; Thaller, G; Tetens, J

    2016-07-01

    The casein genes are known to be highly variable in typical dairy species, such as cattle and goat, but the knowledge about equine casein genes is limited. Nevertheless, mare milk production and consumption is gaining importance because of its high nutritive value, use in naturopathy, and hypoallergenic properties with respect to cow milk protein allergies. In the current study, the open reading frames of the 4 casein genes CSN1S1 (αS1-casein), CSN2 (β-casein), CSN1S2 (αS2-casein), and CSN3 (κ-casein) were resequenced in 253 horses of 14 breeds. The analysis revealed 21 nonsynonymous nucleotide exchanges, as well as 11 synonymous nucleotide exchanges, leading to a total of 31 putative protein isoforms predicted at the DNA level, 26 of which considered novel. Although the majority of the alleles need to be confirmed at the transcript and protein level, a preliminary nomenclature was established for the equine casein alleles. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  15. On the interannual variability of the Bonin high associated with the East Asian summer monsoon rain

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Kyung-Ja; Lee, Sun-Seon [Pusan National University, Department of Atmospheric Sciences, Busan (Korea)

    2007-01-15

    In order to assess how the Bonin high affects interannual variability of the East Asian summer monsoon (EASM) around the Korean Peninsula, the pulsation of the Bonin high and its association with teleconnection patterns was examined. The major factor for the interannual intensity of the EASM is the center position of the Bonin high rather than its center pressure. Up to 12 harmonics over time can be used to reconstruct the Bonin high, demonstrating its intraseasonal variation. The interannual variability of the Bonin high correlates with the Tibet high. This correlation is dominant for the EASM onset time, though not its retreat. The primary teleconnection pattern, reliant up on the interannual variability of the Bonin high, is the Western Pacific oscillation (WPO) in April. In relation to long-term variability, the correlation between the WPO and the Bonin high appears to contribute to the retreat stage of the EASM, which has itself increased since the mid-1970s. Furthermore, the WPO in May and the Tibet correlation has marked the onset rather than the retreat of the EASM since the 1970s. This highly correlated pattern since the mid-1970s may be the result of El Nino. (orig.)

  16. Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon (Citrullus lanatus [Thunb.] Matsum. and Nakai) constructed using whole-genome re-sequencing data.

    Science.gov (United States)

    Liu, Shi; Gao, Peng; Zhu, Qianglong; Luan, Feishi; Davis, Angela R; Wang, Xiaolu

    2016-03-01

    Cleaved amplified polymorphic sequence (CAPS) markers are useful tools for detecting single nucleotide polymorphisms (SNPs). This study detected and converted SNP sites into CAPS markers based on high-throughput re-sequencing data in watermelon, for linkage map construction and quantitative trait locus (QTL) analysis. Two inbred lines, Cream of Saskatchewan (COS) and LSW-177 had been re-sequenced and analyzed by Perl self-compiled script for CAPS marker development. 88.7% and 78.5% of the assembled sequences of the two parental materials could map to the reference watermelon genome, respectively. Comparative assembled genome data analysis provided 225,693 and 19,268 SNPs and indels between the two materials. 532 pairs of CAPS markers were designed with 16 restriction enzymes, among which 271 pairs of primers gave distinct bands of the expected length and polymorphic bands, via PCR and enzyme digestion, with a polymorphic rate of 50.94%. Using the new CAPS markers, an initial CAPS-based genetic linkage map was constructed with the F2 population, spanning 1836.51 cM with 11 linkage groups and 301 markers. 12 QTLs were detected related to fruit flesh color, length, width, shape index, and brix content. These newly CAPS markers will be a valuable resource for breeding programs and genetic studies of watermelon.

  17. Optimization of a variable-stiffness skin for morphing high-lift devices

    NARCIS (Netherlands)

    Thuwis, G.A.A.; Abdalla, M.M.; Gürdal, Z.

    2010-01-01

    One of the possibilities for the next generation of smart high-lift devices is to use a seamless morphing structure. A passive composite variable-stiffness skin as a solution to the dilemma of designing the structure to have high enough stiffness to withstand aerodynamic loading and low stiffness to

  18. Testing and Validation of High Density Resequencing Microarray for Broad Range Biothreat Agents Detection

    Science.gov (United States)

    2009-08-11

    concentration of the virus was expressed in plaque forming units (pfu). For synthetic DNA templates, the DNA concentration was used to calculate the...cells ATCC Escherichia coli O157:H7 ATCC 43985 (CDC EDL933) Nucleic acid ATCC Francisella tularensis SHU4 Nucleic acid AFIP Leptospira interrogans ATCC...2% on the nucleotide level and 0.6% on the protein level. Similar strain discrimination was obtained in case of Machupo virus strains Carvallo and

  19. High-speed limnology: using advanced sensors to investigate spatial variability in biogeochemistry and hydrology.

    Science.gov (United States)

    Crawford, John T; Loken, Luke C; Casson, Nora J; Smith, Colin; Stone, Amanda G; Winslow, Luke A

    2015-01-06

    Advanced sensor technology is widely used in aquatic monitoring and research. Most applications focus on temporal variability, whereas spatial variability has been challenging to document. We assess the capability of water chemistry sensors embedded in a high-speed water intake system to document spatial variability. This new sensor platform continuously samples surface water at a range of speeds (0 to >45 km h(-1)) resulting in high-density, mesoscale spatial data. These novel observations reveal previously unknown variability in physical, chemical, and biological factors in streams, rivers, and lakes. By combining multiple sensors into one platform, we were able to detect terrestrial-aquatic hydrologic connections in a small dystrophic lake, to infer the role of main-channel vs backwater nutrient processing in a large river and to detect sharp chemical changes across aquatic ecosystem boundaries in a stream/lake complex. Spatial sensor data were verified in our examples by comparing with standard lab-based measurements of selected variables. Spatial fDOM data showed strong correlation with wet chemistry measurements of DOC, and optical NO3 concentrations were highly correlated with lab-based measurements. High-frequency spatial data similar to our examples could be used to further understand aquatic biogeochemical fluxes, ecological patterns, and ecosystem processes, and will both inform and benefit from fixed-site data.

  20. Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

    Directory of Open Access Journals (Sweden)

    Clive J Hoggart

    2008-07-01

    Full Text Available Testing one SNP at a time does not fully realise the potential of genome-wide association studies to identify multiple causal variants, which is a plausible scenario for many complex diseases. We show that simultaneous analysis of the entire set of SNPs from a genome-wide study to identify the subset that best predicts disease outcome is now feasible, thanks to developments in stochastic search methods. We used a Bayesian-inspired penalised maximum likelihood approach in which every SNP can be considered for additive, dominant, and recessive contributions to disease risk. Posterior mode estimates were obtained for regression coefficients that were each assigned a prior with a sharp mode at zero. A non-zero coefficient estimate was interpreted as corresponding to a significant SNP. We investigated two prior distributions and show that the normal-exponential-gamma prior leads to improved SNP selection in comparison with single-SNP tests. We also derived an explicit approximation for type-I error that avoids the need to use permutation procedures. As well as genome-wide analyses, our method is well-suited to fine mapping with very dense SNP sets obtained from re-sequencing and/or imputation. It can accommodate quantitative as well as case-control phenotypes, covariate adjustment, and can be extended to search for interactions. Here, we demonstrate the power and empirical type-I error of our approach using simulated case-control data sets of up to 500 K SNPs, a real genome-wide data set of 300 K SNPs, and a sequence-based dataset, each of which can be analysed in a few hours on a desktop workstation.

  1. Human apolipoprotein e resequencing by proteomic analysis and its application to serotyping.

    Directory of Open Access Journals (Sweden)

    Motoi Nishimura

    Full Text Available BACKGROUND: Apolipoprotein E (ApoE typing is considered important because of the association between ApoE and Alzheimer's disease and familial dyslipidemia and is currently performed by genetic testing (APOE genotyping. ApoE levels in plasma and serum are clinically determined by immunoassay. METHODS: Combining an ApoE immunoassay reagent with proteomic analysis using an Orbitrap mass spectrometer, we attempted to resequence ApoE from trace amounts of serum for typing (serotyping. Most (24 of 33 ApoE mutant proteins registered to date with Online Mendelian Inheritance in Man, such as ApoE2 and ApoE4, involve lysine and arginine mutations. Digestion of mutant ApoE with trypsin will thus result in fragments that differ substantially from wild-type ApoE3 in terms of mass, making serotyping ideally suited to mass spectrometry analysis. RESULTS: The mean coverage of the amino acid sequence of full-length ApoE was 91.6% in the protein resequence. Residues 112 and 158 (which are mutated in ApoE2 and ApoE4 were covered in all samples, and the protein sequences were used for serotyping. Serotypes including all heterozygous combinations (ApoE2/E3, E2/E4, E3/E4 corresponded exactly to the APOE genotyping results in each of the subjects. CONCLUSION: Our novel ApoE serotyping method with protein resequencing requires no synthesis of stable isotope-labeled peptides or genome analysis. The method can use residual blood from samples collected for routine clinical tests, thus enabling retrospective studies with preserved body fluids. The test could be applied to samples from subjects whose DNA is unavailable. In future studies, we hope to demonstrate the capability of our method to detect rare ApoE mutations.

  2. Match-to-match variability in high-speed running activity in a professional soccer team.

    Science.gov (United States)

    Carling, Christopher; Bradley, Paul; McCall, Alan; Dupont, Gregory

    2016-12-01

    This study investigated variability in competitive high-speed running performance in an elite soccer team. A semi-automated tracking system quantified running performance in 12 players over a season (median 17 matches per player, 207 observations). Variability [coefficient of variation (CV)] was compared for total sprint distance (TSD, >25.2 km/h), high-speed running (HSR, 19.8-25.2 km/h), total high-speed running (THSR, ≥19.8 km/h); THSR when the team was in and out of ball possession, in individual ball possession, in the peak 5 min activity period; and distance run according to individual maximal aerobic speed (MAS). Variability for % declines in THSR and distance covered at ≥80% MAS across halves, at the end of play (final 15 min vs. mean for all 15 min periods) and transiently (5 min period following peak 5 min activity period), was analysed. Collectively, variability was higher for TSD versus HSR and THSR and lowest for distance run at ≥80% MAS (CVs: 37.1%, 18.1%, 19.8% and 11.8%). THSR CVs when the team was in/out of ball possession, in individual ball possession and during the peak 5 min period were 31.5%, 26.1%, 60.1% and 23.9%. Variability in THSR declines across halves, at the end of play and transiently, ranged from 37.1% to 142.6%, while lower CVs were observed in these metrics for running at ≥80% MAS (20.9-53.3%).These results cast doubt on the appropriateness of general measures of high-speed activity for determining variability in an elite soccer team, although individualisation of HSR thresholds according to fitness characteristics might provide more stable indicators of running performance and fatigue occurrence.

  3. Incorporation of gene-specific variability improves expression analysis using high-density DNA microarrays

    Directory of Open Access Journals (Sweden)

    Spitznagel Edward

    2003-11-01

    Full Text Available Abstract Background The assessment of data reproducibility is essential for application of microarray technology to exploration of biological pathways and disease states. Technical variability in data analysis largely depends on signal intensity. Within that context, the reproducibility of individual probe sets has not been hitherto addressed. Results We used an extraordinarily large replicate data set derived from human placental trophoblast to analyze probe-specific contribution to variability of gene expression. We found that signal variability, in addition to being signal-intensity dependant, is probe set-specific. Importantly, we developed a novel method to quantify the contribution of this probe set-specific variability. Furthermore, we devised a formula that incorporates a priori-computed, replicate-based information on probe set- and intensity-specific variability in determination of expression changes even without technical replicates. Conclusion The strategy of incorporating probe set-specific variability is superior to analysis based on arbitrary fold-change thresholds. We recommend its incorporation to any computation of gene expression changes using high-density DNA microarrays. A Java application implementing our T-score is available at http://www.sadovsky.wustl.edu/tscore.html.

  4. Catch, effort and sampling strategies in the highly variable sardine fisheries around East Java, Indonesia.

    NARCIS (Netherlands)

    Pet, J.S.; Densen, van W.L.T.; Machiels, M.A.M.; Sukkel, M.; Setyohady, D.; Tumuljadi, A.

    1997-01-01

    Temporal and spatial patterns in the fishery for Sardinella spp. around East Java, Indonesia, were studied in an attempt to develop an efficient catch and effort sampling strategy for this highly variable fishery. The inter-annual and monthly variation in catch, effort and catch per unit of effort

  5. Investigation of High School Students' Environmental Attitudes in Terms of Some Demographic Variables

    Science.gov (United States)

    Koruoglu, Nergiz; Ugulu, Ilker; Yorek, Nurettin

    2015-01-01

    Studying individuals and students' attitudes towards environment and factors affecting students to be responsible individuals towards their environment may provide help towards the solution of environmental problems. In this study, it is aimed to evaluate environmental attitudes of high school students in terms of some variables. The sample of the…

  6. Variability of Photovoltaic Power in the State of Gujarat Using High Resolution Solar Data

    Energy Technology Data Exchange (ETDEWEB)

    Hummon, M. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Cochran, J. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Weekley, A. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Lopez, A. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Zhang, J. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Stoltenberg, B. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Parsons, B. [Evergreen Renewable Consulting, CO (United States); Batra, P. [Central Electricity Authority, New Delhi (India); Mehta, B. [Gujarat Energy Transmission Corporation Ltd., Vadodara (India); Patel, D. [Gujarat Energy Transmission Corporation Ltd., Vadodara (India)

    2014-03-01

    India has ambitious goals for high utilization of variable renewable power from wind and solar, and deployment has been proceeding at a rapid pace. The western state of Gujarat currently has the largest amount of solar generation of any Indian state, with over 855 Megawatts direct current (MWDC). Combined with over 3,240 MW of wind, variable generation renewables comprise nearly 18% of the electric-generating capacity in the state. A new historic 10-kilometer (km) gridded solar radiation data set capturing hourly insolation values for 2002-2011 is available for India. We apply an established method for downscaling hourly irradiance data to one-minute irradiance data at potential PV power production locations for one year, 2006. The objective of this report is to characterize the intra-hour variability of existing and planned photovoltaic solar power generation in the state of Gujarat (a total of 1.9 gigawatts direct current (GWDC)), and of five possible expansion scenarios of solar generation that reflect a range of geographic diversity (each scenario totals 500-1,000 MW of additional solar capacity). The report statistically analyzes one year's worth of power variability data, applied to both the baseline and expansion scenarios, to evaluate diurnal and seasonal power fluctuations, different timescales of variability (e.g., from one to 15 minutes), the magnitude of variability (both total megawatts and relative to installed solar capacity), and the extent to which the variability can be anticipated in advance. The paper also examines how Gujarat Energy Transmission Corporation (GETCO) and the Gujarat State Load Dispatch Centre (SLDC) could make use of the solar variability profiles in grid operations and planning.

  7. High beat-to-beat blood pressure variability in atrial fibrillation compared to sinus rhythm.

    Science.gov (United States)

    Olbers, Joakim; Gille, Adam; Ljungman, Petter; Rosenqvist, Mårten; Östergren, Jan; Witt, Nils

    2018-02-07

    Atrial fibrillation (AF) is associated with an increased risk for cardiovascular morbidity and mortality, not entirely explained by thromboembolism. The underlying mechanisms for this association are largely unknown. Similarly, high blood pressure (BP) increases the risk for cardiovascular events. Despite this the interplay between AF and BP is insufficiently studied. The purpose of this study was to examine and quantify the beat-to-beat blood pressure variability in patients with AF in comparison to a control group of patients with sinus rhythm. We studied 33 patients - 21 in atrial fibrillation and 12 in sinus rhythm - undergoing routine coronary angiography. Invasive blood pressure was recorded at three locations: radial artery, brachial artery and ascending aorta. Blood pressure variability, defined as average beat-to-beat blood pressure difference, was calculated for systolic and diastolic blood pressure at each site. We observed a significant difference (p blood pressure variability between the atrial fibrillation and sinus rhythm groups at all locations. Systolic blood pressure variability roughly doubled in the atrial fibrillation group compared to the sinus rhythm group (4.9 and 2.4 mmHg respectively). Diastolic beat-to-beat blood pressure variability was approximately 6 times as high in the atrial fibrillation group compared to the sinus rhythm group (7.5 and 1.2 mmHg respectively). No significant difference in blood pressure variability was seen between measurement locations. Beat-to-beat blood pressure variability in patients with atrial fibrillation was substantially higher than in patients with sinus rhythm. Hemodynamic effects of this beat-to-beat variation in blood pressure may negatively affect vascular structure and function, which may contribute to the increased cardiovascular morbidity and mortality seen in patients with atrial fibrillation.

  8. Volume measurement variability in three-dimensional high-frequency ultrasound images of murine liver metastases

    International Nuclear Information System (INIS)

    Wirtzfeld, L A; Graham, K C; Groom, A C; MacDonald, I C; Chambers, A F; Fenster, A; Lacefield, J C

    2006-01-01

    The identification and quantification of tumour volume measurement variability is imperative for proper study design of longitudinal non-invasive imaging of pre-clinical mouse models of cancer. Measurement variability will dictate the minimum detectable volume change, which in turn influences the scheduling of imaging sessions and the interpretation of observed changes in tumour volume. In this paper, variability is quantified for tumour volume measurements from 3D high-frequency ultrasound images of murine liver metastases. Experimental B16F1 liver metastases were analysed in different size ranges including less than 1 mm 3 , 1-4 mm 3 , 4-8 mm 3 and 8-70 mm 3 . The intra- and inter-observer repeatability was high over a large range of tumour volumes, but the coefficients of variation (COV) varied over the volume ranges. The minimum and maximum intra-observer COV were 4% and 14% for the 1-4 mm 3 and 3 tumours, respectively. For tumour volumes measured by segmenting parallel planes, the maximum inter-slice distance that maintained acceptable measurement variability increased from 100 to 600 μm as tumour volume increased. Comparison of free breathing versus ventilated animals demonstrated that respiratory motion did not significantly change the measured volume. These results enable design of more efficient imaging studies by using the measured variability to estimate the time required to observe a significant change in tumour volume

  9. Land agroecological quality assessment in conditions of high spatial soil cover variability at the Pereslavskoye Opolye.

    Science.gov (United States)

    Morev, Dmitriy; Vasenev, Ivan

    2015-04-01

    The essential spatial variability is mutual feature for most natural and man-changed soils at the Central region of European territory of Russia. The original spatial heterogeneity of forest soils has been further complicated by a specific land-use history and human impacts. For demand-driven land-use planning and decision making the quantitative analysis and agroecological interpretation of representative soil cover spatial variability is an important and challenging task that receives increasing attention from private companies, governmental and environmental bodies. Pereslavskoye Opolye is traditionally actively used in agriculture due to dominated high-quality cultivated soddy-podzoluvisols which are relatively reached in organic matter (especially for conditions of the North part at the European territory of Russia). However, the soil cover patterns are often very complicated even within the field that significantly influences on crop yield variability and have to be considered in farming system development and land agroecological quality evaluation. The detailed investigations of soil regimes and mapping of the winter rye yield have been carried in conditions of two representative fields with slopes sharply contrasted both in aspects and degrees. Rye biological productivity and weed infestation have been measured in elementary plots of 0.25 m2 with the following analysis the quality of the yield. In the same plot soil temperature and moisture have been measured by portable devices. Soil sampling was provided from three upper layers by drilling. The results of ray yield detailed mapping shown high differences both in average values and within-field variability on different slopes. In case of low-gradient slope (field 1) there is variability of ray yield from 39.4 to 44.8 dt/ha. In case of expressed slope (field 2) the same species of winter rye grown with the same technology has essentially lower yield and within-field variability from 20 to 29.6 dt/ha. The

  10. Investigation of High School Students’ Internet Addiction inThe Light of Various Variables

    OpenAIRE

    Deniz Mertkan GEZGİN; Göknur KAPLAN AKILLI

    2016-01-01

    Abstract: The aim of this study was to investigate high school students’ level of internet addiction and to determine internet addiction level according to various variables. The study was designed utilizing a survey model. The participants of the study were 501 high school students randomly selected from different socio-economical districts, i.e., Selcuk district in Izmir and Central district in Edirne within the 2015-2016 academic year. Data were obtained through Internet Addiction Scale. D...

  11. Selection of variables for neural network analysis. Comparisons of several methods with high energy physics data

    International Nuclear Information System (INIS)

    Proriol, J.

    1994-01-01

    Five different methods are compared for selecting the most important variables with a view to classifying high energy physics events with neural networks. The different methods are: the F-test, Principal Component Analysis (PCA), a decision tree method: CART, weight evaluation, and Optimal Cell Damage (OCD). The neural networks use the variables selected with the different methods. We compare the percentages of events properly classified by each neural network. The learning set and the test set are the same for all the neural networks. (author)

  12. Normalization of High Dimensional Genomics Data Where the Distribution of the Altered Variables Is Skewed

    Science.gov (United States)

    Landfors, Mattias; Philip, Philge; Rydén, Patrik; Stenberg, Per

    2011-01-01

    Genome-wide analysis of gene expression or protein binding patterns using different array or sequencing based technologies is now routinely performed to compare different populations, such as treatment and reference groups. It is often necessary to normalize the data obtained to remove technical variation introduced in the course of conducting experimental work, but standard normalization techniques are not capable of eliminating technical bias in cases where the distribution of the truly altered variables is skewed, i.e. when a large fraction of the variables are either positively or negatively affected by the treatment. However, several experiments are likely to generate such skewed distributions, including ChIP-chip experiments for the study of chromatin, gene expression experiments for the study of apoptosis, and SNP-studies of copy number variation in normal and tumour tissues. A preliminary study using spike-in array data established that the capacity of an experiment to identify altered variables and generate unbiased estimates of the fold change decreases as the fraction of altered variables and the skewness increases. We propose the following work-flow for analyzing high-dimensional experiments with regions of altered variables: (1) Pre-process raw data using one of the standard normalization techniques. (2) Investigate if the distribution of the altered variables is skewed. (3) If the distribution is not believed to be skewed, no additional normalization is needed. Otherwise, re-normalize the data using a novel HMM-assisted normalization procedure. (4) Perform downstream analysis. Here, ChIP-chip data and simulated data were used to evaluate the performance of the work-flow. It was found that skewed distributions can be detected by using the novel DSE-test (Detection of Skewed Experiments). Furthermore, applying the HMM-assisted normalization to experiments where the distribution of the truly altered variables is skewed results in considerably higher

  13. Sub-Hour X-Ray Variability of High-Energy Peaked BL Lacertae Objects

    Directory of Open Access Journals (Sweden)

    Bidzina Kapanadze

    2018-03-01

    Full Text Available The study of multi-wavelength flux variability in BL Lacertae objects is very important to discern unstable processes and emission mechanisms underlying their extreme observational features. While the innermost regions of these objects are not accessible from direct observations, we may draw conclusions about their internal structure via the detection of flux variations on various timescales, based on the light-travel argument. In this paper, we review the sub-hour X-ray variability in high-energy peaked BL Lacertae sources (HBLs that are bright at X-rays and provide us with an effective tool to study the details related to the physics of the emitting particles. The X-ray emission of these sources is widely accepted to be a synchrotron radiation from the highest-energy electrons, and the complex spectral variability observed in this band reflects the injection and radiative evolution of freshly-accelerated particles. The detection of sub-hour X-ray flux variability is very important since it can be related to the small-scale jet turbulent structures or triggered by unstable processes occurring in the vicinity of a central supermassive black hole. We summarize the fastest X-ray variability instances detected in bright HBLs and discuss their physical implications.

  14. Non-native Listeners’ Recognition of High-Variability Speech Using PRESTO

    Science.gov (United States)

    Tamati, Terrin N.; Pisoni, David B.

    2015-01-01

    Background Natural variability in speech is a significant challenge to robust successful spoken word recognition. In everyday listening environments, listeners must quickly adapt and adjust to multiple sources of variability in both the signal and listening environments. High-variability speech may be particularly difficult to understand for non-native listeners, who have less experience with the second language (L2) phonological system and less detailed knowledge of sociolinguistic variation of the L2. Purpose The purpose of this study was to investigate the effects of high-variability sentences on non-native speech recognition and to explore the underlying sources of individual differences in speech recognition abilities of non-native listeners. Research Design Participants completed two sentence recognition tasks involving high-variability and low-variability sentences. They also completed a battery of behavioral tasks and self-report questionnaires designed to assess their indexical processing skills, vocabulary knowledge, and several core neurocognitive abilities. Study Sample Native speakers of Mandarin (n = 25) living in the United States recruited from the Indiana University community participated in the current study. A native comparison group consisted of scores obtained from native speakers of English (n = 21) in the Indiana University community taken from an earlier study. Data Collection and Analysis Speech recognition in high-variability listening conditions was assessed with a sentence recognition task using sentences from PRESTO (Perceptually Robust English Sentence Test Open-Set) mixed in 6-talker multitalker babble. Speech recognition in low-variability listening conditions was assessed using sentences from HINT (Hearing In Noise Test) mixed in 6-talker multitalker babble. Indexical processing skills were measured using a talker discrimination task, a gender discrimination task, and a forced-choice regional dialect categorization task. Vocabulary

  15. High inter-specimen variability of baseline data for the tibio-talar contact area.

    Science.gov (United States)

    Matricali, Giovanni A; Bartels, Ward; Labey, Luc; Dereymaeker, Greta Ph E; Luyten, Frank P; Vander Sloten, Jos

    2009-01-01

    The tibio-talar contact area has been widely investigated to monitor biomechanical changes due to articular incongruities or an altered loading. This study aims to investigate for the first time in a systematic way the extent of the inter-specimen variability of the tibio-talar contact area, and its repercussions when analyzing data concerning this parameter. Ten specimens were loaded to record the tibio-talar contact characteristics by use of pressure sensitive film. The size of the talar dome area, the size of the (normalized) tibio-talar contact area, the position of the tibio-talar contact area, and the shape of the latter were determined and analyzed. Inter-specimen variability was expressed as the coefficient of variation and was calculated for the datasets of previous studies as well. The size of the tibio-talar contact area showed a very high inter-specimen variability, as is the case in previous studies. This high variability persisted when a normalized tibio-talar contact area was calculated. The shape of the tibio-talar contact area showed some basic characteristics, but a high variation in details could be observed. Every specimen can be considered to have its own "ankle print". By this variability, articular incongruities are expected to have a different effect on local biomechanical characteristics in every single individual. Therefore, every single case has to be evaluated and reported for significant changes. In case of modeling, this also underscores the need to use subject specific models fed by sets of parameters derived from a series of single specimens.

  16. THE CURIOUS CASE OF GLASS I: HIGH IONIZATION AND VARIABILITY OF DIFFERENT TYPES

    Energy Technology Data Exchange (ETDEWEB)

    Kruger, Andrew J. [Department of Physical Science, Wilbur Wright College, 4300 N. Narragansett Ave., Chicago, IL 60634 (United States); Richter, Matthew J. [Department of Physics, University of California at Davis, One Shields Ave., Davis, CA 95616 (United States); Carr, John S. [Remote Sensing Division, Naval Research Laboratory, Code 7210, Washington, DC 20375 (United States); Najita, Joan R. [National Optical Astronomy Observatory, Tucson, AZ 85719 (United States); Moerchen, Margaret M. [European Southern Observatory, Alonso de Cordova 3107, Santiago (Chile); Doppmann, Greg W. [W. M. Keck Observatory, 65-1120 Mamalahoa Hwy, Kamuela, HI 96743 (United States); Seifahrt, Andreas [Department of Astronomy and Astrophysics, University of Chicago, 5640 S. Ellis Ave., Chicago, IL 60637 (United States)

    2013-02-20

    Our Spitzer IRS observation of the infrared companion Glass Ib revealed fine-structure emission with high ionization ([Ne III]/[Ne II] = 2.1 and [S IV]/[S III] = 0.6) that indicates that the gas is likely illuminated by hard radiation. While models suggest that extreme-ultraviolet radiation could be present in T Tauri stars, this is the first detection of [S IV] and such a high [Ne III]/[Ne II] ratio in a young star. We also find that Glass Ib displays the molecules HCN, CO{sub 2}, and H{sub 2}O in emission. Here we investigate the Glass I binary system and consider possible mechanisms that may have caused the high ionization, whether from an outflow or disk irradiation. We also model the spectral energy distributions of Glass Ia and Ib to test if the system is a young member of the Chameleon I star-forming region, and we consider other possible classifications for the system. We find that Glass Ib is highly variable, showing changes in continuum strength and emission features at optical, near-infrared, and mid-infrared wavelengths. The optical light curve indicates that a central stellar component in Glass Ib became entirely visible for 2.5 years beginning in mid-2002 and possibly displayed periodic variability with repeated, short-period dimming during that time. As the fine-structure emission was not detected in observations before or after our Spitzer IRS observation, we explore whether the variable nature of Glass Ib is related to the gas being highly ionized, possibly due to variable accretion or an X-ray flare.

  17. Design, conditioning, and performance of a high voltage, high brightness dc photoelectron gun with variable gap

    Energy Technology Data Exchange (ETDEWEB)

    Maxson, Jared; Bazarov, Ivan; Dunham, Bruce; Dobbins, John; Liu, Xianghong; Smolenski, Karl [Cornell Laboratory for Accelerator-Based Sciences and Education, Cornell University, Ithaca, New York 14853 (United States)

    2014-09-15

    A new high voltage photoemission gun has been constructed at Cornell University which features a segmented insulator and a movable anode, allowing the cathode-anode gap to be adjusted. In this work, we describe the gun's overall mechanical and high voltage design, the surface preparation of components, as well as the clean construction methods. We present high voltage conditioning data using a 50 mm cathode-anode gap, in which the conditioning voltage exceeds 500 kV, as well as at smaller gaps. Finally, we present simulated emittance results obtained from a genetic optimization scheme using voltage values based on the conditioning data. These results indicate that for charges up to 100 pC, a 30 mm gap at 400 kV has equal or smaller 100% emittance than a 50 mm gap at 450 kV, and also a smaller core emittance, when placed as the source for the Cornell energy recovery linac photoinjector with bunch length constrained to be <3 ps rms. For 100 pC up to 0.5 nC charges, the 50 mm gap has larger core emittance than the 30 mm gap, but conversely smaller 100% emittance.

  18. Increased variability of watershed areas in patients with high-grade carotid stenosis

    DEFF Research Database (Denmark)

    Kaczmarz, Stephan; Griese, Vanessa; Preibisch, Christine

    2018-01-01

    . Despite of high relevance for both clinical diagnostics and research, individual in vivo WSA definition is fairly limited to date. Thus, this study proposes a standardized segmentation approach to delineate individual WSAs by use of time-to-peak (TTP) maps and investigates spatial variability...... of individual WSAs. Methods: We defined individual watershed masks based on relative TTP increases in 30 healthy elderly persons and 28 patients with unilateral, high-grade carotid stenosis, being at risk for watershed-related hemodynamic impairment. Determined WSA location was confirmed by an arterial transit...... time atlas and individual super-selective arterial spin labeling. We compared spatial variability of WSA probability maps between groups and assessed TTP differences between hemispheres in individual and group-average watershed locations. Results: Patients showed significantly higher spatial...

  19. Perhaps a new unified scaling variable for describing the low- and high-psub(T) processes

    International Nuclear Information System (INIS)

    Amaglobeli, N.S.; Esakia, S.M.; Khujadze, A.M.; Kuratashvili, G.O.; Topuria, T.P.; Garsevanishvili, V.R.

    1982-09-01

    A new scale invariant parametrization of single particle inclusive spectra in hadron-hadron collisions is proposed. The variable introduced goes over to the well-known scaling variables xsub(F)=2psub(z)/√s and xsub(T)=2psub(T)/√s in the high-psub(z) and high-psub(T) limits, respectively. Some ''critical'' surfaces are found in the phase space of produced particles, which determine the boundary of the regions with significantly different characteristics (in particular, angular distributions) of generated particles. In one of these two regions a naive statistical model seems to be in good agreement with the data, whereas it does not work in the other region. (author)

  20. Forecasting short-run crude oil price using high- and low-inventory variables

    International Nuclear Information System (INIS)

    Ye, Michael; Zyren, John; Shore, Joanne

    2006-01-01

    Since inventories have a lower bound or a minimum operating level, economic literature suggests a nonlinear relationship between inventory level and commodity prices. This was found to be the case in the short-run crude oil market. In order to explore this inventory-price relationship, two nonlinear inventory variables are defined and derived from the monthly normal level and relative level of OECD crude oil inventories from post 1991 Gulf War to October 2003: one for the low inventory state and another for the high inventory state of the crude oil market. Incorporation of low- and high-inventory variables in a single equation model to forecast short-run WTI crude oil prices enhances the model fit and forecast ability

  1. Optimization of a variable-stiffness skin for morphing high-lift devices

    International Nuclear Information System (INIS)

    Thuwis, G A A; Abdalla, M M; Gürdal, Z

    2010-01-01

    One of the possibilities for the next generation of smart high-lift devices is to use a seamless morphing structure. A passive composite variable-stiffness skin as a solution to the dilemma of designing the structure to have high enough stiffness to withstand aerodynamic loading and low stiffness to enable morphing is proposed. The variable-stiffness skin is achieved by allowing for a spatial fibre angle and skin thickness variation on a morphing high-lift system. The stiffness distribution is tailored to influence the deformation of the structure beneficially. To design a realistic stiffness distribution, it is important to take aerodynamic and actuation loads into account during the optimization. A two-dimensional aero-servo-elastic framework is created for this purpose. Skin optimization is performed using a gradient-based optimizer, where sensitivity information is found through application of the adjoint method. The implementation of the aero-servo-elastic environment is addressed and initial optimization results presented. The results indicate that a variable-stiffness skin increases the design space. Moreover, the importance of taking the change in aerodynamic loads due to morphing skin deformation into account during optimization is demonstrated

  2. Silicon photonic transceiver circuit for high-speed polarization-based discrete variable quantum key distribution.

    Science.gov (United States)

    Cai, Hong; Long, Christopher M; DeRose, Christopher T; Boynton, Nicholas; Urayama, Junji; Camacho, Ryan; Pomerene, Andrew; Starbuck, Andrew L; Trotter, Douglas C; Davids, Paul S; Lentine, Anthony L

    2017-05-29

    We demonstrate a silicon photonic transceiver circuit for high-speed discrete variable quantum key distribution that employs a common structure for transmit and receive functions. The device is intended for use in polarization-based quantum cryptographic protocols, such as BB84. Our characterization indicates that the circuit can generate the four BB84 states (TE/TM/45°/135° linear polarizations) with >30 dB polarization extinction ratios and gigabit per second modulation speed, and is capable of decoding any polarization bases differing by 90° with high extinction ratios.

  3. High Resolution ECG for Evaluation of QT Interval Variability during Exposure to Acute Hypoxia

    Science.gov (United States)

    Zupet, P.; Finderle, Z.; Schlegel, Todd T.; Starc, V.

    2010-01-01

    Ventricular repolarization instability as quantified by the index of QT interval variability (QTVI) is one of the best predictors for risk of malignant ventricular arrhythmias and sudden cardiac death. Because it is difficult to appropriately monitor early signs of organ dysfunction at high altitude, we investigated whether high resolution advanced ECG (HR-ECG) analysis might be helpful as a non-invasive and easy-to-use tool for evaluating the risk of cardiac arrhythmias during exposure to acute hypoxia. 19 non-acclimatized healthy trained alpinists (age 37, 8 plus or minus 4,7 years) participated in the study. Five-minute high-resolution 12-lead electrocardiograms (ECGs) were recorded (Cardiosoft) in each subject at rest in the supine position breathing room air and then after breathing 12.5% oxygen for 30 min. For beat-to-beat RR and QT variability, the program of Starc was utilized to derive standard time domain measures such as root mean square of the successive interval difference (rMSSD) of RRV and QTV, the corrected QT interval (QTc) and the QTVI in lead II. Changes were evaluated with paired-samples t-test with p-values less than 0.05 considered statistically significant. As expected, the RR interval and its variability both decreased with increasing altitude, with p = 0.000 and p = 0.005, respectively. Significant increases were found in both the rMSSDQT and the QTVI in lead II, with p = 0.002 and p = 0.003, respectively. There was no change in QTc interval length (p = non significant). QT variability parameters may be useful for evaluating changes in ventricular repolarization caused by hypoxia. These changes might be driven by increases in sympathetic nervous system activity at ventricular level.

  4. Comparison of environmental forcings affecting suspended sediments variability in two macrotidal, highly-turbid estuaries

    Science.gov (United States)

    Jalón-Rojas, Isabel; Schmidt, Sabine; Sottolichio, Aldo

    2017-11-01

    The relative contribution of environmental forcing frequencies on turbidity variability is, for the first time, quantified at seasonal and multiannual time scales in tidal estuarine systems. With a decade of high-frequency, multi-site turbidity monitoring, the two nearby, macrotidal and highly-turbid Gironde and Loire estuaries (west France) are excellent natural laboratories for this purpose. Singular Spectrum Analyses, combined with Lomb-Scargle periodograms and Wavelet Transforms, were applied to the continuous multiannual turbidity time series. Frequencies of the main environmental factors affecting turbidity were identified: hydrological regime (high versus low river discharges), river flow variability, tidal range, tidal cycles, and turbulence. Their relative influences show similar patterns in both estuaries and depend on the estuarine region (lower or upper estuary) and the time scale (multiannual or seasonal). On the multiannual time scale, the relative contribution of tidal frequencies (tidal cycles and range) to turbidity variability decreases up-estuary from 68% to 47%, while the influence of river flow frequencies increases from 3% to 42%. On the seasonal time scale, the relative influence of forcings frequencies remains almost constant in the lower estuary, dominated by tidal frequencies (60% and 30% for tidal cycles and tidal range, respectively); in the upper reaches, it is variable depending on hydrological regime, even if tidal frequencies are responsible for up 50% of turbidity variance. These quantifications show the potential of combined spectral analyses to compare the behavior of suspended sediment in tidal estuaries throughout the world and to evaluate long-term changes in environmental forcings, especially in a context of global change. The relevance of this approach to compare nearby and overseas systems and to support management strategies is discussed (e.g., selection of effective operation frequencies/regions, prediction of the most

  5. Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

    KAUST Repository

    Hunt, Paul; Martinelli, Axel; Modrzynska, Katarzyna; Borges, Sofia; Creasey, Alison; Rodrigues, Louise; Beraldi, Dario; Loewe, Laurence; Fawcett, Richard; Kumar, Sujai; Thomson, Marian; Trivedi, Urmi; Otto, Thomas D; Pain, Arnab; Blaxter, Mark; Cravo, Pedro

    2010-01-01

    was mapped to a region of chromosome 2 by Linkage Group Selection in two different genetic crosses. Whole-genome deep coverage short-read re-sequencing (IlluminaSolexa) defined the point mutations, insertions, deletions and copy-number variations arising

  6. Kiloampere, Variable-Temperature, Critical-Current Measurements of High-Field Superconductors.

    Science.gov (United States)

    Goodrich, L F; Cheggour, N; Stauffer, T C; Filla, B J; Lu, X F

    2013-01-01

    We review variable-temperature, transport critical-current (I c) measurements made on commercial superconductors over a range of critical currents from less than 0.1 A to about 1 kA. We have developed and used a number of systems to make these measurements over the last 15 years. Two exemplary variable-temperature systems with coil sample geometries will be described: a probe that is only variable-temperature and a probe that is variable-temperature and variable-strain. The most significant challenge for these measurements is temperature stability, since large amounts of heat can be generated by the flow of high current through the resistive sample fixture. Therefore, a significant portion of this review is focused on the reduction of temperature errors to less than ±0.05 K in such measurements. A key feature of our system is a pre-regulator that converts a flow of liquid helium to gas and heats the gas to a temperature close to the target sample temperature. The pre-regulator is not in close proximity to the sample and it is controlled independently of the sample temperature. This allows us to independently control the total cooling power, and thereby fine tune the sample cooling power at any sample temperature. The same general temperature-control philosophy is used in all of our variable-temperature systems, but the addition of another variable, such as strain, forces compromises in design and results in some differences in operation and protocol. These aspects are analyzed to assess the extent to which the protocols for our systems might be generalized to other systems at other laboratories. Our approach to variable-temperature measurements is also placed in the general context of measurement-system design, and the perceived advantages and disadvantages of design choices are presented. To verify the accuracy of the variable-temperature measurements, we compared critical-current values obtained on a specimen immersed in liquid helium ("liquid" or I c liq) at 5

  7. Data re-arranging techniques leading to proper variable selections in high energy physics

    Science.gov (United States)

    Kůs, Václav; Bouř, Petr

    2017-12-01

    We introduce a new data based approach to homogeneity testing and variable selection carried out in high energy physics experiments, where one of the basic tasks is to test the homogeneity of weighted samples, mainly the Monte Carlo simulations (weighted) and real data measurements (unweighted). This technique is called ’data re-arranging’ and it enables variable selection performed by means of the classical statistical homogeneity tests such as Kolmogorov-Smirnov, Anderson-Darling, or Pearson’s chi-square divergence test. P-values of our variants of homogeneity tests are investigated and the empirical verification through 46 dimensional high energy particle physics data sets is accomplished under newly proposed (equiprobable) quantile binning. Particularly, the procedure of homogeneity testing is applied to re-arranged Monte Carlo samples and real DATA sets measured at the particle accelerator Tevatron in Fermilab at DØ experiment originating from top-antitop quark pair production in two decay channels (electron, muon) with 2, 3, or 4+ jets detected. Finally, the variable selections in the electron and muon channels induced by the re-arranging procedure for homogeneity testing are provided for Tevatron top-antitop quark data sets.

  8. Air pollution forecast in cities by an air pollution index highly correlated with meteorological variables

    International Nuclear Information System (INIS)

    Cogliani, E.

    2001-01-01

    There are many different air pollution indexes which represent the global urban air pollution situation. The daily index studied here is also highly correlated with meteorological variables and this index is capable of identifying those variables that significantly affect the air pollution. The index is connected with attention levels of NO 2 , CO and O 3 concentrations. The attention levels are fixed by a law proposed by the Italian Ministries of Health and Environment. The relation of that index with some meteorological variables is analysed by the linear multiple partial correlation statistical method. Florence, Milan and Vicence were selected to show the correlation among the air pollution index and the daily thermic excursion, the previous day's air pollution index and the wind speed. During the January-March period the correlation coefficient reaches 0.85 at Milan. The deterministic methods of forecasting air pollution concentrations show very high evaluation errors and are applied on limited areas around the observation stations, as opposed to the whole urban areas. The global air pollution, instead of the concentrations at specific observation stations, allows the evaluation of the level of the sanitary risk regarding the whole urban population. (Author)

  9. Automated optimization and construction of chemometric models based on highly variable raw chromatographic data.

    Science.gov (United States)

    Sinkov, Nikolai A; Johnston, Brandon M; Sandercock, P Mark L; Harynuk, James J

    2011-07-04

    Direct chemometric interpretation of raw chromatographic data (as opposed to integrated peak tables) has been shown to be advantageous in many circumstances. However, this approach presents two significant challenges: data alignment and feature selection. In order to interpret the data, the time axes must be precisely aligned so that the signal from each analyte is recorded at the same coordinates in the data matrix for each and every analyzed sample. Several alignment approaches exist in the literature and they work well when the samples being aligned are reasonably similar. In cases where the background matrix for a series of samples to be modeled is highly variable, the performance of these approaches suffers. Considering the challenge of feature selection, when the raw data are used each signal at each time is viewed as an individual, independent variable; with the data rates of modern chromatographic systems, this generates hundreds of thousands of candidate variables, or tens of millions of candidate variables if multivariate detectors such as mass spectrometers are utilized. Consequently, an automated approach to identify and select appropriate variables for inclusion in a model is desirable. In this research we present an alignment approach that relies on a series of deuterated alkanes which act as retention anchors for an alignment signal, and couple this with an automated feature selection routine based on our novel cluster resolution metric for the construction of a chemometric model. The model system that we use to demonstrate these approaches is a series of simulated arson debris samples analyzed by passive headspace extraction, GC-MS, and interpreted using partial least squares discriminant analysis (PLS-DA). Copyright © 2011 Elsevier B.V. All rights reserved.

  10. A Novel Technique for Design of Ultra High Tunable Electrostatic Parallel Plate RF MEMS Variable Capacitor

    Science.gov (United States)

    Baghelani, Masoud; Ghavifekr, Habib Badri

    2017-12-01

    This paper introduces a novel method for designing of low actuation voltage, high tuning ratio electrostatic parallel plate RF MEMS variable capacitors. It is feasible to achieve ultra-high tuning ratios way beyond 1.5:1 barrier, imposed by pull-in effect, by the proposed method. The proposed method is based on spring strengthening of the structure just before the unstable region. Spring strengthening could be realized by embedding some dimples on the spring arms with the precise height. These dimples shorten the spring length when achieved to the substrate. By the proposed method, as high tuning ratios as 7.5:1 is attainable by only considering four dimple sets. The required actuation voltage for this high tuning ratio is 14.33 V which is simply achievable on-chip by charge pump circuits. Brownian noise effect is also discussed and mechanical natural frequency of the structure is calculated.

  11. High-resolution regional climate model evaluation using variable-resolution CESM over California

    Science.gov (United States)

    Huang, X.; Rhoades, A.; Ullrich, P. A.; Zarzycki, C. M.

    2015-12-01

    Understanding the effect of climate change at regional scales remains a topic of intensive research. Though computational constraints remain a problem, high horizontal resolution is needed to represent topographic forcing, which is a significant driver of local climate variability. Although regional climate models (RCMs) have traditionally been used at these scales, variable-resolution global climate models (VRGCMs) have recently arisen as an alternative for studying regional weather and climate allowing two-way interaction between these domains without the need for nudging. In this study, the recently developed variable-resolution option within the Community Earth System Model (CESM) is assessed for long-term regional climate modeling over California. Our variable-resolution simulations will focus on relatively high resolutions for climate assessment, namely 28km and 14km regional resolution, which are much more typical for dynamically downscaled studies. For comparison with the more widely used RCM method, the Weather Research and Forecasting (WRF) model will be used for simulations at 27km and 9km. All simulations use the AMIP (Atmospheric Model Intercomparison Project) protocols. The time period is from 1979-01-01 to 2005-12-31 (UTC), and year 1979 was discarded as spin up time. The mean climatology across California's diverse climate zones, including temperature and precipitation, is analyzed and contrasted with the Weather Research and Forcasting (WRF) model (as a traditional RCM), regional reanalysis, gridded observational datasets and uniform high-resolution CESM at 0.25 degree with the finite volume (FV) dynamical core. The results show that variable-resolution CESM is competitive in representing regional climatology on both annual and seasonal time scales. This assessment adds value to the use of VRGCMs for projecting climate change over the coming century and improve our understanding of both past and future regional climate related to fine

  12. Effects of high-carbohydrate and high-fat dietary treatments on measures of heart rate variability and sympathovagal balance.

    Science.gov (United States)

    Millis, Richard M; Austin, Rachel E; Bond, Vernon; Faruque, Mezbah; Goring, Kim L; Hickey, Brian M; Blakely, Raymond; Demeersman, Ronald E

    2009-07-17

    We tested the hypothesis that respiratory quotient (RQ) determines sympathovagal balance associated with metabolism of stored and dietary energy substrates. Six 18-20 year-old African-American males were studied after two control pretreatments of fasting and post-treatments of metabolizing high-fat and high-carbohydrate beverages. RQ, heart rate (HR), energy expenditure (EE) and blood pressure (BP) were recorded at rest and repeated 1 h-3 h after ingesting isocaloric high-carbohydrate and high-fat beverages. Sympathovagal modulation of HR was quantified by the low frequency/high frequency (LF/HF) ratio from fast Fourier transform (spectral) analysis of the electrocardiogram RR intervals during paced breathing at 0.2 Hz. Significance of differences of peak post-treatment values from controls was evaluated by analysis of covariance and of correlations by linear regression at Pcarbohydrate and high-fat treatments increased RQ, EE, HR and LF/HF with significant interactions between covariates. LF/HF values were not significant after eliminating covariance of RQ, EE and HR for the control vs. high-fat and for the high-fat vs. high-carbohydrate and after eliminating covariance of EE and HR for the control vs. high-carbohydrate treatments. Across the RQ values, correlations were significant for EE and LF/HF. These findings imply that high RQ and sympathetic modulation produced by metabolizing carbohydrate is associated with high resting energy expenditure. We conclude that respiratory quotient may be an important determinant of the LF/HF ratio in the heart rate variability spectrum, likely, by a respiratory chemosensory mechanism.

  13. Investigation of High School Students’ Internet Addiction inThe Light of Various Variables

    Directory of Open Access Journals (Sweden)

    Deniz Mertkan GEZGİN

    2016-12-01

    Full Text Available Abstract: The aim of this study was to investigate high school students’ level of internet addiction and to determine internet addiction level according to various variables. The study was designed utilizing a survey model. The participants of the study were 501 high school students randomly selected from different socio-economical districts, i.e., Selcuk district in Izmir and Central district in Edirne within the 2015-2016 academic year. Data were obtained through Internet Addiction Scale. Descriptive statistics utilizing Mann-Whitney and Kruskal-Wallis H tests were used for data analysis. The findings revealed low levels of Internet addiction for high school students along with the potential risk of Internet addiction. Furthermore, the differences between internet addiction level and grade level, mother's education level, smart  phone ownership and mobile internet access were found to be statistically significant.Keywords: Internet addiction, problematic internet use, mobile internet, adolescents

  14. Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing

    Directory of Open Access Journals (Sweden)

    M. Michelle Malmberg

    2018-04-01

    Full Text Available Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD. Complexity reduction genotyping-by-sequencing (GBS methods, including GBS-transcriptomics (GBS-t, enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs, and identify structural variants (SVs. Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.

  15. Snowpack spatial and temporal variability assessment using SMP high-resolution penetrometer

    Science.gov (United States)

    Komarov, Anton; Seliverstov, Yuriy; Sokratov, Sergey; Grebennikov, Pavel

    2017-04-01

    This research is focused on study of spatial and temporal variability of structure and characteristics of snowpack, quick identification of layers based on hardness and dispersion values received from snow micro penetrometer (SMP). We also discuss the detection of weak layers and definition of their parameters in non-alpine terrain. As long as it is the first SMP tool available in Russia, our intent is to test it in different climate and weather conditions. During two separate snowpack studies in plain and mountain landscapes, we derived density and grain size profiles by comparing snow density and grain size from snowpits and SMP measurements. The first case study was MSU meteorological observatory test site in Moscow. SMP data was obtained by 6 consecutive measurements along 10 m transects with a horizontal resolution of approximately 50 cm. The detailed description of snowpack structure, density, grain size, air and snow temperature was also performed. By comparing this information, the detailed scheme of snowpack evolution was created. The second case study was in Khibiny mountains. One 10-meter-long transect was made. SMP, density, grain size and snow temperature data was obtained with horizontal resolution of approximately 50 cm. The high-definition profile of snowpack density variation was acquired using received data. The analysis of data reveals high spatial and temporal variability in snow density and layer structure in both horizontal and vertical dimensions. It indicates that the spatial variability is exhibiting similar spatial patterns as surface topology. This suggests a strong influence from such factors as wind and liquid water pressure on the temporal and spatial evolution of snow structure. It was also defined, that spatial variation of snowpack characteristics is substantial even within homogeneous plain landscape, while in high-latitude mountain regions it grows significantly.

  16. An Auxiliary Variable Method for Markov Chain Monte Carlo Algorithms in High Dimension

    Directory of Open Access Journals (Sweden)

    Yosra Marnissi

    2018-02-01

    Full Text Available In this paper, we are interested in Bayesian inverse problems where either the data fidelity term or the prior distribution is Gaussian or driven from a hierarchical Gaussian model. Generally, Markov chain Monte Carlo (MCMC algorithms allow us to generate sets of samples that are employed to infer some relevant parameters of the underlying distributions. However, when the parameter space is high-dimensional, the performance of stochastic sampling algorithms is very sensitive to existing dependencies between parameters. In particular, this problem arises when one aims to sample from a high-dimensional Gaussian distribution whose covariance matrix does not present a simple structure. Another challenge is the design of Metropolis–Hastings proposals that make use of information about the local geometry of the target density in order to speed up the convergence and improve mixing properties in the parameter space, while not being too computationally expensive. These two contexts are mainly related to the presence of two heterogeneous sources of dependencies stemming either from the prior or the likelihood in the sense that the related covariance matrices cannot be diagonalized in the same basis. In this work, we address these two issues. Our contribution consists of adding auxiliary variables to the model in order to dissociate the two sources of dependencies. In the new augmented space, only one source of correlation remains directly related to the target parameters, the other sources of correlations being captured by the auxiliary variables. Experiments are conducted on two practical image restoration problems—namely the recovery of multichannel blurred images embedded in Gaussian noise and the recovery of signal corrupted by a mixed Gaussian noise. Experimental results indicate that adding the proposed auxiliary variables makes the sampling problem simpler since the new conditional distribution no longer contains highly heterogeneous

  17. The Influence of the Antecedent Variable on the Teachers' Performance through Achievement Motivation in Senior High School

    Science.gov (United States)

    Dewi, Erni R.; Bundu, Patta; Tahmir, Suradi

    2016-01-01

    This study aims at analysing whether the antecedent variable directly affects the performance of the high school teachers or not. In addition, this research strives to find out whether the antecedent variable indirectly affects the teachers' performance through the achievement motivation of the high school teachers. It was a quantitative research…

  18. Masked expression of life-history traits in a highly variable environment

    Science.gov (United States)

    DeBoer, Jason A.; Fontaine, Joseph J.; Chizinski, Christopher J.; Pope, Kevin L.

    2015-01-01

    Differing life-history strategies may act as a constraint on reproductive expression that ultimately limits the ability of individual species to respond to changes in the magnitude or frequency of environmental variation, and potentially underlies the variation often inherent in phenotypic and evolved responses to anthropogenic change. Alternatively, if there are environmental cues that predict reproductive potential, differential expression of life-history strategies may represent differences in the adaptive capacity to optimize current reproductive value given variation in environmental conditions. We compared several aspects of walleye Sander vitreus spawning ecology at two reservoirs that differ in environmental variability (i.e., annual water-level fluctuation) to identify the capacity of phenotypic expression and the corresponding association with age. Despite significant differences in female body and liver masses between reservoirs that differ in environmental variability, we found no difference in reproductive investment measured by egg size and fecundity. Walleye in a highly variable environment appear to exhibit reproductive traits more typical of a short-lived life-history strategy, which may be resultant from the interaction of environmental and anthropogenic pressures. This finding emphasizes the need to identify the degree to which life-history expression represents physiological constraints versus ecological optimization, particularly as anthropogenic change continues to alter environmental conditions. 

  19. High-intensity pulsed electric field variables affecting Staphylococcus aureus inoculated in milk.

    Science.gov (United States)

    Sobrino-López, A; Raybaudi-Massilia, R; Martín-Belloso, O

    2006-10-01

    Staphylococcus aureus is an important milk-related pathogen that is inactivated by high-intensity pulsed electric fields (HIPEF). In this study, inactivation of Staph. aureus suspended in milk by HIPEF was studied using a response surface methodology, in which electric field intensity, pulse number, pulse width, pulse polarity, and the fat content of milk were the controlled variables. It was found that the fat content of milk did not significantly affect the microbial inactivation of Staph. aureus. A maximum value of 4.5 log reductions was obtained by applying 150 bipolar pulses of 8 mus each at 35 kV/cm. Bipolar pulses were more effective than those applied in the monopolar mode. An increase in electric field intensity, pulse number, or pulse width resulted in a drop in the survival fraction of Staph. aureus. Pulse widths close to 6.7 micros lead to greater microbial death with a minimum number of applied pulses. At a constant treatment time, a greater number of shorter pulses achieved better inactivation than those treatments performed at a lower number of longer pulses. The combined action of pulse number and electric field intensity followed a similar pattern, indicating that the same fraction of microbial death can be reached with different combinations of the variables. The behavior and relationship among the electrical variables suggest that the energy input of HIPEF processing might be optimized without decreasing the microbial death.

  20. Affective variables, parental involvement and competence among South Korean high school learners of English

    Directory of Open Access Journals (Sweden)

    Annie Morris

    2013-10-01

    Full Text Available This study investigated the relationships between various affective variables and two measures of competence in English, for 190 South Korean high school students. A 55-item questionnaire was used to measure attitudes (Attitudes toward English Speakers and their Communities and Attitudes toward the English-speaking Culture, motivation (Motivational Intensity, Desire to Learn and Attitudes toward the Learning of English, amotivation, parental involvement (Active Parental Encouragement, Passive Parental Encouragement and Parental Pressure, parental disinterest and students’ competence in L2 (English- EXAM and English-SELF. Pearson product-moment coefficients indicate that active and passive forms of parental encouragement correlate with motivationto learn, as conceptualized by Gardner (1985, 2010, as well as with parental pressure, which suggests that South Korean students report undergoing forms of pressure when their parents actively or passively encourage them. Furthermore, the obtained correlations of the active and passive forms of encouragement with different variables suggest that the two forms represent two distinct concepts. While parental disinterest correlated negatively with motivational variables, parental pressure correlated only with motivational intensity, and only weakly. Therefore, parental pressure seems not to interact significantly with participants’ attitudes, motivation and competence. Multiple linear regression analyses confirm the importance of motivation to learn for students' L2 competence.

  1. High interannual variability of sea ice thickness in the Arctic region.

    Science.gov (United States)

    Laxon, Seymour; Peacock, Neil; Smith, Doug

    2003-10-30

    Possible future changes in Arctic sea ice cover and thickness, and consequent changes in the ice-albedo feedback, represent one of the largest uncertainties in the prediction of future temperature rise. Knowledge of the natural variability of sea ice thickness is therefore critical for its representation in global climate models. Numerical simulations suggest that Arctic ice thickness varies primarily on decadal timescales owing to changes in wind and ocean stresses on the ice, but observations have been unable to provide a synoptic view of sea ice thickness, which is required to validate the model results. Here we use an eight-year time-series of Arctic ice thickness, derived from satellite altimeter measurements of ice freeboard, to determine the mean thickness field and its variability from 65 degrees N to 81.5 degrees N. Our data reveal a high-frequency interannual variability in mean Arctic ice thickness that is dominated by changes in the amount of summer melt, rather than by changes in circulation. Our results suggest that a continued increase in melt season length would lead to further thinning of Arctic sea ice.

  2. Quantifying uncertainty due to internal variability using high-resolution regional climate model simulations

    Science.gov (United States)

    Gutmann, E. D.; Ikeda, K.; Deser, C.; Rasmussen, R.; Clark, M. P.; Arnold, J. R.

    2015-12-01

    The uncertainty in future climate predictions is as large or larger than the mean climate change signal. As such, any predictions of future climate need to incorporate and quantify the sources of this uncertainty. One of the largest sources comes from the internal, chaotic, variability within the climate system itself. This variability has been approximated using the 30 ensemble members of the Community Earth System Model (CESM) large ensemble. Here we examine the wet and dry end members of this ensemble for cool-season precipitation in the Colorado Rocky Mountains with a set of high-resolution regional climate model simulations. We have used the Weather Research and Forecasting model (WRF) to simulate the periods 1990-2000, 2025-2035, and 2070-2080 on a 4km grid. These simulations show that the broad patterns of change depicted in CESM are inherited by the high-resolution simulations; however, the differences in the height and location of the mountains in the WRF simulation, relative to the CESM simulation, means that the location and magnitude of the precipitation changes are very different. We further show that high-resolution simulations with the Intermediate Complexity Atmospheric Research model (ICAR) predict a similar spatial pattern in the change signal as WRF for these ensemble members. We then use ICAR to examine the rest of the CESM Large Ensemble as well as the uncertainty in the regional climate model due to the choice of physics parameterizations.

  3. Small scale denitrification variability in riparian zones: Results from a high-resolution dataset

    Science.gov (United States)

    Gassen, Niklas; Knöller, Kay; Musolff, Andreas; Popp, Felix; Lüders, Tillmann; Stumpp, Christine

    2017-04-01

    Riparian zones are important compartments at the interface between groundwater and surface water where biogeochemical processes like denitrification are often enhanced. Nitrate loads of either groundwater entering a stream through the riparian zone or streamwater infiltrating into the riparian zone can be substantially reduced. These processes are spatially and temporally highly variable, making it difficult to capture solute variabilities, estimate realistic turnover rates and thus to quantify integral mass removal. A crucial step towards a more detailed characterization is to monitor solutes on a scale which adequately resemble the highly heterogeneous distribution and on a scale where processes occur. We measured biogeochemical parameters in a spatial high resolution within a riparian corridor of a German lowland river system over the course of one year. Samples were taken from three newly developed high-resolution multi-level wells with a maximum vertical resolution of 5 cm and analyzed for major ions, DOC and N-O isotopes. Sediment derived during installation of the wells was analyzed for specific denitrifying enzymes. Results showed a distinct depth zonation of hydrochemistry within the shallow alluvial aquifer, with a 1 m thick zone just below the water table with lower nitrate concentrations and EC values similar to the nearby river. Conservative parameters were consistent inbetween the three wells, but nitrate was highly variable. In addition, spots with low nitrate concentrations showed isotopic and microbial evidence for higher denitrification activities. The depth zonation was observed throughout the year, with stronger temporal variations of nitrate concentrations just below the water table compared to deeper layers. Nitrate isotopes showed a clear seasonal trend of denitrification activities (high in summer, low in winter). Our dataset gives new insight into river-groundwater exchange processes and shows the highly heterogeneous distribution of

  4. IAS15 inflation adjustments and EVA: empirical evidence from a highly variable inflation regime

    Directory of Open Access Journals (Sweden)

    Pierre Erasmus

    2011-08-01

    Full Text Available Inflation can have a pronounced effect on the financial performance of a firm. This study makes inflation adjustments to a firm’s cost of sales, depreciation, level of gearing and assets in line with International Accounting Standard 15 (IAS15 in order to calculate an inflation-adjusted version of the economic value added (EVA measure. The study was conducted using data from South African industrial firms during a period characterised by highly variable inflation levels (1991-2005. The results indicate that during this period there were significant differences between the nominal and real values of the firms’ EVAs

  5. High Intrapatient Variability of Tacrolimus Levels and Outpatient Clinic Nonattendance Are Associated With Inferior Outcomes in Renal Transplant Patients

    Directory of Open Access Journals (Sweden)

    Dawn L. Goodall, MSc

    2017-08-01

    Conclusions. This study shows that high tacrolimus IPV and clinic nonattendance are associated with inferior allograft survival. Interventions to minimize the causes of high variability, particularly nonadherence are essential to improve long-term allograft outcomes.

  6. Variability in rainfall over tropical Australia during summer and relationships with the Bilybara High

    Science.gov (United States)

    Reason, C. J. C.

    2018-04-01

    Variability in summer rainfall over tropical Australia, defined here as that part of the continent north of 25° S, and its linkages with regional circulation are examined. In particular, relationships with the mid-level anticyclone (termed the Bilybara High) that exists over the northwestern Australia/Timor Sea region between August and April are considered. This High forms to the southwest of the upper-level anticyclone via a balance between the upper-level divergence over the region of tropical precipitation maximum and planetary vorticity advection and moves south and strengthens during the spring and summer. It is shown that variations in the strength and position of the Bilybara High are related to anomalies in precipitation and temperature over large parts of tropical Australia as well as some areas in the south and southeast of the landmass. Some of the interannual variations in the High are related to ENSO, but there are also a number of neutral years with large anomalies in the High and hence in rainfall. On decadal time scales, a strong relationship exists between the leading mode of tropical Australian rainfall and the Bilybara High. On both interannual and decadal scales, the relationships between the High and the regional rainfall involve changes in the monsoonal northwesterlies blowing towards northern Australia, and further south, in the easterly trade winds over the region.

  7. Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using next-generation sequencer.

    Science.gov (United States)

    Mitsui, Jun; Fukuda, Yoko; Azuma, Kyo; Tozaki, Hirokazu; Ishiura, Hiroyuki; Takahashi, Yuji; Goto, Jun; Tsuji, Shoji

    2010-07-01

    We have recently found that multiple rare variants of the glucocerebrosidase gene (GBA) confer a robust risk for Parkinson disease, supporting the 'common disease-multiple rare variants' hypothesis. To develop an efficient method of identifying rare variants in a large number of samples, we applied multiplexed resequencing using a next-generation sequencer to identification of rare variants of GBA. Sixteen sets of pooled DNAs from six pooled DNA samples were prepared. Each set of pooled DNAs was subjected to polymerase chain reaction to amplify the target gene (GBA) covering 6.5 kb, pooled into one tube with barcode indexing, and then subjected to extensive sequence analysis using the SOLiD System. Individual samples were also subjected to direct nucleotide sequence analysis. With the optimization of data processing, we were able to extract all the variants from 96 samples with acceptable rates of false-positive single-nucleotide variants.

  8. Downscaling reanalysis data to high-resolution variables above a glacier surface (Cordillera Blanca, Peru)

    Science.gov (United States)

    Hofer, Marlis; Mölg, Thomas; Marzeion, Ben; Kaser, Georg

    2010-05-01

    Recently initiated observation networks in the Cordillera Blanca provide temporally high-resolution, yet short-term atmospheric data. The aim of this study is to extend the existing time series into the past. We present an empirical-statistical downscaling (ESD) model that links 6-hourly NCEP/NCAR reanalysis data to the local target variables, measured at the tropical glacier Artesonraju (Northern Cordillera Blanca). The approach is particular in the context of ESD for two reasons. First, the observational time series for model calibration are short (only about two years). Second, unlike most ESD studies in climate research, we focus on variables at a high temporal resolution (i.e., six-hourly values). Our target variables are two important drivers in the surface energy balance of tropical glaciers; air temperature and specific humidity. The selection of predictor fields from the reanalysis data is based on regression analyses and climatologic considerations. The ESD modelling procedure includes combined empirical orthogonal function and multiple regression analyses. Principal component screening is based on cross-validation using the Akaike Information Criterion as model selection criterion. Double cross-validation is applied for model evaluation. Potential autocorrelation in the time series is considered by defining the block length in the resampling procedure. Apart from the selection of predictor fields, the modelling procedure is automated and does not include subjective choices. We assess the ESD model sensitivity to the predictor choice by using both single- and mixed-field predictors of the variables air temperature (1000 hPa), specific humidity (1000 hPa), and zonal wind speed (500 hPa). The chosen downscaling domain ranges from 80 to 50 degrees west and from 0 to 20 degrees south. Statistical transfer functions are derived individually for different months and times of day (month/hour-models). The forecast skill of the month/hour-models largely depends on

  9. Analysis Methodology for Balancing Authority Cooperation in High Penetration of Variable Generation

    Energy Technology Data Exchange (ETDEWEB)

    Makarov, Yuri V.; Etingov, Pavel V.; Zhou, Ning; Ma, Jian; Samaan, Nader A.; Diao, Ruisheng; Malhara, Sunita V.; Guttromson, Ross T.; Du, Pengwei; Sastry, Chellury

    2010-02-01

    With the rapidly growing penetration level of wind and solar generation, the challenges of managing variability and the uncertainty of intermittent renewable generation become more and more significant. The problem of power variability and uncertainty gets exacerbated when each balancing authority (BA) works locally and separately to balance its own subsystem. The virtual BA concept means various forms of collaboration between individual BAs must manage power variability and uncertainty. The virtual BA will have a wide area control capability in managing its operational balancing requirements in different time frames. This coordination results in the improvement of efficiency and reliability of power system operation while facilitating the high level integration of green, intermittent energy resources. Several strategies for virtual BA implementation, such as ACE diversity interchange (ADI), wind only BA, BA consolidation, dynamic scheduling, regulation and load following sharing, extreme event impact study are discussed in this report. The objective of such strategies is to allow individual BAs within a large power grid to help each other deal with power variability. Innovative methods have been developed to simulate the balancing operation of BAs. These methods evaluate the BA operation through a number of metrics — such as capacity, ramp rate, ramp duration, energy and cycling requirements — to evaluate the performances of different virtual BA strategies. The report builds a systematic framework for evaluating BA consolidation and coordination. Results for case studies show that significant economic and reliability benefits can be gained. The merits and limitation of each virtual BA strategy are investigated. The report provides guidelines for the power industry to evaluate the coordination or consolidation method. The application of the developed strategies in cooperation with several regional BAs is in progress for several off-spring projects.

  10. Whole Genome Re-Sequencing and Characterization of Powdery Mildew Disease-Associated Allelic Variation in Melon.

    Directory of Open Access Journals (Sweden)

    Sathishkumar Natarajan

    Full Text Available Powdery mildew is one of the most common fungal diseases in the world. This disease frequently affects melon (Cucumis melo L. and other Cucurbitaceous family crops in both open field and greenhouse cultivation. One of the goals of genomics is to identify the polymorphic loci responsible for variation in phenotypic traits. In this study, powdery mildew disease assessment scores were calculated for four melon accessions, 'SCNU1154', 'Edisto47', 'MR-1', and 'PMR5'. To investigate the genetic variation of these accessions, whole genome re-sequencing using the Illumina HiSeq 2000 platform was performed. A total of 754,759,704 quality-filtered reads were generated, with an average of 82.64% coverage relative to the reference genome. Comparisons of the sequences for the melon accessions revealed around 7.4 million single nucleotide polymorphisms (SNPs, 1.9 million InDels, and 182,398 putative structural variations (SVs. Functional enrichment analysis of detected variations classified them into biological process, cellular component and molecular function categories. Further, a disease-associated QTL map was constructed for 390 SNPs and 45 InDels identified as related to defense-response genes. Among them 112 SNPs and 12 InDels were observed in powdery mildew responsive chromosomes. Accordingly, this whole genome re-sequencing study identified SNPs and InDels associated with defense genes that will serve as candidate polymorphisms in the search for sources of resistance against powdery mildew disease and could accelerate marker-assisted breeding in melon.

  11. Prediction of Genes Related to Positive Selection Using Whole-Genome Resequencing in Three Commercial Pig Breeds

    Directory of Open Access Journals (Sweden)

    HyoYoung Kim

    2015-12-01

    Full Text Available Selective sweep can cause genetic differentiation across populations, which allows for the identification of possible causative regions/genes underlying important traits. The pig has experienced a long history of allele frequency changes through artificial selection in the domestication process. We obtained an average of 329,482,871 sequence reads for 24 pigs from three pig breeds: Yorkshire (n = 5, Landrace (n = 13, and Duroc (n = 6. An average read depth of 11.7 was obtained using whole-genome resequencing on an Illumina HiSeq2000 platform. In this study, cross-population extended haplotype homozygosity and cross-population composite likelihood ratio tests were implemented to detect genes experiencing positive selection for the genome-wide resequencing data generated from three commercial pig breeds. In our results, 26, 7, and 14 genes from Yorkshire, Landrace, and Duroc, respectively were detected by two kinds of statistical tests. Significant evidence for positive selection was identified on genes ST6GALNAC2 and EPHX1 in Yorkshire, PARK2 in Landrace, and BMP6, SLA-DQA1, and PRKG1 in Duroc.These genes are reportedly relevant to lactation, reproduction, meat quality, and growth traits. To understand how these single nucleotide polymorphisms (SNPs related positive selection affect protein function, we analyzed the effect of non-synonymous SNPs. Three SNPs (rs324509622, rs80931851, and rs80937718 in the SLA-DQA1 gene were significant in the enrichment tests, indicating strong evidence for positive selection in Duroc. Our analyses identified genes under positive selection for lactation, reproduction, and meat-quality and growth traits in Yorkshire, Landrace, and Duroc, respectively.

  12. Whole Genome Re-Sequencing and Characterization of Powdery Mildew Disease-Associated Allelic Variation in Melon.

    Science.gov (United States)

    Natarajan, Sathishkumar; Kim, Hoy-Taek; Thamilarasan, Senthil Kumar; Veerappan, Karpagam; Park, Jong-In; Nou, Ill-Sup

    2016-01-01

    Powdery mildew is one of the most common fungal diseases in the world. This disease frequently affects melon (Cucumis melo L.) and other Cucurbitaceous family crops in both open field and greenhouse cultivation. One of the goals of genomics is to identify the polymorphic loci responsible for variation in phenotypic traits. In this study, powdery mildew disease assessment scores were calculated for four melon accessions, 'SCNU1154', 'Edisto47', 'MR-1', and 'PMR5'. To investigate the genetic variation of these accessions, whole genome re-sequencing using the Illumina HiSeq 2000 platform was performed. A total of 754,759,704 quality-filtered reads were generated, with an average of 82.64% coverage relative to the reference genome. Comparisons of the sequences for the melon accessions revealed around 7.4 million single nucleotide polymorphisms (SNPs), 1.9 million InDels, and 182,398 putative structural variations (SVs). Functional enrichment analysis of detected variations classified them into biological process, cellular component and molecular function categories. Further, a disease-associated QTL map was constructed for 390 SNPs and 45 InDels identified as related to defense-response genes. Among them 112 SNPs and 12 InDels were observed in powdery mildew responsive chromosomes. Accordingly, this whole genome re-sequencing study identified SNPs and InDels associated with defense genes that will serve as candidate polymorphisms in the search for sources of resistance against powdery mildew disease and could accelerate marker-assisted breeding in melon.

  13. Resequencing three candidate genes discovers seven potentially deleterious variants susceptibility to major depressive disorder and suicide attempts in Chinese.

    Science.gov (United States)

    Rao, Shitao; Leung, Cherry She Ting; Lam, Macro Hb; Wing, Yun Kwok; Waye, Mary Miu Yee; Tsui, Stephen Kwok Wing

    2017-03-01

    To date almost 200 genes were found to be associated with major depressive disorder (MDD) or suicide attempts (SA), but very few genes were reported for their molecular mechanisms. This study aimed to find out whether there were common or rare variants in three candidate genes altering the risk for MDD and SA in Chinese. Three candidate genes (HOMER1, SLC6A4 and TEF) were chosen for resequencing analysis and association studies as they were reported to be involved in the etiology of MDD and SA. Following that, bioinformatics analyses were applied on those variants of interest. After resequencing analysis and alignment for the amplicons, a total of 34 common or rare variants were found in the randomly selected 36 Hong Kong Chinese patients with both MDD and SA. Among those, seven variants show potentially deleterious features. Rs60029191 and a rare variant located in regulatory region of the HOMER1 gene may affect the promoter activities through interacting with predicted transcription factors. Two missense mutations existed in the SLC6A4 coding regions were firstly reported in Hong Kong Chinese MDD and SA patients, and both of them could affect the transport efficiency of SLC6A4 to serotonin. Moreover, a common variant rs6354 located in the untranslated region of this gene may affect the expression level or exonic splicing of serotonin transporter. In addition, both of a most studied polymorphism rs738499 and a low-frequency variant in the promoter region of the TEF gene were found to be located in potential transcription factor binding sites, which may let the two variants be able to influence the promoter activities of the gene. This study elucidated the potentially molecular mechanisms of the three candidate genes altering the risk for MDD and SA. These findings implied that not only common variants but rare variants could make contributions to the genetic susceptibility to MDD and SA in Chinese. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Allelic association, DNA resequencing and copy number variation at the metabotropic glutamate receptor GRM7 gene locus in bipolar disorder.

    Science.gov (United States)

    Kandaswamy, Radhika; McQuillin, Andrew; Curtis, David; Gurling, Hugh

    2014-06-01

    Genetic markers at the GRM7 gene have shown allelic association with bipolar disorder (BP) in several case-control samples including our own sample. In this report, we present results of resequencing the GRM7 gene in 32 bipolar samples and 32 random controls selected from 553 bipolar cases and 547 control samples (UCL1). Novel and potential etiological base pair changes discovered by resequencing were genotyped in the entire UCL case-control sample. We also report on the association between GRM7 and BP in a second sample of 593 patients and 642 controls (UCL2). The three most significantly associated SNPs in the original UCL1 BP GWAS sample were genotyped in the UCL2 sample, of which none were associated. After combining the genotype data for the two samples only two (rs1508724 and rs6769814) of the original three SNP markers remained significantly associated with BP. DNA sequencing revealed mutations in three cases which were absent in control subjects. A 3'-UTR SNP rs56173829 was found to be significantly associated with BP in the whole UCL sample (P = 0.035; OR = 0.482), the rare allele being less common in cases compared to controls. Bioinformatic analyses predicted a change in the centroid secondary structure of RNA and alterations in the miRNA binding sites for the mutated base of rs56173829. We also validated two deletions and a duplication within GRM7 using quantitative-PCR which provides further support for the pre-existing evidence that copy number variants at GRM7 may have a role in the etiology of BP. © 2014 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Published by Wiley Periodicals, Inc.

  15. Polarized training has greater impact on key endurance variables than threshold, high intensity or high volume training

    Directory of Open Access Journals (Sweden)

    Thomas eStöggl

    2014-02-01

    Full Text Available Endurance athletes integrate four conditioning concepts in their training programs: high-volume training (HVT, ‘threshold-training’ (THR, high-intensity interval training (HIIT and a combination of these aforementioned concepts known as polarized training (POL. The purpose of this study was to explore which of these four training concepts provides the greatest response on key components of endurance performance in well-trained endurance athletes. Methods: Forty eight runners, cyclists, triathletes and cross-country skiers (peak oxygen uptake: (VO2peak: 62.6±7.1 mL∙min-1∙kg-1 were randomly assigned to one of four groups performing over nine weeks. An incremental test, work economy and a VO2peak tests were performed. Training intensity was heart rate controlled. Results: POL demonstrated the greatest increase in VO2peak (+6.8 ml∙min∙kg-1 or 11.7%, P0.05. Conclusion: POL resulted in the greatest improvements in most key variables of endurance performance in well-trained endurance athletes. THR or HVT did not lead to further improvements in performance related variables.

  16. A new variable-resolution associative memory for high energy physics

    International Nuclear Information System (INIS)

    Annovi, A.; Amerio, S.; Beretta, M.; Bossini, E.; Crescioli, F.; Dell'Orso, M.; Giannetti, P.; Hoff, J.; Liu, T.; Magalotti, D.; Piendibene, M.; Sacco, I.; Schoening, A.; Soltveit, H. K.; Stabile, A.; Tripiccione, R.; Liberali, V.; Vitillo, R.; Volpi, G.

    2011-01-01

    We describe an important advancement for the Associative Memory device (AM). The AM is a VLSI processor for pattern recognition based on Content Addressable Memory (CAM) architecture. The AM is optimized for on-line track finding in high-energy physics experiments. Pattern matching is carried out by finding track candidates in coarse resolution 'roads'. A large AM bank stores all trajectories of interest, called 'patterns', for a given detector resolution. The AM extracts roads compatible with a given event during detector read-out. Two important variables characterize the quality of the AM bank: its 'coverage' and the level of fake roads. The coverage, which describes the geometric efficiency of a bank, is defined as the fraction of tracks that match at least one pattern in the bank. Given a certain road size, the coverage of the bank can be increased just adding patterns to the bank, while the number of fakes unfortunately is roughly proportional to the number of patterns in the bank. Moreover, as the luminosity increases, the fake rate increases rapidly because of the increased silicon occupancy. To counter that, we must reduce the width of our roads. If we decrease the road width using the current technology, the system will become very large and extremely expensive. We propose an elegant solution to this problem: the 'variable resolution patterns'. Each pattern and each detector layer within a pattern will be able to use the optimal width, but we will use a 'don't care' feature (inspired from ternary CAMs) to increase the width when that is more appropriate. In other words we can use patterns of variable shape. As a result we reduce the number of fake roads, while keeping the efficiency high and avoiding excessive bank size due to the reduced width. We describe the idea, the implementation in the new AM design and the implementation of the algorithm in the simulation. Finally we show the effectiveness of the 'variable resolution patterns' idea using simulated

  17. A Meta-analysis on Resting State High-frequency Heart Rate Variability in Bulimia Nervosa.

    Science.gov (United States)

    Peschel, Stephanie K V; Feeling, Nicole R; Vögele, Claus; Kaess, Michael; Thayer, Julian F; Koenig, Julian

    2016-09-01

    Autonomic nervous system function is altered in eating disorders. We aimed to quantify differences in resting state vagal activity, indexed by high-frequency heart rate variability comparing patients with bulimia nervosa (BN) and healthy controls. A systematic search of the literature to identify studies eligible for inclusion and meta-analytical methods were applied. Meta-regression was used to identify potential covariates. Eight studies reporting measures of resting high-frequency heart rate variability in individuals with BN (n = 137) and controls (n = 190) were included. Random-effects meta-analysis revealed a sizeable main effect (Z = 2.22, p = .03; Hedge's g = 0.52, 95% CI [0.06;0.98]) indicating higher resting state vagal activity in individuals with BN. Meta-regression showed that body mass index and medication intake are significant covariates. Findings suggest higher vagal activity in BN at rest, particularly in unmedicated samples with lower body mass index. Potential mechanisms underlying these findings and implications for routine clinical care are discussed. Copyright © 2016 John Wiley & Sons, Ltd and Eating Disorders Association. Copyright © 2016 John Wiley & Sons, Ltd and Eating Disorders Association.

  18. Initiating an ergonomic analysis. A process for jobs with highly variable tasks.

    Science.gov (United States)

    Conrad, K M; Lavender, S A; Reichelt, P A; Meyer, F T

    2000-09-01

    Occupational health nurses play a vital role in addressing ergonomic problems in the workplace. Describing and documenting exposure to ergonomic risk factors is a relatively straightforward process in jobs in which the work is repetitive. In other types of work, the analysis becomes much more challenging because tasks may be repeated infrequently, or at irregular time intervals, or under different environmental and temporal conditions, thereby making it difficult to observe a "representative" sample of the work performed. This article describes a process used to identify highly variable job tasks for ergonomic analyses. The identification of tasks for ergonomic analysis was a two step process involving interviews and a survey of firefighters and paramedics from a consortium of 14 suburban fire departments. The interviews were used to generate a list of frequently performed, physically strenuous job tasks and to capture clear descriptions of those tasks and associated roles. The goals of the survey were to confirm the interview findings across the entire target population and to quantify the frequency and degree of strenuousness of each task. In turn, the quantitative results from the survey were used to prioritize job tasks for simulation. Although this process was used to study firefighters and paramedics, the approach is likely to be suitable for many other types of occupations in which the tasks are highly variable in content and irregular in frequency.

  19. Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data.

    Science.gov (United States)

    Li, Yongle; Ruperao, Pradeep; Batley, Jacqueline; Edwards, David; Khan, Tanveer; Colmer, Timothy D; Pang, Jiayin; Siddique, Kadambot H M; Sutton, Tim

    2018-01-01

    Drought tolerance is a complex trait that involves numerous genes. Identifying key causal genes or linked molecular markers can facilitate the fast development of drought tolerant varieties. Using a whole-genome resequencing approach, we sequenced 132 chickpea varieties and advanced breeding lines and found more than 144,000 single nucleotide polymorphisms (SNPs). We measured 13 yield and yield-related traits in three drought-prone environments of Western Australia. The genotypic effects were significant for all traits, and many traits showed highly significant correlations, ranging from 0.83 between grain yield and biomass to -0.67 between seed weight and seed emergence rate. To identify candidate genes, the SNP and trait data were incorporated into the SUPER genome-wide association study (GWAS) model, a modified version of the linear mixed model. We found that several SNPs from auxin-related genes, including auxin efflux carrier protein (PIN3), p-glycoprotein, and nodulin MtN21/EamA-like transporter, were significantly associated with yield and yield-related traits under drought-prone environments. We identified four genetic regions containing SNPs significantly associated with several different traits, which was an indication of pleiotropic effects. We also investigated the possibility of incorporating the GWAS results into a genomic selection (GS) model, which is another approach to deal with complex traits. Compared to using all SNPs, application of the GS model using subsets of SNPs significantly associated with the traits under investigation increased the prediction accuracies of three yield and yield-related traits by more than twofold. This has important implication for implementing GS in plant breeding programs.

  20. Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data

    Directory of Open Access Journals (Sweden)

    Yongle Li

    2018-02-01

    Full Text Available Drought tolerance is a complex trait that involves numerous genes. Identifying key causal genes or linked molecular markers can facilitate the fast development of drought tolerant varieties. Using a whole-genome resequencing approach, we sequenced 132 chickpea varieties and advanced breeding lines and found more than 144,000 single nucleotide polymorphisms (SNPs. We measured 13 yield and yield-related traits in three drought-prone environments of Western Australia. The genotypic effects were significant for all traits, and many traits showed highly significant correlations, ranging from 0.83 between grain yield and biomass to -0.67 between seed weight and seed emergence rate. To identify candidate genes, the SNP and trait data were incorporated into the SUPER genome-wide association study (GWAS model, a modified version of the linear mixed model. We found that several SNPs from auxin-related genes, including auxin efflux carrier protein (PIN3, p-glycoprotein, and nodulin MtN21/EamA-like transporter, were significantly associated with yield and yield-related traits under drought-prone environments. We identified four genetic regions containing SNPs significantly associated with several different traits, which was an indication of pleiotropic effects. We also investigated the possibility of incorporating the GWAS results into a genomic selection (GS model, which is another approach to deal with complex traits. Compared to using all SNPs, application of the GS model using subsets of SNPs significantly associated with the traits under investigation increased the prediction accuracies of three yield and yield-related traits by more than twofold. This has important implication for implementing GS in plant breeding programs.

  1. Variable Delay Element For Jitter Control In High Speed Data Links

    Science.gov (United States)

    Livolsi, Robert R.

    2002-06-11

    A circuit and method for decreasing the amount of jitter present at the receiver input of high speed data links which uses a driver circuit for input from a high speed data link which comprises a logic circuit having a first section (1) which provides data latches, a second section (2) which provides a circuit generates a pre-destorted output and for compensating for level dependent jitter having an OR function element and a NOR function element each of which is coupled to two inputs and to a variable delay element as an input which provides a bi-modal delay for pulse width pre-distortion, a third section (3) which provides a muxing circuit, and a forth section (4) for clock distribution in the driver circuit. A fifth section is used for logic testing the driver circuit.

  2. High performance reconciliation for continuous-variable quantum key distribution with LDPC code

    Science.gov (United States)

    Lin, Dakai; Huang, Duan; Huang, Peng; Peng, Jinye; Zeng, Guihua

    2015-03-01

    Reconciliation is a significant procedure in a continuous-variable quantum key distribution (CV-QKD) system. It is employed to extract secure secret key from the resulted string through quantum channel between two users. However, the efficiency and the speed of previous reconciliation algorithms are low. These problems limit the secure communication distance and the secure key rate of CV-QKD systems. In this paper, we proposed a high-speed reconciliation algorithm through employing a well-structured decoding scheme based on low density parity-check (LDPC) code. The complexity of the proposed algorithm is reduced obviously. By using a graphics processing unit (GPU) device, our method may reach a reconciliation speed of 25 Mb/s for a CV-QKD system, which is currently the highest level and paves the way to high-speed CV-QKD.

  3. High-efficiency Gaussian key reconciliation in continuous variable quantum key distribution

    Science.gov (United States)

    Bai, ZengLiang; Wang, XuYang; Yang, ShenShen; Li, YongMin

    2016-01-01

    Efficient reconciliation is a crucial step in continuous variable quantum key distribution. The progressive-edge-growth (PEG) algorithm is an efficient method to construct relatively short block length low-density parity-check (LDPC) codes. The qua-sicyclic construction method can extend short block length codes and further eliminate the shortest cycle. In this paper, by combining the PEG algorithm and qua-si-cyclic construction method, we design long block length irregular LDPC codes with high error-correcting capacity. Based on these LDPC codes, we achieve high-efficiency Gaussian key reconciliation with slice recon-ciliation based on multilevel coding/multistage decoding with an efficiency of 93.7%.

  4. Winter cloudiness variability over Northern Eurasia related to the Siberian High during 1966–2010

    International Nuclear Information System (INIS)

    Chernokulsky, Alexander; Mokhov, Igor I; Nikitina, Natalia

    2013-01-01

    This letter presents an assessment of winter cloudiness variability over Northern Eurasia regions related to the Siberian High intensity (SHI) variations during 1966–2010. An analysis of cloud fraction and the occurrence of different cloud types was carried out based on visual observations from almost 500 Russian meteorological stations. The moonlight criterion was implemented to reduce the uncertainty of night observations. The SHI was defined based on sea-level pressure fields from different reanalyses. We found a statistically significant negative correlation of cloud cover with the SHI over central and southern Siberia and the southern Urals with regression coefficients around 3% hPa −1 for total cloud fraction (TCF) for particular stations near the Siberian High center. Cross-wavelet analysis of TCF and SHI revealed a long-term relationship between cloudiness and the Siberian High. Generally, the Siberian High intensification by 1 hPa leads to a replacement of one overcast day with one day without clouds, which is associated mainly with a decrease in precipitating and stratiform clouds. These changes point to a positive feedback between cloudiness and the Siberian High. (letter)

  5. LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instability.

    Directory of Open Access Journals (Sweden)

    Marcos R H Estécio

    2007-05-01

    Full Text Available Alterations in DNA methylation in cancer include global hypomethylation and gene-specific hypermethylation. It is not clear whether these two epigenetic errors are mechanistically linked or occur independently. This study was performed to determine the relationship between DNA hypomethylation, hypermethylation and microsatellite instability in cancer.We examined 61 cancer cell lines and 60 colorectal carcinomas and their adjacent tissues using LINE-1 bisulfite-PCR as a surrogate for global demethylation. Colorectal carcinomas with sporadic microsatellite instability (MSI, most of which are due to a CpG island methylation phenotype (CIMP and associated MLH1 promoter methylation, showed in average no difference in LINE-1 methylation between normal adjacent and cancer tissues. Interestingly, some tumor samples in this group showed increase in LINE-1 methylation. In contrast, MSI-showed a significant decrease in LINE-1 methylation between normal adjacent and cancer tissues (P<0.001. Microarray analysis of repetitive element methylation confirmed this observation and showed a high degree of variability in hypomethylation between samples. Additionally, unsupervised hierarchical clustering identified a group of highly hypomethylated tumors, composed mostly of tumors without microsatellite instability. We extended LINE-1 analysis to cancer cell lines from different tissues and found that 50/61 were hypomethylated compared to peripheral blood lymphocytes and normal colon mucosa. Interestingly, these cancer cell lines also exhibited a large variation in demethylation, which was tissue-specific and thus unlikely to be resultant from a stochastic process.Global hypomethylation is partially reversed in cancers with microsatellite instability and also shows high variability in cancer, which may reflect alternative progression pathways in cancer.

  6. Seasonal and diurnal variability of the meteor flux at high latitudes observed using PFISR

    Science.gov (United States)

    Sparks, J. J.; Janches, D.; Nicolls, M. J.; Heinselman, C. J.

    2009-05-01

    We report in this and a companion paper [Fentzke, J.T., Janches, D., Sparks, J.J., 2008. Latitudinal and seasonal variability of the micrometeor input function: A study using model predictions and observations from Arecibo and PFISR. Journal of Atmospheric and Solar-Terrestrial Physics, this issue, doi:10.1016/j.jastp.2008.07.015] a complete seasonal study of the micrometeor input function (MIF) at high latitudes using meteor head-echo radar observations performed with the Poker Flat Incoherent Scatter Radar (PFISR). This flux is responsible for a number of atmospheric phenomena; for example, it could be the source of meteoric smoke that is thought to act as condensation nuclei in the formation of ice particles in the polar mesosphere. The observations presented here were performed for full 24-h periods near the summer and winter solstices and spring and autumn equinoxes, times at which the seasonal variability of the MIF is predicted to be large at high latitudes [Janches, D., Heinselman, C.J., Chau, J.L., Chandran, A., Woodman, R., 2006. Modeling of the micrometeor input function in the upper atmosphere observed by High Power and Large Aperture Radars, JGR, 11, A07317, doi:10.1029/2006JA011628]. Precise altitude and radar instantaneous line-of-sight (radial) Doppler velocity information are obtained for each of the hundreds of events detected every day. We show that meteor rates, altitude, and radial velocity distributions have a large seasonal dependence. This seasonal variability can be explained by a change in the relative location of the meteoroid sources with respect to the observer. Our results show that the meteor flux into the upper atmosphere is strongly anisotropic and its characteristics must be accounted for when including this flux into models attempting to explain related aeronomical phenomena. In addition, the measured acceleration and received signal strength distribution do not seem to depend on season; which may suggest that these observed

  7. Detecting high spatial variability of ice shelf basal mass balance, Roi Baudouin Ice Shelf, Antarctica

    Directory of Open Access Journals (Sweden)

    S. Berger

    2017-11-01

    Full Text Available Ice shelves control the dynamic mass loss of ice sheets through buttressing and their integrity depends on the spatial variability of their basal mass balance (BMB, i.e. the difference between refreezing and melting. Here, we present an improved technique – based on satellite observations – to capture the small-scale variability in the BMB of ice shelves. As a case study, we apply the methodology to the Roi Baudouin Ice Shelf, Dronning Maud Land, East Antarctica, and derive its yearly averaged BMB at 10 m horizontal gridding. We use mass conservation in a Lagrangian framework based on high-resolution surface velocities, atmospheric-model surface mass balance and hydrostatic ice-thickness fields (derived from TanDEM-X surface elevation. Spatial derivatives are implemented using the total-variation differentiation, which preserves abrupt changes in flow velocities and their spatial gradients. Such changes may reflect a dynamic response to localized basal melting and should be included in the mass budget. Our BMB field exhibits much spatial detail and ranges from −14.7 to 8.6 m a−1 ice equivalent. Highest melt rates are found close to the grounding line where the pressure melting point is high, and the ice shelf slope is steep. The BMB field agrees well with on-site measurements from phase-sensitive radar, although independent radar profiling indicates unresolved spatial variations in firn density. We show that an elliptical surface depression (10 m deep and with an extent of 0.7 km × 1.3 km lowers by 0.5 to 1.4 m a−1, which we tentatively attribute to a transient adaptation to hydrostatic equilibrium. We find evidence for elevated melting beneath ice shelf channels (with melting being concentrated on the channel's flanks. However, farther downstream from the grounding line, the majority of ice shelf channels advect passively (i.e. no melting nor refreezing toward the ice shelf front. Although the absolute, satellite

  8. Radiology reports for incidental thyroid nodules on CT and MRI: high variability across subspecialties.

    Science.gov (United States)

    Grady, A T; Sosa, J A; Tanpitukpongse, T P; Choudhury, K R; Gupta, R T; Hoang, J K

    2015-02-01

    practices for incidental thyroid nodules detected on CT and MR imaging are predominantly influenced by nodule size and the radiologist's subspecialty. Reporting was highly variable for nodules measuring 10-19 mm; this finding can be partially attributed to different reporting styles among radiology subspecialty divisions. The variability demonstrated in this study further underscores the need to develop CT and MR imaging practice guidelines with the goal of standardizing reporting of incidental thyroid nodules and thereby potentially improving the consistency and quality of patient care. © 2015 by American Journal of Neuroradiology.

  9. Latest Holocene Climate Variability revealed by a high-resolution multiple Proxy Record off Lisbon (Portugal)

    Science.gov (United States)

    Abrantes, F.; Lebreiro, S.; Ferreira, A.; Gil, I.; Jonsdottir, H.; Rodrigues, T.; Kissel, C.; Grimalt, J.

    2003-04-01

    The North Atlantic Oscillation (NAO) is known to have a major influence on the wintertime climate of the Atlantic basin and surrounding countries, determining precipitation and wind conditions at mid-latitudes. A comparison of Hurrel's NAO index to the mean winter (January-March) discharge of the Iberian Tagus River reveals a good negative correlation to negative NAO, while the years of largest upwelling anomalies, as referred in the literature, appear to be in good agreement with positive NAO. On this basis, a better understanding of the long-term variability of the NAO and Atlantic climate variability can be gained from high-resolution climate records from the Lisbon area. Climate variability of the last 2,000 years is assessed through a multiple proxy study of sedimentary sequences recovered from the Tagus prodelta deposition center, off Lisbon (Western Iberia). Physical properties, XRF and magnetic properties from core logging, grain size, δ18O, TOC, CaCO3, total alkenones, n-alkanes, alkenone SST, diatoms, benthic and planktonic foraminiferal assemblage compositions and fluxes are the proxies employed. The age model for site D13902 is based on AMS C-14 dates from mollusc and planktonic foraminifera shells, the reservoir correction for which was obtained by dating 3 pre-bomb, mollusc shells from the study area. Preliminary results indicate a Little Ice Age (LIA - 1300 - 1600 AD) alkenone derived SSTs around 15 degC followed by a sharp and rapid increase towards 19 degC. In spite the strong variability observed for most records, this low temperature interval is marked by a general increase in organic carbon, total alkenone concentration, diatom and foraminiferal abundances, as well as an increase in the sediment fine fraction and XRF determined Fe content, pointing to important river input and higher productivity. The Medieval Warm Period (1080 - 1300 AD) is characterized by 17-18 degC SSTs, increased mean grain size, but lower magnetic susceptibility and Fe

  10. Flip, flop and fly: modulated motor control and highly variable movement patterns of autotomized gecko tails.

    Science.gov (United States)

    Higham, Timothy E; Russell, Anthony P

    2010-02-23

    Many animals lose and regenerate appendages, and tail autotomy in lizards is an extremely well-studied example of this. Whereas the energetic, ecological and functional ramifications of tail loss for many lizards have been extensively documented, little is known about the behaviour and neuromuscular control of the autotomized tail. We used electromyography and high-speed video to quantify the motor control and movement patterns of autotomized tails of leopard geckos (Eublepharis macularius). In addition to rhythmic swinging, we show that they exhibit extremely complex movement patterns for up to 30 min following autotomy, including acrobatic flips up to 3 cm in height. Unlike the output of most central pattern generators (CPGs), muscular control of the tail is variable and can be arrhythmic. We suggest that the gecko tail is well suited for studies involving CPGs, given that this spinal preparation is naturally occurring, requires no surgery and exhibits complex modulation.

  11. High Power Tm3+-Doped Fiber Lasers Tuned by a Variable Reflective Output Coupler

    Directory of Open Access Journals (Sweden)

    Yulong Tang

    2008-01-01

    Full Text Available Wide wavelength tuning by a variable reflective output coupler is demonstrated in high-power double-clad Tm3+-doped silica fiber lasers diode-pumped at ∼790  nm. Varying the output coupling from 96% to 5%, the laser wavelength is tuned over a range of 106  nm from 1949 to 2055  nm. The output power exceeds 20  W over 90-nm range and the maximum output power is 32  W at 1949  nm for 51-W launched pump power, corresponding to a slope efficiency of ∼70%. Assisted with different fiber lengths, the tuning range is expanded to 240  nm from 1866 to 2107  nm with the output power larger than 10  W.

  12. Challenges of characterization of radioactive waste with High composition variability and their consequences measurement methodology

    International Nuclear Information System (INIS)

    Lexa, D.

    2014-01-01

    Radioactive waste characterization is a key step in every nuclear decommissioning project. It normally relies on a combination of facility operational history with results of destructive and non-destructive analysis. A particularly challenging situation arises when historical waste from a nuclear research facility is to be characterized, meaning little or no radiological information is available and the composition of the waste is highly variable. The nuclide vector concept is of limited utility, resulting in increased requirements placed on both the extent and performance of destructive and non-destructive analysis. Specific challenges are illustrated on an example of the decommissioning project underway at the Joint Research Center of the European Commission in Ispra. (author)

  13. High spatial variability in biogeochemical rates and microbial communities across Louisiana salt marsh landscapes

    Science.gov (United States)

    Roberts, B. J.; Chelsky, A.; Bernhard, A. E.; Giblin, A. E.

    2017-12-01

    Salt marshes are important sites for retention and transformation of carbon and nutrients. Much of our current marsh biogeochemistry knowledge is based on sampling at times and in locations that are convenient, most often vegetated marsh platforms during low tide. Wetland loss rates are high in many coastal regions including Louisiana which has the highest loss rates in the US. This loss not only reduces total marsh area but also changes the relative allocation of subhabitats in the remaining marsh. Climate and other anthropogenic changes lead to further changes including inundation patterns, redox conditions, salinity regimes, and shifts in vegetation patterns across marsh landscapes. We present results from a series of studies examining biogeochemical rates, microbial communities, and soil properties along multiple edge to interior transects within Spartina alterniflora across the Louisiana coast; between expanding patches of Avicennia germinans and adjacent S. alterniflora marshes; in soils associated with the four most common Louisiana salt marsh plants species; and across six different marsh subhabitats. Spartina alterniflora marsh biogeochemistry and microbial populations display high spatial variability related to variability in soil properties which appear to be, at least in part, regulated by differences in elevation, hydrology, and redox conditions. Differences in rates between soils associated with different vegetation types were also related to soil properties with S. alterniflora soils often yielding the lowest rates. Biogeochemical process rates vary significantly across marsh subhabitats with individual process rates differing in their hotspot habitat(s) across the marsh. Distinct spatial patterns may influence the roles that marshes play in retaining and transforming nutrients in coastal regions and highlight the importance of incorporating spatial sampling when scaling up plot level measurements to landscape or regional scales.

  14. High Interannual Variability in Connectivity and Genetic Pool of a Temperate Clingfish Matches Oceanographic Transport Predictions

    Science.gov (United States)

    Teixeira, Sara; Assis, Jorge; Serrão, Ester A.; Gonçalves, Emanuel J.; Borges, Rita

    2016-01-01

    Adults of most marine benthic and demersal fish are site-attached, with the dispersal of their larval stages ensuring connectivity among populations. In this study we aimed to infer spatial and temporal variation in population connectivity and dispersal of a marine fish species, using genetic tools and comparing these with oceanographic transport. We focused on an intertidal rocky reef fish species, the shore clingfish Lepadogaster lepadogaster, along the southwest Iberian Peninsula, in 2011 and 2012. We predicted high levels of self-recruitment and distinct populations, due to short pelagic larval duration and because all its developmental stages have previously been found near adult habitats. Genetic analyses based on microsatellites countered our prediction and a biophysical dispersal model showed that oceanographic transport was a good explanation for the patterns observed. Adult sub-populations separated by up to 300 km of coastline displayed no genetic differentiation, revealing a single connected population with larvae potentially dispersing long distances over hundreds of km. Despite this, parentage analysis performed on recruits from one focal site within the Marine Park of Arrábida (Portugal), revealed self-recruitment levels of 2.5% and 7.7% in 2011 and 2012, respectively, suggesting that both long- and short-distance dispersal play an important role in the replenishment of these populations. Population differentiation and patterns of dispersal, which were highly variable between years, could be linked to the variability inherent in local oceanographic processes. Overall, our measures of connectivity based on genetic and oceanographic data highlight the relevance of long-distance dispersal in determining the degree of connectivity, even in species with short pelagic larval durations. PMID:27911952

  15. Relating Psychosocial Variables in High School to Alcohol Use Trajectories During the Transition to Young Adulthood

    National Research Council Canada - National Science Library

    Morrow, Craig

    2000-01-01

    .... This study examined psychosocial variables-including peer focus, social skills, affect, antisocial behavior, gender, and sex-role attitudes-in an attempt to uncover variables related to changes...

  16. High variability impairs motor learning regardless of whether it affects task performance.

    Science.gov (United States)

    Cardis, Marco; Casadio, Maura; Ranganathan, Rajiv

    2018-01-01

    Motor variability plays an important role in motor learning, although the exact mechanisms of how variability affects learning are not well understood. Recent evidence suggests that motor variability may have different effects on learning in redundant tasks, depending on whether it is present in the task space (where it affects task performance) or in the null space (where it has no effect on task performance). We examined the effect of directly introducing null and task space variability using a manipulandum during the learning of a motor task. Participants learned a bimanual shuffleboard task for 2 days, where their goal was to slide a virtual puck as close as possible toward a target. Critically, the distance traveled by the puck was determined by the sum of the left- and right-hand velocities, which meant that there was redundancy in the task. Participants were divided into five groups, based on both the dimension in which the variability was introduced and the amount of variability that was introduced during training. Results showed that although all groups were able to reduce error with practice, learning was affected more by the amount of variability introduced rather than the dimension in which variability was introduced. Specifically, groups with higher movement variability during practice showed larger errors at the end of practice compared with groups that had low variability during learning. These results suggest that although introducing variability can increase exploration of new solutions, this may adversely affect the ability to retain the learned solution. NEW & NOTEWORTHY We examined the role of introducing variability during motor learning in a redundant task. The presence of redundancy allows variability to be introduced in different dimensions: the task space (where it affects task performance) or the null space (where it does not affect task performance). We found that introducing variability affected learning adversely, but the amount of

  17. Variable high-resolution color CCD camera system with online capability for professional photo studio application

    Science.gov (United States)

    Breitfelder, Stefan; Reichel, Frank R.; Gaertner, Ernst; Hacker, Erich J.; Cappellaro, Markus; Rudolf, Peter; Voelk, Ute

    1998-04-01

    Digital cameras are of increasing significance for professional applications in photo studios where fashion, portrait, product and catalog photographs or advertising photos of high quality have to be taken. The eyelike is a digital camera system which has been developed for such applications. It is capable of working online with high frame rates and images of full sensor size and it provides a resolution that can be varied between 2048 by 2048 and 6144 by 6144 pixel at a RGB color depth of 12 Bit per channel with an also variable exposure time of 1/60s to 1s. With an exposure time of 100 ms digitization takes approx. 2 seconds for an image of 2048 by 2048 pixels (12 Mbyte), 8 seconds for the image of 4096 by 4096 pixels (48 Mbyte) and 40 seconds for the image of 6144 by 6144 pixels (108 MByte). The eyelike can be used in various configurations. Used as a camera body most commercial lenses can be connected to the camera via existing lens adaptors. On the other hand the eyelike can be used as a back to most commercial 4' by 5' view cameras. This paper describes the eyelike camera concept with the essential system components. The article finishes with a description of the software, which is needed to bring the high quality of the camera to the user.

  18. Seasonal and high-resolution variability in hydrochemistry of the Andes-Amazon

    Science.gov (United States)

    Burt, E.; West, A. J.

    2017-12-01

    Stream hydrochemistry acts as a record of integrated catchment processes such as the amount of time it takes precipitation to flow through the subsurface and become streamflow (water transit times), water-rock interaction and biogeochemical cycling. Although it is understood that sampling interval affects observed patterns in hydrochemistry, most studies collect samples on a weekly, bi-weekly or monthly schedule due to lack of resources or the difficulty of maintaining automated sampling devices. Here, we attempt to combine information from two sampling time scales, comparing a year-long hydrochemical time series to data from a recent sub-daily sampling campaign. Starting in April 2016, river, soil and rain waters have been collected every two weeks at five small catchments spanning the tropical Andes and Amazon - a natural laboratory for its gradients in topography, erosion rates, precipitation, temperature and flora. Between January and March, 2017, we conducted high frequency sampling for approximately one week at each catchment, sampling at least every four hours including overnight. We will constrain young water fractions (Kirchner, 2016) and storm water fluxes for the experimental catchments using stable isotopes of water as conservative tracers. Major element data will provide the opportunity to make initial constraints on geochemical and hydrologic coupling. Preliminary results suggest that in the Amazon, hydrochemistry patterns are dependent on sampling frequency: the seasonal cycle in stable isotopes of water is highly damped, while the high resolution sampling displays large variability. This suggests that a two-week sampling interval is not frequent enough to capture rapid transport of water, perhaps through preferential flow networks. In the Andes, stable isotopes of water are highly damped in both the seasonal and high resolution cycle, suggesting that the catchment behaves as a "well-mixed" system.

  19. Variable load failure mechanism for high-speed load sensing electro-hydrostatic actuator pump of aircraft

    Directory of Open Access Journals (Sweden)

    Cun SHI

    2018-05-01

    Full Text Available This paper presents a novel transient lubrication model for the analysis of the variable load failure mechanism of high-speed pump used in Load Sensing Electro-Hydrostatic Actuator (LS-EHA. Focusing on the slipper/swashplate pair partial abrasion, which is considered as the dominant failure mode in the high-speed condition, slipper dynamic models are established. A forth sliding motion of the slipper on the swashplate surface is presented under the fact that the slipper center of mass will rotate around the center of piston ball when the swashplate angle is dynamically adjusted. Besides, extra inertial tilting moments will be produced for the slipper based on the theorem on translation of force, which will increase rapidly when LS-EHA pump operates under high-speed condition. Then, a dynamic lubricating model coupling with fluid film thickness field, temperature field and pressure field is proposed. The deformation effects caused by thermal deflection and hydrostatic pressure are considered. A numerical simulation model is established to validate the effectiveness and accuracy of the proposed model. Finally, based on the load spectrum of aircraft flight profile, the variable load conditions and the oil film characteristics are analyzed, and series of variable load rules of oil film thickness with variable speed/variable pressure/variable displacement are concluded. Keywords: Coupling lubrication model, Electro-Hydrostatic Actuator (EHA, High-speed pump, Partial abrasion, Slipper pair, Variable load

  20. High glycemic variability assessed by continuous glucose monitoring after surgical treatment of obesity by gastric bypass.

    Science.gov (United States)

    Hanaire, Helene; Bertrand, Monelle; Guerci, Bruno; Anduze, Yves; Guillaume, Eric; Ritz, Patrick

    2011-06-01

    Obesity surgery elicits complex changes in glucose metabolism that are difficult to observe with discontinuous glucose measurements. We aimed to evaluate glucose variability after gastric bypass by continuous glucose monitoring (CGM) in a real-life setting. CGM was performed for 4.2 ± 1.3 days in three groups of 10 subjects each: patients who had undergone gastric bypass and who were referred for postprandial symptoms compatible with mild hypoglycemia, nonoperated diabetes controls, and healthy controls. The maximum interstitial glucose (IG), SD of IG values, and mean amplitude of glucose excursions (MAGE) were significantly higher in operated patients and in diabetes controls than in healthy controls. The time to the postprandial peak IG was significantly shorter in operated patients (42.8 ± 6.0 min) than in diabetes controls (82.2 ± 11.1 min, P = 0.0002), as were the rates of glucose increase to the peak (2.4 ± 1.6 vs. 1.2 ± 0.3 mg/mL/min; P = 0.041). True hypoglycemia (glucose fasting state and 2 h postmeal. Glucose variability is exaggerated after gastric bypass, combining unusually high and early hyperglycemic peaks and rapid IG decreases. This might account for postprandial symptoms mimicking hypoglycemia but often seen without true hypoglycemia. Early postprandial hyperglycemia might be underestimated if glucose measurements are done 2 h postmeal.

  1. Ecosystem responses to recent oceanographic variability in high-latitude Northern Hemisphere ecosystems

    Science.gov (United States)

    Mueter, Franz J.; Broms, Cecilie; Drinkwater, Kenneth F.; Friedland, Kevin D.; Hare, Jonathan A.; Hunt, George L., Jr.; Melle, Webjørn; Taylor, Maureen

    2009-04-01

    As part of the international MENU collaboration, we compared and contrasted ecosystem responses to climate-forced oceanographic variability across several high latitude regions of the North Pacific (Eastern Bering Sea (EBS) and Gulf of Alaska (GOA)) and North Atlantic Oceans (Gulf of Maine/Georges Bank (GOM/GB) and the Norwegian/Barents Seas (NOR/BAR)). Differences in the nitrate content of deep source waters and incoming solar radiation largely explain differences in average primary productivity among these ecosystems. We compared trends in productivity and abundance at various trophic levels and their relationships with sea-surface temperature. Annual net primary production generally increases with annual mean sea-surface temperature between systems and within the EBS, BAR, and GOM/GB. Zooplankton biomass appears to be controlled by both top-down (predation by fish) and bottom-up forcing (advection, SST) in the BAR and NOR regions. In contrast, zooplankton in the GOM/GB region showed no evidence of top-down forcing but appeared to control production of major fish populations through bottom-up processes that are independent of temperature variability. Recruitment of several fish stocks is significantly and positively correlated with temperature in the EBS and BAR, but cod and pollock recruitment in the EBS has been negatively correlated with temperature since the 1977 shift to generally warmer conditions. In each of the ecosystems, fish species showed a general poleward movement in response to warming. In addition, the distribution of groundfish in the EBS has shown a more complex, non-linear response to warming resulting from internal community dynamics. Responses to recent warming differ across systems and appear to be more direct and more pronounced in the higher latitude systems where food webs and trophic interactions are simpler and where both zooplankton and fish species are often limited by cold temperatures.

  2. High-Frequency X-ray Variability Detection in A Black Hole Transient with USA.

    Energy Technology Data Exchange (ETDEWEB)

    Shabad, Gayane

    2000-10-16

    Studies of high-frequency variability (above {approx}100 Hz) in X-ray binaries provide a unique opportunity to explore the fundamental physics of spacetime and matter, since the orbital timescale on the order of several milliseconds is a timescale of the motion of matter through the region located in close proximity to a compact stellar object. The detection of weak high-frequency signals in X-ray binaries depends on how well we understand the level of Poisson noise due to the photon counting statistics, i.e. how well we can understand and model the detector deadtime and other instrumental systematic effects. We describe the preflight timing calibration work performed on the Unconventional Stellar Aspect (USA) X-ray detector to study deadtime and timing issues. We developed a Monte Carlo deadtime model and deadtime correction methods for the USA experiment. The instrumental noise power spectrum can be estimated within {approx}0.1% accuracy in the case when no energy-dependent instrumental effect is present. We also developed correction techniques to account for an energy-dependent instrumental effect. The developed methods were successfully tested on USA Cas A and Cygnus X-1 data. This work allowed us to make a detection of a weak signal in a black hole candidate (BHC) transient.

  3. Evaluation of variability in high-resolution protein structures by global distance scoring

    Directory of Open Access Journals (Sweden)

    Risa Anzai

    2018-01-01

    Full Text Available Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.

  4. Evaluation of variability in high-resolution protein structures by global distance scoring.

    Science.gov (United States)

    Anzai, Risa; Asami, Yoshiki; Inoue, Waka; Ueno, Hina; Yamada, Koya; Okada, Tetsuji

    2018-01-01

    Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.

  5. Effects of variable specific heat on energy transfer in a high-temperature supersonic channel flow

    Science.gov (United States)

    Chen, Xiaoping; Li, Xiaopeng; Dou, Hua-Shu; Zhu, Zuchao

    2018-05-01

    An energy transfer mechanism in high-temperature supersonic turbulent flow for variable specific heat (VSH) condition through turbulent kinetic energy (TKE), mean kinetic energy (MKE), turbulent internal energy (TIE) and mean internal energy (MIE) is proposed. The similarities of energy budgets between VSH and constant specific heat (CSH) conditions are investigated by introducing a vibrational energy excited degree and considering the effects of fluctuating specific heat. Direct numerical simulation (DNS) of temporally evolving high-temperature supersonic turbulent channel flow is conducted at Mach number 3.0 and Reynolds number 4800 combined with a constant dimensional wall temperature 1192.60 K for VSH and CSH conditions to validate the proposed energy transfer mechanism. The differences between the terms in the two kinetic energy budgets for VSH and CSH conditions are small; however, the magnitude of molecular diffusion term for VSH condition is significantly smaller than that for CSH condition. The non-negligible energy transfer is obtained after neglecting several small terms of diffusion, dissipation and compressibility related. The non-negligible energy transfer involving TIE includes three processes, in which energy can be gained from TKE and MIE and lost to MIE. The same non-negligible energy transfer through TKE, MKE and MIE is observed for both the conditions.

  6. Local variability in growth and reproduction of Salix arctica in the High Arctic

    Directory of Open Access Journals (Sweden)

    Noémie Boulanger-Lapointe

    2016-06-01

    Full Text Available Arctic terrestrial ecosystems are heterogeneous because of the strong influences of microtopography, soil moisture and snow accumulation on vegetation distribution. The interaction between local biotic and abiotic factors and global climate patterns will influence species responses to climate change. Salix arctica (Arctic willow is a structuring species, ubiquitous and widespread, and as such is one of the most important shrub species in the High Arctic. In this study, we measured S. arctica reproductive effort, early establishment, survival and growth in the Zackenberg valley, north-east Greenland. We sampled four plant communities that varied with respect to snow conditions, soil moisture, nutrient content and plant composition. We found large variability in reproductive effort and success with total catkin density ranging from 0.6 to 66 catkins/m2 and seedling density from <1 to 101 seedlings/m2. There were also major differences in crown area increment (4–23 cm2/year and stem radial growth (40–74 µm/year. The snowbed community, which experienced a recent reduction in snow cover, supported young populations with high reproductive effort, establishment and growth. Soil nutrient content and herbivore activity apparently did not strongly constrain plant reproduction and growth, but competition by Cassiope tetragona and low soil moisture may inhibit performance. Our results show that local environmental factors, such as snow accumulation, have a significant impact on tundra plant response to climate change and will affect the understanding of regional vegetation response to climate change.

  7. Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

    Directory of Open Access Journals (Sweden)

    Jiandong YANG, Zhihe ZHANG, Fujun SHEN, Xuyu YANG, Liang ZHANG, Limin CHEN, Wenping ZHANG, Qing ZHU, Rong HOU

    2011-12-01

    Full Text Available Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A, Allelic richness (AR and mean expected heterozygosity (HE for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort [Current Zoology 57 (6: 717–724, 2011].

  8. High frequency sonar variability in littoral environments: Irregular particles and bubbles

    Science.gov (United States)

    Richards, Simon D.; Leighton, Timothy G.; White, Paul R.

    2002-11-01

    Littoral environments may be characterized by high concentrations of suspended particles. Such suspensions contribute to attenuation through visco-inertial absorption and scattering and may therefore be partially responsible for the observed variability in high frequency sonar performance in littoral environments. Microbubbles which are prevalent in littoral waters also contribute to volume attenuation through radiation, viscous and thermal damping and cause dispersion. The attenuation due to a polydisperse suspension of particles with depth-dependent concentration has been included in a sonar model. The effects of a depth-dependent, polydisperse population of microbubbles on attenuation, sound speed and volume reverberation are also included. Marine suspensions are characterized by nonspherical particles, often plate-like clay particles. Measurements of absorption in dilute suspensions of nonspherical particles have shown disagreement with predictions of spherical particle models. These measurements have been reanalyzed using three techniques for particle sizing: laser diffraction, gravitational sedimentation, and centrifugal sedimentation, highlighting the difficulty of characterizing polydisperse suspensions of irregular particles. The measurements have been compared with predictions of a model for suspensions of oblate spheroids. Excellent agreement is obtained between this model and the measurements for kaolin particles, without requiring any a priori knowledge of the measurements.

  9. Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice

    Science.gov (United States)

    Wilson, Robert; Geyer, Stefan H.; Reissig, Lukas; Rose, Julia; Szumska, Dorota; Hardman, Emily; Prin, Fabrice; McGuire, Christina; Ramirez-Solis, Ramiro; White, Jacqui; Galli, Antonella; Tudor, Catherine; Tuck, Elizabeth; Mazzeo, Cecilia Icoresi; Smith, James C.; Robertson, Elizabeth; Adams, David J.; Mohun, Timothy; Weninger, Wolfgang J.

    2017-01-01

    Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD) programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve. Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates. PMID:27996060

  10. Measurement of high-departure aspheres using subaperture stitching with the Variable Optical Null (VON)

    Science.gov (United States)

    Kulawiec, Andrew; Murphy, Paul; DeMarco, Michael

    2010-10-01

    Aspheric surfaces are proven to provide significant benefits to a wide variety of optical systems, but the ability to produce high-precision aspheric surfaces has historically been limited by the ability (or lack thereof) to measure them. Traditionally, aspheric measurements have required dedicated null optics, but the cost, lead time, and calibration difficulty of using null optics has made the use of aspheres more challenging and less attractive. In the past three years, QED has developed the Subaperture Stitching Interferometer for Aspheres (SSI-A®) to help address this limitation, providing flexible aspheric measurement capability of up to 200 waves of aspheric departure from best-fit sphere. Some aspheres, however, have thousands of waves of departure. We have recently developed Variable Optical Null (VON) technology that can null much of the aspheric departure in a subaperture. The VON is automatically configurable and is adjusted to nearly null each specific subaperture of an asphere. This ability to nearly null a local subaperture of an asphere provides a significant boost in aspheric measurement capability, enabling aspheres with up to 1000 waves of departure to be measured, without the use of dedicated null optics. We outline the basic principles of subaperture stitching and VON technology, demonstrate the extended capability provided by the VON, and present measurement results from the new Aspheric Stitching Interferometer (ASI®).

  11. Consumer's risk in the EMA and FDA regulatory approaches for bioequivalence in highly variable drugs.

    Science.gov (United States)

    Muñoz, Joel; Alcaide, Daniel; Ocaña, Jordi

    2016-05-30

    The 2010 US Food and Drug Administration and European Medicines Agency regulatory approaches to establish bioequivalence in highly variable drugs are both based on linearly scaling the bioequivalence limits, both take a 'scaled average bioequivalence' approach. The present paper corroborates previous work suggesting that none of them adequately controls type I error or consumer's risk, so they result in invalid test procedures in the neighbourhood of a within-subject coefficient of variation osf 30% for the reference (R) formulation. The problem is particularly serious in the US Food and Drug Administration regulation, but it is also appreciable in the European Medicines Agency one. For the partially replicated TRR/RTR/RRT and the replicated TRTR/RTRT crossover designs, we quantify these type I error problems by means of a simulation study, discuss their possible causes and propose straightforward improvements on both regulatory procedures that improve their type I error control while maintaining an adequate power. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  12. A new “Variable Resolution Associative Memory” for High Energy Physics

    CERN Document Server

    Annovi, A; The ATLAS collaboration; Beretta, M; Bossini, E; Crescioli, F; Dell'Orso, M; Giannetti, P; Hoff, J; Liberali, V; Liu, T; Magalotti, D; Piendibene, M; Sacco, A; Schoening, A; Soltveit, H K; Stabile, A; Tripiccione, R; Vitillo, R; Volpi, G

    2011-01-01

    We describe an important advancement for the Associative Memory device (AM). The AM is a VLSI processor for pattern recognition based on Content Addressable Memory (CAM) architecture. The AM is optimized for on-line track finding in high-energy physics experiments. Pattern matching is carried out finding track candidates in coarse resolution “roads”. A large AM bank stores all trajectories of interest, called “patterns”, for a given detector resolution. The AM extracts roads compatible with a given event during detector read-out. Two important variables characterize the quality of the AM bank: its “coverage” and the level of “found fakes”. The coverage, which describes the geometric efficiency of a bank, is defined as the fraction of tracks that match at least a pattern in the bank. Given a certain road size, the coverage of the bank can be increased just adding patterns to the bank, while the number of found fakes unfortunately is roughly proportional to this number of patterns in the bank. M...

  13. Transformations of gold nanoparticles investigated using variable temperature high-resolution transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Young, N.P. [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Huis, M.A. van; Zandbergen, H.W. [Kavli Institute of Nanoscience, Delft University of Technolgy, Lorentzweg 1, NL-2628CJ, Delft, The Netherlands. (Netherlands); Xu, H. [Department of Geology and Geophysics, and Materials Science Program, University of Wisconsin-Madison, Madison, WI (United States); Kirkland, A.I., E-mail: angus.kirkland@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom)

    2010-04-15

    Recently designed advanced in-situ specimen holders for transmission electron microscopy (TEM) have been used in studies of gold nanoparticles. We report results of variable temperature TEM experiments in which structural transformations have been correlated with specimen temperature, allowing general trends to be identified. Transformation to a decahedral morphology for particles in the size range 5-12 nm was observed for the majority of particles regardless of their initial structure. Following in-situ annealing, decahedra were found to be stable at room temperature, confirming this as the equilibrium morphology, in agreement with recently calculated phase diagrams. Other transitions at low temperature in addition to surface roughening have also been observed and correlated with the same nanoscale phase diagram. Investigations of gold particles at high temperature have revealed evidence for co-existing solid and liquid phases. Overall, these results are important in a more precise understanding of the structure and action of catalytic gold nanoparticles and in the experimental verification of theoretical calculations.

  14. Variability induced by spaceflight environment on high oil and normal maize lines

    International Nuclear Information System (INIS)

    Xu Xiaowei; Xu Li; Dong Xin; Jin Weiwei; Chen Shaojiang

    2011-01-01

    High oil inbred line BY815 and two normal inbred lines 1145 and F349 treated with spaceflight were used for variability analysis. Results showed that the mutation rate of BY815 was 21.61% in SP 1 , while the mutation rates of 1145 and F349 were 2.57% and 3.13% respectively. Only six mutants were found from these three materials in SP 2 , of which two mutants, HT-3 from BY815 exhibiting albino leaf color and HT-5 from 1145 exhibiting stripe-like spots leaves, were worthy of further study. Genetic analysis of the two mutants showed that the segregation ratio of normal and mutant phenotypes was 3 : 1, which was in accordance with Mendel's single gene inheritance law. Cytological observation of all the six mutants showed no chromosome abnormalities. By using SSR (simple sequence repeat) method, 130 pairs of primers were employed and only one mutant originated from inbred line 1145 showed polymorphic and the mutated loci rate of the genome in this mutant was 8.46%. (authors)

  15. The analytical description of high temperature tensile creep for cavitating materials subjected to time variable loads

    International Nuclear Information System (INIS)

    Bocek, M.

    A phenomenological cavitation model is presented by means of which the life time as well as the creep curve equations can be calculated for cavitating materials subjected to time variable tensile loads. The model precludes the proportionality between the damage A and the damage rate (dA/dt) resp. Both are connected by the life time function tau. The latter is derived from static stress rupture tests and contains the loading conditions. From this model the life fraction rule (LFR) is derived. The model is used to calculate the creep curves of cavitating materials subjected at high temperatures to non-stationary tensile loading conditions. In the present paper the following loading procedures are considered: creep at constant load F and true stress s; creep at linear load increase ((dF/dt)=const) and creep at constant load amplitude cycling (CLAC). For these loading procedures the creep equations for cavitating and non-cavitating specimens are derived. Under comparable conditions the creep rate of cavitating materials are higher than for non-cavitating ones. (author)

  16. Design of a High Temperature Radiator for the Variable Specific Impulse Magnetoplasma Rocket

    Science.gov (United States)

    Sheth, Rubik B.; Ungar, Eugene K.; Chambliss, Joe P.

    2012-01-01

    The Variable Specific Impulse Magnetoplasma Rocket (VASIMR), currently under development by Ad Astra Rocket Company (Webster, TX), is a unique propulsion system that could change the way space propulsion is performed. VASIMR's efficiency, when compared to that of a conventional chemical rocket, reduces the propellant needed for exploration missions by a factor of 10. Currently plans include flight tests of a 200 kW VASIMR system, titled VF-200, on the International Space Station (ISS). The VF-200 will consist of two 100 kW thruster units packaged together in one engine bus. Each thruster core generates 27 kW of waste heat during its 15 minute firing time. The rocket core will be maintained between 283 and 573 K by a pumped thermal control loop. The design of a high temperature radiator is a unique challenge for the vehicle design. This paper will discuss the path taken to develop a steady state and transient-based radiator design. The paper will describe the radiator design option selected for the VASIMR thermal control system for use on ISS, and how the system relates to future exploration vehicles.

  17. Design Analysis of a High Temperature Radiator for the Variable Specific Impulse Magnetoplasma Rocket (VASIMR)

    Science.gov (United States)

    Sheth, Rubik B.; Ungar, Eugene K.; Chambliss, Joe P.; Cassady, Leonard D.

    2011-01-01

    The Variable Specific Impulse Magnetoplasma Rocket (VASIMR), currently under development by Ad Astra Rocket Company, is a unique propulsion system that can potentially change the way space propulsion is performed. VASIMR's efficiency, when compared to that of a conventional chemical rocket, reduce propellant needed for exploration missions by a factor of 10. Currently plans include flight tests of a 200 kW VASIMR system, titled VF-200, on the International Space Station. The VF-200 will consist of two 100 kW thruster units packaged together in one engine bus. Each thruster unit has a unique heat rejection requirement of about 27 kW over a firing time of 15 minutes. In order to control rocket core temperatures, peak operating temperatures of about 300 C are expected within the thermal control loop. Design of a high temperature radiator is a unique challenge for the vehicle design. This paper will discuss the path taken to develop a steady state and transient based radiator design. The paper will describe radiator design options for the VASIMR thermal control system for use on ISS as well as future exploration vehicles.

  18. Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data.

    Science.gov (United States)

    Yip, Shun H; Sham, Pak Chung; Wang, Junwen

    2018-02-21

    Traditional RNA sequencing (RNA-seq) allows the detection of gene expression variations between two or more cell populations through differentially expressed gene (DEG) analysis. However, genes that contribute to cell-to-cell differences are not discoverable with RNA-seq because RNA-seq samples are obtained from a mixture of cells. Single-cell RNA-seq (scRNA-seq) allows the detection of gene expression in each cell. With scRNA-seq, highly variable gene (HVG) discovery allows the detection of genes that contribute strongly to cell-to-cell variation within a homogeneous cell population, such as a population of embryonic stem cells. This analysis is implemented in many software packages. In this study, we compare seven HVG methods from six software packages, including BASiCS, Brennecke, scLVM, scran, scVEGs and Seurat. Our results demonstrate that reproducibility in HVG analysis requires a larger sample size than DEG analysis. Discrepancies between methods and potential issues in these tools are discussed and recommendations are made.

  19. Carbon dioxide in northern high latitude oceans: Anthropogenic increase and air-sea flux variability

    International Nuclear Information System (INIS)

    Omar, Abdirahman M.

    2003-01-01

    The aim of this thesis is to further our knowledge of carbon dioxide in the northern high latitude oceans (northern North Atlantic, Barents Sea, and Arctic Ocean) by studying the anthropogenic change in the oceanic CO2, the inter-annual variability of the air-sea CO2 flux, and the relationship between this variability and changes in other oceanic processes. An introductory chapter and four papers are presented. Descriptions of the seawater carbonate system parameters, air-sea exchange of CO2, and related processes are given in the introduction chapter. The anthropogenic increase in partial pressure of CO2 (pCO2) in the surface water of the Barents Sea is evaluated in paper I. The effect of alternations of the Barents Sea climate between cold and warm modes on the annual cycles of seawater fugacity and air-sea flux of CO2 is investigated in paper II. Oceanic uptake of atmospheric CO2 associated with the seasonal formation of sea ice in Storfjorden and the implication for the entire Arctic Ocean is studied in paper III. An assessment of the variations of the air-sea flux of CO2 in the northern North Atlantic for 20 winters (1981-2001) is carried out in paper IV. PCO2 in the surface water of the Barents Sea is shown to have increased parallel with the atmospheric pCO2 between 1967 and 2000-2001 (paper I). This was determined by comparing seawater pCO2 from 1967 with that from 2000-2001. The former was estimated from surface seawater temperature (SST) while the latter was computed from data of total dissolved inorganic carbon and alkalinity. A procedure which accounts for the natural variability was applied and the difference between seawater pC02 of 1967 and that of 2000-2001 is attributed to the uptake of excess CO2. In the Atlantic sector of the Barents Sea, the surface seawater fugacity of CO2 (fCO s''w) is shown to be lower than the atmospheric fCO2 throughout the year, implying that the area is an annual sink of atmospheric CO2 (paper II). Additionally, changes

  20. Carbon dioxide in northern high latitude oceans: Anthropogenic increase and air-sea flux variability

    Energy Technology Data Exchange (ETDEWEB)

    Omar, Abdirahman M.

    2003-07-01

    The aim of this thesis is to further our knowledge of carbon dioxide in the northern high latitude oceans (northern North Atlantic, Barents Sea, and Arctic Ocean) by studying the anthropogenic change in the oceanic CO2, the inter-annual variability of the air-sea CO2 flux, and the relationship between this variability and changes in other oceanic processes. An introductory chapter and four papers are presented. Descriptions of the seawater carbonate system parameters, air-sea exchange of CO2, and related processes are given in the introduction chapter. The anthropogenic increase in partial pressure of CO2 (pCO2) in the surface water of the Barents Sea is evaluated in paper I. The effect of alternations of the Barents Sea climate between cold and warm modes on the annual cycles of seawater fugacity and air-sea flux of CO2 is investigated in paper II. Oceanic uptake of atmospheric CO2 associated with the seasonal formation of sea ice in Storfjorden and the implication for the entire Arctic Ocean is studied in paper III. An assessment of the variations of the air-sea flux of CO2 in the northern North Atlantic for 20 winters (1981-2001) is carried out in paper IV. PCO2 in the surface water of the Barents Sea is shown to have increased parallel with the atmospheric pCO2 between 1967 and 2000-2001 (paper I). This was determined by comparing seawater pCO2 from 1967 with that from 2000-2001. The former was estimated from surface seawater temperature (SST) while the latter was computed from data of total dissolved inorganic carbon and alkalinity. A procedure which accounts for the natural variability was applied and the difference between seawater pC02 of 1967 and that of 2000-2001 is attributed to the uptake of excess CO2. In the Atlantic sector of the Barents Sea, the surface seawater fugacity of CO2 (fCO s''w) is shown to be lower than the atmospheric fCO2 throughout the year, implying that the area is an annual sink of atmospheric CO2 (paper II). Additionally

  1. Population-based resequencing revealed an ancestral winter group of cultivated flax: implication for flax domestication processes

    Science.gov (United States)

    Fu, Yong-Bi

    2012-01-01

    Cultivated flax (Linum usitatissimum L.) is the earliest oil and fiber crop and its early domestication history may involve multiple events of domestication for oil, fiber, capsular indehiscence, and winter hardiness. Genetic studies have demonstrated that winter cultivated flax is closely related to oil and fiber cultivated flax and shows little relatedness to its progenitor, pale flax (L. bienne Mill.), but winter hardiness is one major characteristic of pale flax. Here, we assessed the genetic relationships of 48 Linum samples representing pale flax and four trait-specific groups of cultivated flax (dehiscent, fiber, oil, and winter) through population-based resequencing at 24 genomic regions, and revealed a winter group of cultivated flax that displayed close relatedness to the pale flax samples. Overall, the cultivated flax showed a 27% reduction of nucleotide diversity when compared with the pale flax. Recombination frequently occurred at these sampled genomic regions, but the signal of selection and bottleneck was relatively weak. These findings provide some insight into the impact and processes of flax domestication and are significant for expanding our knowledge about early flax domestication, particularly for winter hardiness. PMID:22822439

  2. Genetic diversity, molecular phylogeny and selection evidence of the silkworm mitochondria implicated by complete resequencing of 41 genomes

    Directory of Open Access Journals (Sweden)

    Tellier Laurent C

    2010-03-01

    Full Text Available Abstract Background Mitochondria are a valuable resource for studying the evolutionary process and deducing phylogeny. A few mitochondria genomes have been sequenced, but a comprehensive picture of the domestication event for silkworm mitochondria remains to be established. In this study, we integrate the extant data, and perform a whole genome resequencing of Japanese wild silkworm to obtain breakthrough results in silkworm mitochondrial (mt population, and finally use these to deduce a more comprehensive phylogeny of the Bombycidae. Results We identified 347 single nucleotide polymorphisms (SNPs in the mt genome, but found no past recombination event to have occurred in the silkworm progenitor. A phylogeny inferred from these whole genome SNPs resulted in a well-classified tree, confirming that the domesticated silkworm, Bombyx mori, most recently diverged from the Chinese wild silkworm, rather than from the Japanese wild silkworm. We showed that the population sizes of the domesticated and Chinese wild silkworms both experience neither expansion nor contraction. We also discovered that one mt gene, named cytochrome b, shows a strong signal of positive selection in the domesticated clade. This gene is related to energy metabolism, and may have played an important role during silkworm domestication. Conclusions We present a comparative analysis on 41 mt genomes of B. mori and B. mandarina from China and Japan. With these, we obtain a much clearer picture of the evolution history of the silkworm. The data and analyses presented here aid our understanding of the silkworm in general, and provide a crucial insight into silkworm phylogeny.

  3. Gene expression profiling and candidate gene resequencing identifies pathways and mutations important for malignant transformation caused by leukemogenic fusion genes.

    Science.gov (United States)

    Novak, Rachel L; Harper, David P; Caudell, David; Slape, Christopher; Beachy, Sarah H; Aplan, Peter D

    2012-12-01

    NUP98-HOXD13 (NHD13) and CALM-AF10 (CA10) are oncogenic fusion proteins produced by recurrent chromosomal translocations in patients with acute myeloid leukemia (AML). Transgenic mice that express these fusions develop AML with a long latency and incomplete penetrance, suggesting that collaborating genetic events are required for leukemic transformation. We employed genetic techniques to identify both preleukemic abnormalities in healthy transgenic mice as well as collaborating events leading to leukemic transformation. Candidate gene resequencing revealed that 6 of 27 (22%) CA10 AMLs spontaneously acquired a Ras pathway mutation and 8 of 27 (30%) acquired an Flt3 mutation. Two CA10 AMLs acquired an Flt3 internal-tandem duplication, demonstrating that these mutations can be acquired in murine as well as human AML. Gene expression profiles revealed a marked upregulation of Hox genes, particularly Hoxa5, Hoxa9, and Hoxa10 in both NHD13 and CA10 mice. Furthermore, mir196b, which is embedded within the Hoxa locus, was overexpressed in both CA10 and NHD13 samples. In contrast, the Hox cofactors Meis1 and Pbx3 were differentially expressed; Meis1 was increased in CA10 AMLs but not NHD13 AMLs, whereas Pbx3 was consistently increased in NHD13 but not CA10 AMLs. Silencing of Pbx3 in NHD13 cells led to decreased proliferation, increased apoptosis, and decreased colony formation in vitro, suggesting a previously unexpected role for Pbx3 in leukemic transformation. Published by Elsevier Inc.

  4. Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas L Turner

    2011-03-01

    Full Text Available Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size.

  5. The Salience of Selected Variables on Choice for Movie Attendance among High School Students.

    Science.gov (United States)

    Austin, Bruce A.

    A questionnaire was designed for a study assessing both the importance of 28 variables in movie attendance and the importance of movie-going as a leisure-time activity. Respondents were 130 ninth and twelfth grade students. The 28 variables were broadly organized into eight categories: movie production personnel, production elements, advertising,…

  6. Scalable Active Optical Access Network Using Variable High-Speed PLZT Optical Switch/Splitter

    Science.gov (United States)

    Ashizawa, Kunitaka; Sato, Takehiro; Tokuhashi, Kazumasa; Ishii, Daisuke; Okamoto, Satoru; Yamanaka, Naoaki; Oki, Eiji

    This paper proposes a scalable active optical access network using high-speed Plumbum Lanthanum Zirconate Titanate (PLZT) optical switch/splitter. The Active Optical Network, called ActiON, using PLZT switching technology has been presented to increase the number of subscribers and the maximum transmission distance, compared to the Passive Optical Network (PON). ActiON supports the multicast slot allocation realized by running the PLZT switch elements in the splitter mode, which forces the switch to behave as an optical splitter. However, the previous ActiON creates a tradeoff between the network scalability and the power loss experienced by the optical signal to each user. It does not use the optical power efficiently because the optical power is simply divided into 0.5 to 0.5 without considering transmission distance from OLT to each ONU. The proposed network adopts PLZT switch elements in the variable splitter mode, which controls the split ratio of the optical power considering the transmission distance from OLT to each ONU, in addition to PLZT switch elements in existing two modes, the switching mode and the splitter mode. The proposed network introduces the flexible multicast slot allocation according to the transmission distance from OLT to each user and the number of required users using three modes, while keeping the advantages of ActiON, which are to support scalable and secure access services. Numerical results show that the proposed network dramatically reduces the required number of slots and supports high bandwidth efficiency services and extends the coverage of access network, compared to the previous ActiON, and the required computation time for selecting multicast users is less than 30msec, which is acceptable for on-demand broadcast services.

  7. The Effect of Sex on Heart Rate Variability at High Altitude.

    Science.gov (United States)

    Boos, Christopher John; Vincent, Emma; Mellor, Adrian; O'Hara, John; Newman, Caroline; Cruttenden, Richard; Scott, Phylip; Cooke, Mark; Matu, Jamie; Woods, David Richard

    2017-12-01

    There is evidence suggesting that high altitude (HA) exposure leads to a fall in heart rate variability (HRV) that is linked to the development of acute mountain sickness (AMS). The effects of sex on changes in HRV at HA and its relationship to AMS are unknown. HRV (5-min single-lead ECG) was measured in 63 healthy adults (41 men and 22 women) 18-56 yr of age at sea level (SL) and during a HA trek at 3619, 4600, and 5140 m, respectively. The main effects of altitude (SL, 3619 m, 4600 m, and 5140 m) and sex (men vs women) and their potential interaction were assessed using a factorial repeated-measures ANOVA. Logistic regression analyses were performed to assess the ability of HRV to predict AMS. Men and women were of similar age (31.2 ± 9.3 vs 31.7 ± 7.5 yr), ethnicity, and body and mass index. There was main effect for altitude on heart rate, SD of normal-to-normal (NN) intervals (SDNN), root mean square of successive differences (RMSSD), number of pairs of successive NN differing by >50 ms (NN50), NN50/total number of NN, very low-frequency power, low-frequency (LF) power, high-frequency (HF) power, and total power (TP). The most consistent effect on post hoc analysis was reduction in these HRV measures between 3619 and 5140 m at HA. Heart rate was significantly lower and SDNN, RMSSD, LF power, HF power, and TP were higher in men compared with women at HA. There was no interaction between sex and altitude for any of the HRV indices measured. HRV was not predictive of AMS development. Increasing HA leads to a reduction in HRV. Significant differences between men and women emerge at HA. HRV was not predictive of AMS.

  8. Exploring the stochastic and deterministic aspects of cyclic emission variability on a high speed spark-ignition engine

    International Nuclear Information System (INIS)

    Karvountzis-Kontakiotis, A.; Dimaratos, A.; Ntziachristos, L.; Samaras, Z.

    2017-01-01

    This study contributes to the understanding of cycle-to-cycle emissions variability (CEV) in premixed spark-ignition combustion engines. A number of experimental investigations of cycle-to-cycle combustion variability (CCV) exist in published literature; however only a handful of studies deal with CEV. This study experimentally investigates the impact of CCV on CEV of NO and CO, utilizing experimental results from a high-speed spark-ignition engine. Both CEV and CCV are shown to comprise a deterministic and a stochastic component. Results show that at maximum break torque (MBT) operation, the indicated mean effective pressure (IMEP) maximizes and its coefficient of variation (COV_I_M_E_P) minimizes, leading to minimum variation of NO. NO variability and hence mean NO levels can be reduced by more than 50% and 30%, respectively, at advanced ignition timing, by controlling the deterministic CCV using cycle resolved combustion control. The deterministic component of CEV increases at lean combustion (lambda = 1.12) and this overall increases NO variability. CEV was also found to decrease with engine load. At steady speed, increasing throttle position from 20% to 80%, decreased COV_I_M_E_P, COV_N_O and COV_C_O by 59%, 46%, and 6% respectively. Highly resolved engine control, by means of cycle-to-cycle combustion control, appears as key to limit the deterministic feature of cyclic variability and by that to overall reduce emission levels. - Highlights: • Engine emissions variability comprise both stochastic and deterministic components. • Lean and diluted combustion conditions increase emissions variability. • Advanced ignition timing enhances the deterministic component of variability. • Load increase decreases the deterministic component of variability. • The deterministic component can be reduced by highly resolved combustion control.

  9. High Resolution Spatiotemporal Climate Reconstruction and Variability in East Asia during Little Ice Age

    Science.gov (United States)

    Lin, K. H. E.; Wang, P. K.; Lee, S. Y.; Liao, Y. C.; Fan, I. C.; Liao, H. M.

    2017-12-01

    The Little ice Age (LIA) is one of the most prominent epochs in paleoclimate reconstruction of the Common Era. While the signals of LIA were generally discovered across hemispheres, wide arrays of regional variability were found, and the reconstructed anomalies were sometimes inconsistent across studies by using various proxy data or historical records. This inconsistency is mainly attributed to limited data coverage at fine resolution that can assist high-resolution climate reconstruction in the continuous spatiotemporal trends. Qing dynasty (1644-1911 CE) of China existed in the coldest period of LIA. Owing to a long-standing tradition that acquired local officials to record odds and social or meteorological events, thousands of local chronicles were left. Zhang eds. (2004) took two decades to compile all these meteorological records in a compendium, for which we then digitized and coded all records into our REACHS database system for reconstructing climate. There were in total 1,435 points (sites) in our database for over 80,000 events in the period of time. After implementing two-rounds coding check for data quality control (accuracy rate 87.2%), multiple indexes were retrieved for reconstructing annually and seasonally resolved temperature and precipitation series for North, Central, and South China. The reconstruction methods include frequency count and grading, with usage of multiple regression models to test sensitivity and to calculate correlations among several reconstructed series. Validation was also conducted through comparison with instrumental data and with other reconstructed series in previous studies. Major research results reveal interannual (3-5 years), decadal (8-12 years), and interdecadal (≈30 years) variabilities with strong regional expressions across East China. Cooling effect was not homogenously distributed in space and time. Flood and drought conditions frequently repeated but the spatiotemporal pattern was variant, indicating likely

  10. Short Communication. Using high resolution UAV imagery to estimate tree variables in Pinus pinea plantation in Portugal

    Directory of Open Access Journals (Sweden)

    Juan Guerra Hernandez

    2016-07-01

    Research highlights: The results demonstrate that tree variables can be automatically extracted from high resolution imagery. We highlight the use of UAV systems as a fast, reliable and cost‑effective technique for small scale applications. Keywords: Unmanned aerial systems (UAS; forest inventory; tree crown variables; 3D image modelling; canopy height model (CHM; object‑based image analysis (OBIA, structure‑from‑motion (SfM.

  11. Can Images Obtained With High Field Strength Magnetic Resonance Imaging Reduce Contouring Variability of the Prostate?

    International Nuclear Information System (INIS)

    Usmani, Nawaid; Sloboda, Ron; Kamal, Wafa; Ghosh, Sunita; Pervez, Nadeem; Pedersen, John; Yee, Don; Danielson, Brita; Murtha, Albert; Amanie, John; Monajemi, Tara

    2011-01-01

    Purpose: The objective of this study is to determine whether there is less contouring variability of the prostate using higher-strength magnetic resonance images (MRI) compared with standard MRI and computed tomography (CT). Methods and Materials: Forty patients treated with prostate brachytherapy were accrued to a prospective study that included the acquisition of 1.5-T MR and CT images at specified time points. A subset of 10 patients had additional 3.0-T MR images acquired at the same time as their 1.5-T MR scans. Images from each of these patients were contoured by 5 radiation oncologists, with a random subset of patients repeated to quantify intraobserver contouring variability. To minimize bias in contouring the prostate, the image sets were placed in folders in a random order with all identifiers removed from the images. Results: Although there was less interobserver contouring variability in the overall prostate volumes in 1.5-T MRI compared with 3.0-T MRI (p < 0.01), there was no significant differences in contouring variability in the different regions of the prostate between 1.5-T MRI and 3.0-T MRI. MRI demonstrated significantly less interobserver contouring variability in both 1.5-T and 3.0-T compared with CT in overall prostate volumes (p < 0.01, p = 0.01), with the greatest benefits being appreciated in the base of the prostate. Overall, there was less intraobserver contouring variability than interobserver contouring variability for all of the measurements analyzed. Conclusions: Use of 3.0-T MRI does not demonstrate a significant improvement in contouring variability compared with 1.5-T MRI, although both magnetic strengths demonstrated less contouring variability compared with CT.

  12. Discovery of a highly variable dipping ultraluminous X-ray source in M94

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Dacheng; Irwin, Jimmy A. [Department of Physics and Astronomy, University of Alabama, Box 870324, Tuscaloosa, AL 35487 (United States); Webb, Natalie A.; Barret, Didier [CNRS, IRAP, 9 avenue du Colonel Roche, BP 44346, F-31028 Toulouse Cedex 4 (France); Remillard, Ronald A., E-mail: dlin@ua.edu [MIT Kavli Institute for Astrophysics and Space Research, MIT, 70 Vassar Street, Cambridge, MA 02139-4307 (United States)

    2013-12-20

    We report the discovery of a new ultraluminous X-ray source (ULX) 2XMM J125048.6+410743 within the spiral galaxy M94. The source has been observed by ROSAT, Chandra, and XMM-Newton on several occasions, exhibiting as a highly variable persistent source or a recurrent transient with a flux variation factor of ≳100, a high duty cycle (at least ∼70%), and a peak luminosity of L {sub X} ∼ 2 × 10{sup 39} erg s{sup –1} (0.2-10 keV, absorbed). In the brightest observation, the source is similar to typical low-luminosity ULXs, with the spectrum showing a high-energy cutoff but harder than that from a standard accretion disk. There are also sporadical short dips, accompanied by spectral softening. In a fainter observation with L {sub X} ∼ 3.6 × 10{sup 38} erg s{sup –1}, the source appears softer and is probably in the thermal state seen in Galactic black hole X-ray binaries (BHBs). In an even fainter observation (L {sub X} ∼ 9 × 10{sup 37} erg s{sup –1}), the spectrum is harder again, and the source might be in the steep-power-law state or the hard state of BHBs. In this observation, the light curve might exhibit ∼7 hr (quasi-)periodic large modulations over two cycles. The source also has a possible point-like optical counterpart from Hubble Space Telescope images. In terms of the colors and the luminosity, the counterpart is probably a G8 supergiant or a compact red globular cluster containing ∼2 × 10{sup 5} K dwarfs, with some possible weak UV excess that might be ascribed to accretion activity. Thus, our source is a candidate stellar-mass BHB with a supergiant companion or with a dwarf companion residing in a globular cluster. Our study supports that some low-luminosity ULXs are supercritically accreting stellar-mass BHBs.

  13. Meteo-marine parameters for highly variable environment in coastal regions from satellite radar images

    Science.gov (United States)

    Pleskachevsky, A. L.; Rosenthal, W.; Lehner, S.

    2016-09-01

    The German Bight of the North Sea is the area with highly variable sea state conditions, intensive ship traffic and with a high density of offshore installations, e.g. wind farms in use and under construction. Ship navigation and the docking on offshore constructions is impeded by significant wave heights HS > 1.3 m. For these reasons, improvements are required in recognition and forecasting of sea state HS in the range 0-3 m. Thus, this necessitates the development of new methods to determine the distribution of meteo-marine parameters from remote sensing data with an accuracy of decimetres for HS. The operationalization of these methods then allows the robust automatic processing in near real time (NRT) to support forecast agencies by providing validations for model results. A new empirical algorithm XWAVE_C (C = coastal) for estimation of significant wave height from X-band satellite-borne Synthetic Aperture Radar (SAR) data has been developed, adopted for coastal applications using TerraSAR-X (TS-X) and Tandem-X (TD-X) satellites in the German Bight and implemented into the Sea Sate Processor (SSP) for fully automatic processing for NRT services. The algorithm is based on the spectral analysis of subscenes and the model function uses integrated image spectra parameters as well as local wind information from the analyzed subscene. The algorithm is able to recognize and remove the influence of non-sea state produced signals in the Wadden Sea areas such as dry sandbars as well as nonlinear SAR image distortions produced by e.g. short wind waves and breaking waves. Also parameters of very short waves, which are not visible in SAR images and produce only unsystematic clutter, can be accurately estimated. The SSP includes XWAVE_C, a pre-filtering procedure for removing artefacts such as ships, seamarks, buoys, offshore constructions and slicks, and an additional procedure performing a check of results based on the statistics of the whole scene. The SSP allows an

  14. MULTI-EPOCH OBSERVATIONS OF HD 69830: HIGH-RESOLUTION SPECTROSCOPY AND LIMITS TO VARIABILITY

    Energy Technology Data Exchange (ETDEWEB)

    Beichman, C. A.; Tanner, A. M.; Bryden, G.; Akeson, R. L.; Ciardi, D. R. [NASA Exoplanet Science Institute, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91125 (United States); Lisse, C. M. [Johns Hopkins University, Applied Physics Laboratory, Laurel, MD 20723 (United States); Boden, A. F. [Caltech Optical Observatories, California Institute of Technology, Pasadena, CA 91125 (United States); Dodson-Robinson, S. E.; Salyk, C. [University of Texas, Astronomy Department, Austin, TX 78712 (United States); Wyatt, M. C., E-mail: chas@pop.jpl.nasa.gov [Institute of Astronomy, University of Cambridge, Cambridge, CB3 0HA (United Kingdom)

    2011-12-10

    The main-sequence solar-type star HD 69830 has an unusually large amount of dusty debris orbiting close to three planets found via the radial velocity technique. In order to explore the dynamical interaction between the dust and planets, we have performed multi-epoch photometry and spectroscopy of the system over several orbits of the outer dust. We find no evidence for changes in either the dust amount or its composition, with upper limits of 5%-7% (1{sigma} per spectral element) on the variability of the dust spectrum over 1 year, 3.3% (1{sigma}) on the broadband disk emission over 4 years, and 33% (1{sigma}) on the broadband disk emission over 24 years. Detailed modeling of the spectrum of the emitting dust indicates that the dust is located outside of the orbits of the three planets and has a composition similar to main-belt, C-type asteroids in our solar system. Additionally, we find no evidence for a wide variety of gas species associated with the dust. Our new higher signal-to-noise spectra do not confirm our previously claimed detection of H{sub 2}O ice leading to a firm conclusion that the debris can be associated with the break-up of one or more C-type asteroids formed in the dry, inner regions of the protoplanetary disk of the HD 69830 system. The modeling of the spectral energy distribution and high spatial resolution observations in the mid-infrared are consistent with a {approx}1 AU location for the emitting material.

  15. Home ranges of lions in the Kalahari, Botswana exhibit vast sizes and high temporal variability.

    Science.gov (United States)

    Zehnder, André; Henley, Stephen; Weibel, Robert

    2018-06-01

    The central Kalahari region in Botswana is one of the few remaining ecosystems with a stable lion population. Yet, relatively little is known about the ecology of the lions there. As an entry point, home range estimations provide information about the space utilization of the studied animals. The home ranges of eight lions in this region were determined to investigate their spatial overlaps and spatiotemporal variations. We found that, except for MCP, all home range estimators yielded comparable results regarding size and shape. The home ranges of all individuals were located predominantly inside the protected reserves. Their areas were among the largest known for lions with 1131 - 4314km 2 (95%), with no significant differences between males and females. Numerous overlaps between lions of different sexes were detected, although these originate from different groups. A distance chart confirmed that most of these lions directly encountered each other once or several times. Strong temporal variations of the home ranges were observed that did not match a seasonal pattern. The exceptionally large home ranges are likely to be caused by the sparse and dynamic prey populations. Since the ungulates in the study area move in an opportunistic way, too, strong spatiotemporal home range variations emerge. This can lead to misleading home ranges. We therefore recommend clarifying the stability of the home ranges by applying several levels of temporal aggregation. The lack of strict territoriality is likely an adaptation to the variable prey base and the high energetic costs associated with defending a large area. Copyright © 2018 Elsevier GmbH. All rights reserved.

  16. High-intensity intermittent exercise and its effects on heart rate variability and subsequent strength performance

    Directory of Open Access Journals (Sweden)

    Valéria Leme Gonçalves Panissa

    2016-03-01

    Full Text Available PRUPOSE: To investigate the effects of a 5-km high-intensity interval exercise (HIIE on heart rate variability (HRV and subsequent strength performance. METHODS: nine trained males performed a control session composed of a half-squat strength exercise (4 x 80% of one repetition maximum – 1RM in isolation and 30-min, 1-, 4-, 8- and 24-h after an HIIE (1-min at the velocity peak:1-min passive recovery. All experimental sessions were performed on different days. The maximum number of repetitions and total weight lifted during the strength exercise were registered in all conditions; in addition, prior to each session, HRV were assessed [beat-to-beat intervals (RR and log-transformed of root means square of successive differences in the normal-to-normal intervals (lnRMSSD]. RESULTS: Performance in the strength exercise dropped at 30-min (31% and 1-h (19% post-HIIE concomitantly with lower values of RR (781±79 ms; 799±134 ms, respectively in the same recovery intervals compared to the control (1015±197 ms. Inferential analysis did not detect any effect of condition on lnRMSSD, however, values were lower after 30-min (3.5±0.4 ms and 1-h (3.3±0.5 ms with moderate and large effect sizes (0.9 and 1.2, respectively compared with the control condition (3.9±0.4 ms. CONCLUSION: Both RR and lnRMSSD seem to be associated with deleterious effects on strength performance, although further studies should be conducted to clarify this association.

  17. Oceanic mesoscale turbulence drives large biogeochemical interannual variability at middle and high latitudes

    Digital Repository Service at National Institute of Oceanography (India)

    Levy, M.; Resplandy, L.; Lengaigne, M.

    variability was responsible for interannual fluctuations of the subpolar phytoplankton bloom reaching 80% in amplitude and 2 weeks in timing. Over broader scales, the largest impact occurred in the subtropics with interannual variations of 20% in new...

  18. High performance continuously variable transmission control through robust-control-relevant model validation

    NARCIS (Netherlands)

    Oomen, T.A.E.; Meulen, van der S.H.

    2013-01-01

    Optimal operation of continuously variable transmissions (CVTs) is essential to meet tightening emission and fuel consumption requirements. This is achieved by accurately tracking a prescribed transmission ratio reference and simultaneously optimizing the internal efficiency of the CVT. To reduce

  19. Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip

    Directory of Open Access Journals (Sweden)

    Carr Steven M

    2007-09-01

    Full Text Available Abstract Background Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mitochondrial (mtDNA genomes. However, costs of single-species design and microarray fabrication are prohibitive. A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide sets from multiple, homologous reference genomes. Such a strategy requires that cross-hybridization between the experimental DNAs and reference oligos from the different species not interfere with the accurate recovery of species-specific data. To determine the pattern and limits of such interspecific hybridization, we compared the efficiency of sequence recovery and accuracy of SNP identification by a 15,452-base human-specific microarray challenged with human, chimpanzee, gorilla, and codfish mtDNA genomes. Results In the human genome, 99.67% of the sequence was recovered with 100.0% accuracy. Accuracy of SNP identification declines log-linearly with sequence divergence from the reference, from 0.067 to 0.247 errors per SNP in the chimpanzee and gorilla genomes, respectively. Efficiency of sequence recovery declines with the increase of the number of interspecific SNPs in the 25b interval tiled by the reference oligonucleotides. In the gorilla genome, which differs from the human reference by 10%, and in which 46% of these 25b regions contain 3 or more SNP differences from the reference, only 88% of the sequence is recoverable. In the codfish genome, which differs from the reference by > 30%, less than 4% of the sequence is recoverable, in short islands ≥ 12b that are conserved between primates and fish. Conclusion Experimental DNAs bind inefficiently to homologous reference oligonucleotide sets on a re-sequencing microarray when their sequences differ by

  20. Evaluation of Candidate Linear Variable Displacement Transducers for High Temperature Irradiations in the Advanced Test Reactor

    International Nuclear Information System (INIS)

    Knudson, D.L.; Rempe, J.L.; Daw, J.E.

    2009-01-01

    The United States (U.S.) Department of Energy (DOE) designated the Advanced Test Reactor (ATR) as a National Scientific User Facility (NSUF) in April 2007 to promote nuclear science and technology in the U.S. Given this designation, the ATR is supporting new users from universities, laboratories, and industry as they conduct basic and applied nuclear research and development to advance the nation's energy security needs. A fundamental component of the ATR NSUF program is to develop in-pile instrumentation capable of providing real-time measurements of key parameters during irradiation experiments. Dimensional change is a key parameter that must be monitored during irradiation of new materials being considered for fuel, cladding, and structures in next generation and existing nuclear reactors. Such materials can experience significant changes during high temperature irradiation. Currently, dimensional changes are determined by repeatedly irradiating a specimen for a defined period of time in the ATR and then removing it from the reactor for evaluation. The time and labor to remove, examine, and return irradiated samples for each measurement makes this approach very expensive. In addition, such techniques provide limited data (i.e., only characterizing the end state when samples are removed from the reactor) and may disturb the phenomena of interest. To address these issues, the Idaho National Laboratory (INL) recently initiated efforts to evaluate candidate linear variable displacement transducers (LVDTs) for use during high temperature irradiation experiments in typical ATR test locations. Two nuclear grade LVDT vendor designs were identified for consideration - a smaller diameter design qualified for temperatures up to 350 C and a larger design with capabilities to 500 C. Initial evaluation efforts include collecting calibration data as a function of temperature, long duration testing of LVDT response while held at high temperature, and the assessment of changes

  1. Cognitive Variability

    Science.gov (United States)

    Siegler, Robert S.

    2007-01-01

    Children's thinking is highly variable at every level of analysis, from neural and associative levels to the level of strategies, theories, and other aspects of high-level cognition. This variability exists within people as well as between them; individual children often rely on different strategies or representations on closely related problems…

  2. Lightweight Potential of Welded High-strength Steel Joints from S700 Under Constant and Variable Amplitude Loading by High-frequency Mechanical Impact (HFMI) Treatment

    OpenAIRE

    Yıldırım, Halid Can; Marquis, Gary; Sonsino, Cetin Morris

    2015-01-01

    Investigations with longitudinal stiffeners of the steel grade S700 under fully-reversed, constant amplitude loading and under variable amplitude loading with a straight-line spectrum show impressive fatigue strength improvement by high-frequency mechanical impact (HFMI) treatment. However, the degree of improvement was for variable amplitude loading lower when compared to constant amplitude loading due to local plasticity which occurs during larger load levels and consequently reduces the be...

  3. The employment of Support Vector Machine to classify high and low performance archers based on bio-physiological variables

    Science.gov (United States)

    Taha, Zahari; Muazu Musa, Rabiu; Majeed, Anwar P. P. Abdul; Razali Abdullah, Mohamad; Amirul Abdullah, Muhammad; Hasnun Arif Hassan, Mohd; Khalil, Zubair

    2018-04-01

    The present study employs a machine learning algorithm namely support vector machine (SVM) to classify high and low potential archers from a collection of bio-physiological variables trained on different SVMs. 50 youth archers with the average age and standard deviation of (17.0 ±.056) gathered from various archery programmes completed a one end shooting score test. The bio-physiological variables namely resting heart rate, resting respiratory rate, resting diastolic blood pressure, resting systolic blood pressure, as well as calories intake, were measured prior to their shooting tests. k-means cluster analysis was applied to cluster the archers based on their scores on variables assessed. SVM models i.e. linear, quadratic and cubic kernel functions, were trained on the aforementioned variables. The k-means clustered the archers into high (HPA) and low potential archers (LPA), respectively. It was demonstrated that the linear SVM exhibited good accuracy with a classification accuracy of 94% in comparison the other tested models. The findings of this investigation can be valuable to coaches and sports managers to recognise high potential athletes from the selected bio-physiological variables examined.

  4. High Altitude Affects Nocturnal Non-linear Heart Rate Variability: PATCH-HA Study

    Directory of Open Access Journals (Sweden)

    Christopher J. Boos

    2018-04-01

    Full Text Available Background: High altitude (HA exposure can lead to changes in resting heart rate variability (HRV, which may be linked to acute mountain sickness (AMS development. Compared with traditional HRV measures, non-linear HRV appears to offer incremental and prognostic data, yet its utility and relationship to AMS have been barely examined at HA. This study sought to examine this relationship at terrestrial HA.Methods: Sixteen healthy British military servicemen were studied at baseline (800 m, first night and over eight consecutive nights, at a sleeping altitude of up to 3600 m. A disposable cardiac patch monitor was used, to record the nocturnal cardiac inter-beat interval data, over 1 h (0200–0300 h, for offline HRV assessment. Non-linear HRV measures included Sample entropy (SampEn, the short (α1, 4–12 beats and long-term (α2, 13–64 beats detrend fluctuation analysis slope and the correlation dimension (D2. The maximal rating of perceived exertion (RPE, during daily exercise, was assessed using the Borg 6–20 RPE scale.Results: All subjects completed the HA exposure. The average age of included subjects was 31.4 ± 8.1 years. HA led to a significant fall in SpO2 and increase in heart rate, LLS and RPE. There were no significant changes in the ECG-derived respiratory rate or in any of the time domain measures of HRV during sleep. The only notable changes in frequency domain measures of HRV were an increase in LF and fall in HFnu power at the highest altitude. Conversely, SampEn, SD1/SD2 and D2 all fell, whereas α1 and α2 increased (p < 0.05. RPE inversely correlated with SD1/SD2 (r = -0.31; p = 0.002, SampEn (r = -0.22; p = 0.03, HFnu (r = -0.27; p = 0.007 and positively correlated with LF (r = 0.24; p = 0.02, LF/HF (r = 0.24; p = 0.02, α1 (r = 0.32; p = 0.002 and α2 (r = 0.21; p = 0.04. AMS occurred in 7/16 subjects (43.8% and was very mild in 85.7% of cases. HRV failed to predict AMS.Conclusion: Non-linear HRV is more sensitive to the

  5. A Capillary-Based Static Phase Separator for Highly Variable Wetting Conditions

    Science.gov (United States)

    Thomas, Evan A.; Graf, John C.; Weislogel, Mark M.

    2010-01-01

    The invention, a static phase separator (SPS), uses airflow and capillary wetting characteristics to passively separate a two-phase (liquid and air) flow. The device accommodates highly variable liquid wetting characteristics. The resultant design allows for a range of wetting properties from about 0 to over 90 advancing contact angle, with frequent complete separation of liquid from gas observed when using appropriately scaled test conditions. Additionally, the design accommodates a range of air-to-liquid flow-rate ratios from only liquid flow to over 200:1 air-to-liquid flow rate. The SPS uses a helix input section with an ice-cream-cone-shaped constant area cross section (see figure). The wedge portion of the cross section is on the outer edge of the helix, and collects the liquid via centripetal acceleration. The helix then passes into an increasing cross-sectional area vane region. The liquid in the helix wedge is directed into the top of capillary wedges in the liquid containment section. The transition from diffuser to containment section includes a 90 change in capillary pumping direction, while maintaining inertial direction. This serves to impinge the liquid into the two off-center symmetrical vanes by the airflow. Rather than the airflow serving to shear liquid away from the capillary vanes, the design allows for further penetration of the liquid into the vanes by the air shear. This is also assisted by locating the air exit ports downstream of the liquid drain port. Additionally, any droplets not contained in the capillary vanes are re-entrained downstream by a third opposing capillary vane, which directs liquid back toward the liquid drain port. Finally, the dual air exit ports serve to slow the airflow down, and to reduce the likelihood of shear. The ports are stove-piped into the cavity to form an unfriendly capillary surface for a wetting fluid to carryover. The liquid drain port is located at the start of the containment region, allowing for

  6. Hydroclimate variability of High Arctic Svalbard during the Holocene inferred from hydrogen isotopes of leaf waxes

    Science.gov (United States)

    Balascio, Nicholas L.; D'Andrea, William J.; Gjerde, Marthe; Bakke, Jostein

    2018-03-01

    The response of the Arctic hydrologic cycle to global warming includes changes in precipitation patterns and moisture availability associated with variable sea ice extent and modes of atmospheric circulation. Reconstructions of past hydroclimate changes help constrain the natural range of these systems, identify the manners in which they respond to different forcing mechanisms, and reveal their connections to other components of the climate system, all of which lead to a better understanding of present and future changes. Here we examine hydroclimate changes during the Holocene in the High Arctic archipelago of Svalbard by reconstructing the isotopic composition of precipitation. We measured the hydrogen isotopic composition (δD values) of leaf wax compounds (n-alkanes; C25-C31) in a sediment core from Lake Hakluytvatnet on the island of Amsterdamøya, northwest Spitsbergen. We interpret δD values of mid-chain (C25) and long-chain (C29, C31) length n-alkanes to represent changes in the isotopic composition of lake water and precipitation over the last 12.9 ka. After deglaciation of the catchment, water supply became restricted and the lake experienced significant evaporative isotopic enrichment indicating warmer conditions from 12.8 to 7.5 ka. The isotope values suggest an increase in the delivery of moisture from warmer sub-polar air masses between 12.8 and 9.5 ka, followed by generally warm, but unstable conditions between 9.5 and 7.5 ka, possibly indicating a response to meltwater forcing. Sedimentary evidence indicates a hiatus in deposition c. 7.5-5.0 ka, likely as a result of desiccation of the lake. At c. 5.0 ka lacustrine sedimentation resumed and over the last 5 ka there was a progressive increase in the influence of polar air masses and colder conditions, which culminated in an abrupt shift to colder conditions at c. 1.8 ka. This late Holocene cooling ended c. 0.18 ka, when isotopic data indicate warmer conditions and greater influence of moisture

  7. High-fidelity teleportation of continuous-variable quantum States using delocalized single photons

    DEFF Research Database (Denmark)

    Andersen, Ulrik L; Ralph, Timothy C

    2013-01-01

    Traditional continuous-variable teleportation can only approach unit fidelity in the limit of an infinite (and unphysical) amount of squeezing. We describe a new method for continuous-variable teleportation that approaches unit fidelity with finite resources. The protocol is not based on squeezed...... states as in traditional teleportation but on an ensemble of single photon entangled states. We characterize the teleportation scheme with coherent states, mesoscopic superposition states, and two-mode squeezed states and we find several situations in which near-unity teleportation fidelity can...

  8. Inferring the demographic history of African farmers and pygmy hunter-gatherers using a multilocus resequencing data set.

    Directory of Open Access Journals (Sweden)

    Etienne Patin

    2009-04-01

    Full Text Available The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunter-gatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunter-gatherers of Africa. They dwell in equatorial rainforests and are characterized by their short mean stature. However, little is known about the chronology of the demographic events-size changes, population splits, and gene flow--ultimately giving rise to contemporary Pygmy (Western and Eastern groups and neighboring agricultural populations. We studied the branching history of Pygmy hunter-gatherers and agricultural populations from Africa and estimated separation times and gene flow between these populations. We resequenced 24 independent noncoding regions across the genome, corresponding to a total of approximately 33 kb per individual, in 236 samples from seven Pygmy and five agricultural populations dispersed over the African continent. We used simulation-based inference to identify the historical model best fitting our data. The model identified included the early divergence of the ancestors of Pygmy hunter-gatherers and farming populations approximately 60,000 years ago, followed by a split of the Pygmies' ancestors into the Western and Eastern Pygmy groups approximately 20,000 years ago. Our findings increase knowledge of the history of the peopling of the African continent in a region lacking archaeological data. An appreciation of the demographic and adaptive history of African populations with different modes of subsistence should improve our understanding of the influence of human lifestyles on genome diversity.

  9. Variables that impact the implementation of project-based learning in high school science

    Science.gov (United States)

    Cunningham, Kellie

    Wagner and colleagues (2006) state the mediocrity of teaching and instructional leadership is the central problem that must be addressed if we are to improve student achievement. Educational reform efforts have been initiated to improve student performance and to hold teachers and school leaders accountable for student achievement (Wagner et al., 2006). Specifically, in the area of science, goals for improving student learning have led reformers to establish standards for what students should know and be able to do, as well as what instructional methods should be used. Key concepts and principles have been identified for student learning. Additionally, reformers recommend student-centered, inquiry-based practices that promote a deep understanding of how science is embedded in the everyday world. These new approaches to science education emphasize inquiry as an essential element for student learning (Schneider, Krajcik, Marx, & Soloway, 2002). Project-based learning (PBL) is an inquiry-based instructional approach that addresses these recommendations for science education reform. The objective of this research was to study the implementation of project-based learning (PBL) in an urban school undergoing reform efforts and identify the variables that positively or negatively impacted the PBL implementation process and its outcomes. This study responded to the need to change how science is taught by focusing on the implementation of project-based learning as an instructional approach to improve student achievement in science and identify the role of both school leaders and teachers in the creation of a school environment that supports project-based learning. A case study design using a mixed-method approach was used in this study. Data were collected through individual interviews with the school principal, science instructional coach, and PBL facilitator. A survey, classroom observations and interviews involving three high school science teachers teaching grades 9

  10. High Variability Is a Defining Component of Mediterranean-Climate Rivers and Their Biota

    Directory of Open Access Journals (Sweden)

    Núria Cid

    2017-01-01

    Full Text Available Variability in flow as a result of seasonal precipitation patterns is a defining element of streams and rivers in Mediterranean-climate regions of the world and strongly influences the biota of these unique systems. Mediterranean-climate areas include the Mediterranean Basin and parts of Australia, California, Chile, and South Africa. Mediterranean streams and rivers can experience wet winters and consequent floods to severe droughts, when intermittency in otherwise perennial systems can occur. Inter-annual variation in precipitation can include multi-year droughts or consecutive wet years. Spatial variation in patterns of precipitation (rain vs. snow combined with topographic variability lead to spatial variability in hydrologic patterns that influence populations and communities. Mediterranean streams and rivers are global biodiversity hotspots and are particularly vulnerable to human impacts. Biomonitoring, conservation efforts, and management responses to climate change require approaches that account for spatial and temporal variability (including both intra- and inter-annual. The importance of long-term data sets for understanding and managing these systems highlights the need for sustained and coordinated research efforts in Mediterranean-climate streams and rivers.

  11. High-Q Variable Bandwidth Passive Filters for Software Defined Radio

    NARCIS (Netherlands)

    Arkesteijn, V.J.; Klumperink, Eric A.M.; Nauta, Bram

    2001-01-01

    An important aspect of Software Defined Radio is the ability to define the bandwidth of the filter that selects the desired channel. This paper describes a technique for channel filtering, in which two passive filters are combined to obtain a variable bandwidth. Passive filters have the advantage of

  12. High-Q variable bandwidth passive filters for Software Defined Radio

    NARCIS (Netherlands)

    Arkesteijn, V.J.; Klumperink, Eric A.M.; Nauta, Bram

    An important aspect of Software Defined Radio is the ability to define the bandwidth of the filter that selects the desired channel. This paper describes a technique for channel filtering, in which two passive filters are combined to obtain a variable bandwidth. Passive filters have the advantage of

  13. A Robust Supervised Variable Selection for Noisy High-Dimensional Data

    Czech Academy of Sciences Publication Activity Database

    Kalina, Jan; Schlenker, Anna

    2015-01-01

    Roč. 2015, Article 320385 (2015), s. 1-10 ISSN 2314-6133 R&D Projects: GA ČR GA13-17187S Institutional support: RVO:67985807 Keywords : dimensionality reduction * variable selection * robustness Subject RIV: BA - General Mathematics Impact factor: 2.134, year: 2015

  14. Still Motivated to Teach? A Study of School Context Variables, Stress and Job Satisfaction among Teachers in Senior High School

    Science.gov (United States)

    Skaalvik, Einar M.; Skaalvik, Sidsel

    2017-01-01

    This study explored how teachers' working conditions or school context variables (job demands and job resources) were related to their teaching self-concept, teacher burnout, job satisfaction, and motivation to leave the teaching profession among teachers in Norwegian senior high school. Participants were 546 teachers in three counties in central…

  15. The predictive value of baseline variables in the treatment of benign prostatic hyperplasia using high-energy transurethral microwave thermotherapy

    NARCIS (Netherlands)

    D'Ancona, F. C.; Francisca, E. A.; Hendriks, J. C.; Debruyne, F. M.; de la Rosette, J. J.

    1998-01-01

    To evaluate the combination of patient age, prostate size, grade of outlet obstruction and total amount of energy, all independent predictive variables of treatment outcome in patients with lower urinary tract symptoms (LUTS) and benign prostatic hyperplasia (BPH) treated with high-energy

  16. High-resolution rock-magnetic variability in shallow marine sediment: a sensitive paleoclimatic metronome

    Science.gov (United States)

    Arai, Kohsaku; Sakai, Hideo; Konishi, Kenji

    1997-05-01

    An outer shelf deposit in central Japan centered on the Olduvai normal polarity event in the reversed Matuyama chron reveals a close correlation of both the magnetic susceptibility and remanent intensity with the sedimentary cyclicities apparent in lithologies and molluscan assemblages. Two sedimentary cycles are characterized by distinctly similar, but double-peaked magnetic cyclicities. The rock-magnetic variability is primarily attributed to the relative abundance of terrigenous magnetic minerals, and the double peak of the variability is characterized by the concentration of finer-grained magnetic minerals. The concentration is suspected to be controlled by both climatic change and shifting proximity of the shoreline as a function of rise and fall of the sea level due to glacio-eustasy. Rock-magnetic study reveals the record of a 21 ka period of orbital precession cycles within the sedimentary cyclicity attributable to a 41 ka period of orbital obliquity forcing.

  17. A High-Linearity Low-Noise Amplifier with Variable Bandwidth for Neural Recoding Systems

    Science.gov (United States)

    Yoshida, Takeshi; Sueishi, Katsuya; Iwata, Atsushi; Matsushita, Kojiro; Hirata, Masayuki; Suzuki, Takafumi

    2011-04-01

    This paper describes a low-noise amplifier with multiple adjustable parameters for neural recording applications. An adjustable pseudo-resistor implemented by cascade metal-oxide-silicon field-effect transistors (MOSFETs) is proposed to achieve low-signal distortion and wide variable bandwidth range. The amplifier has been implemented in 0.18 µm standard complementary metal-oxide-semiconductor (CMOS) process and occupies 0.09 mm2 on chip. The amplifier achieved a selectable voltage gain of 28 and 40 dB, variable bandwidth from 0.04 to 2.6 Hz, total harmonic distortion (THD) of 0.2% with 200 mV output swing, input referred noise of 2.5 µVrms over 0.1-100 Hz and 18.7 µW power consumption at a supply voltage of 1.8 V.

  18. Graphical user interface for input output characterization of single variable and multivariable highly nonlinear systems

    Directory of Open Access Journals (Sweden)

    Shahrukh Adnan Khan M. D.

    2017-01-01

    Full Text Available This paper presents a Graphical User Interface (GUI software utility for the input/output characterization of single variable and multivariable nonlinear systems by obtaining the sinusoidal input describing function (SIDF of the plant. The software utility is developed on MATLAB R2011a environment. The developed GUI holds no restriction on the nonlinearity type, arrangement and system order; provided that output(s of the system is obtainable either though simulation or experiments. An insight to the GUI and its features are presented in this paper and example problems from both single variable and multivariable cases are demonstrated. The formulation of input/output behavior of the system is discussed and the nucleus of the MATLAB command underlying the user interface has been outlined. Some of the industries that would benefit from this software utility includes but not limited to aerospace, defense technology, robotics and automotive.

  19. Highly variable aerodynamic roughness length (z0) for a hummocky debris-covered glacier

    Science.gov (United States)

    Miles, Evan S.; Steiner, Jakob F.; Brun, Fanny

    2017-08-01

    The aerodynamic roughness length (z0) is an essential parameter in surface energy balance studies, but few literature values exist for debris-covered glaciers. We use microtopographic and aerodynamic methods to assess the spatial variability of z0 for Lirung Glacier, Nepal. We apply structure from motion to produce digital elevation models for three nested domains: five 1 m2 plots, a 21,300 m2 surface depression, and the lower 550,000 m2 of the debris-mantled tongue. Wind and temperature sensor towers were installed in the vicinity of the plots within the surface depression in October 2014. We calculate z0 according to a variety of transect-based microtopographic parameterizations for each plot, then develop a grid version of the algorithms by aggregating data from all transects. This grid approach is applied to the surface depression digital elevation model to characterize z0 spatial variability. The algorithms reproduce the same variability among transects and plots, but z0 estimates vary by an order of magnitude between algorithms. Across the study depression, results from different algorithms are strongly correlated. Using Monin-Obukov similarity theory, we derive z0 values from the meteorological data. Using different stability criteria, we derive median values of z0 between 0.03 m and 0.05 m, but with considerable uncertainty due to the glacier's complex topography. Considering estimates from these algorithms, results suggest that z0 varies across Lirung Glacier between ˜0.005 m (gravels) to ˜0.5 m (boulders). Future efforts should assess the importance of such variable z0 values in a distributed energy balance model.

  20. A study of applying variable valve timing to highly rated diesel engines

    Energy Technology Data Exchange (ETDEWEB)

    Stone, C R; Leonard, H J [comps.; Brunel Univ., Uxbridge (United Kingdom); Charlton, S J [comp.; Bath Univ. (United Kingdom)

    1992-10-01

    The main objective of the research was to use Simulation Program for Internal Combustion Engines (SPICE) to quantify the potential offered by Variable Valve Timing (VVT) in improving engine performance. A model has been constructed of a particular engine using SPICE. The model has been validated with experimental data, and it has been shown that accurate predictions are made when the valve timing is changed. (author)

  1. Joint High-Dimensional Bayesian Variable and Covariance Selection with an Application to eQTL Analysis

    KAUST Repository

    Bhadra, Anindya

    2013-04-22

    We describe a Bayesian technique to (a) perform a sparse joint selection of significant predictor variables and significant inverse covariance matrix elements of the response variables in a high-dimensional linear Gaussian sparse seemingly unrelated regression (SSUR) setting and (b) perform an association analysis between the high-dimensional sets of predictors and responses in such a setting. To search the high-dimensional model space, where both the number of predictors and the number of possibly correlated responses can be larger than the sample size, we demonstrate that a marginalization-based collapsed Gibbs sampler, in combination with spike and slab type of priors, offers a computationally feasible and efficient solution. As an example, we apply our method to an expression quantitative trait loci (eQTL) analysis on publicly available single nucleotide polymorphism (SNP) and gene expression data for humans where the primary interest lies in finding the significant associations between the sets of SNPs and possibly correlated genetic transcripts. Our method also allows for inference on the sparse interaction network of the transcripts (response variables) after accounting for the effect of the SNPs (predictor variables). We exploit properties of Gaussian graphical models to make statements concerning conditional independence of the responses. Our method compares favorably to existing Bayesian approaches developed for this purpose. © 2013, The International Biometric Society.

  2. The identification of high potential archers based on relative psychological coping skills variables: A Support Vector Machine approach

    Science.gov (United States)

    Taha, Zahari; Muazu Musa, Rabiu; Majeed, A. P. P. Abdul; Razali Abdullah, Mohamad; Aizzat Zakaria, Muhammad; Muaz Alim, Muhammad; Arif Mat Jizat, Jessnor; Fauzi Ibrahim, Mohamad

    2018-03-01

    Support Vector Machine (SVM) has been revealed to be a powerful learning algorithm for classification and prediction. However, the use of SVM for prediction and classification in sport is at its inception. The present study classified and predicted high and low potential archers from a collection of psychological coping skills variables trained on different SVMs. 50 youth archers with the average age and standard deviation of (17.0 ±.056) gathered from various archery programmes completed a one end shooting score test. Psychological coping skills inventory which evaluates the archers level of related coping skills were filled out by the archers prior to their shooting tests. k-means cluster analysis was applied to cluster the archers based on their scores on variables assessed. SVM models, i.e. linear and fine radial basis function (RBF) kernel functions, were trained on the psychological variables. The k-means clustered the archers into high psychologically prepared archers (HPPA) and low psychologically prepared archers (LPPA), respectively. It was demonstrated that the linear SVM exhibited good accuracy and precision throughout the exercise with an accuracy of 92% and considerably fewer error rate for the prediction of the HPPA and the LPPA as compared to the fine RBF SVM. The findings of this investigation can be valuable to coaches and sports managers to recognise high potential athletes from the selected psychological coping skills variables examined which would consequently save time and energy during talent identification and development programme.

  3. A highly variable segment of human subterminal 16p reveals a history of population growth for modern humans outside Africa

    Science.gov (United States)

    Alonso, Santos; Armour, John A. L.

    2001-01-01

    We have sequenced a highly polymorphic subterminal noncoding region from human chromosome 16p13.3, flanking the 5′ end of the hypervariable minisatellite MS205, in 100 chromosomes sampled from different African and Euroasiatic populations. Coalescence analysis indicates that the time to the most recent common ancestor (approximately 1 million years) predates the appearance of anatomically modern human forms. The root of the network describing this variability lies in Africa. African populations show a greater level of diversity and deeper branches. Most Euroasiatic variability seems to have been generated after a recent out-of-Africa range expansion. A history of population growth is the most likely scenario for the Euroasiatic populations. This pattern of nuclear variability can be reconciled with inferences based on mitochondrial DNA. PMID:11158547

  4. Variability Extraction and Synthesis via Multi-Resolution Analysis using Distribution Transformer High-Speed Power Data

    Energy Technology Data Exchange (ETDEWEB)

    Chamana, Manohar [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Mather, Barry A [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-10-19

    A library of load variability classes is created to produce scalable synthetic data sets using historical high-speed raw data. These data are collected from distribution monitoring units connected at the secondary side of a distribution transformer. Because of the irregular patterns and large volume of historical high-speed data sets, the utilization of current load characterization and modeling techniques are challenging. Multi-resolution analysis techniques are applied to extract the necessary components and eliminate the unnecessary components from the historical high-speed raw data to create the library of classes, which are then utilized to create new synthetic load data sets. A validation is performed to ensure that the synthesized data sets contain the same variability characteristics as the training data sets. The synthesized data sets are intended to be utilized in quasi-static time-series studies for distribution system planning studies on a granular scale, such as detailed PV interconnection studies.

  5. Low- and high-anxious hypermobile Ehlers-Danlos syndrome patients: comparison of psychosocial and health variables.

    Science.gov (United States)

    Baeza-Velasco, Carolina; Bourdon, Caroline; Montalescot, Lucile; de Cazotte, Cécile; Pailhez, Guillem; Bulbena, Antonio; Hamonet, Claude

    2018-05-01

    Despite the frequent co-ocurrence of hypermobile Ehler-Danlos syndrome (hEDS) and pathological anxiety, little is known about the psychosocial and health implications of such comorbidity. Our aim was to explore the association between high levels of anxiety and psychosocial (catastrophizing, kinesiophobia, somatosensory amplification, social support and functioning), health (pain, fatigue, BMI, tobacco/alcohol use, depression, diagnosis delay, general health), and sociodemographic factors in people with hEDS. In this cross-sectional study, 80 hEDS patients were divided into two groups according to self-reported anxiety levels: low and high. Psychosocial, sociodemographic and health variables were compared between the groups. Forty-one participants reported a high level of anxiety (51.2%). No differences were found in the sociodemographic variables between high-anxious and low-anxious patients. The percentage of participants with severe fatigue and high depressive symptomatology was significantly higher in the high-anxious group (80.5 vs 56.4; 26.8 vs 12.8%, respectively). High-anxious hEDS patients also showed significantly higher levels of pain catastrophizing, somatosensory amplification as well as a poorer social functioning and general health. Multivariate analyses showed that somatosensory amplification, pain catastrophizing and poor social functioning are variables that increase the probability of belonging to the high-anxious group. Despite limitations, this first study comparing high-anxious versus low-anxious hEDS patients with respect to health aspects, highlight the importance of considering the psychosocial factors (many susceptible to modification), to improve the adjustment to this chronic condition and provide support to those affected through a biopsychosocial approach.

  6. Variability of residual stresses and superposition effect in multipass grinding of high-carbon high-chromium steel

    Science.gov (United States)

    Karabelchtchikova, Olga; Rivero, Iris V.

    2005-02-01

    The distribution of residual stresses (RS) and surface integrity generated in heat treatment and subsequent multipass grinding was investigated in this experimental study to examine the source of variability and the nature of the interactions of the experimental factors. A nested experimental design was implemented to (a) compare the sources of the RS variability, (b) to examine RS distribution and tensile peak location due to experimental factors, and (c) to analyze the superposition relationship in the RS distribution due to multipass grinding technique. To characterize the material responses, several techniques were used, including microstructural analysis, hardness-toughness and roughness examinations, and retained austenite and RS measurements using x-ray diffraction. The causality of the RS was explained through the strong correlation of the surface integrity characteristics and RS patterns. The main sources of variation were the depth of the RS distribution and the multipass grinding technique. The grinding effect on the RS was statistically significant; however, it was mostly predetermined by the preexisting RS induced in heat treatment. Regardless of the preceding treatments, the effect of the multipass grinding technique exhibited similar RS patterns, which suggests the existence of the superposition relationship and orthogonal memory between the passes of the grinding operation.

  7. High-frequency paleoclimatic variability: a spectral analysis of the Vostok ice-core isotopic record

    Energy Technology Data Exchange (ETDEWEB)

    Yiou, P.; Genthon, C.; Jouzel, J.; Le Treut, H.; Lorius, C.; Ghil, M.; Korotkevich, Y.S.

    1988-01-01

    This paper uses a recently analysed isotopic record from an ice core drilled at the Soviet Antartic Station VOSTOK, representing a total time span of about 160,000 years. Results obtained show the existence of a significative climatic variability at the time scale of 10,000 years and below. The many spectral peaks appear to be approximate linear combination of a little number among them, a clear indication of the non linear nature of climate fluctuations at these ''short'' time scales.

  8. Investigation of Acoustic Vector Sensor Data Processing in the Presence of Highly Variable Bathymetry

    Science.gov (United States)

    2014-06-01

    shelf 10 region to the north of the canyon. The impact of this 3-dimensional (3D) variable bathymetry, which may be combined with the effects of...weaker arrivals at large negative angles, consistent with the earliest bottom reflections on the left. The impact of the bottom-path reflections from...nzout*(nrout+1)*ny))),’bof’); for ifr =1:64, for ir=1:nrout+1, for iy=1:ny, data=fread(fid3,2*nzout,’float32’); fwrite(fid,data

  9. Climate drives inter-annual variability in probability of high severity fire occurrence in the western United States

    Science.gov (United States)

    Keyser, Alisa; Westerling, Anthony LeRoy

    2017-05-01

    A long history of fire suppression in the western United States has significantly changed forest structure and ecological function, leading to increasingly uncharacteristic fires in terms of size and severity. Prior analyses of fire severity in California forests showed that time since last fire and fire weather conditions predicted fire severity very well, while a larger regional analysis showed that topography and climate were important predictors of high severity fire. There has not yet been a large-scale study that incorporates topography, vegetation and fire-year climate to determine regional scale high severity fire occurrence. We developed models to predict the probability of high severity fire occurrence for the western US. We predict high severity fire occurrence with some accuracy, and identify the relative importance of predictor classes in determining the probability of high severity fire. The inclusion of both vegetation and fire-year climate predictors was critical for model skill in identifying fires with high fractional fire severity. The inclusion of fire-year climate variables allows this model to forecast inter-annual variability in areas at future risk of high severity fire, beyond what slower-changing fuel conditions alone can accomplish. This allows for more targeted land management, including resource allocation for fuels reduction treatments to decrease the risk of high severity fire.

  10. Investigation of High School Students' Attitude and Anxiety Levels towards Mathematics in Terms of Some Variables

    Science.gov (United States)

    Dursun, Semsettin

    2015-01-01

    The purpose of this study was to investigate Turkish high school students' attitude and anxiety levels towards mathematics. For this purpose, the methodology employed in this study was a descriptive study. The participants of the study consisted of 361 high school students from three different high school types from a province in Turkey during…

  11. High vacuum test of the dynamic components of the cyclotron dee chamber at the 224 cm variable energy cyclotron

    International Nuclear Information System (INIS)

    Chintalapudi, S.N.; Bandopadhyay, D.K.; Ghosh, D.K.; Gowariker, S.R.

    1979-01-01

    The 224 cm Variable Energy Cyclotron constructed and commissioned at Calcutta comprises a number of dynamic components in the high vacuum Dee Chamber. The static and dynamic conditions of these components have to be tested for high vacuum worthiness prior to their installation in the Dee Tank. A special set up was fabricated and used for simulating the Dee Chamber conditions and testing the components. A high vacuum of the order of 1 x 10 -5 torr was achieved under both dynamic and static conditions with and without coolant hydraulic pressures. The details of the set up, methods employed for the various tests carried out and the results obtained are described. (auth.)

  12. Investigation into the Effects of the Variable Displacement Mechanism on Swash Plate Oscillation in High-Speed Piston Pumps

    Directory of Open Access Journals (Sweden)

    Xu Fang

    2018-04-01

    Full Text Available High-speed, pressure-compensated variable displacement piston pumps are widely used in aircraft hydraulic systems for their high power density. The swash plate is controlled by the pressure-compensated valve, which uses pressure feedback so that the instantaneous output flow of the pump is exactly enough to maintain a presetting pressure. The oscillation of the swash plate is one of the major excitation sources in the high-speed piston pump, which may cause lower efficiency, shorter service life, and even serious damage. This paper presents an improved model to investigate the influence of the variable displacement mechanism on the swash plate oscillation and introduces some feasible ways to reduce oscillation of the swash plate. Most of the variable structural parameters of the variable displacement mechanism are taken into consideration, and their influences on swash plate oscillation are discussed in detail. The influence of the load pipe on the oscillation of the swash plate is considered in the improved model. A test rig is built and similarities between the experiments and simulated results prove that the simulation model can effectively predict the variable displacement mechanism state. The simulation results show that increasing the volume of the outlet chamber, the spring stiffness of the control valve, the action area of the actuator piston, and offset distance of the actuator piston can significantly reduce the oscillation amplitude of the swash plate. Furthermore, reducing the diameter of the control valve spool and the dead volume of the actuator piston chamber can also have a positive effect on oscillation amplitude reduction.

  13. High glucose variability is associated with poor neurodevelopmental outcomes in neonatal hypoxic ischemic encephalopathy.

    Science.gov (United States)

    Al Shafouri, N; Narvey, M; Srinivasan, G; Vallance, J; Hansen, G

    2015-01-01

    In neonatal hypoxic ischemic encephalopathy (HIE), hypo- and hyperglycemia have been associated with poor outcomes. However, glucose variability has not been reported in this population. To examine the association between serum glucose variability within the first 24 hours and two-year neurodevelopmental outcomes in neonates cooled for HIE. In this retrospective cohort study, glucose, clinical and demographic data were documented from 23 term newborns treated with whole body therapeutic hypothermia. Severe neurodevelopmental outcomes from planned two-year assessments were defined as the presence of any one of the following: Gross Motor Function Classification System levels 3 to 5, Bayley III Motor Standard Score neurodevelopmental outcomes from 8 of 23 patients were considered severe, and this group demonstrated a significant increase of mean absolute glucose (MAG) change (-0.28 to -0.03, 95% CI, p = 0.032). There were no significant differences between outcome groups with regards to number of patients with hyperglycemic means, one or multiple hypo- or hyperglycemic measurement(s). There were also no differences between both groups with mean glucose, although mean glucose standard deviation was approaching significance. Poor neurodevelopmental outcomes in whole body cooled HIE neonates are significantly associated with MAG changes. This information may be relevant for prognostication and potential management strategies.

  14. Different histories of two highly variable LTR retrotransposons in sunflower species.

    Science.gov (United States)

    Mascagni, Flavia; Cavallini, Andrea; Giordani, Tommaso; Natali, Lucia

    2017-11-15

    In the Helianthus genus, very large intra- and interspecific variability related to two specific retrotransposons of Helianthus annuus (Helicopia and SURE) exists. When comparing these two sequences to sunflower sequence databases recently produced by our lab, the Helicopia family was shown to belong to the Maximus/SIRE lineage of the Sirevirus genus of the Copia superfamily, whereas the SURE element (whose superfamily was not even previously identified) was classified as a Gypsy element of the Ogre/Tat lineage of the Metavirus genus. Bioinformatic analysis of the two retrotransposon families revealed their genomic abundance and relative proliferation timing. The genomic abundance of these families differed significantly among 12 Helianthus species. The ratio between the abundance of long terminal repeats and their reverse transcriptases suggested that the SURE family has relatively more solo long terminal repeats than does Helicopia. Pairwise comparisons of Illumina reads encoding the reverse transcriptase domain indicated that SURE amplification may have occurred more recently than that of Helicopia. Finally, the analysis of population structure based on the SURE and Helicopia polymorphisms of 32 Helianthus species evidenced two subpopulations, which roughly corresponded to species of the Helianthus and Divaricati/Ciliares sections. However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when studying genome evolution. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. A high-peak-power passively Q-switched composite variable-cut vanadate laser

    International Nuclear Information System (INIS)

    Sirotkin, A A

    2014-01-01

    We present laser sources based on a novel method of controlling spectral parameters in diode-pumped vanadate lasers. Angular dependences of the luminescence intensity of Stark transitions at the 4F3/2‒4I11/2 transition in vanadate crystals are investigated. The operation of diode-pumped passively Q-switched composite variable-cut (θ = var, φ = 0) YVO 4 –Nd 3+  : YVO 4 lasers with Cr 4+  : YAG saturable absorber is demonstrated (the narrowest pulse of 2 ns with the highest peak power of 24.3 kW). In the experiment, an efficient self-Raman laser was realized, based on the multifunctional variable-cut (θ = 25°, φ = 0) YVO 4 –Nd 3+  : YVO 4 laser crystal with the passive Q-switched. (letters)

  16. Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing.

    Directory of Open Access Journals (Sweden)

    Zhen-Hui Wang

    Full Text Available BACKGROUND: Hybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizanialatifolia Griseb. in general, 131 millions 90 base pair (bp paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs and 17,839 homozygous insertions/deletions (indels were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a

  17. Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data.

    Science.gov (United States)

    Liu, San-Xu; Hou, Wei; Zhang, Xue-Yan; Peng, Chang-Jun; Yue, Bi-Song; Fan, Zhen-Xin; Li, Jing

    2018-07-18

    The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (lobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (Pgenome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.

  18. Pooled Resequencing of 122 Ulcerative Colitis Genes in a Large Dutch Cohort Suggests Population-Specific Associations of Rare Variants in MUC2.

    Science.gov (United States)

    Visschedijk, Marijn C; Alberts, Rudi; Mucha, Soren; Deelen, Patrick; de Jong, Dirk J; Pierik, Marieke; Spekhorst, Lieke M; Imhann, Floris; van der Meulen-de Jong, Andrea E; van der Woude, C Janneke; van Bodegraven, Adriaan A; Oldenburg, Bas; Löwenberg, Mark; Dijkstra, Gerard; Ellinghaus, David; Schreiber, Stefan; Wijmenga, Cisca; Rivas, Manuel A; Franke, Andre; van Diemen, Cleo C; Weersma, Rinse K

    2016-01-01

    Genome-wide association studies have revealed several common genetic risk variants for ulcerative colitis (UC). However, little is known about the contribution of rare, large effect genetic variants to UC susceptibility. In this study, we performed a deep targeted re-sequencing of 122 genes in Dutch UC patients in order to investigate the contribution of rare variants to the genetic susceptibility to UC. The selection of genes consists of 111 established human UC susceptibility genes and 11 genes that lead to spontaneous colitis when knocked-out in mice. In addition, we sequenced the promoter regions of 45 genes where known variants exert cis-eQTL-effects. Targeted pooled re-sequencing was performed on DNA of 790 Dutch UC cases. The Genome of the Netherlands project provided sequence data of 500 healthy controls. After quality control and prioritization based on allele frequency and pathogenicity probability, follow-up genotyping of 171 rare variants was performed on 1021 Dutch UC cases and 1166 Dutch controls. Single-variant association and gene-based analyses identified an association of rare variants in the MUC2 gene with UC. The associated variants in the Dutch population could not be replicated in a German replication cohort (1026 UC cases, 3532 controls). In conclusion, this study has identified a putative role for MUC2 on UC susceptibility in the Dutch population and suggests a population-specific contribution of rare variants to UC.

  19. Rapid Genome-wide Single Nucleotide Polymorphism Discovery in Soybean and Rice via Deep Resequencing of Reduced Representation Libraries with the Illumina Genome Analyzer

    Directory of Open Access Journals (Sweden)

    Stéphane Deschamps

    2010-07-01

    Full Text Available Massively parallel sequencing platforms have allowed for the rapid discovery of single nucleotide polymorphisms (SNPs among related genotypes within a species. We describe the creation of reduced representation libraries (RRLs using an initial digestion of nuclear genomic DNA with a methylation-sensitive restriction endonuclease followed by a secondary digestion with the 4bp-restriction endonuclease This strategy allows for the enrichment of hypomethylated genomic DNA, which has been shown to be rich in genic sequences, and the digestion with serves to increase the number of common loci resequenced between individuals. Deep resequencing of these RRLs performed with the Illumina Genome Analyzer led to the identification of 2618 SNPs in rice and 1682 SNPs in soybean for two representative genotypes in each of the species. A subset of these SNPs was validated via Sanger sequencing, exhibiting validation rates of 96.4 and 97.0%, in rice ( and soybean (, respectively. Comparative analysis of the read distribution relative to annotated genes in the reference genome assemblies indicated that the RRL strategy was primarily sampling within genic regions for both species. The massively parallel sequencing of methylation-sensitive RRLs for genome-wide SNP discovery can be applied across a wide range of plant species having sufficient reference genomic sequence.

  20. Experimental Evaluation of a Low Emissions High Performance Duct Burner for Variable Cycle Engines (VCE)

    Science.gov (United States)

    Lohmann, R. P.; Mador, R. J.

    1979-01-01

    An evaluation was conducted with a three stage Vorbix duct burner to determine the performance and emissions characteristics of the concept and to refine the configuration to provide acceptable durability and operational characteristics for its use in the variable cycle engine (VCE) testbed program. The tests were conducted at representative takeoff, transonic climb, and supersonic cruise inlet conditions for the VSCE-502B study engine. The test stand, the emissions sampling and analysis equipment, and the supporting flow visualization rigs are described. The performance parameters including the fuel-air ratio, the combustion efficiency/exit temperature, thrust efficiency, and gaseous emissions calculations are defined. The test procedures are reviewed and the results are discussed.

  1. High-precision 41K/39K measurements by MC-ICP-MS indicate terrestrial variability of δ41K

    Science.gov (United States)

    Morgan, Leah; Santiago Ramos, Danielle P.; Davidheiser-Kroll, Brett; Faithfull, John; Lloyd, Nicholas S.; Ellam, Rob M.; Higgins, John A.

    2018-01-01

    Potassium is a major component in continental crust, the fourth-most abundant cation in seawater, and a key element in biological processes. Until recently, difficulties with existing analytical techniques hindered our ability to identify natural isotopic variability of potassium isotopes in terrestrial materials. However, measurement precision has greatly improved and a range of K isotopic compositions has now been demonstrated in natural samples. In this study, we present a new technique for high-precision measurement of K isotopic ratios using high-resolution, cold plasma multi-collector mass spectrometry. We apply this technique to demonstrate natural variability in the ratio of 41K to 39K in a diverse group of geological and biological samples, including silicate and evaporite minerals, seawater, and plant and animal tissues. The total range in 41K/39K ratios is ca. 2.6‰, with a long-term external reproducibility of 0.17‰ (2, N=108). Seawater and seawater-derived evaporite minerals are systematically enriched in 41K compared to silicate minerals by ca. 0.6‰, a result consistent with recent findings1, 2. Although our average bulk-silicate Earth value (-0.54‰) is indistinguishable from previously published values, we find systematic δ41K variability in some high-temperature sample suites, particularly those with evidence for the presence of fluids. The δ41K values of biological samples span a range of ca. 1.2‰ between terrestrial mammals, plants, and marine organisms. Implications of terrestrial K isotope variability for the atomic weight of K and K-based geochronology are discussed. Our results indicate that high-precision measurements of stable K isotopes, made using commercially available mass spectrometers, can provide unique insights into the chemistry of potassium in geological and biological systems. 

  2. The identification of high potential archers based on fitness and motor ability variables: A Support Vector Machine approach.

    Science.gov (United States)

    Taha, Zahari; Musa, Rabiu Muazu; P P Abdul Majeed, Anwar; Alim, Muhammad Muaz; Abdullah, Mohamad Razali

    2018-02-01

    Support Vector Machine (SVM) has been shown to be an effective learning algorithm for classification and prediction. However, the application of SVM for prediction and classification in specific sport has rarely been used to quantify/discriminate low and high-performance athletes. The present study classified and predicted high and low-potential archers from a set of fitness and motor ability variables trained on different SVMs kernel algorithms. 50 youth archers with the mean age and standard deviation of 17.0 ± 0.6 years drawn from various archery programmes completed a six arrows shooting score test. Standard fitness and ability measurements namely hand grip, vertical jump, standing broad jump, static balance, upper muscle strength and the core muscle strength were also recorded. Hierarchical agglomerative cluster analysis (HACA) was used to cluster the archers based on the performance variables tested. SVM models with linear, quadratic, cubic, fine RBF, medium RBF, as well as the coarse RBF kernel functions, were trained based on the measured performance variables. The HACA clustered the archers into high-potential archers (HPA) and low-potential archers (LPA), respectively. The linear, quadratic, cubic, as well as the medium RBF kernel functions models, demonstrated reasonably excellent classification accuracy of 97.5% and 2.5% error rate for the prediction of the HPA and the LPA. The findings of this investigation can be valuable to coaches and sports managers to recognise high potential athletes from a combination of the selected few measured fitness and motor ability performance variables examined which would consequently save cost, time and effort during talent identification programme. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. High Variability of Observed Weight Bearing During Standing Foot and Ankle Radiographs.

    Science.gov (United States)

    Miller, Christopher P; Ghorbanhoseini, Mohammad; Ehrlichman, Lauren K; Walley, Kempland C; Ghaheri, Azadeh; Kwon, John Y

    2017-06-01

    Weight-bearing radiographs are a critical component of evaluating foot and ankle pathology. An underlying assumption is that patients are placing 50% of their body weight on the affected foot during image acquisition. The accuracy of weight bearing during radiographs is unknown and, presumably, variable, which may result in uncertain ability of the resultant radiographs to appropriately portray the pathology of interest. Fifty subjects were tested. The percentage body weight through the foot of interest was measured at the moment of radiographic image acquisition. The subject was then instructed to bear "half [their] weight" prior to the next radiograph. The percentage body weight was calculated and compared to ideal 50% weight bearing. The mean percentage body weight in trial 1 and 2 was 45.7% ± 3.2% ( P = .012 compared to the 50% mark) and 49.2% ± 2.4%, respectively ( P = .428 compared to 50%). The mean absolute difference in percentage weight bearing compared to 50% in trials 1 and 2 was 9.3% ± 2.3% and 5.8% ± 1.8%, respectively ( P = .005). For trial 1, 18/50 subjects were within the "ideal" (45%-55%) range for weight bearing compared to 32/50 on trial 2 ( P = .005). In trial 1, 24/50 subjects had "appropriate" (>45%) weight bearing compared to 39/50 on trial 2 ( P = .002). There was substantial variability in the weight applied during radiograph acquisition. This study raises questions regarding the assumptions, reliability, and interpretation when evaluating weight-bearing radiographs. Level III, comparative study.

  4. School-Related Variables in the Dimensions of Anger in High School Students in Turkey

    Science.gov (United States)

    Siyez, Digdem M.

    2018-01-01

    The study aimed to examine the effects of perceived social support from teachers, expectation of academic achievement, school control, and gender on anger dimensions in high school students in Izmir, Turkey. In total, 446 high school students (234 girls, 212 boys) participated in the study. Pearson's correlation and multiple regression analyses…

  5. Dissociated control as a signature of typological variability in high hypnotic suggestibility.

    Science.gov (United States)

    Terhune, Devin Blair; Cardeña, Etzel; Lindgren, Magnus

    2011-09-01

    This study tested the prediction that dissociative tendencies modulate the impact of a hypnotic induction on cognitive control in different subtypes of highly suggestible individuals. Low suggestible (LS), low dissociative highly suggestible (LDHS), and high dissociative highly suggestible (HDHS) participants completed the Stroop color-naming task in control and hypnosis conditions. The magnitude of conflict adaptation (faster response times on incongruent trials preceded by an incongruent trial than those preceded by a congruent trial) was used as a measure of cognitive control. LS and LDHS participants displayed marginally superior up-regulation of cognitive control following a hypnotic induction, whereas HDHS participants' performance declined. These findings indicate that dissociative tendencies modulate the influence of a hypnotic induction on cognitive control in high hypnotic suggestibility and suggest that HS individuals are comprised of distinct subtypes with dissimilar cognitive profiles. Copyright © 2010 Elsevier Inc. All rights reserved.

  6. The effect of highly variable topography on the spatial distribution of Aniba perutilis (Lauraceae in the Colombian Andes

    Directory of Open Access Journals (Sweden)

    José C. Fagua

    2013-03-01

    Full Text Available Topography is a factor that can significantly affect the diversity and the distribution of trees species in tropical forests. Aniba perutilis, a timber species listed as vulnerable to extinction, is widely distributed in Andean forest fragments, especially in those with highly variable topography. Based on field surveys and logistic regression analyses, we studied the population structure and the effect of highly variable topography on the spatial distribution of this tree in three protected forest fragments in the central Andes of Colombia. Individuals of A. perutilis were mainly found on mountain ridges and hills with gentle slopes; no individuals were found in valleys. Using a species distribution model with presence/absence data, we showed that the available habitat for A. perutilis is significantly smaller than the extension of the fragments and much smaller than the extension of the currently protected areas. Our results have important implications for the conservation of A. perutilis and likely for other threatened Andean tree species, which can also have locally restricted distributions due to highly variable local topography.

  7. High variability of dung beetle diversity patterns at four mountains of the Trans-Mexican Volcanic Belt

    Directory of Open Access Journals (Sweden)

    Alfonsina Arriaga-Jiménez

    2018-02-01

    Full Text Available Insect diversity patterns of high mountain ecosystems remain poorly studied in the tropics. Sampling dung beetles of the subfamilies Aphodiinae, Scarabaeinae, and Geotrupinae was carried out at four volcanoes in the Trans-Mexican Volcanic Belt (TMVB in the Mexican transition zone at 2,700 and 3,400 MASL, and on the windward and leeward sides. Sampling units represented a forest–shrubland–pasture (FSP mosaic typical of this mountain region. A total of 3,430 individuals of 29 dung beetle species were collected. Diversity, abundance and compositional similarity (CS displayed a high variability at all scales; elevation, cardinal direction, or FSP mosaics did not show any patterns of higher or lower values of those measures. The four mountains were different regarding dispersion patterns and taxonomic groups, both for species and individuals. Onthophagus chevrolati dominated all four mountains with an overall relative abundance of 63%. CS was not related to distance among mountains, but when O. chevrolati was excluded from the analysis, CS values based on species abundance decreased with increasing distance. Speciation, dispersion, and environmental instability are suggested as the main drivers of high mountain diversity patterns, acting together at different spatial and temporal scales. Three species new to science were collected (>10% of all species sampled. These discoveries may indicate that speciation rate is high among these volcanoes—a hypothesis that is also supported by the elevated number of collected species with a restricted montane distribution. Dispersion is an important factor in driving species composition, although naturally limited between high mountains; horizontal colonization events at different time scales may best explain the observed species composition in the TMVB, complemented by vertical colonization events to a lesser extent. Environmental instability may be the main factor causing the high variability of diversity

  8. High variability of dung beetle diversity patterns at four mountains of the Trans-Mexican Volcanic Belt.

    Science.gov (United States)

    Arriaga-Jiménez, Alfonsina; Rös, Matthias; Halffter, Gonzalo

    2018-01-01

    Insect diversity patterns of high mountain ecosystems remain poorly studied in the tropics. Sampling dung beetles of the subfamilies Aphodiinae, Scarabaeinae, and Geotrupinae was carried out at four volcanoes in the Trans-Mexican Volcanic Belt (TMVB) in the Mexican transition zone at 2,700 and 3,400 MASL, and on the windward and leeward sides. Sampling units represented a forest-shrubland-pasture (FSP) mosaic typical of this mountain region. A total of 3,430 individuals of 29 dung beetle species were collected. Diversity, abundance and compositional similarity (CS) displayed a high variability at all scales; elevation, cardinal direction, or FSP mosaics did not show any patterns of higher or lower values of those measures. The four mountains were different regarding dispersion patterns and taxonomic groups, both for species and individuals. Onthophagus chevrolati dominated all four mountains with an overall relative abundance of 63%. CS was not related to distance among mountains, but when O. chevrolati was excluded from the analysis, CS values based on species abundance decreased with increasing distance. Speciation, dispersion, and environmental instability are suggested as the main drivers of high mountain diversity patterns, acting together at different spatial and temporal scales. Three species new to science were collected (>10% of all species sampled). These discoveries may indicate that speciation rate is high among these volcanoes-a hypothesis that is also supported by the elevated number of collected species with a restricted montane distribution. Dispersion is an important factor in driving species composition, although naturally limited between high mountains; horizontal colonization events at different time scales may best explain the observed species composition in the TMVB, complemented by vertical colonization events to a lesser extent. Environmental instability may be the main factor causing the high variability of diversity and abundance patterns

  9. INDUCED GENETIC VARIABILITY AND SELECTION FOR HIGH YIELDING MUTANTS IN BREAD WHEAT(TRITICUM AESTIVUM L.)

    International Nuclear Information System (INIS)

    SOBIEH, S.EL-S.S.

    2007-01-01

    This study was conducted during the two winter seasons of 2004/2005 and 2005/2006 at the experimental farm belonging to Plant Research Department, Nuclear Research Centre, AEA, Egypt.The aim of this study is to determine the effect of gamma rays(150, 200 and 250 Gy) on means of yield and its attributes for exotic wheat variety (vir-25) and induction of genetic variability that permits to perform visual selection through the irradiated populations, as well as to determine difference in seed protein patterns between vir-25 parent variety and some selectants in M2 generation.The results showed that the different doses of gamma rays had non-significant effect on mean value of yield/plant and significant effect on mean values of it's attributes. 0n the other hand, the considered genetic variability was generated as result of applying gamma irradiation. The highest amount of induced genetic variability was detected for number of grains/ spike, spike length and number of spikes/plant. Additionally, these three traits exhibited strong association with grain yield/plant, hence, they were used as a criterion for selection.Some variant plants were selected from radiation treatment 250 Gy, with 2-10 spikes per plant.These variant plants exhibited increasing in spike length and number of gains/spike.The results also revealed that protein electrophoresis were varied in the number and position of bands from genotype to another and various genotypes share bands with molecular weights 31.4 and 3.2 KD.Many bands were found to be specific for the genotype and the nine wheat mutants were characterized by the presence of bands of molecular weights: 151.9, 125.7, 14.1 and 5.7 KD at M-167.4, 21.7 and 8.2 at M-299.7 KD at M-3136.1, 97.6, 49.8, 27.9 and 20.6 KD at M-4 135.2, 95.3 and 28.1 KD at M-5 135.5, 67.7, 47.1, 32.3, 21.9 and 9.6 KD at M-6 126.1, 112.1, 103.3, 58.8, 20.9 and 12.1 KD at M-7 127.7, 116.6, 93.9, 55.0 and 47.4 KD at M-8 141.7, 96.1, 79.8, 68.9, 42.1, 32.7, 22.0 and 13

  10. Mode Transition Variable Geometry for High Speed Inlets for Hypersonic Aircraft, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Hypersonic propulsion research has been a focus of the NASA aeronautics program for years. Previous high-speed cruise and space access programs have examined the...

  11. Stress Recovery Effects of High- and Low-Frequency Amplified Music on Heart Rate Variability.

    Science.gov (United States)

    Nakajima, Yoshie; Tanaka, Naofumi; Mima, Tatsuya; Izumi, Shin-Ichi

    Sounds can induce autonomic responses in listeners. However, the modulatory effect of specific frequency components of music is not fully understood. Here, we examined the role of the frequency component of music on autonomic responses. Specifically, we presented music that had been amplified in the high- or low-frequency domains. Twelve healthy women listened to white noise, a stress-inducing noise, and then one of three versions of a piece of music: original, low-, or high-frequency amplified. To measure autonomic response, we calculated the high-frequency normalized unit (HFnu), low-frequency normalized unit, and the LF/HF ratio from the heart rate using electrocardiography. We defined the stress recovery ratio as the value obtained after participants listened to music following scratching noise, normalized by the value obtained after participants listened to white noise after the stress noise, in terms of the HFnu, low-frequency normalized unit, LF/HF ratio, and heart rate. Results indicated that high-frequency amplified music had the highest HFnu of the three versions. The stress recovery ratio of HFnu under the high-frequency amplified stimulus was significantly larger than that under the low-frequency stimulus. Our results suggest that the high-frequency component of music plays a greater role in stress relief than low-frequency components.

  12. LONG-TERM LIGHT CURVE OF HIGHLY VARIABLE PROTOSTELLAR STAR GM CEP

    International Nuclear Information System (INIS)

    Xiao Limin; Kroll, Peter; Henden, Arne A.

    2010-01-01

    We present data from the archival plates at Harvard College Observatory and Sonneberg Observatory showing the field of the solar-type pre-main-sequence star GM Cep. A total of 186 magnitudes of GM Cep have been measured on these archival plates, with 176 in blue sensitivity, six in visible, and four in red. We combine our data with data from the literature and from the American Association of Variable Star Observers to depict the long-term light curves of GM Cep in both B and V wavelengths. The light curves span from 1895 until now, with two densely sampled regions (1935-1945 in the B band, and 2006 until now in the V band). The long-term light curves do not show any fast rise behavior as predicted by an accretion mechanism. Both the light curves and the magnitude histograms confirm the conclusion that the light curves are dominated by dips (possibly from extinction) superposed on some quiescence state, instead of outbursts caused by accretion flares. Our result excludes the possibility of GM Cep being a FUor, EXor, or McNeil's Nebula-type star. Several special cases of T Tauri stars were checked, but none of these light curves were compatible with that of GM Cep. The lack of periodicity in the light curve excludes the possibility of GM Cep being a KH 15D system.

  13. MT-ND5 Mutation Exhibits Highly Variable Neurological Manifestations at Low Mutant Load

    Directory of Open Access Journals (Sweden)

    Yi Shiau Ng

    2018-04-01

    Full Text Available Mutations in the m.13094T>C MT-ND5 gene have been previously described in three cases of Leigh Syndrome (LS. In this retrospective, international cohort study we identified 20 clinically affected individuals (13 families and four asymptomatic carriers. Ten patients were deceased at the time of analysis (median age of death was 10 years (range: 5·4 months−37 years, IQR = 17·9 years. Nine patients manifested with LS, one with mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS, and one with Leber hereditary optic neuropathy. The remaining nine patients presented with either overlapping syndromes or isolated neurological symptoms. Mitochondrial respiratory chain activity analysis was normal in five out of ten muscle biopsies. We confirmed maternal inheritance in six families, and demonstrated marked variability in tissue segregation, and phenotypic expression at relatively low blood mutant loads. Neuropathological studies of two patients manifesting with LS/MELAS showed prominent capillary proliferation, microvacuolation and severe neuronal cell loss in the brainstem and cerebellum, with conspicuous absence of basal ganglia involvement. These findings suggest that whole mtDNA genome sequencing should be considered in patients with suspected mitochondrial disease presenting with complex neurological manifestations, which would identify over 300 known pathogenic variants including the m.13094T>C. Keywords: Mitochondrial encephalomyopathy, Lactic acidosis and stroke-like episodes (MELAS, Leigh syndrome (LS, Mitochondrial DNA, Heteroplasmy, Neuropathology

  14. High spatial variability of coral, sponges and gorgonian assemblages in a well preserved reef

    Directory of Open Access Journals (Sweden)

    Patricia González-Díaz

    2010-06-01

    Full Text Available The main goal of this research was to obtain baseline field data of the composition of sponges, corals, and gorgonian assemblages that can be used as a reference for future analyses of anthropogenic impact. We tested the hypothesis that relatively homogeneous and well preserved reef units can present notable natural variability in the composition of their communities which are unassociated with changes in land proximity or a human impact gradient. Research was carried out in July 2006 at Los Colorados reef, located in the northwestern region of Pinar del Río Province, Cuba at 12 sampling stations. The biotopes selected were crest, terrace edge and spur and grove. Ecological indicators were diversity of corals, species composition, density of corals, hydrocorals, gorgonians and sponges, and density of selected coral species. A total of 2659 colonies of scleractineans corals representing 36 species were counted. The most abundant species in the crest biotope were Millepora alcicornis, Acropora palmata and Porites astreoides; in the terrace edge and spur and grove, the most abundant species were Siderastrea siderea, Stephanocoenia intersepta, Porites astreoides, Agaricia agaricites and Montastraea cavernosa. We found differences among sites for several indicators (e.g. density of corals, sponges and gorgonians and for selected species, but they could not be associated to any gradient of land influence or human impact. Therefore, sites inside a relatively homogeneous reef unit can present notable natural differences in the composition of their communities. Rev. Biol. Trop. 58 (2: 621-634. Epub 2010 June 02.

  15. High population variability and source-sink dynamics in a solitary bee species.

    Science.gov (United States)

    Franzén, Markus; Nilsson, Sven G

    2013-06-01

    Although solitary bees are considered to play key roles in ecosystem functions, surprisingly few studies have explored their population dynamics. We investigated the population dynamics of a rare, declining, solitary bee (Andrena humilis) in a landscape of 80 km2 in southern Sweden from 2003 to 2011. Only one population was persistent throughout all years studied; most likely this population supplied the surrounding landscape with 11 smaller, temporary local populations. Despite stable pollen availability, the size of the persistent population fluctuated dramatically in a two-year cycle over the nine years, with 490-1230 nests in odd-numbered years and 21-48 nests in even-numbered years. These fluctuations were not significantly related to climatic variables or pollen availability. Nineteen colonization and 14 extinction events were recorded. Occupancy decreased with distance from the persistent population and increased with increasing resource (pollen) availability. There were significant positive correlations between the size of the persistent population and patch occupancy and colonization. Colonizations were generally more common in patches closer to the persistent population, whereas extinctions were independent of distance from the persistent population. Our results highlight the complex population dynamics that exist for this solitary bee species, which could be due to source-sink dynamics, a prolonged diapause, or can represent a bet-hedging strategy to avoid natural enemies and survive in small habitat patches. If large fluctuations in solitary bee populations prove to be widespread, it will have important implications for interpreting ecological relationships, bee conservation, and pollination.

  16. A HIGH-VELOCITY BULGE RR LYRAE VARIABLE ON A HALO-LIKE ORBIT

    International Nuclear Information System (INIS)

    Kunder, Andrea; Storm, J.; Rich, R. M.; Hawkins, K.; Poleski, R.; Johnson, C. I.; Shen, J.; Li, Z.-Y.; Cordero, M. J.; Nataf, D. M.; Bono, G.; Walker, A. R.; Koch, A.; De Propris, R.; Udalski, A.; Szymanski, M. K.; Soszynski, I.; Pietrzynski, G.; Ulaczyk, K.; Wyrzykowski, Ł.

    2015-01-01

    We report on the RR Lyrae variable star, MACHO 176.18833.411, located toward the Galactic bulge and observed within the data from the ongoing Bulge RR Lyrae Radial Velocity Assay, which has the unusual radial velocity of −372 ± 8 km s −1 and true space velocity of −482 ± 22 km s −1 relative to the Galactic rest frame. Located less than 1 kpc from the Galactic center and toward a field at (l, b) = (3, −2.5), this pulsating star has properties suggesting it belongs to the bulge RR Lyrae star population, yet a velocity indicating it is abnormal, at least with respect to bulge giants and red clump stars. We show that this star is most likely a halo interloper and therefore suggest that halo contamination is not insignificant when studying metal-poor stars found within the bulge area, even for stars within 1 kpc of the Galactic center. We discuss the possibility that MACHO 176.18833.411 is on the extreme edge of the bulge RR Lyrae radial velocity distribution, and also consider a more exotic scenario in which it is a runaway star moving through the Galaxy

  17. Behavior problems at ages 6 and 11 and high school academic achievement: longitudinal latent variable modeling.

    Science.gov (United States)

    Breslau, Naomi; Breslau, Joshua; Miller, Elizabeth; Raykov, Tenko

    2011-02-28

    Previous studies documented long-run effects of behavior problems at the start of school on academic achievement. However, these studies did not examine whether the observed effects of early behavior problems are explained by more proximate behavior problems, given the tendency of children's behavior problems to persist. Latent variable modeling was applied to estimate the effects of behavior problems at ages 6 and 11 on academic achievement at age 17, using data from a longitudinal study (n=823). Behavior problems at ages 6 and 11, each stage independently of the other, predicted lower math and reading test scores at age 17, controlling for intelligence quotient (IQ), birth weight, maternal characteristics, family and community environment, and taking into account behavior problems at age 17. Behavior problems at the start of school, independent of later behavior problems, exert lingering effects on achievement by impeding the acquisition of cognitive skills that are the foundation for later academic progress. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  18. High spatial variability of coral, sponges and gorgonian assemblages in a well preserved reef.

    Science.gov (United States)

    González-Díaz, Patricia; González-Sansón, Gaspar; Alvarez Fernández, Sergio; Perera Pérez, Orlando

    2010-06-01

    The main goal of this research was to obtain baseline field data of the composition of sponges, corals, and gorgonian assemblages that can be used as a reference for future analyses of anthropogenic impact. We tested the hypothesis that relatively homogeneous and well preserved reef units can present notable natural variability in the composition of their communities which are unassociated with changes in land proximity or a human impact gradient. Research was carried out in July 2006 at Los Colorados reef, located in the northwestern region of Pinar del Río Province, Cuba at 12 sampling stations. The biotopes selected were crest, terrace edge and spur and grove. Ecological indicators were diversity of corals, species composition, density of corals, hydrocorals, gorgonians and sponges, and density of selected coral species. A total of 2659 colonies of scleractineans corals representing 36 species were counted. The most abundant species in the crest biotope were Millepora alcicornis, Acropora palmata and Porites astreoides; in the terrace edge and spur and grove, the most abundant species were Siderastrea siderea, Stephanocoenia intersepta, Porites astreoides, Agaricia agaricites and Montastraea cavernosa. We found differences among sites for several indicators (e.g. density of corals, sponges and gorgonians and for selected species), but they could not be associated to any gradient of land influence or human impact. Therefore, sites inside a relatively homogeneous reef unit can present notable natural differences in the composition of their communities.

  19. Heart rate variability biofeedback reduces food cravings in high food cravers.

    Science.gov (United States)

    Meule, Adrian; Freund, Rebecca; Skirde, Ann Kathrin; Vögele, Claus; Kübler, Andrea

    2012-12-01

    Heart rate variability (HRV) biofeedback has been reported to increase HRV while decreasing symptoms in patients with mental disorders. In addition, associations between low HRV and lowered self-regulation were found in non-clinical samples, e.g., in individuals with strong chocolate cravings or unsuccessful dieting. The current study aimed at decreasing food cravings with HRV-biofeedback in individuals frequently experiencing such cravings. Participants (N = 56) with strong or low food cravings associated with a lack of control over eating were selected from the local community. Half of the participants with strong cravings (craving-biofeedback; n = 14) performed 12 sessions of HRV-biofeedback while the other half (craving-control; n = 14) and a group with low cravings (non-craving-control; n = 28) received no intervention. Subjective food cravings related to a lack of control over eating decreased from pre- to post-measurement in the craving-biofeedback group, but remained constant in the control groups. Moreover, only the craving-biofeedback group showed a decrease in eating and weight concerns. Although HRV-biofeedback was successful in reducing food cravings, this change was not accompanied by an increase in HRV. Instead, HRV decreased in the craving-control group. This study provides preliminary evidence that HRV-biofeedback could be beneficial for attenuating dysfunctional eating behavior although specific mechanisms remain to be elucidated.

  20. MAPA distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber.

    Science.gov (United States)

    Hoehenwarter, Wolfgang; Larhlimi, Abdelhalim; Hummel, Jan; Egelhofer, Volker; Selbig, Joachim; van Dongen, Joost T; Wienkoop, Stefanie; Weckwerth, Wolfram

    2011-07-01

    Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers of shotgun proteomics analyses on a personal computer in a matter of hours. We compared 183 LC-MS analyses and more than 2 million MS/MS spectra and could define and separate the proteomic phenotypes of field grown tubers of 12 tetraploid cultivars of the crop plant Solanum tuberosum. Protein isoforms of patatin as well as other major gene families such as lipoxygenase and cysteine protease inhibitor that regulate tuber development were found to be the primary source of variability between the cultivars. This suggests that differentially expressed protein isoforms modulate genotype specific tuber development and the plant phenotype. We properly assigned the measured abundance of tryptic peptides to different protein isoforms that share extensive stretches of primary structure and thus inferred their abundance. Peptides unique to different protein isoforms were used to classify the remaining peptides assigned to the entire subset of isoforms based on a common abundance profile using multivariate statistical procedures. We identified nearly 4000 proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date.

  1. A HIGH-VELOCITY BULGE RR LYRAE VARIABLE ON A HALO-LIKE ORBIT

    Energy Technology Data Exchange (ETDEWEB)

    Kunder, Andrea; Storm, J. [Leibniz-Institut für Astrophysik Potsdam (AIP), An der Sternwarte 16, D-14482 Potsdam (Germany); Rich, R. M. [Department of Physics and Astronomy, University of California at Los Angeles, Los Angeles, CA 90095-1562 (United States); Hawkins, K. [Institute of Astronomy, Madingley Road, Cambridge CB3 0HA (United Kingdom); Poleski, R. [Department of Astronomy, Ohio State University, 140 W. 18th Avenue, Columbus, OH 43210 (United States); Johnson, C. I. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA 02138 (United States); Shen, J.; Li, Z.-Y. [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Chinese Academy of Sciences, 80 Nandan Road, Shanghai 200030 (China); Cordero, M. J. [Astronomisches Rechen-Institut: Zentrum für Astronomie, Mönchhofstr. 12-14, D-69120 Heidelberg (Germany); Nataf, D. M. [Research School of Astronomy and Astrophysics, The Australian National University, Canberra, ACT 2611 (Australia); Bono, G. [Dipartimento di Fisica, Universita di Roma Tor Vergata, Via della Ricerca Scientifica 1, I-00133 Roma (Italy); Walker, A. R. [Cerro Tololo Inter-American Observatory, National Optical Astronomy Observatory, Casilla 603, La Serena (Chile); Koch, A. [Landessternwarte, Zentrum für Astronomie der Universität Heidelberg, Königstuhl 12, D-69117 Heidelberg (Germany); De Propris, R. [Finnish Centre for Astronomy with ESO (FINCA), University of Turku, Turku (Finland); Udalski, A.; Szymanski, M. K.; Soszynski, I.; Pietrzynski, G.; Ulaczyk, K.; Wyrzykowski, Ł. [Warsaw University Observatory, Al. Ujazdowskie 4, 00-478 Warszawa (Poland); and others

    2015-07-20

    We report on the RR Lyrae variable star, MACHO 176.18833.411, located toward the Galactic bulge and observed within the data from the ongoing Bulge RR Lyrae Radial Velocity Assay, which has the unusual radial velocity of −372 ± 8 km s{sup −1} and true space velocity of −482 ± 22 km s{sup −1} relative to the Galactic rest frame. Located less than 1 kpc from the Galactic center and toward a field at (l, b) = (3, −2.5), this pulsating star has properties suggesting it belongs to the bulge RR Lyrae star population, yet a velocity indicating it is abnormal, at least with respect to bulge giants and red clump stars. We show that this star is most likely a halo interloper and therefore suggest that halo contamination is not insignificant when studying metal-poor stars found within the bulge area, even for stars within 1 kpc of the Galactic center. We discuss the possibility that MACHO 176.18833.411 is on the extreme edge of the bulge RR Lyrae radial velocity distribution, and also consider a more exotic scenario in which it is a runaway star moving through the Galaxy.

  2. A novel program to design siRNAs simultaneously effective to highly variable virus genomes.

    Science.gov (United States)

    Lee, Hui Sun; Ahn, Jeonghyun; Jun, Eun Jung; Yang, Sanghwa; Joo, Chul Hyun; Kim, Yoo Kyum; Lee, Heuiran

    2009-07-10

    A major concern of antiviral therapy using small interfering RNAs (siRNAs) targeting RNA viral genome is high sequence diversity and mutation rate due to genetic instability. To overcome this problem, it is indispensable to design siRNAs targeting highly conserved regions. We thus designed CAPSID (Convenient Application Program for siRNA Design), a novel bioinformatics program to identify siRNAs targeting highly conserved regions within RNA viral genomes. From a set of input RNAs of diverse sequences, CAPSID rapidly searches conserved patterns and suggests highly potent siRNA candidates in a hierarchical manner. To validate the usefulness of this novel program, we investigated the antiviral potency of universal siRNA for various Human enterovirus B (HEB) serotypes. Assessment of antiviral efficacy using Hela cells, clearly demonstrates that HEB-specific siRNAs exhibit protective effects against all HEBs examined. These findings strongly indicate that CAPSID can be applied to select universal antiviral siRNAs against highly divergent viral genomes.

  3. High-intensity endurance training increases nocturnal heart rate variability in sedentary participants

    Directory of Open Access Journals (Sweden)

    A Nummela

    2016-01-01

    Full Text Available The effects of endurance training on endurance performance characteristics and cardiac autonomic modulation during night sleep were investigated during two 4-week training periods. After the first 4-week training period (3 x 40 min per week, at 75% of HRR the subjects were divided into HIGH group (n = 7, who performed three high-intensity endurance training sessions per week; and CONTROL group (n = 8 who did not change their training. An incremental treadmill test was performed before and after the two 4-weektraining periods. Furthermore, nocturnal RR-intervals were recorded after each training day. In the second 4-weektraining period HIGH group increased their V0Zmax (P = 0.005 more than CONTROL group. At the same time, nocturnal HR decreased (P = 0.039 and high-frequency power (HFP increased (P = 0.003 in HIGH group while no changes were observed in CONTROL group. Furthermore, a correlation was observed between the changes in nocturnal HFP and changes in V0Zmax during the second 4-week training period (r = 0.90, P < 0.001. The present study showed that the increased HFP is related to improved VO2max in sedentary subjects suggesting that nocturnal HFP can provide a useful method in monitoring individual responses to endurance training.

  4. Establishment of in vitro-in vivo equivalence of highly variable drugs - a generic product development perspective.

    Science.gov (United States)

    Pathak, Shriram M; Aggarwal, Deepika; Venkateswarlu, V

    2014-06-01

    In vivo equivalence of highly variable drugs (HVD) has always been a subject of great concern, in terms of both safety and efficacy, for regulatory agencies. Successful demonstration of their bioequivalence thus presents the most crucial component of a generic application, significantly contributing toward the cost and time of development. For poorly soluble drugs, such as telmisartan, dissolution represents the rate-limiting step in the gastric region and in many cases may not be complete, thereby contributing to low and highly variable bioavailability. Consequently, simulation of gastrointestinal conditions is essential to adequately predict the in vivo behavior of drug formulations. In this study, we evaluated usefulness of physiologically relevant dissolution method over commonly used acidic media to forecast comparable in vivo performance of telmisartan formulation to that of reference samples. In the present study, telmisartan was classified as a HVD and a partial replicate design with repeating the reference product and scaling the bioequivalence for the reference variability has been presented. The design has effectively decreased sample size, without increasing patient risk. Results from this project suggest that scaled average bioequivalence (SABE) provides a good approach for evaluating the bioequivalence of HVD, meeting the need for international guidelines for bioequivalence.

  5. Comparing measured and modelled soil carbon: which site-specific variables are linked to high stability?

    Science.gov (United States)

    Robertson, Andy; Schipanski, Meagan; Ma, Liwang; Ahuja, Lajpat; McNamara, Niall; Smith, Pete; Davies, Christian

    2016-04-01

    Changes in soil carbon (C) stocks have been studied in depth over the last two decades, as net greenhouse gas (GHG) sinks are highlighted to be a partial solution to the causes of climate change. However, the stability of this soil C is often overlooked when measuring these changes. Ultimately a net sequestration in soils is far less beneficial if labile C is replacing more stable forms. To date there is no accepted framework for measuring soil C stability, and as a result there is considerable uncertainty associated with the simulated impacts of land management and land use change when using process-based systems models. However, a recent effort to equate measurable soil C fractions to model pools has generated data that help to assess the impacts of land management, and can ultimately help to reduce the uncertainty of model predictions. Our research compiles this existing fractionation data along with site metadata to create a simplistic statistical model able to quantify the relative importance of different site-specific conditions. Data was mined from 23 published studies and combined with original data to generate a dataset of 100+ land use change sites across Europe. For sites to be included they required soil C fractions isolated using the Zimmermann et al. (2007) method and specific site metadata (mean annual precipitation, MAP; mean annual temperature, MAT; soil pH; land use; altitude). Of the sites, 75% were used to develop a generalized linear mixed model (GLMM) to create coefficients where site parameters can be used to predict influence on the measured soil fraction C stocks. The remaining 25% of sites were used to evaluate uncertainty and validate this empirical model. Further, four of the aforementioned sites were used to simulate soil C dynamics using the RothC, DayCent and RZWQM2 models. A sensitivity analysis (4096 model runs for each variable applying Latin hypercube random sampling techniques) was then used to observe whether these models place

  6. High interpatient variability of raltegravir CSF concentrations in HIV-positive patients: a pharmacogenetic analysis.

    Science.gov (United States)

    Calcagno, Andrea; Cusato, Jessica; Simiele, Marco; Motta, Ilaria; Audagnotto, Sabrina; Bracchi, Margherita; D'Avolio, Antonio; Di Perri, Giovanni; Bonora, Stefano

    2014-01-01

    To analyse the determinants of raltegravir CSF penetration, including the pharmacogenetics of drug transporters located at the blood-brain barrier or blood-CSF barrier. Plasma and CSF raltegravir concentrations were determined by a validated HPLC coupled with mass spectrometry method in adults on raltegravir-based combination antiretroviral therapy undergoing a lumbar puncture. Single nucleotide polymorphisms in the genes encoding drugs transporters (ABCB1 3435, SLCO1A2, ABCC2 and SLC22A6) and the gene encoding hepatocyte nuclear factor 4 α (HNF4α) were determined by real-time PCR. In 41 patients (73.2% male, 95.1% Caucasians), the median raltegravir plasma and CSF concentrations were 165 ng/mL (83-552) and 31 ng/mL (21-56), respectively. CSF-to-plasma ratios (CPRs) ranged from 0.005 to 1.33 (median 0.20, IQR 0.04-0.36). Raltegravir trough CSF concentrations (n = 35) correlated with raltegravir plasma levels (ρ = 0.395, P = 0.019); CPRs were higher in patients with blood-brain barrier damage (0.47 versus 0.18, P = 0.02). HNF4α 613 CG genotype carriers had lower trough CSF concentrations (20 versus 37 ng/mL, P = 0.03) and CPRs (0.12 versus 0.27, P = 0.02). Following multivariate linear regression analysis, the CSF-to-serum albumin ratio was the only independent predictor of raltegravir penetration into the CSF. Raltegravir penetration into the CSF shows a large interpatient variability, although CSF concentrations were above the wild-type IC50 in all patients (and above IC95 in 28.6%). In this cohort, blood-brain barrier permeability is the only independent predictor of raltegravir CPR. The impact of single nucleotide polymorphisms in selected genes on raltegravir penetration warrants further studies.

  7. Spatiotemporal variability of Canadian High Arctic glacier surface albedo from MODIS data, 2001-2016

    Science.gov (United States)

    Mortimer, Colleen A.; Sharp, Martin

    2018-02-01

    Inter-annual variations and longer-term trends in the annual mass balance of glaciers in Canada's Queen Elizabeth Islands (QEI) are largely attributable to changes in summer melt. The largest source of melt energy in the QEI in summer is net shortwave radiation, which is modulated by changes in glacier surface albedo. We used measurements from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensors to investigate large-scale spatial patterns, temporal trends, and variability in the summer surface albedo of QEI glaciers from 2001 to 2016. Mean summer black-sky shortwave broadband albedo (BSA) decreased at a rate of 0.029±0.025 decade-1 over that period. Larger reductions in BSA occurred in July (-0.050±0.031 decade-1). No change in BSA was observed in either June or August. Most of the decrease in BSA, which was greatest at lower elevations around the margins of the ice masses, occurred between 2007 and 2012, when mean summer BSA was anomalously low. The first principal component of the 16-year record of mean summer BSA was well correlated with the mean summer North Atlantic Oscillation index, except in 2006, 2010, and 2016, when the mean summer BSA appears to have been dominated by the August BSA. During the period 2001-2016, the mean summer land surface temperature (LST) over the QEI glaciers and ice caps increased by 0.049±0.038 °C yr-1, and the BSA record was negatively correlated (r: -0.86) with the LST record, indicative of a positive ice-albedo feedback that would increase rates of mass loss from the QEI glaciers.

  8. Microscale profiling of photosynthesis-related variables in a highly productive biofilm photobioreactor.

    Science.gov (United States)

    Li, Tong; Piltz, Bastian; Podola, Björn; Dron, Anthony; de Beer, Dirk; Melkonian, Michael

    2016-05-01

    In the present study depth profiles of light, oxygen, pH and photosynthetic performance in an artificial biofilm of the green alga Halochlorella rubescens in a porous substrate photobioreactor (PSBR) were recorded with microsensors. Biofilms were exposed to different light intensities (50-1,000 μmol photons m(-2) s(-1) ) and CO2 levels (0.04-5% v/v in air). The distribution of photosynthetically active radiation showed almost identical trends for different surface irradiances, namely: a relatively fast drop to a depth of about 250 µm, (to 5% of the incident), followed by a slower decrease. Light penetrated into the biofilm deeper than the Lambert-Beer Law predicted, which may be attributed to forward scattering of light, thus improving the overall light availability. Oxygen concentration profiles showed maxima at a depth between 50 and 150 μm, depending on the incident light intensity. A very fast gas exchange was observed at the biofilm surface. The highest oxygen concentration of 3.2 mM was measured with 1,000 μmol photons m(-2) s(-1) and 5% supplementary CO2. Photosynthetic productivity increased with light intensity and/or CO2 concentration and was always highest at the biofilm surface; the stimulating effect of elevated CO2 concentration in the gas phase on photosynthesis was enhanced by higher light intensities. The dissolved inorganic carbon concentration profiles suggest that the availability of the dissolved free CO2 has the strongest impact on photosynthetic productivity. The results suggest that dark respiration could explain previously observed decrease in growth rate over cultivation time in this type of PSBR. Our results represent a basis for understanding the complex dynamics of environmental variables and metabolic processes in artificial phototrophic biofilms exposed to a gas phase and can be used to improve the design and operational parameters of PSBRs. © 2015 Wiley Periodicals, Inc.

  9. Practices for Identifying and Rejecting Hemolyzed Specimens Are Highly Variable in Clinical Laboratories.

    Science.gov (United States)

    Howanitz, Peter J; Lehman, Christopher M; Jones, Bruce A; Meier, Frederick A; Horowitz, Gary L

    2015-08-01

    Hemolysis is an important clinical laboratory quality attribute that influences result reliability. To determine hemolysis identification and rejection practices occurring in clinical laboratories. We used the College of American Pathologists Survey program to distribute a Q-Probes-type questionnaire about hemolysis practices to Chemistry Survey participants. Of 3495 participants sent the questionnaire, 846 (24%) responded. In 71% of 772 laboratories, the hemolysis rate was less than 3.0%, whereas in 5%, it was 6.0% or greater. A visual scale, an instrument scale, and combination of visual and instrument scales were used to identify hemolysis in 48%, 11%, and 41% of laboratories, respectively. A picture of the hemolysis level was used as an aid to technologists' visual interpretation of hemolysis levels in 40% of laboratories. In 7.0% of laboratories, all hemolyzed specimens were rejected; in 4% of laboratories, no hemolyzed specimens were rejected; and in 88% of laboratories, some specimens were rejected depending on hemolysis levels. Participants used 69 different terms to describe hemolysis scales, with 21 terms used in more than 10 laboratories. Slight and moderate were the terms used most commonly. Of 16 different cutoffs used to reject hemolyzed specimens, moderate was the most common, occurring in 30% of laboratories. For whole blood electrolyte measurements performed in 86 laboratories, 57% did not evaluate the presence of hemolysis, but for those that did, the most common practice in 21 laboratories (24%) was centrifuging and visually determining the presence of hemolysis in all specimens. Hemolysis practices vary widely. Standard assessment and consistent reporting are the first steps in reducing interlaboratory variability among results.

  10. Estimating trans-seasonal variability in water column biomass for a highly migratory, deep diving predator.

    Directory of Open Access Journals (Sweden)

    Malcolm D O'Toole

    Full Text Available The deployment of animal-borne electronic tags is revolutionizing our understanding of how pelagic species respond to their environment by providing in situ oceanographic information such as temperature, salinity, and light measurements. These tags, deployed on pelagic animals, provide data that can be used to study the ecological context of their foraging behaviour and surrounding environment. Satellite-derived measures of ocean colour reveal temporal and spatial variability of surface chlorophyll-a (a useful proxy for phytoplankton distribution. However, this information can be patchy in space and time resulting in poor correspondence with marine animal behaviour. Alternatively, light data collected by animal-borne tag sensors can be used to estimate chlorophyll-a distribution. Here, we use light level and depth data to generate a phytoplankton index that matches daily seal movements. Time-depth-light recorders (TDLRs were deployed on 89 southern elephant seals (Mirounga leonina over a period of 6 years (1999-2005. TDLR data were used to calculate integrated light attenuation of the top 250 m of the water column (LA(250, which provided an index of phytoplankton density at the daily scale that was concurrent with the movement and behaviour of seals throughout their entire foraging trip. These index values were consistent with typical seasonal chl-a patterns as measured from 8-daySea-viewing Wide Field-of-view Sensor (SeaWiFs images. The availability of data recorded by the TDLRs was far greater than concurrent remotely sensed chl-a at higher latitudes and during winter months. Improving the spatial and temporal availability of phytoplankton information concurrent with animal behaviour has ecological implications for understanding the movement of deep diving predators in relation to lower trophic levels in the Southern Ocean. Light attenuation profiles recorded by animal-borne electronic tags can be used more broadly and routinely to estimate

  11. Inside Student Government: The Variable Quality of High School Student Councils

    Science.gov (United States)

    McFarland, Daniel; Starmanns, Carlos E.

    2009-01-01

    Background/Context: Student governments are the first direct experience that youth have of representative government. However, very little research has been done on student councils in spite of their ubiquity in American high schools and consistent references to their positive effects on the political socialization of youth.…

  12. Saharan dust transport and high-latitude glacial climate variability: the Alboran Sea record

    NARCIS (Netherlands)

    Moreno, A.; Cacho, I.; Canals, M.; Prins, M.A.; Sánchez-Goñi, M.F.; Grimalt, J.O.; Weltje, G.J.

    2002-01-01

    Millennial to submillennial marine oscillations that are linked with the North Atlantic's Heinrich events and Dansgaard-Oeschger cycles have been reported recently from the Alboran Sea, revealing a close ocean-atmosphere coupling in the Mediterranean region. We present a high-resolution record of

  13. Estimating the effect of a variable in a high-dimensional regression model

    DEFF Research Database (Denmark)

    Jensen, Peter Sandholt; Wurtz, Allan

    assume that the effect is identified in a high-dimensional linear model specified by unconditional moment restrictions. We consider  properties of the following methods, which rely on lowdimensional models to infer the effect: Extreme bounds analysis, the minimum t-statistic over models, Sala...

  14. Effect of resin variables on the creep behavior of high density hardwood composite panels

    Science.gov (United States)

    R.C. Tang; Jianhua Pu; C.Y Hse

    1993-01-01

    The flexural creep behavior of oriented strandboards (OSB) fabricated with mixed high, density hardwood flakes was investigated. Three types of adhesives, liquid phenolic-formaldehyde (LPF), melamine modified urea-formaldehyde (MUF), and LPF (face)/MUF (core) were chosen in this investigation. The resin contents (RC) used were 3.5 percent and 5.0 percent. The flakes...

  15. Application of multi-pass high pressure homogenization under variable temperature regimes to induce autolysis of wine yeasts.

    Science.gov (United States)

    Comuzzo, Piergiorgio; Calligaris, Sonia; Iacumin, Lucilla; Ginaldi, Federica; Voce, Sabrina; Zironi, Roberto

    2017-06-01

    The effects of the number of passes and processing temperature management (controlled vs. uncontrolled) were investigated during high pressure homogenization-induced autolysis of Saccharomyces bayanus wine yeasts, treated at 150MPa. Both variables were able to affect cell viability, and the release of soluble molecules (free amino acids, proteins and glucidic colloids), but the effect of temperature was more important. S. bayanus cells were completely inactivated in 10 passes without temperature control (corresponding to a processing temperature of 75°C). The two processing variables also affected the volatile composition of the autolysates produced: higher temperatures led to a lower concentration of volatile compounds. The management of the operating conditions may allow the compositional characteristics of the products to be modulated, making them suitable for different winemaking applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. A set of high quality colour images with Spanish norms for seven relevant psycholinguistic variables: the Nombela naming test.

    Science.gov (United States)

    Moreno-Martinez, Francisco Javier; Montoro, Pedro R; Laws, Keith R

    2011-05-01

    This paper presents a new corpus of 140 high quality colour images belonging to 14 subcategories and covering a range of naming difficulty. One hundred and six Spanish speakers named the items and provided data for several psycholinguistic variables: age of acquisition, familiarity, manipulability, name agreement, typicality and visual complexity. Furthermore, we also present lexical frequency data derived internet search hits. Apart from the large number of variables evaluated, these stimuli present an important advantage with respect to other comparable image corpora in so far as naming performance in healthy individuals is less prone to ceiling effect problems. Reliability and validity indexes showed that our items display similar psycholinguistic characteristics to those of other corpora. In sum, this set of ecologically valid stimuli provides a useful tool for scientists engaged in cognitive and neuroscience-based research.

  17. Inferior outcomes for black children with high risk acute lymphoblastic leukemia and the impact of socioeconomic variables.

    Science.gov (United States)

    Walsh, Alexandra; Chewning, Joseph; Li, Xuelin; Dai, Chen; Whelan, Kimberly; Madan-Swain, Avi; Waterbor, John; Baskin, Monica L; Goldman, Frederick D

    2017-02-01

    While significant improvements have been made for children with acute lymphoblastic leukemia (ALL) in the United States over the past 20 years, black patients continue to have inferior outcomes. The full impact of socioeconomic variables on outcomes in this minority population is not entirely understood. Disease characteristics, demographic, and socioeconomic status (SES) variables were collected on black (n = 44) and white (n = 178) patients diagnosed at the University of Alabama at Birmingham. Cox proportional hazard regression was used to evaluate the influence of SES and insurance status on survival. As a cohort, 5-year overall survival (OS) was 87% (82-91%), with a median follow-up of 99 months. In univariable analysis, black race was not significantly associated with a higher risk of death or relapse and death. White and black patients with standard-risk leukemia had excellent outcomes, with 97% (91-99%) and 96% (75-99%) 5-year OS, respectively. In contrast, for high-risk disease, white patients had a statistically significant improved 5-year OS rates compared with black patients (79% [68-87%] vs. 52% [28-72%]). Black children were more likely to have public insurance, and, in multivariable analysis, this was associated with a trend toward an improved outcome. Black patients also had poorer census tract-level SES parameters, but these variables were not associated with survival. Our study demonstrates significantly inferior outcomes for black children with high-risk leukemia. These outcome disparities were not related to SES variables, including poverty or private insurance coverage, suggesting the involvement of other factors and highlighting the need for a prospective investigative analysis. © 2016 Wiley Periodicals, Inc.

  18. Effect of climatic variability on childhood diarrhea and its high risk periods in northwestern parts of Ethiopia

    Science.gov (United States)

    Kumie, Abera; Worku, Alemayehu; C. Bagtzoglou, Amvrossios; Anagnostou, Emmanouil

    2017-01-01

    Background Increasing climate variability as a result of climate change will be one of the public health challenges to control infectious diseases in the future, particularly in sub-Saharan Africa including Ethiopia. Objective To investigate the effect of climate variability on childhood diarrhea (CDD) and identify high risk periods of diarrheal diseases. Methods The study was conducted in all districts located in three Zones (Awi, West and East Gojjam) of Amhara Region in northwestern parts of Ethiopia. Monthly CDD cases for 24 months (from July 2013 to June 2015) reported to each district health office from the routine surveillance system were used for the study. Temperature, rainfall and humidity data for each district were extracted from satellite precipitation estimates and global atmospheric reanalysis. The space-time permutation scan statistic was used to identify high risk periods of CDD. A negative binomial regression was used to investigate the relationship between cases of CDD and climate variables. Statistical analyses were conducted using SaTScan program and StataSE v. 12. Results The monthly average incidence rate of CDD was 11.4 per 1000 (95%CI 10.8–12.0) with significant variation between males [12.5 per 1000 (95%CI 11.9 to 13.2)] and females [10.2 per 1000 (95%CI 9.6 to 10.8)]. The space-time permutation scan statistic identified the most likely high risk period of CDD between March and June 2014 located in Huletej Enese district of East Gojjam Zone. Monthly average temperature and monthly average rainfall were positively associated with the rate of CDD, whereas the relative humidity was negatively associated with the rate of CDD. Conclusions This study found that the most likely high risk period is in the beginning of the dry season. Climatic factors have an association with the occurrence of CDD. Therefore, CDD prevention and control strategy should consider local weather variations to improve programs on CDD. PMID:29073259

  19. High-Intensity Interval Exercises' Acute Impact on Heart Rate Variability: Comparison Between Whole-Body and Cycle Ergometer Protocols.

    Science.gov (United States)

    Schaun, Gustavo Z; Del Vecchio, Fabrício B

    2018-01-01

    Schaun, GZ and Del Vecchio, FB. High-intensity interval exercises' acute impact on heart rate variability: comparison between whole-body and cycle ergometer protocols. J Strength Cond Res 32(1): 223-229, 2018-Study aimed to compare the effects of 2 high-intensity interval training (HIIT) protocols on heart rate variability. Twelve young adult males (23.3 ± 3.9 years, 177.8 ± 7.4 cm, 76.9 ± 12.9 kg) volunteered to participate. In a randomized cross-over design, subjects performed 2 HIIT protocols, 1 on a cycle ergometer (Tabata protocol [TBT]; eight 20-second bouts at 170% Pmax interspersed by 10-second rest) and another with whole-body calisthenic exercises (McRae protocol; eight 20-second all-out intervals interspersed by 10-second rest). Heart rate variability outcomes in the time, frequency, and nonlinear domains were assessed on 3 moments: (a) presession; (b) immediately postsession; and (c) 24 hours postsession. Results revealed that RRmean, Ln rMSSD, Ln high frequency (HF), and Ln low frequency (LF) were significantly reduced immediately postsession (p ≤ 0.001) and returned to baseline 24 h after both protocols. In addition, LF/HF ratio was reduced 24 h postsession (p ≤ 0.01) and SD2 was significantly lower immediately postsession only in TBT. Our main finding was that responses from heart rate autonomic control were similar in both protocols, despite different modes of exercise performed. Specifically, exercises resulted in a high parasympathetic inhibition immediately after session with subsequent recovery within 1 day. These results suggest that subjects were already recovered the day after and can help coaches to better program training sessions with such protocols.

  20. Plant hydraulic strategies and their variability at high latitudes: insights from a southern Canadian boreal forest site

    Science.gov (United States)

    Pappas, C.; Matheny, A. M.; Maillet, J.; Baltzer, J. L.; Stephens, J.; Barr, A.; Black, T. A.; Sonnentag, O.

    2016-12-01

    Boreal forests cover about one third of the world's forested area with a large part of the boreal zone located in Canada. These high-latitude ecosystems respond rapidly to environmental changes. Plant water stress and the resulting drought-induced mortality has been recently hypothesised as a major driver of forest changes in western Canada. Although boreal forests often exhibit low floristic complexity, local scale abiotic heterogeneities may lead to highly variable plant functional traits and thus to diverging plant responses to environmental changes. However, detailed measurements of plant hydraulic strategies and their inter- and intra-specific variability are still lacking for these ecosystems. Here, we quantify plant water use and hydraulic strategies of black spruce (Picea mariana) and larch (Larix laricina), that are widespread in the boreal zone, at a long-term monitoring site located in central Saskatchewan (53.99° N, 105.12° W; elevation 628.94 m a.s.l.). The site is characterized by a mature black spruce overstorey that dominates the landscape with few larch individuals. The ground cover consists mainly of mosses with some peat moss and lichens over a rich soil organic layer. Tree-level sap flux density, measured with Granier-style thermal dissipation probes (N=39), and concurrently recorded radial stem dynamics, measured with high frequency dendrometers (N=13), are used to quantify plant hydraulic functioning during the 2016 growing season. Hydrometeorological measurements, including soil moisture and micrometeorological data, are used to describe environmental constraints in plant water use. Tree-level dynamics are then integrated to the landscape and compared with ecosystem-level evapotranspiration measurements from an adjacent eddy-covariance flux tower. This experimental design allows us to quantify the main environmental drivers that shape plant hydraulic strategies in this southern boreal zone and to provide new insights into the inter- and

  1. Insights Into Deglacial Through Holocene Climate Variability At The Peru-Chile Margin From Very High Sedimentation Rate Marine Cores

    Science.gov (United States)

    Chazen, C.; Dejong, H.; Altabet, M.; Herbert, T.

    2007-12-01

    The Peru-Chile upwelling system is situated at the epicenter of the modern ENSO System. The high settling flux of organic materials and poor ventilation of subsurface waters makes the Peru upwelling system one of the world's three major oxygen minimum/denitrification zones (Codispoti and Christensen, 1985). Extremely high sedimentation rates and permanent hypoxic/anoxic subsurface waters create excellent conditions for the preservation of organic matter. Despite the significance of this region in regards to paleoceanography and paleoclimatology, relatively little work has been done to characterize past Peruvian climate because carbonate dissolution hinders the use of conventional paleoclimate methods and hiatuses frequently interrupt the record. However, using nitrogen isotopes and alkenone paleothermometry on multiple sediment cores from the Margin we have managed to overcome many of these challenges to create a nearly continuous SST (Uk`37), productivity (C37total), biogenic opal and denitrification (δN15) record from the LGM through the late Holocene. Remarkably, recent work has revealed an annually laminated core, which spans from 1.4-8.0ka uninterrupted, providing a unique window into Holocene climate variability. Modern-day upwelling induced climate at the Peru-Chile margin is characterized by cold temperatures (21.5°C) high productivity and strong denitrification, which has persisted since the mid Holocene (4ka). The mid Holocene also marks the beginning of a dramatic increase in seasonality and ENSO variability consistent with other tropical climate indicators. Climate variability in the Mid-early Holocene shows a distinctively different pattern from that of the late Holocene; unproductive warm temperatures persist through the early Holocene in what can be described as a permanent El Niño-like state. Early tropical warming occurred near 17ka along with an unprecedented increase in denitrification, which is decoupled from local productivity. Early onset

  2. Serological diagnosis of paracoccidioidomycosis: high rate of inter-laboratorial variability among medical mycology reference centers.

    Directory of Open Access Journals (Sweden)

    Monica Scarpelli Martinelli Vidal

    2014-09-01

    Full Text Available Serological tests have long been established as rapid, simple and inexpensive tools for the diagnosis and follow-up of PCM. However, different protocols and antigen preparations are used and the few attempts to standardize the routine serological methods have not succeeded.We compared the performance of six Brazilian reference centers for serological diagnosis of PCM. Each center provided 30 sera of PCM patients, with positive high, intermediate and low titers, which were defined as the "reference" titers. Each center then applied its own antigen preparation and serological routine test, either semiquantitative double immunodifusion or counterimmmunoelectrophoresis, in the 150 sera from the other five centers blindly as regard to the "reference" titers. Titers were transformed into scores: 0 (negative, 1 (healing titers, 2 (active disease, low titers and 3 (active disease, high titers according to each center's criteria. Major discordances were considered between scores indicating active disease and scores indicating negative or healing titers; such discordance when associated with proper clinical and other laboratorial data, may correspond to different approaches to the patient's treatment. Surprisingly, all centers exhibited a high rate of "major" discordances with a mean of 31 (20% discordant scores. Alternatively, when the scores given by one center to their own sera were compared with the scores given to their sera by the remaining five other centers, a high rate of major discordances was also found, with a mean number of 14.8 sera in 30 presenting a discordance with at least one other center. The data also suggest that centers that used CIE and pool of isolates for antigen preparation performed better.There are inconsistencies among the laboratories that are strong enough to result in conflicting information regarding the patients' treatment. Renewed efforts should be promoted to improve standardization of the serological diagnosis of PCM.

  3. The variability and controls of rock strength along rocky coasts of central Spitsbergen, High Arctic

    Science.gov (United States)

    Strzelecki, Mateusz Czesław

    2017-09-01

    This paper presents the results of the Schmidt Hammer Rock Tests (SHRTs) across a range of rocky coastal landforms. Northern Billefjorden (central Spitsbergen), represents typical High Arctic microtidal fjord environment. Sheltered location and prolonged sea-ice conditions limit wave action. Coastal cliffs, shore platforms and skerries are developed in various rock types including limestone, sandstone, anhydrite/gypsum, dolomite and metamorphic outcrops. SHRT demonstrated a broad variety of relationships between rock strength and distance from shoreline, presence of sediment cover, distribution of snow patches and icefoot, and accumulations of seaweed and driftwood. In general, rock cliff surfaces were the most resistant in their lower and middle zones, that are thermally insulated by thick winter snowdrifts. More exposed cliff tops were fractured and weathered. The differences in rock strength observed along the shore platforms were highly dependent on thickness of sediment cover and shoreline configuration promoting stronger rock surfaces in areas exposed to the longest wave fetch and washed from gravel deposits. Rock strength of skerry islands is influenced by tidal action controlling the duration of tide inundation and movement of sea-ice scratching boulder surfaces. The results presented in this paper emphasize the richness of rock coast geomorphology and processes operating in High Arctic settings.

  4. High energy fast neutrons from the Harwell variable energy cyclotron. II. Biologic studies in mammalian systems

    International Nuclear Information System (INIS)

    Berry, R.J.; Bance, D.A.; Barnes, D.W.H.; Cox, R.; Goodhead, D.T.; Sansom, J.M.; Thacker, J.

    1977-01-01

    A high energy fast neutron beam potentially suitable for radiotherapy has been described in a companion paper. Its biologic effects have been studied in the following experimental systems: clonal survival and mutation induction after irradiation in vitro in Chinese hamster cells and human diploid fibroblasts; survival of reproductive capacity in vivo of murine hemopoietic colony-forming cells and murine intestinal crypts after irradiation in vivo; survival of reproductive capacity in vivo after irradiation in vitro or in vivo of murine lymphocytic leukemia cells; acute intestinal death following total body irradiation of mice and guinea pigs; and hemopoietic death following total body irradiation of mice and guinea pigs. The relative biologic effectiveness of these high energy neutrons varied among the different biologic systems, and in several cases varied with the size of the radiation dose. The oxygen enhancement ratio was studied in murine lymphocytic leukemia cells irradiated under aerobic or hypoxic conditions in vitro and assayed for survival of reproductive capacity in vivo. Compared with x-rays, the potential therapeutic gain factor for these neutrons was about 1.5. This work represents a ''radiobiologic calibration'' program which it is suggested should be undertaken before new and unknown fast neutron spectra are used for experimental radiotherapy. The results are compared with biologic studies carried out at high energy fast neutron generators in the United States

  5. High-resolution ultrasound imaging and noninvasive optoacoustic monitoring of blood variables in peripheral blood vessels

    Science.gov (United States)

    Petrov, Irene Y.; Petrov, Yuriy; Prough, Donald S.; Esenaliev, Rinat O.

    2011-03-01

    Ultrasound imaging is being widely used in clinics to obtain diagnostic information non-invasively and in real time. A high-resolution ultrasound imaging platform, Vevo (VisualSonics, Inc.) provides in vivo, real-time images with exceptional resolution (up to 30 microns) using high-frequency transducers (up to 80 MHz). Recently, we built optoacoustic systems for probing radial artery and peripheral veins that can be used for noninvasive monitoring of total hemoglobin concentration, oxyhemoglobin saturation, and concentration of important endogenous and exogenous chromophores (such as ICG). In this work we used the high-resolution ultrasound imaging system Vevo 770 for visualization of the radial artery and peripheral veins and acquired corresponding optoacoustic signals from them using the optoacoustic systems. Analysis of the optoacoustic data with a specially developed algorithm allowed for measurement of blood oxygenation in the blood vessels as well as for continuous, real-time monitoring of arterial and venous blood oxygenation. Our results indicate that: 1) the optoacoustic technique (unlike pure optical approaches and other noninvasive techniques) is capable of accurate peripheral venous oxygenation measurement; and 2) peripheral venous oxygenation is dependent on skin temperature and local hemodynamics. Moreover, we performed for the first time (to the best of our knowledge) a comparative study of optoacoustic arterial oximetry and a standard pulse oximeter in humans and demonstrated superior performance of the optoacoustic arterial oximeter, in particular at low blood flow.

  6. High Variability in Nosocomial Clostridium difficile Infection Rates Across Hospitals After Colorectal Resection.

    Science.gov (United States)

    Aquina, Christopher T; Probst, Christian P; Becerra, Adan Z; Hensley, Bradley J; Iannuzzi, James C; Noyes, Katia; Monson, John R T; Fleming, Fergal J

    2016-04-01

    Hospital-acquired Clostridium difficile infection is associated with adverse patient outcomes and high medical costs. The incidence and severity of C. difficile has been rising in both medical and surgical patients. Our aim was to assess risk factors and variation associated with the development of nosocomial C. difficile colitis among patients undergoing colorectal resection. This was a retrospective cohort study. The study included segmental colectomy and proctectomy cases in New York State from 2005 to 2013. The study cohort included 150,878 colorectal resections. Patients with a documented previous history of C. difficile infection or residence outside of New York State were excluded. A diagnosis of C. difficile colitis either during the index hospital stay or on readmission within 30 days was the main measure. C. difficile colitis occurred in 3323 patients (2.2%). Unadjusted C. difficile colitis rates ranged from 0% to 11.3% among surgeons and 0% to 6.8% among hospitals. After controlling for patient, surgeon, and hospital characteristics using mixed-effects multivariable analysis, significant unexplained variation in C. difficile rates remained present across hospitals but not surgeons. Patient factors explained only 24% of the total hospital-level variation, and known surgeon and hospital-level characteristics explained an additional 8% of the total hospital-level variation. Therefore, ≈70% of the hospital variation in C. difficile infection rates remained unexplained by captured patient, surgeon, and hospital factors. Furthermore, there was an ≈5-fold difference in adjusted C. difficile rates across hospitals. A limited set of hospital and surgeon characteristics was available. Colorectal surgery patients appear to be at high risk for C. difficile infection, and alarming variation in nosocomial C. difficile infection rates currently exists among hospitals after colorectal resection. Given the high morbidity and cost associated with C. difficile colitis

  7. Estimation of the high-spatial-resolution variability in extreme wind speeds for forestry applications

    Directory of Open Access Journals (Sweden)

    A. Venäläinen

    2017-07-01

    Full Text Available The bioeconomy has an increasing role to play in climate change mitigation and the sustainable development of national economies. In Finland, a forested country, over 50 % of the current bioeconomy relies on the sustainable management and utilization of forest resources. Wind storms are a major risk that forests are exposed to and high-spatial-resolution analysis of the most vulnerable locations can produce risk assessment of forest management planning. In this paper, we examine the feasibility of the wind multiplier approach for downscaling of maximum wind speed, using 20 m spatial resolution CORINE land-use dataset and high-resolution digital elevation data. A coarse spatial resolution estimate of the 10-year return level of maximum wind speed was obtained from the ERA-Interim reanalyzed data. Using a geospatial re-mapping technique the data were downscaled to 26 meteorological station locations to represent very diverse environments. Applying a comparison, we find that the downscaled 10-year return levels represent 66 % of the observed variation among the stations examined. In addition, the spatial variation in wind-multiplier-downscaled 10-year return level wind was compared with the WAsP model-simulated wind. The heterogeneous test area was situated in northern Finland, and it was found that the major features of the spatial variation were similar, but in some locations, there were relatively large differences. The results indicate that the wind multiplier method offers a pragmatic and computationally feasible tool for identifying at a high spatial resolution those locations with the highest forest wind damage risks. It can also be used to provide the necessary wind climate information for wind damage risk model calculations, thus making it possible to estimate the probability of predicted threshold wind speeds for wind damage and consequently the probability (and amount of wind damage for certain forest stand configurations.

  8. Mobile high-voltage switchboard. Variable and uncomplicated; Mobile Hochspannungsschaltanlage. Variabel und unkompliziert in der Anwendung

    Energy Technology Data Exchange (ETDEWEB)

    Albert, Andreas [Siemens AG, Erlangen (Germany). Sector Energy

    2009-07-13

    The mobile high-voltage switchboard ''REE-Movil 2'' for voltages up to 245 kV provides a complete and nearly autonomous switchboard in a container, a solution that has been available in the medium-voltage sector for some time already. It can be used whenever a quick replacement of a switchboard section or a temporary supplement to a switching substation is needed. The container is mounted on a trailer for maximum flexibility and mobility. (orig.)

  9. High spatial variability of coral, sponges and gorgonian assemblages in a well preserved reef

    Directory of Open Access Journals (Sweden)

    Patricia González-Díaz

    2010-06-01

    Full Text Available The main goal of this research was to obtain baseline field data of the composition of sponges, corals, and gorgonian assemblages that can be used as a reference for future analyses of anthropogenic impact. We tested the hypothesis that relatively homogeneous and well preserved reef units can present notable natural variability in the composition of their communities which are unassociated with changes in land proximity or a human impact gradient. Research was carried out in July 2006 at Los Colorados reef, located in the northwestern region of Pinar del Río Province, Cuba at 12 sampling stations. The biotopes selected were crest, terrace edge and spur and grove. Ecological indicators were diversity of corals, species composition, density of corals, hydrocorals, gorgonians and sponges, and density of selected coral species. A total of 2659 colonies of scleractineans corals representing 36 species were counted. The most abundant species in the crest biotope were Millepora alcicornis, Acropora palmata and Porites astreoides; in the terrace edge and spur and grove, the most abundant species were Siderastrea siderea, Stephanocoenia intersepta, Porites astreoides, Agaricia agaricites and Montastraea cavernosa. We found differences among sites for several indicators (e.g. density of corals, sponges and gorgonians and for selected species, but they could not be associated to any gradient of land influence or human impact. Therefore, sites inside a relatively homogeneous reef unit can present notable natural differences in the composition of their communities. Rev. Biol. Trop. 58 (2: 621-634. Epub 2010 June 02.El objetivo principal de la investigación fue obtener una línea base de la composición de las comunidades de esponjas, corales y gorgonias que pueda ser utilizada como referencia para futuros análisis de impacto antrópico. Nuestra hipótesis es que un arrecife relativamente homogéneo y bien conservado, presenta una variabilidad natural

  10. Portable gamma-ray holdup and attributes measurements of high- and variable-burnup plutonium

    International Nuclear Information System (INIS)

    Wenz, T.R.; Russo, P.A.; Miller, M.C.; Menlove, H.O.; Takahashi, S.; Yamamoto, Y.; Aoki, I.

    1991-01-01

    High burnup-plutonium holdup has been assayed quantitatively by low resolution gamma-ray spectrometry. The assay was calibrated with four plutonium standards representing a range of fuel burnup and 241 Am content. Selection of a calibration standard based on its qualitative spectral similarity to gamma-ray spectra of the process material is partially responsible for the success of these holdup measurements. The spectral analysis method is based on the determination of net counts in a single spectral region of interest (ROI). However, the low-resolution gamma-ray assay signal for the high-burnup plutonium includes unknown amounts of contamination from 241 Am. For most needs, the range of calibration standards required for this selection procedure is not available. A new low-resolution gamma-ray spectral analysis procedure for assay of 239 Pu has been developed. The procedure uses the calculated isotope activity ratios and the measured net counts in three spectral ROIs to evaluate and remove the 241 Am contamination from the 239 Pu assay signal on a spectrum-by-spectrum basis. The calibration for the new procedure requires only a single plutonium standard. The procedure also provides a measure of the burnup and age attributes of holdup deposits. The new procedure has been demonstrated using portable gamma-ray spectroscopy equipment for a wide range of plutonium standards and has also been applied to the assay of 239 Pu holdup in a mixed oxide fuel fabrication facility. 10 refs., 5 figs., 3 tabs

  11. High repetition rate laser-driven MeV ion acceleration at variable background pressures

    Science.gov (United States)

    Snyder, Joseph; Ngirmang, Gregory; Orban, Chris; Feister, Scott; Morrison, John; Frische, Kyle; Chowdhury, Enam; Roquemore, W. M.

    2017-10-01

    Ultra-intense laser-plasma interactions (LPI) can produce highly energetic photons, electrons, and ions with numerous potential real-world applications. Many of these applications will require repeatable, high repetition targets that are suitable for LPI experiments. Liquid targets can meet many of these needs, but they typically require higher chamber pressure than is used for many low repetition rate experiments. The effect of background pressure on the LPI has not been thoroughly studied. With this in mind, the Extreme Light group at the Air Force Research Lab has carried out MeV ion and electron acceleration experiments at kHz repetition rate with background pressures ranging from 30 mTorr to >1 Torr using a submicron ethylene glycol liquid sheet target. We present these results and provide two-dimensional particle-in-cell simulation results that offer insight on the thresholds for the efficient acceleration of electrons and ions. This research is supported by the Air Force Office of Scientific Research under LRIR Project 17RQCOR504 under the management of Dr. Riq Parra and Dr. Jean-Luc Cambier. Support was also provided by the DOD HPCMP Internship Program.

  12. Predicting abundance and variability of ice nucleating particles in precipitation at the high-altitude observatory Jungfraujoch

    Directory of Open Access Journals (Sweden)

    E. Stopelli

    2016-07-01

    Full Text Available Nucleation of ice affects the properties of clouds and the formation of precipitation. Quantitative data on how ice nucleating particles (INPs determine the distribution, occurrence and intensity of precipitation are still scarce. INPs active at −8 °C (INPs−8 were observed for 2 years in precipitation samples at the High-Altitude Research Station Jungfraujoch (Switzerland at 3580 m a.s.l. Several environmental parameters were scanned for their capability to predict the observed abundance and variability of INPs−8. Those singularly presenting the best correlations with observed number of INPs−8 (residual fraction of water vapour, wind speed, air temperature, number of particles with diameter larger than 0.5 µm, season, and source region of particles were implemented as potential predictor variables in statistical multiple linear regression models. These models were calibrated with 84 precipitation samples collected during the first year of observations; their predictive power was successively validated on the set of 15 precipitation samples collected during the second year. The model performing best in calibration and validation explains more than 75 % of the whole variability of INPs−8 in precipitation and indicates that a high abundance of INPs−8 is to be expected whenever high wind speed coincides with air masses having experienced little or no precipitation prior to sampling. Such conditions occur during frontal passages, often accompanied by precipitation. Therefore, the circumstances when INPs−8 could be sufficiently abundant to initiate the ice phase in clouds may frequently coincide with meteorological conditions favourable to the onset of precipitation events.

  13. High Variability in Cellular Stoichiometry of Carbon, Nitrogen, and Phosphorus Within Classes of Marine Eukaryotic Phytoplankton Under Sufficient Nutrient Conditions.

    Science.gov (United States)

    Garcia, Nathan S; Sexton, Julie; Riggins, Tracey; Brown, Jeff; Lomas, Michael W; Martiny, Adam C

    2018-01-01

    Current hypotheses suggest that cellular elemental stoichiometry of marine eukaryotic phytoplankton such as the ratios of cellular carbon:nitrogen:phosphorus (C:N:P) vary between phylogenetic groups. To investigate how phylogenetic structure, cell volume, growth rate, and temperature interact to affect the cellular elemental stoichiometry of marine eukaryotic phytoplankton, we examined the C:N:P composition in 30 isolates across 7 classes of marine phytoplankton that were grown with a sufficient supply of nutrients and nitrate as the nitrogen source. The isolates covered a wide range in cell volume (5 orders of magnitude), growth rate (temperature (2-24°C). Our analysis indicates that C:N:P is highly variable, with statistical model residuals accounting for over half of the total variance and no relationship between phylogeny and elemental stoichiometry. Furthermore, our data indicated that variability in C:P, N:P, and C:N within Bacillariophyceae (diatoms) was as high as that among all of the isolates that we examined. In addition, a linear statistical model identified a positive relationship between diatom cell volume and C:P and N:P. Among all of the isolates that we examined, the statistical model identified temperature as a significant factor, consistent with the temperature-dependent translation efficiency model, but temperature only explained 5% of the total statistical model variance. While some of our results support data from previous field studies, the high variability of elemental ratios within Bacillariophyceae contradicts previous work that suggests that this cosmopolitan group of microalgae has consistently low C:P and N:P ratios in comparison with other groups.

  14. A universal system for highly efficient cardiac differentiation of human induced pluripotent stem cells that eliminates interline variability.

    Directory of Open Access Journals (Sweden)

    Paul W Burridge

    2011-04-01

    Full Text Available The production of cardiomyocytes from human induced pluripotent stem cells (hiPSC holds great promise for patient-specific cardiotoxicity drug testing, disease modeling, and cardiac regeneration. However, existing protocols for the differentiation of hiPSC to the cardiac lineage are inefficient and highly variable. We describe a highly efficient system for differentiation of human embryonic stem cells (hESC and hiPSC to the cardiac lineage. This system eliminated the variability in cardiac differentiation capacity of a variety of human pluripotent stem cells (hPSC, including hiPSC generated from CD34(+ cord blood using non-viral, non-integrating methods.We systematically and rigorously optimized >45 experimental variables to develop a universal cardiac differentiation system that produced contracting human embryoid bodies (hEB with an improved efficiency of 94.7±2.4% in an accelerated nine days from four hESC and seven hiPSC lines tested, including hiPSC derived from neonatal CD34(+ cord blood and adult fibroblasts using non-integrating episomal plasmids. This cost-effective differentiation method employed forced aggregation hEB formation in a chemically defined medium, along with staged exposure to physiological (5% oxygen, and optimized concentrations of mesodermal morphogens BMP4 and FGF2, polyvinyl alcohol, serum, and insulin. The contracting hEB derived using these methods were composed of high percentages (64-89% of cardiac troponin I(+ cells that displayed ultrastructural properties of functional cardiomyocytes and uniform electrophysiological profiles responsive to cardioactive drugs.This efficient and cost-effective universal system for cardiac differentiation of hiPSC allows a potentially unlimited production of functional cardiomyocytes suitable for application to hPSC-based drug development, cardiac disease modeling, and the future generation of clinically-safe nonviral human cardiac cells for regenerative medicine.

  15. High Levels of Genetic Diversity of Plasmodium falciparum Populations in Papua New Guinea despite Variable Infection Prevalence

    Science.gov (United States)

    Barry, Alyssa E.; Schultz, Lee; Senn, Nicholas; Nale, Joe; Kiniboro, Benson; Siba, Peter M.; Mueller, Ivo; Reeder, John C.

    2013-01-01

    High levels of genetic diversity in Plasmodium falciparum populations are an obstacle to malaria control. Here, we investigate the relationship between local variation in malaria epidemiology and parasite genetic diversity in Papua New Guinea (PNG). Cross-sectional malaria surveys were performed in 14 villages spanning four distinct malaria-endemic areas on the north coast, including one area that was sampled during the dry season. High-resolution msp2 genotyping of 2,147 blood samples identified 761 P. falciparum infections containing a total of 1,392 clones whose genotypes were used to measure genetic diversity. Considerable variability in infection prevalence and mean multiplicity of infection was observed at all of the study sites, with the area sampled during the dry season showing particularly striking local variability. Genetic diversity was strongly associated with multiplicity of infection but not with infection prevalence. In highly endemic areas, differences in infection prevalence may not translate into a decrease in parasite population diversity. PMID:23400571

  16. Variable High Order Multiblock Overlapping Grid Methods for Mixed Steady and Unsteady Multiscale Viscous Flows

    Science.gov (United States)

    Sjogreen, Bjoern; Yee, H. C.

    2007-01-01

    Flows containing steady or nearly steady strong shocks in parts of the flow field, and unsteady turbulence with shocklets on other parts of the flow field are difficult to capture accurately and efficiently employing the same numerical scheme even under the multiblock grid or adaptive grid refinement framework. On one hand, sixth-order or higher shock-capturing methods are appropriate for unsteady turbulence with shocklets. On the other hand, lower order shock-capturing methods are more effective for strong steady shocks in terms of convergence. In order to minimize the shortcomings of low order and high order shock-capturing schemes for the subject flows,a multi- block overlapping grid with different orders of accuracy on different blocks is proposed. Test cases to illustrate the performance of the new solver are included.

  17. Multivariate linear regression of high-dimensional fMRI data with multiple target variables.

    Science.gov (United States)

    Valente, Giancarlo; Castellanos, Agustin Lage; Vanacore, Gianluca; Formisano, Elia

    2014-05-01

    Multivariate regression is increasingly used to study the relation between fMRI spatial activation patterns and experimental stimuli or behavioral ratings. With linear models, informative brain locations are identified by mapping the model coefficients. This is a central aspect in neuroimaging, as it provides the sought-after link between the activity of neuronal populations and subject's perception, cognition or behavior. Here, we show that mapping of informative brain locations using multivariate linear regression (MLR) may lead to incorrect conclusions and interpretations. MLR algorithms for high dimensional data are designed to deal with targets (stimuli or behavioral ratings, in fMRI) separately, and the predictive map of a model integrates information deriving from both neural activity patterns and experimental design. Not accounting explicitly for the presence of other targets whose associated activity spatially overlaps with the one of interest may lead to predictive maps of troublesome interpretation. We propose a new model that can correctly identify the spatial patterns associated with a target while achieving good generalization. For each target, the training is based on an augmented dataset, which includes all remaining targets. The estimation on such datasets produces both maps and interaction coefficients, which are then used to generalize. The proposed formulation is independent of the regression algorithm employed. We validate this model on simulated fMRI data and on a publicly available dataset. Results indicate that our method achieves high spatial sensitivity and good generalization and that it helps disentangle specific neural effects from interaction with predictive maps associated with other targets. Copyright © 2013 Wiley Periodicals, Inc.

  18. A highly efficient SDRAM controller supporting variable-length burst access and batch process for discrete reads

    Science.gov (United States)

    Li, Nan; Wang, Junzheng

    2016-03-01

    A highly efficient Synchronous Dynamic Random Access Memory (SDRAM) controller supporting variable-length burst access and batch process for discrete reads is proposed in this paper. Based on the Principle of Locality, command First In First Out (FIFO) and address range detector are designed within this controller to accelerate its responses to discrete read requests, which dramatically improves the average Effective Bus Utilization Ratio (EBUR) of SDRAM. Our controller is finally verified by driving the Micron 256-Mb SDRAM MT48LC16M16A2. Successful simulation and verification results show that our controller exhibits much higher EBUR than do most existing designs in case of discrete reads.

  19. A novel smart rotor support with shape memory alloy metal rubber for high temperatures and variable amplitude vibrations

    International Nuclear Information System (INIS)

    Ma, Yanhong; Zhang, Qicheng; Zhang, Dayi; Hong, Jie; Scarpa, Fabrizio; Liu, Baolong

    2014-01-01

    The work describes the design, manufacturing and testing of a smart rotor support with shape memory alloy metal rubber (SMA-MR) elements, able to provide variable stiffness and damping characteristics with temperature, motion amplitude and excitation frequency. Differences in damping behavior and nonlinear stiffness between SMA-MR and more traditional metal rubber supports are discussed. The mechanical performance shown by the prototype demonstrates the feasibility of using the SMA-MR concept for active vibration control in rotordynamics, in particular at high temperatures and large amplitude vibrations. (paper)

  20. A study of flux control for high-efficiency speed control of variable flux permanent magnet motor

    Directory of Open Access Journals (Sweden)

    Young Hyun Kim

    2018-05-01

    Full Text Available In this study, we evaluate the performance of permanent magnets (PMs. The efficiency of attraction in the high speed region was studied using the variable flux memory motor (VFMM. It is presented in order to analyze the magnetic characteristics of PMs, using the second quadrant plan data with re- and de-magnetization. In addition, this study focuses on the evaluation of operational characteristics relative to the magnetizing directions according to the d-axis currents, by using one of the finite element solutions. The feasibility of application for the VFMM has been experimentally demonstrated.

  1. A study of flux control for high-efficiency speed control of variable flux permanent magnet motor

    Science.gov (United States)

    Kim, Young Hyun; Lee, Seong Soo; Lee, Jung Ho

    2018-05-01

    In this study, we evaluate the performance of permanent magnets (PMs). The efficiency of attraction in the high speed region was studied using the variable flux memory motor (VFMM). It is presented in order to analyze the magnetic characteristics of PMs, using the second quadrant plan data with re- and de-magnetization. In addition, this study focuses on the evaluation of operational characteristics relative to the magnetizing directions according to the d-axis currents, by using one of the finite element solutions. The feasibility of application for the VFMM has been experimentally demonstrated.

  2. Cross-sectional associations between high-deprivation home and neighbourhood environments, and health-related variables among Liverpool children

    Science.gov (United States)

    Noonan, Robert J; Boddy, Lynne M; Knowles, Zoe R; Fairclough, Stuart J

    2016-01-01

    Objectives (1) To investigate differences in health-related, home and neighbourhood environmental variables between Liverpool children living in areas of high deprivation (HD) and medium-to-high deprivation (MD) and (2) to assess associations between these perceived home and neighbourhood environments and health-related variables stratified by deprivation group. Design Cross-sectional study. Setting 10 Liverpool primary schools in 2014. Participants 194 children aged 9–10 years. Main outcome measures Health-related variables (self-reported physical activity (PA) (Physical Activity Questionnaire for Older Children, PAQ-C), cardiorespiratory fitness, body mass index (BMI) z-scores, waist circumference), home environment variables: (garden/backyard access, independent mobility, screen-based media restrictions, bedroom media) and neighbourhood walkability (Neighbourhood Environment Walkability Scale for Youth, NEWS-Y). Explanatory measures Area deprivation. Results There were significant differences between HD and MD children's BMI z-scores (p<0.01), waist circumference (p<0.001) and cardiorespiratory fitness (p<0.01). HD children had significantly higher bedroom media availability (p<0.05) and independent mobility scores than MD children (p<0.05). MD children had significantly higher residential density and neighbourhood aesthetics scores, and lower crime safety, pedestrian and road traffic safety scores than HD children, all of which indicated higher walkability (p<0.01). HD children's BMI z-scores (β=−0.29, p<0.01) and waist circumferences (β=−0.27, p<0.01) were inversely associated with neighbourhood aesthetics. HD children's PA was negatively associated with bedroom media (β=−0.24, p<0.01), and MD children's PA was positively associated with independent mobility (β=0.25, p<0.01). MD children's independent mobility was inversely associated with crime safety (β=−0.28, p<0.01) and neighbourhood aesthetics (β=−0.24, p<0.05). Conclusions Children

  3. High variability of the heterogeneous ice nucleation potential of oxalic acid dihydrate and sodium oxalate

    Directory of Open Access Journals (Sweden)

    R. Wagner

    2010-08-01

    Full Text Available The heterogeneous ice nucleation potential of airborne oxalic acid dihydrate and sodium oxalate particles in the deposition and condensation mode has been investigated by controlled expansion cooling cycles in the AIDA aerosol and cloud chamber of the Karlsruhe Institute of Technology at temperatures between 244 and 228 K. Previous laboratory studies have highlighted the particular role of oxalic acid dihydrate as the only species amongst a variety of other investigated dicarboxylic acids to be capable of acting as a heterogeneous ice nucleus in both the deposition and immersion mode. We could confirm a high deposition mode ice activity for 0.03 to 0.8 μm sized oxalic acid dihydrate particles that were either formed by nucleation from a gaseous oxalic acid/air mixture or by rapid crystallisation of highly supersaturated aqueous oxalic acid solution droplets. The critical saturation ratio with respect to ice required for deposition nucleation was found to be less than 1.1 and the size-dependent ice-active fraction of the aerosol population was in the range from 0.1 to 22%. In contrast, oxalic acid dihydrate particles that had crystallised from less supersaturated solution droplets and had been allowed to slowly grow in a supersaturated environment from still unfrozen oxalic acid solution droplets over a time period of several hours were found to be much poorer heterogeneous ice nuclei. We speculate that under these conditions a crystal surface structure with less-active sites for the initiation of ice nucleation was generated. Such particles partially proved to be almost ice-inactive in both the deposition and condensation mode. At times, the heterogeneous ice nucleation ability of oxalic acid dihydrate significantly changed when the particles had been processed in preceding cloud droplet activation steps. Such behaviour was also observed for the second investigated species, namely sodium oxalate. Our experiments address the atmospheric scenario

  4. High variability of the heterogeneous ice nucleation potential of oxalic acid dihydrate and sodium oxalate

    Science.gov (United States)

    Wagner, R.; Möhler, O.; Saathoff, H.; Schnaiter, M.; Leisner, T.

    2010-08-01

    The heterogeneous ice nucleation potential of airborne oxalic acid dihydrate and sodium oxalate particles in the deposition and condensation mode has been investigated by controlled expansion cooling cycles in the AIDA aerosol and cloud chamber of the Karlsruhe Institute of Technology at temperatures between 244 and 228 K. Previous laboratory studies have highlighted the particular role of oxalic acid dihydrate as the only species amongst a variety of other investigated dicarboxylic acids to be capable of acting as a heterogeneous ice nucleus in both the deposition and immersion mode. We could confirm a high deposition mode ice activity for 0.03 to 0.8 μm sized oxalic acid dihydrate particles that were either formed by nucleation from a gaseous oxalic acid/air mixture or by rapid crystallisation of highly supersaturated aqueous oxalic acid solution droplets. The critical saturation ratio with respect to ice required for deposition nucleation was found to be less than 1.1 and the size-dependent ice-active fraction of the aerosol population was in the range from 0.1 to 22%. In contrast, oxalic acid dihydrate particles that had crystallised from less supersaturated solution droplets and had been allowed to slowly grow in a supersaturated environment from still unfrozen oxalic acid solution droplets over a time period of several hours were found to be much poorer heterogeneous ice nuclei. We speculate that under these conditions a crystal surface structure with less-active sites for the initiation of ice nucleation was generated. Such particles partially proved to be almost ice-inactive in both the deposition and condensation mode. At times, the heterogeneous ice nucleation ability of oxalic acid dihydrate significantly changed when the particles had been processed in preceding cloud droplet activation steps. Such behaviour was also observed for the second investigated species, namely sodium oxalate. Our experiments address the atmospheric scenario that coating layers

  5. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    Directory of Open Access Journals (Sweden)

    Huaiyong Luo

    Full Text Available The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

  6. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

    Science.gov (United States)

    Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

    2015-01-01

    The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

  7. Eelgrass Leaf Surface Microbiomes Are Locally Variable and Highly Correlated with Epibiotic Eukaryotes

    Directory of Open Access Journals (Sweden)

    Mia M. Bengtsson

    2017-07-01

    Full Text Available Eelgrass (Zostera marina is a marine foundation species essential for coastal ecosystem services around the northern hemisphere. Like all macroscopic organisms, it possesses a microbiome (here defined as an associated prokaryotic community which may play critical roles in modulating the interaction of eelgrass with its environment. For example, its leaf surface microbiome could inhibit or attract eukaryotic epibionts which may overgrow the eelgrass leading to reduced primary productivity and subsequent eelgrass meadow decline. We used amplicon sequencing of the 16S and 18S rRNA genes of prokaryotes and eukaryotes to assess the leaf surface microbiome (prokaryotes as well as eukaryotic epibionts in- and outside lagoons on the German Baltic Sea coast. Prokaryote microbiomes varied substantially both between sites inside lagoons and between open coastal and lagoon sites. Water depth, leaf area and biofilm chlorophyll a concentration explained a large amount of variation in both prokaryotic and eukaryotic community composition. The prokaryotic microbiome and eukaryotic epibiont communities were highly correlated, and network analysis revealed disproportionate co-occurrence between a limited number of eukaryotic taxa and several bacterial taxa. This suggests that eelgrass leaf surfaces are home to a mosaic of microbiomes of several epibiotic eukaryotes, in addition to the microbiome of the eelgrass itself. Our findings thereby underline that eukaryotic diversity should be taken into account in order to explain prokaryotic microbiome assembly and dynamics in aquatic environments.

  8. The evolution of highly variable immunity genes across a passerine bird radiation.

    Science.gov (United States)

    O'Connor, E A; Strandh, M; Hasselquist, D; Nilsson, J-Å; Westerdahl, H

    2016-02-01

    To survive, individuals must be able to recognize and eliminate pathogens. The genes of the major histocompatibility complex (MHC) play an essential role in this process in vertebrates as their diversity affects the repertoire of pathogens that can be recognized by the immune system. Emerging evidence suggests that birds within the parvorder Passerida possess an exceptionally high number of MHC genes. However, this has yet to be directly investigated using a consistent framework, and the question of how this MHC diversity has evolved has not been addressed. We used next-generation sequencing to investigate how MHC class I gene copy number and sequence diversity varies across the Passerida radiation using twelve species chosen to represent the phylogenetic range of this group. Additionally, we performed phylogenetic analyses on this data to identify, for the first time, the evolutionary model that best describes how MHC class I gene diversity has evolved within Passerida. We found evidence of multiple MHC class I genes in every family tested, with an extremely broad range in gene copy number across Passerida. There was a strong phylogenetic signal in MHC gene copy number and diversity, and these traits appear to have evolved through a process of Brownian motion in the species studied, that is following the pattern of genetic drift or fluctuating selection, as opposed to towards a single optimal value or through evolutionary 'bursts'. By characterizing MHC class I gene diversity across Passerida in a systematic framework, this study provides a first step towards understanding this huge variation. © 2016 John Wiley & Sons Ltd.

  9. Sodium bicarbonate and high-intensity-cycling capacity: variability in responses.

    Science.gov (United States)

    Saunders, Bryan; Sale, Craig; Harris, Roger C; Sunderland, Caroline

    2014-07-01

    To determine whether gastrointestinal (GI) distress affects the ergogenicity of sodium bicarbonate and whether the degree of alkalemia or other metabolic responses is different between individuals who improve exercise capacity and those who do not. Twenty-one men completed 2 cycling-capacity tests at 110% of maximum power output. Participants were supplemented with 0.3 g/kg body mass of either placebo (maltodextrin) or sodium bicarbonate (SB). Blood pH, bicarbonate, base excess, and lactate were determined at baseline, preexercise, immediately postexercise, and 5 min postexercise. SB supplementation did not significantly increase total work done (TWD; P = .16, 46.8 ± 9.1 vs 45.6 ± 8.4 kJ, d = 0.14), although magnitude-based inferences suggested a 63% likelihood of a positive effect. When data were analyzed without 4 participants who experienced GI discomfort, TWD (P = .01) was significantly improved with SB. Immediately postexercise blood lactate was higher in SB for the individuals who improved but not for those who did not. There were also differences in the preexercise-to-postexercise change in blood pH, bicarbonate, and base excess between individuals who improved and those who did not. SB improved high-intensity-cycling capacity but only with the exclusion of participants experiencing GI discomfort. Differences in blood responses suggest that SB may not be beneficial to all individuals. Magnitude-based inferences suggested that the exercise effects are unlikely to be negative; therefore, individuals should determine whether they respond well to SB supplementation before competition.

  10. Genetic diversity of dispersed seeds is highly variable among leks of the long-wattled umbrellabird

    Science.gov (United States)

    Ottewell, Kym; Browne, Luke; Cabrera, Domingo; Olivo, Jorge; Karubian, Jordan

    2018-01-01

    Frugivorous animals frequently generate clumped distributions of seeds away from source trees, but genetic consequences of this phenomenon remain poorly resolved. Seed dispersal of the palm Oenocarpus bataua by long-wattled umbrellabirds Cephalopterus penduliger generates high seed densities in leks (i.e., multi-male display sites), providing a suitable venue to investigate how dispersal by this frugivore may influence seed source diversity and genetic structure at local and landscape levels. We found moderate levels of maternal seed source diversity in primary seed rain across five leks in northwest Ecuador (unweighted mean alpha diversity α = 9.52, weighted mean αr = 3.52), with considerable variation among leks (αr range: 1.81-24.55). Qualitatively similar findings were obtained for allelic diversity and heterozygosity. Higher densities of O. bataua adults around leks were associated with higher values of αr and heterozygosity (non-significant trends) and allelic diversity (significant correlation). Seed source overlap between different leks was not common but did occur at low frequency, providing evidence for long-distance seed dispersal by umbrellabirds into leks. Our findings are consistent with the idea that seed pool diversity within leks may be shaped by the interaction between density of local trees, which can vary considerably between leks, and umbrellabird foraging ecology, particularly a lack of territorial defense of fruiting trees. Taken as a whole, this work adds to our growing appreciation of the ways resource distribution and associated frugivore foraging behaviors mechanistically shape seed dispersal outcomes and the distribution of plant genotypes across the landscape.

  11. High Resolution Simulations of Future Climate in West Africa Using a Variable-Resolution Atmospheric Model

    Science.gov (United States)

    Adegoke, J. O.; Engelbrecht, F.; Vezhapparambu, S.

    2013-12-01

    In previous work demonstrated the application of a var¬iable-resolution global atmospheric model, the conformal-cubic atmospheric model (CCAM), across a wide range of spatial and time scales to investigate the ability of the model to provide realistic simulations of present-day climate and plausible projections of future climate change over sub-Saharan Africa. By applying the model in stretched-grid mode the versatility of the model dynamics, numerical formulation and physical parameterizations to function across a range of length scales over the region of interest, was also explored. We primarily used CCAM to illustrate the capability of the model to function as a flexible downscaling tool at the climate-change time scale. Here we report on additional long term climate projection studies performed by downscaling at much higher resolutions (8 Km) over an area that stretches from just south of Sahara desert to the southern coast of the Niger Delta and into the Gulf of Guinea. To perform these simulations, CCAM was provided with synoptic-scale forcing of atmospheric circulation from 2.5 deg resolution NCEP reanalysis at 6-hourly interval and SSTs from NCEP reanalysis data uses as lower boundary forcing. CCAM 60 Km resolution downscaled to 8 Km (Schmidt factor 24.75) then 8 Km resolution simulation downscaled to 1 Km (Schmidt factor 200) over an area approximately 50 Km x 50 Km in the southern Lake Chad Basin (LCB). Our intent in conducting these high resolution model runs was to obtain a deeper understanding of linkages between the projected future climate and the hydrological processes that control the surface water regime in this part of sub-Saharan Africa.

  12. The effect of highly variable topography on the spatial distribution of Aniba perutilis (Lauraceae in the Colombian Andes

    Directory of Open Access Journals (Sweden)

    José C. Fagua

    2013-03-01

    Full Text Available Topography is a factor that can significantly affect the diversity and the distribution of trees species in tropical forests. Aniba perutilis, a timber species listed as vulnerable to extinction, is widely distributed in Andean forest fragments, especially in those with highly variable topography. Based on field surveys and logistic regression analyses, we studied the population structure and the effect of highly variable topography on the spatial distribution of this tree in three protected forest fragments in the central Andes of Colombia. Individuals of A. perutilis were mainly found on mountain ridges and hills with gentle slopes; no individuals were found in valleys. Using a species distribution model with presence/absence data, we showed that the available habitat for A. perutilis is significantly smaller than the extension of the fragments and much smaller than the extension of the currently protected areas. Our results have important implications for the conservation of A. perutilis and likely for other threatened Andean tree species, which can also have locally restricted distributions due to highly variable local topography.La topografía es un factor que puede afectar considerablemente la diversidad y la distribución de las especies de árboles tropicales. Aniba perutilis, una especie de árbol maderable vulnerable a la extinción, está ampliamente distribuida en fragmentos de bosques andinos, especialmente en aquellos con topografía altamente variable. A partir de trabajo de campo y análisis de regresión logística, estudiamos la estructura de la población y los efectos de la topografía sobre la distribución espacial de este árbol en tres fragmentos de bosque en la cordillera central de Colombia que actualmente se encuentran protegidos. Los individuos de A. perutilis se encontraron principalmente en los filos de montaña y colinas con gradientes topográficos suaves; no se encontraron individuos en los valles. A partir de un

  13. Mid-Holocene onset of high-amplitude decadal to centennial scale variability along the Peru Chile Margin

    Science.gov (United States)

    Chazen, C. R.; Altabet, M.; Herbert, T. D.

    2008-12-01

    Understanding the natural climate variations in the eastern tropical Pacific is crucial for predicting the evolution of the El Niño-Southern Oscillation (ENSO) system and for anticipating the ways in which increases in atmospheric CO2 will affect climate. Here we present the first continuous, high-resolution (11-12 yr) climate record across the mid-Holocene transition (10ka-1.4ka) from the Peru-Chile Margin near the epicenter of the modern ENSO system. Although the high productivity of the Peru margin should promote high deposition rates, and the anaerobic bottom water conditions should inhibit sediment mixing by benthic organisms, nearly all sediment cores recovered from this region suffer from major gaps in Holocene sedimentation. Our data comes from a ~5 meter piston core collected from the mid-Peruvian shelf (15° 15"S, 75° 58"W, ~250mwd) in the heart of the oxygen minimum/denitrification zone that provides the first uninterrupted archive of conditions along the Peru-Chile margin. A suite of geochemical proxies allow us to reconstruct sea surface temperature (SST- Uk'37), phytoplankton productivity (C37total and %BSi), and thermocline ventilation (δ15N), variables that are tightly correlated to ENSO events today. Despite the observation that the mean late Holocene state of all three variables did not change over the last 10,000 years, our data reveal a dramatic increase in climate variability after the mid Holocene (~5ka); represented by prolonged periods (50-200yrs) of climate extremes, which are absent in the early Holocene. To further investigate these climate extremes we examine benthic foraminiferal assemblages and oxygen isotopes in combination with our other proxy records in selected late Holocene sections. The roughly centennial-scale oscillations do not show typical El Niño-La Niña correlations between proxies. We therefore posit that a significant fraction of super-ENSO variance during the course of the Holocene may originate outside the tropics

  14. High Intrapatient Variability of Tacrolimus Exposure in the Early Period After Liver Transplantation Is Associated With Poorer Outcomes.

    Science.gov (United States)

    Rayar, Michel; Tron, Camille; Jézéquel, Caroline; Beaurepaire, Jean Marie; Petitcollin, Antoine; Houssel-Debry, Pauline; Camus, Christophe; Verdier, Marie Clémence; Dehlawi, Ammar; Lakéhal, Mohamed; Desfourneaux, Véronique; Meunier, Bernard; Sulpice, Laurent; Bellissant, Eric; Boudjema, Karim; Lemaitre, Florian

    2018-03-01

    Tacrolimus (TAC) is the cornerstone of immunosuppressive regimen in liver transplantation (LT). Its pharmacokinetics is characterized by a high interpatient and intrapatient variability (IPV) leading to an unpredictable dose-response relationship. The aim of our study was to evaluate the impact of TAC IPV (IPV) on graft and patient outcomes after LT. We retrospectively analyzed 812 LT recipients treated with TAC. The IPV of TAC concentrations was estimated by calculating the coefficient of variation (CV) of whole blood trough concentrations. Patients were categorized in 2 groups: low IPV (CV < 40%) and high IPV (CV ≥ 40%). There were significantly more neurologic complications (31.2% vs 16.6%, P < 0.001), cardiovascular complications (19.7% vs 9.7%, P < 0.001), and acute renal failure requiring dialysis (8.5% vs 2.2%, P < 0.001) in the high CV group than in the low CV group. Moreover, graft survival was significantly poorer in the high CV group (hazard ratio, 1.42; 95% confidence interval, 1.04-1.95; P = 0.03). A pretransplantation elevated Model for End-Stage Liver Disease score (P < 0.001) and Child-Pugh grade (P < 0.001) were identified as risk factors for presenting a high CV. A high CV of TAC concentrations was found to be predictive of TAC-related toxicity and poorer survival.

  15. Low vagally-mediated heart rate variability and increased susceptibility to ventricular arrhythmias in rats bred for high anxiety.

    Science.gov (United States)

    Carnevali, Luca; Trombini, Mimosa; Graiani, Gallia; Madeddu, Denise; Quaini, Federico; Landgraf, Rainer; Neumann, Inga D; Nalivaiko, Eugene; Sgoifo, Andrea

    2014-04-10

    In humans, there is a documented association between anxiety disorders and cardiovascular disease. Putative underlying mechanisms may include an impairment of the autonomic nervous system control of cardiac function. The primary objective of the present study was to characterize cardiac autonomic modulation and susceptibility to arrhythmias in genetic lines of rats that differ largely in their anxiety level. To reach this goal, electrocardiographic recordings were performed in high-anxiety behavior (HAB, n=10) and low-anxiety behavior (LAB, n=10) rats at rest, during stressful stimuli and under autonomic pharmacological manipulations, and analyzed by means of time- and frequency-domain indexes of heart rate variability. During resting conditions, HAB rats displayed a reduced heart rate variability, mostly in terms of lower parasympathetic (vagal) modulation compared to LAB rats. In HAB rats, this relatively low cardiac vagal control was associated with smaller heart rate responsiveness to acute stressors compared to LAB counterparts. In addition, beta-adrenergic pharmacological stimulation induced a larger incidence of ventricular tachyarrhythmias in HABs compared to LABs. At sacrifice, a moderate increase in heart-body weight ratio was observed in HAB rats. We conclude that high levels of anxiety-related behavior in rats are associated with signs of i) impaired autonomic modulation of heart rate (low vagally-mediated heart rate variability), ii) poor adaptive heart rate responsiveness to stressful stimuli, iii) increased arrhythmia susceptibility, and iv) cardiac hypertrophy. These results highlight the utility of the HAB/LAB model for investigating the mechanistic basis of the comorbidity between anxiety disorders and cardiovascular disease. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Geostatistical characterization of the Callovo-Oxfordian clay variability: from conventional and high resolution log data

    International Nuclear Information System (INIS)

    Lefranc, Marie

    2007-01-01

    Andra (National Radioactive Waste Management Agency) has conducted studies in its Meuse/Haute-Marne Underground Research Laboratory located at a depth of about 490 m in a 155-million-year-old argillaceous rock: the Callovo-Oxfordian argillite. The purpose of the present work is to obtain as much information as possible from high-resolution log data and to optimize their analysis to specify and characterize space-time variations of the argillites from the Meuse/Haute-Marne site and subsequently predict the evolution of argillite properties on a 250 km 2 zone around the underground laboratory (transposition zone). The aim is to outline a methodology to transform depth intervals into geological time intervals and thus to quantify precisely the sedimentation rate variation, estimate duration; for example the duration of bio-stratigraphical units or of hiatuses. The latter point is particularly important because a continuous time recording is often assumed in geological modelling. The spatial variations can be studied on various scales. First, well-to-well correlations are established between seven wells at different scales. Relative variations of the thickness are observed locally. Second, FMI (Full-bore Formation Micro-Imager, Schlumberger) data are studied in detail to extract as much information as possible. For example, the analysis of FMI images reveals a clear carbonate - clay inter-bedding which displays cycles. Third, geostatistical tools are used to study these cycles. The vario-graphic analysis of conventional log data shows one metre cycles. With FMI data, smaller periods can be detected. Variogram modelling and factorial kriging analysis suggest that three spatial periods exist. They vary vertically and laterally in the boreholes but cycle ratios are stable and similar to orbital-cycle ratios (Milankovitch cycles). The three periods correspond to eccentricity, obliquity and precession. Since the duration of these orbital cycles is known, depth intervals can

  17. High variability of TB, HIV, hepatitis C treatment and opioid substitution therapy among prisoners in Germany.

    Science.gov (United States)

    Müller, Jana; Schmidt, Daniel; Kollan, Christian; Lehmann, Marc; Bremer, Viviane; Zimmermann, Ruth

    2017-10-25

    In Germany, medical care of prisoners is completely separated from extramural health care. The extent and quality of medical care among prisoners in Germany are therefore largely unknown. We performed a secondary data analysis of pharmacy sales data for tuberculosis (TB), HIV, hepatitis C (HCV) and opioid substitution treatment (OST) delivered to prisons in 11 federal states (FS) in Germany between 01/2012 and 03/2013. The aims of this study were to assess (i) the treatment availability for the selected diseases and OST in German prisons, (ii) the proportion of prisoners treated per FS and overall for TB, HIV, HCV and OST during the study period. Substances unique to or typically used for the treatment of each disease were defined as marker substances with defined daily doses (DDD). For each marker substance we assessed the cumulative number of DDD, the average daily number of DDD (DDD d ) and average treatment prevalence per day in percent (adTP). Accordingly, the DDD d represents one person treated per day and the adTP means the proportion of prisoners treated per day. We compared the adTP of the diseases with previously measured prevalences. We obtained data from pharmacies supplying prisons in 11 of 16 German FS. Of the included prisons, 41% were supplied with medicines for TB, 71% for HIV and 58% for HCV and OST. Twice as many delivered marker substances for TB were indicated for the continuation phase and chemoprevention than the intensive phase. The HIV adTP ranged from 0.06% to 0.94%, HCV adTP ranged from 0.03% to 0.59% and OST adTP ranged from 0% to 7.90%. The overall adTP for the respective treatment was 0.39% for HIV, 0.12% for HCV and 2.18% for OST. According to our findings treatment rates for TB were consistent with the expected TB prevalence, at least in Berlin. HIV treatment seems to be offered to an adequate proportion of estimated infected prisoners. In contrast, the HCV treatment prevalence was low. High variation among FS in provision of all

  18. High-frequency and meso-scale winter sea-ice variability in the Southern Ocean in a high-resolution global ocean model

    Science.gov (United States)

    Stössel, Achim; von Storch, Jin-Song; Notz, Dirk; Haak, Helmuth; Gerdes, Rüdiger

    2018-03-01

    This study is on high-frequency temporal variability (HFV) and meso-scale spatial variability (MSV) of winter sea-ice drift in the Southern Ocean simulated with a global high-resolution (0.1°) sea ice-ocean model. Hourly model output is used to distinguish MSV characteristics via patterns of mean kinetic energy (MKE) and turbulent kinetic energy (TKE) of ice drift, surface currents, and wind stress, and HFV characteristics via time series of raw variables and correlations. We find that (1) along the ice edge, the MSV of ice drift coincides with that of surface currents, in particular such due to ocean eddies; (2) along the coast, the MKE of ice drift is substantially larger than its TKE and coincides with the MKE of wind stress; (3) in the interior of the ice pack, the TKE of ice drift is larger than its MKE, mostly following the TKE pattern of wind stress; (4) the HFV of ice drift is dominated by weather events, and, in the absence of tidal currents, locally and to a much smaller degree by inertial oscillations; (5) along the ice edge, the curl of the ice drift is highly correlated with that of surface currents, mostly reflecting the impact of ocean eddies. Where ocean eddies occur and the ice is relatively thin, ice velocity is characterized by enhanced relative vorticity, largely matching that of surface currents. Along the ice edge, ocean eddies produce distinct ice filaments, the realism of which is largely confirmed by high-resolution satellite passive-microwave data.

  19. Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

    KAUST Repository

    Hunt, Paul

    2010-09-16

    Background: Classical and quantitative linkage analyses of genetic crosses have traditionally been used to map genes of interest, such as those conferring chloroquine or quinine resistance in malaria parasites. Next-generation sequencing technologies now present the possibility of determining genome-wide genetic variation at single base-pair resolution. Here, we combine in vivo experimental evolution, a rapid genetic strategy and whole genome re-sequencing to identify the precise genetic basis of artemisinin resistance in a lineage of the rodent malaria parasite, Plasmodium chabaudi. Such genetic markers will further the investigation of resistance and its control in natural infections of the human malaria, P. falciparum.Results: A lineage of isogenic in vivo drug-selected mutant P. chabaudi parasites was investigated. By measuring the artemisinin responses of these clones, the appearance of an in vivo artemisinin resistance phenotype within the lineage was defined. The underlying genetic locus was mapped to a region of chromosome 2 by Linkage Group Selection in two different genetic crosses. Whole-genome deep coverage short-read re-sequencing (IlluminaSolexa) defined the point mutations, insertions, deletions and copy-number variations arising in the lineage. Eight point mutations arise within the mutant lineage, only one of which appears on chromosome 2. This missense mutation arises contemporaneously with artemisinin resistance and maps to a gene encoding a de-ubiquitinating enzyme.Conclusions: This integrated approach facilitates the rapid identification of mutations conferring selectable phenotypes, without prior knowledge of biological and molecular mechanisms. For malaria, this model can identify candidate genes before resistant parasites are commonly observed in natural human malaria populations. 2010 Hunt et al; licensee BioMed Central Ltd.

  20. Seasonal variability of stream water quality response to storm events captured using high-frequency and multi-parameter data

    Science.gov (United States)

    Fovet, O.; Humbert, G.; Dupas, R.; Gascuel-Odoux, C.; Gruau, G.; Jaffrezic, A.; Thelusma, G.; Faucheux, M.; Gilliet, N.; Hamon, Y.; Grimaldi, C.

    2018-04-01

    The response of stream chemistry to storm is of major interest for understanding the export of dissolved and particulate species from catchments. The related challenge is the identification of active hydrological flow paths during these events and of the sources of chemical elements for which these events are hot moments of exports. An original four-year data set that combines high frequency records of stream flow, turbidity, nitrate and dissolved organic carbon concentrations, and piezometric levels was used to characterize storm responses in a headwater agricultural catchment. The data set was used to test to which extend the shallow groundwater was impacting the variability of storm responses. A total of 177 events were described using a set of quantitative and functional descriptors related to precipitation, stream and groundwater pre-event status and event dynamics, and to the relative dynamics between water quality parameters and flow via hysteresis indices. This approach led to identify different types of response for each water quality parameter which occurrence can be quantified and related to the seasonal functioning of the catchment. This study demonstrates that high-frequency records of water quality are precious tools to study/unique in their ability to emphasize the variability of catchment storm responses.

  1. Proposal and Development of a High Voltage Variable Frequency Alternating Current Power System for Hybrid Electric Aircraft

    Science.gov (United States)

    Sadey, David J.; Taylor, Linda M.; Beach, Raymond F.

    2017-01-01

    The development of ultra-efficient commercial vehicles and the transition to low-carbon emission propulsion are seen as strategic thrust paths within NASA Aeronautics. A critical enabler to these paths comes in the form of hybrid electric propulsion systems. For megawatt-class systems, the best power system topology for these hybrid electric propulsion systems is debatable. Current proposals within NASA and the Aero community suggest using a combination of alternating current (AC) and direct current (DC) for power generation, transmission, and distribution. This paper proposes an alternative to the current thought model through the use of a primarily high voltage AC power system, supported by the Convergent Aeronautics Solutions (CAS) Project. This system relies heavily on the use of doubly-fed induction machines (DFIMs), which provide high power densities, minimal power conversion, and variable speed operation. The paper presents background on the activity along with the system architecture, development status, and preliminary results.

  2. Potential of deterministic and geostatistical rainfall interpolation under high rainfall variability and dry spells: case of Kenya's Central Highlands

    Science.gov (United States)

    Kisaka, M. Oscar; Mucheru-Muna, M.; Ngetich, F. K.; Mugwe, J.; Mugendi, D.; Mairura, F.; Shisanya, C.; Makokha, G. L.

    2016-04-01

    Drier parts of Kenya's Central Highlands endure persistent crop failure and declining agricultural productivity. These have, in part, attributed to high temperatures, prolonged dry spells and erratic rainfall. Understanding spatial-temporal variability of climatic indices such as rainfall at seasonal level is critical for optimal rain-fed agricultural productivity and natural resource management in the study area. However, the predominant setbacks in analysing hydro-meteorological events are occasioned by either lack, inadequate, or inconsistent meteorological data. Like in most other places, the sole sources of climatic data in the study region are scarce and only limited to single stations, yet with persistent missing/unrecorded data making their utilization a challenge. This study examined seasonal anomalies and variability in rainfall, drought occurrence and the efficacy of interpolation techniques in the drier regions of eastern Kenyan. Rainfall data from five stations (Machang'a, Kiritiri, Kiambere and Kindaruma and Embu) were sourced from both the Kenya Meteorology Department and on-site primary recording. Owing to some experimental work ongoing, automated recording for primary dailies in Machang'a have been ongoing since the year 2000 to date; thus, Machang'a was treated as reference (for period of record) station for selection of other stations in the region. The other stations had data sets of over 15 years with missing data of less than 10 % as required by the world meteorological organization whose quality check is subject to the Centre for Climate Systems Modeling (C2SM) through MeteoSwiss and EMPA bodies. The dailies were also subjected to homogeneity testing to evaluate whether they came from the same population. Rainfall anomaly index, coefficients of variance and probability were utilized in the analyses of rainfall variability. Spline, kriging and inverse distance weighting interpolation techniques were assessed using daily rainfall data and

  3. Highly variable recurrence of tsunamis in the 7,400 years before the 2004 Indian Ocean tsunami

    Science.gov (United States)

    Horton, B.; Rubin, C. M.; Sieh, K.; Jessica, P.; Daly, P.; Ismail, N.; Parnell, A. C.

    2017-12-01

    The devastating 2004 Indian Ocean tsunami caught millions of coastal residents and the scientific community off-guard. Subsequent research in the Indian Ocean basin has identified prehistoric tsunamis, but the timing and recurrence intervals of such events are uncertain. Here, we identify coastal caves as a new depositional environment for reconstructing tsunami records and present a 5,000 year record of continuous tsunami deposits from a coastal cave in Sumatra, Indonesia which shows the irregular recurrence of 11 tsunamis between 7,400 and 2,900 years BP. The data demonstrates that the 2004 tsunami was just the latest in a sequence of devastating tsunamis stretching back to at least the early Holocene and suggests a high likelihood for future tsunamis in the Indian Ocean. The sedimentary record in the cave shows that ruptures of the Sunda megathrust vary between large (which generated the 2004 Indian Ocean tsunami) and smaller slip failures. The chronology of events suggests the recurrence of multiple smaller tsunamis within relatively short time periods, interrupted by long periods of strain accumulation followed by giant tsunamis. The average time period between tsunamis is about 450 years with intervals ranging from a long, dormant period of over 2,000 years, to multiple tsunamis within the span of a century. The very long dormant period suggests that the Sunda megathrust is capable of accumulating large slip deficits between earthquakes. Such a high slip rupture would produce a substantially larger earthquake than the 2004 event. Although there is evidence that the likelihood of another tsunamigenic earthquake in Aceh province is high, these variable recurrence intervals suggest that long dormant periods may follow Sunda Megathrust ruptures as large as that of 2004 Indian Ocean tsunami. The remarkable variability of recurrence suggests that regional hazard mitigation plans should be based upon the high likelihood of future destructive tsunami demonstrated by

  4. The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences.

    Directory of Open Access Journals (Sweden)

    Fabian König

    Full Text Available The monoclonal antibody S9.6 is a widely-used tool to purify, analyse and quantify R-loop structures in cells. A previous study using the surface plasmon resonance technology and a single-chain variable fragment (scFv of S9.6 showed high affinity (0.6 nM for DNA-RNA and also a high affinity (2.7 nM for RNA-RNA hybrids. We used the microscale thermophoresis method allowing surface independent interaction studies and electromobility shift assays to evaluate additional RNA-DNA hybrid sequences and to quantify the binding affinities of the S9.6 antibody with respect to distinct sequences and their GC-content. Our results confirm high affinity binding to previously analysed sequences, but reveals that binding affinities are highly sequence specific. Our study presents R-loop sequences that independent of GC-content and in different sequence variations exhibit either no binding, binding affinities in the micromolar range and as well high affinity binding in the nanomolar range. Our study questions the usefulness of the S9.6 antibody in the quantitative analysis of R-loop sequences in vivo.

  5. New gentle-wing high-shear granulator: impact of processing variables on granules and tablets characteristics of high-drug loading formulation using design of experiment approach.

    Science.gov (United States)

    Fayed, Mohamed H; Abdel-Rahman, Sayed I; Alanazi, Fars K; Ahmed, Mahrous O; Tawfeek, Hesham M; Al-Shdefat, Ramadan I

    2017-10-01

    The aim of this work was to study the application of design of experiment (DoE) approach in defining design space for granulation and tableting processes using a novel gentle-wing high-shear granulator. According to quality-by-design (QbD) prospective, critical attributes of granules, and tablets should be ensured by manufacturing process design. A face-centered central composite design has been employed in order to investigate the effect of water amount (X 1 ), impeller speed (X 2 ), wet massing time (X 3 ), and water addition rate (X 4 ) as independent process variables on granules and tablets characteristics. Acetaminophen was used as a model drug and granulation experiments were carried out using dry addition of povidone k30. The dried granules have been analyzed for their size distribution, density, and flow pattern. Additionally, the produced tablets have been investigated for; weight uniformity, breaking force, friability and percent capping, disintegration time, and drug dissolution. Results of regression analysis showed that water amount, impeller speed and wet massing time have significant (p tablets characteristics. However, the water amount had the most pronounced effect as indicated by its higher parameter estimate. On the other hand, water addition rate showed a minimal impact on granules and tablets properties. In conclusion, water amount, impeller speed, and wet massing time could be considered as critical process variables. Thus, understanding the relationship between these variables and quality attributes of granules and corresponding tablets provides the basis for adjusting granulation variables in order to optimize product performance.

  6. High-resolution paleoclimate records of Holocene hydroclimatic variability in the Eastern Colombian Andes from Lago de Tota

    Science.gov (United States)

    Ahmed, M. N.; Bird, B. W.; Escobar, J.; Polissar, P. J.

    2017-12-01

    The Northern Hemisphere (NH) South American Monsoon (SAM) is a significant source of precipitation for the North Andes (north of 0˚) and has major control over regional hydroclimate variability. Holocene-length histories of NH SAM variability are few compared to the Southern Hemisphere (SH), limiting understanding of how these systems are connected on orbital and shorter timescales. Here, we present multi-proxy lake-sediment-based paleoclimate and paleohydrologic reconstructions from Lago de Tota, Colombia, using sedimentological, geochemical and leaf-wax hydrogen isotopic indicators from radiometically dated cores. The results indicate periods of wet and dry climate phases during the past 9000 BP with an average Holocene sedimentation rate 33cm/kyr. An increase in total organic matter (TOM) content and finer grain-size distributions was observed from 8000 to 3200 BP, suggesting a period of high lake level. This was followed by lower TOM and coarser grain sizes, suggesting lower lake levels from 3200 BP to the present. Although Tota's lake level pattern is antiphased with other lake level reconstructions from the NH and SH Andes, it is consistent with hypothesized changes in atmospheric convection over the Andes during the Holocene and the way in which they would be modified by the so-called dry island effect in the Colombian Andes. This suggests that a common forcing mechanism can be invoked to explain differing millennial-scale Andean hydroclimate changes, namely atmospheric convection. Orbital and Pacific atmosphere-forcing are therefore likely to have played a significant role in driving pan-Andean hydroclimate variability based on their inter-hemispheric influence on Andean convection.

  7. CALIDAD DE RED COMO VARIABLE MODULADORA DE DEPRESIÓN EN ADOLESCENTES ESTUDIANTES DE NIVEL MEDIO/ QUALITY NETWORK AS MODERATOR VARIABLE OF DEPRESSION IN TEENAGERS HIGH SCHOOL STUDENTS

    Directory of Open Access Journals (Sweden)

    Rocío Soria Trujano

    2010-04-01

    Full Text Available RESUMENEn un estudio previo (Nava & Vega, 2008 quisimos probar si alguna alteración emocional (depresión podía seratribuida a la lejanía de la red familiar, los análisis mostraron que sí era posible encontrar diferencias entre jóvenes recluidosy estudiantes universitarios. Sin embargo, los resultados del estudio anterior dejaban una duda, ¿sería posible encontrardepresión aun cuando no hay ausencia de familia de origen? Y, ¿qué variables explicarían tal fenómeno, en caso de encontrardiferencias? Por lo anterior, decidimos realizar un estudio en el cual los participantes fueran adolescentes sin ningunacarencia de familia o alteración psicológica aparente. Evaluamos diferentes variables: apoyo social, estrés, calidad de redy depresión. Los resultados mostraron que sí fue posible replicar los resultados del primer estudio, a pesar de que noexistieron alteraciones emocionales o de red graves. Las conclusiones son discutidas a la luz de los hallazgos empíricos yteóricos correspondientes.ABSTRACTIn a previous study (Nava & Vega, 2008 we wanted to prove if some emotional alterations (depression could beattributed to the remoteness of the family network, the analyses showed that it was possible to find differences betweenyoung adults to imprison and university students. Nevertheless, the results of the previous study left a doubt, would it bepossible to find depression even though there is no absence of origin of family? And what variable would explain suchphenomenon, in case of finding differences? By the previous thing, we decided to make a study where the participants wereadolescents without deficiency of family or apparent psychological alteration. We evaluated different variables, socialsupport, stress, quality of network and depression. The results showed that it was possible to talk back the results of the firststudy, although emotional alterations or of network did not exist seriously. The conclusions are discussed to the

  8. Erosion of the Alberta badlands produces highly variable and elevated heavy metal concentrations in the Red Deer River, Alberta.

    Science.gov (United States)

    Kerr, Jason G; Cooke, Colin A

    2017-10-15

    Erosion is important in the transport of heavy metals from terrestrial to fluvial environments. In this study, we investigated riverine heavy metal (Cd, Cu, Hg and Pb) dynamics in the Red Deer River (RDR) watershed at sites upstream (n=2) and downstream (n=7) of the Alberta badlands, an area of naturally high erosion. At sites draining the badlands, total water column Cd, Cu, Hg and Pb concentrations frequently exceeded guidelines for the protection of freshwater biota. Furthermore, peak concentrations of total Cd (9.8μgL -1 ), Cu (212μgL -1 ), Hg (649ngL -1 ) and Pb (361μgL -1 ) were higher than, or comparable to, values reported for rivers and streams heavily impacted by anthropogenic activities. Total suspended solids (TSS) explained a large proportion (r 2 =0.34-0.83) of the variation in total metal concentrations in the RDR and tributaries and metal fluxes were dominated by the particulate fraction (60-98%). Suspended sediment concentrations (C sed ) and metal to aluminum ratios were generally not indicative of substantial sediment enrichment. Rather, the highly variable and elevated metal concentrations in the RDR watershed were a function of the high and variable suspended sediment fluxes which characterize the river system. While the impact of this on aquatic biota requires further investigation, we suggest erosion in the Alberta badlands may be contributing to Hg-based fish consumption advisories in the RDR. Importantly, this highlights a broader need for information on contaminant dynamics in watersheds subject to elevated rates of erosion. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  9. Genetic variability, partial regression, Co-heritability studies and their implication in selection of high yielding potato gen

    International Nuclear Information System (INIS)

    Iqbal, Z.M.; Khan, S.A.

    2003-01-01

    Partial regression coefficient, genotypic and phenotypic variabilities, heritability co-heritability and genetic advance were studied in 15 Potato varieties of exotic and local origin. Both genotypic and phenotypic coefficients of variations were high for scab and rhizoctonia incidence percentage. Significant partial regression coefficient for emergence percentage indicated its relative importance in tuber yield. High heritability (broadsense) estimates coupled with high genetic advance for plant height, number of stems per plant and scab percentage revealed substantial contribution of additive genetic variance in the expression of these traits. Hence, the selection based on these characters could play a significant role in their improvement the dominance and epistatic variance was more important for character expression of yield ha/sup -1/, emergence and rhizoctonia percentage. This phenomenon is mainly due to the accumulative effects of low heritability and low to moderate genetic advance. The high co-heritability coupled with negative genotypic and phenotypic covariance revealed that selection of varieties having low scab and rhizoctonia percentage resulted in more potato yield. (author)

  10. High resolution heart rate variability analysis in patients with angina pectoris during coronary artery bypass graft surgery

    Science.gov (United States)

    Mironov, V. A.; Mironova, T. F.; Kuvatov, V. A.; Nokhrina, O. Yu.; Kuvatova, E. V.

    2017-12-01

    The purpose of the study is approbation of the capabilities of high-resolution rhythmocardiography (RCG) for the determination of the actual cardiovascular status of operated patients with angina pectoris during coronary artery bypass graft surgery (CABGS) for myocardial revascularization. The research was done by means of a KAP-RK-02-Mikor hardware-software complex with a monitor record and the time- and frequency-domain analyses of heart rate variability (HRV). Monitor records were made at each stage of CABGS in 123 patients. As a result, HRV manifested itself as a fairly adequate and promising method for the determination of the cardiovascular status during CABGS. In addition, the data of the HRV study during CABGS testify to the capability of RCG to determine the high risk of life-threatening cardioarrhythmias before and during operation, to different changes in sinoatrial heart node (SN) dysregulation, and contain the HRV symptoms of a high death risk before, during and after shunting. The loss of the peripheral autonomic sympathetic and parasympathetic control in SN in the form of the autonomic cardioneuropathy syndrome is a predictor of the complications related to CABGS. The obtained data on RCG monitoring of HRV recording are suggestive of wide prospects of the high-resolution RCG method to be used in cardiac surgery as a whole. The actual multivariant dysregulations of SN pacemaker activity testify to its adequacy to the pathophysiology of each period of the cardiac operation, according to the initial ischemic damages and localization of cardiosurgical manipulations during CABGS.

  11. Short Communication. Using high resolution UAV imagery to estimate tree variables in Pinus pinea plantation in Portugal

    Energy Technology Data Exchange (ETDEWEB)

    Guerra Hernandez, J.; Gonzalez-Ferreiro, E.; Sarmento, A.; Silva, J.; Nunes, A.; Correia, A.C.; Fontes, L.; Tomé, M.; Diaz-Varela, D.

    2016-07-01

    Aim of the study: The study aims to analyse the potential use of low‑cost unmanned aerial vehicle (UAV) imagery for the estimation of Pinus pinea L. variables at the individual tree level (position, tree height and crown diameter). Area of study: This study was conducted under the PINEA project focused on 16 ha of umbrella pine afforestation (Portugal) subjected to different treatments. Material and methods: The workflow involved: a) image acquisition with consumer‑grade cameras on board an UAV; b) orthomosaic and digital surface model (DSM) generation using structure-from-motion (SfM) image reconstruction; and c) automatic individual tree segmentation by using a mixed pixel‑ and region‑based based algorithm. Main results: The results of individual tree segmentation (position, height and crown diameter) were validated using field measurements from 3 inventory plots in the study area. All the trees of the plots were correctly detected. The RMSE values for the predicted heights and crown widths were 0.45 m and 0.63 m, respectively. Research highlights: The results demonstrate that tree variables can be automatically extracted from high resolution imagery. We highlight the use of UAV systems as a fast, reliable and cost‑effective technique for small scale applications. (Author)

  12. In silico, experimental, mechanistic model for extended-release felodipine disposition exhibiting complex absorption and a highly variable food interaction.

    Directory of Open Access Journals (Sweden)

    Sean H J Kim

    Full Text Available The objective of this study was to develop and explore new, in silico experimental methods for deciphering complex, highly variable absorption and food interaction pharmacokinetics observed for a modified-release drug product. Toward that aim, we constructed an executable software analog of study participants to whom product was administered orally. The analog is an object- and agent-oriented, discrete event system, which consists of grid spaces and event mechanisms that map abstractly to different physiological features and processes. Analog mechanisms were made sufficiently complicated to achieve prespecified similarity criteria. An equation-based gastrointestinal transit model with nonlinear mixed effects analysis provided a standard for comparison. Subject-specific parameterizations enabled each executed analog's plasma profile to mimic features of the corresponding six individual pairs of subject plasma profiles. All achieved prespecified, quantitative similarity criteria, and outperformed the gastrointestinal transit model estimations. We observed important subject-specific interactions within the simulation and mechanistic differences between the two models. We hypothesize that mechanisms, events, and their causes occurring during simulations had counterparts within the food interaction study: they are working, evolvable, concrete theories of dynamic interactions occurring within individual subjects. The approach presented provides new, experimental strategies for unraveling the mechanistic basis of complex pharmacological interactions and observed variability.

  13. Genetic Variability of Beauveria bassiana and a DNA Marker for Environmental Monitoring of a Highly Virulent Isolate Against Cosmopolites sordidus.

    Science.gov (United States)

    Ferri, D V; Munhoz, C F; Neves, P M O; Ferracin, L M; Sartori, D; Vieira, M L C; Fungaro, M H P

    2012-12-01

    The banana weevil Cosmopolites sordidus (Germar) is one of a number of pests that attack banana crops. The use of the entomopathogenic fungus Beauveria bassiana as a biological control agent for this pest may contribute towards reducing the application of chemical insecticides on banana crops. In this study, the genetic variability of a collection of Brazilian isolates of B. bassiana was evaluated. Samples were obtained from various geographic regions of Brazil, and from different hosts of the Curculionidae family. Based on the DNA fingerprints generated by RAPD and AFLP, we found that 92 and 88 % of the loci were polymorphic, respectively. The B. bassiana isolates were attributed to two genotypic clusters based on the RAPD data, and to three genotypic clusters, when analyzed with AFLP. The nucleotide sequences of nuclear ribosomal DNA intergenic spacers confirmed that all isolates are in fact B. bassiana. Analysis of molecular variance showed that variability among the isolates was not correlated with geographic origin or hosts. A RAPD-specific marker for isolate CG 1024, which is highly virulent to C. sordidus, was cloned and sequenced. Based on the sequences obtained, specific PCR primers BbasCG1024F (5'-TGC GGC TGA GGA GGA CT-3') and BbasCG1024R (5'-TGC GGC TGA GTG TAG AAC-3') were designed for detecting and monitoring this isolate in the field.

  14. The many ways sputum flows - Dealing with high within-subject variability in cystic fibrosis sputum rheology.

    Science.gov (United States)

    Radtke, Thomas; Böni, Lukas; Bohnacker, Peter; Fischer, Peter; Benden, Christian; Dressel, Holger

    2018-08-01

    We evaluated test-retest reliability of sputum viscoelastic properties in clinically stable patients with cystic fibrosis (CF). Data from a prospective, randomized crossover study was used to determine within-subject variability of sputum viscoelasticity (G', storage modulus and G", loss modulus at 1 and 10 rad s -1 ) and solids content over three consecutive visits. Precision of sputum properties was quantified by within-subject standard deviation (SD ws ), coefficient of variation (CV) and intraclass correlation coefficients (ICC). Fifteen clinically stable adults with CF (FEV 1 range 24-94% predicted) were included. No differences between study visits (mean ± SD 8 ± 2 days) were observed for any sputum rheology measure. CV's for G', G" and solids content ranged between 40.3-45.3% and ICC's between 0.21-0.42 indicating poor to fair test-retest reliability. Short-term within-subject variability of sputum properties is high in clinically stable adults with CF. Investigators applying shear rheology experiments in future prospective studies should consider using multiple measurements aiming to increase precision of sputum rheological outcomes. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Short Communication. Using high resolution UAV imagery to estimate tree variables in Pinus pinea plantation in Portugal

    International Nuclear Information System (INIS)

    Guerra Hernandez, J.; Gonzalez-Ferreiro, E.; Sarmento, A.; Silva, J.; Nunes, A.; Correia, A.C.; Fontes, L.; Tomé, M.; Diaz-Varela, D.

    2016-01-01

    Aim of the study: The study aims to analyse the potential use of low‑cost unmanned aerial vehicle (UAV) imagery for the estimation of Pinus pinea L. variables at the individual tree level (position, tree height and crown diameter). Area of study: This study was conducted under the PINEA project focused on 16 ha of umbrella pine afforestation (Portugal) subjected to different treatments. Material and methods: The workflow involved: a) image acquisition with consumer‑grade cameras on board an UAV; b) orthomosaic and digital surface model (DSM) generation using structure-from-motion (SfM) image reconstruction; and c) automatic individual tree segmentation by using a mixed pixel‑ and region‑based based algorithm. Main results: The results of individual tree segmentation (position, height and crown diameter) were validated using field measurements from 3 inventory plots in the study area. All the trees of the plots were correctly detected. The RMSE values for the predicted heights and crown widths were 0.45 m and 0.63 m, respectively. Research highlights: The results demonstrate that tree variables can be automatically extracted from high resolution imagery. We highlight the use of UAV systems as a fast, reliable and cost‑effective technique for small scale applications. (Author)

  16. Effects of Per-Pixel Variability on Uncertainties in Bathymetric Retrievals from High-Resolution Satellite Images

    Directory of Open Access Journals (Sweden)

    Elizabeth J. Botha

    2016-05-01

    Full Text Available Increased sophistication of high spatial resolution multispectral satellite sensors provides enhanced bathymetric mapping capability. However, the enhancements are counter-acted by per-pixel variability in sunglint, atmospheric path length and directional effects. This case-study highlights retrieval errors from images acquired at non-optimal geometrical combinations. The effects of variations in the environmental noise on water surface reflectance and the accuracy of environmental variable retrievals were quantified. Two WorldView-2 satellite images were acquired, within one minute of each other, with Image 1 placed in a near-optimal sun-sensor geometric configuration and Image 2 placed close to the specular point of the Bidirectional Reflectance Distribution Function (BRDF. Image 2 had higher total environmental noise due to increased surface glint and higher atmospheric path-scattering. Generally, depths were under-estimated from Image 2, compared to Image 1. A partial improvement in retrieval error after glint correction of Image 2 resulted in an increase of the maximum depth to which accurate depth estimations were returned. This case-study indicates that critical analysis of individual images, accounting for the entire sun elevation and azimuth and satellite sensor pointing and geometry as well as anticipated wave height and direction, is required to ensure an image is fit for purpose for aquatic data analysis.

  17. Highly variable recurrence of tsunamis in the 7,400 years before the 2004 Indian Ocean tsunami.

    Science.gov (United States)

    Rubin, Charles M; Horton, Benjamin P; Sieh, Kerry; Pilarczyk, Jessica E; Daly, Patrick; Ismail, Nazli; Parnell, Andrew C

    2017-07-19

    The devastating 2004 Indian Ocean tsunami caught millions of coastal residents and the scientific community off-guard. Subsequent research in the Indian Ocean basin has identified prehistoric tsunamis, but the timing and recurrence intervals of such events are uncertain. Here we present an extraordinary 7,400 year stratigraphic sequence of prehistoric tsunami deposits from a coastal cave in Aceh, Indonesia. This record demonstrates that at least 11 prehistoric tsunamis struck the Aceh coast between 7,400 and 2,900 years ago. The average time period between tsunamis is about 450 years with intervals ranging from a long, dormant period of over 2,000 years, to multiple tsunamis within the span of a century. Although there is evidence that the likelihood of another tsunamigenic earthquake in Aceh province is high, these variable recurrence intervals suggest that long dormant periods may follow Sunda megathrust ruptures as large as that of the 2004 Indian Ocean tsunami.

  18. Resistor capacitor, primitive variable solution of buoyant fluid flow within an enclosure with highly temperature dependent viscosity

    Energy Technology Data Exchange (ETDEWEB)

    Burns, S.P. [Texas Univ., Austin, TX (United States); Gianoulakis, S.E. [Sandia National Labs., Albuquerque, NM (United States)

    1995-07-01

    A numerical solution for buoyant natural convection within a square enclosure containing a fluid with highly temperature dependent viscosity is presented. Although the fluid properties employed do not represent any real fluid, the large variation in the fluid viscosity with temperature is characteristic of turbulent flow modeling with eddy-viscosity concepts. Results are obtained using a primitive variable formulation and the resistor method. The results presented include velocity, temperature and pressure distributions within the enclosure as well as shear stress and heat flux distributions along the enclosure walls. Three mesh refinements were employed and uncertainty values are suggested for the final mesh refinement. These solutions are part of a contributed benchmark solution set for the subject problem.

  19. Assessment of local variability by high-throughput e-beam metrology for prediction of patterning defect probabilities

    Science.gov (United States)

    Wang, Fuming; Hunsche, Stefan; Anunciado, Roy; Corradi, Antonio; Tien, Hung Yu; Tang, Peng; Wei, Junwei; Wang, Yongjun; Fang, Wei; Wong, Patrick; van Oosten, Anton; van Ingen Schenau, Koen; Slachter, Bram

    2018-03-01

    We present an experimental study of pattern variability and defectivity, based on a large data set with more than 112 million SEM measurements from an HMI high-throughput e-beam tool. The test case is a 10nm node SRAM via array patterned with a DUV immersion LELE process, where we see a variation in mean size and litho sensitivities between different unique via patterns that leads to a seemingly qualitative differences in defectivity. The large available data volume enables further analysis to reliably distinguish global and local CDU variations, including a breakdown into local systematics and stochastics. A closer inspection of the tail end of the distributions and estimation of defect probabilities concludes that there is a common defect mechanism and defect threshold despite the observed differences of specific pattern characteristics. We expect that the analysis methodology can be applied for defect probability modeling as well as general process qualification in the future.

  20. Achieving a 100% Renewable Grid: Operating Electric Power Systems with Extremely High Levels of Variable Renewable Energy

    Energy Technology Data Exchange (ETDEWEB)

    Kroposki, Benjamin; Johnson, Brian; Zhang, Yingchen; Gevorgian, Vahan; Denholm, Paul; Hodge, Bri-Mathias; Hannegan, Bryan

    2017-03-01

    What does it mean to achieve a 100% renewable grid? Several countries already meet or come close to achieving this goal. Iceland, for example, supplies 100% of its electricity needs with either geothermal or hydropower. Other countries that have electric grids with high fractions of renewables based on hydropower include Norway (97%), Costa Rica (93%), Brazil (76%), and Canada (62%). Hydropower plants have been used for decades to create a relatively inexpensive, renewable form of energy, but these systems are limited by natural rainfall and geographic topology. Around the world, most good sites for large hydropower resources have already been developed. So how do other areas achieve 100% renewable grids? Variable renewable energy (VRE), such as wind and solar photovoltaic (PV) systems, will be a major contributor, and with the reduction in costs for these technologies during the last five years, large-scale deployments are happening around the world.

  1. MULTIWAVELENGTH VARIABILITY OF THE BLAZARS Mrk 421 AND 3C 454.3 IN THE HIGH STATE

    Energy Technology Data Exchange (ETDEWEB)

    Gaur, Haritma; Gupta, Alok C. [Aryabhatta Research Institute of Observational Sciences (ARIES), Manora Peak, Nainital 263129 (India); Wiita, Paul J., E-mail: haritma@aries.res.in [Department of Physics, College of New Jersey, P.O. Box 7718, Ewing, NJ 08628 (United States)

    2012-01-15

    We report the results of photometric observations of the blazars Mrk 421 and 3C 454.3 designed to search for intraday variability (IDV) and short-term variability (STV). Optical photometric observations were spread over 18 nights for Mrk 421 and 7 nights for 3C 454.3 during our observing run in 2009-2010 at the 1.04 m telescope at Aryabhatta Research Institute of Observational Sciences, India. Genuine IDV is found for the source 3C 454.3 but not for Mrk 421. Genuine STV is found for both sources. Mrk 421 was revealed by the Monitor of All-sky X-ray Image (MAXI) X-ray detector on the International Space Station to be in an exceptionally high flux state in 2010 January-February. We performed a correlation between the X-ray and optical bands to search for time delays and found a weak correlation with higher frequencies leading the lower frequencies by about 10 days. The blazar 3C 454.3 was found to be in a high flux state in 2009 November-December. We performed correlations in optical observations made at three telescopes, along with X-ray data from the MAXI camera and public release {gamma}-ray data from the Fermi space telescope. We found strong correlations between the {gamma}-ray and optical bands at a time lag of about four days, but the X-ray flux is not correlated with either. We briefly discuss the possible reasons for the time delays between these bands within the framework of existing models for X-ray and {gamma}-ray emission mechanisms.

  2. Effect of process variables on the density and durability of the pellets made from high moisture corn stover

    Energy Technology Data Exchange (ETDEWEB)

    Jaya Shankar Tumuluru

    2014-03-01

    A flat die pellet mill was used to understand the effect of high levels of feedstock moisture content in the range of 28–38% (w.b.), with die rotational speeds of 40–60 Hz, and preheating temperatures of 30–110 °C on the pelleting characteristics of 4.8 mm screen size ground corn stover using an 8 mm pellet die. The physical properties of the pelletised biomass studied are: (a) pellet moisture content, (b) unit, bulk and tapped density, and (c) durability. Pelletisation experiments were conducted based on central composite design. Analysis of variance (ANOVA) indicated that feedstock moisture content influenced all of the physical properties at P < 0.001. Pellet moisture content decreased with increase in preheating temperature to about 110 °C and decreasing the feedstock moisture content to about 28% (w.b.). Response surface models developed for quality attributes with respect to process variables has adequately described the process with coefficient of determination (R2) values of >0.88. The other pellet quality attributes such as unit, bulk, tapped density, were maximised at feedstock moisture content of 30–33% (w.b.), die speeds of >50 Hz and preheating temperature of >90 °C. In case of durability a medium moisture content of 33–34% (w.b.) and preheating temperatures of >70 °C and higher die speeds >50 Hz resulted in high durable pellets. It can be concluded from the present study that feedstock moisture content, followed by preheating, and die rotational speed are the interacting process variables influencing pellet moisture content, unit, bulk and tapped density and durability.

  3. Development of a split-flow system for high precision variable sample introduction in supercritical fluid chromatography.

    Science.gov (United States)

    Sakai, Miho; Hayakawa, Yoshihiro; Funada, Yasuhiro; Ando, Takashi; Fukusaki, Eiichiro; Bamba, Takeshi

    2017-09-15

    In this study, we propose a novel variable sample injection system based on full-loop injection, named the split-flow sample introduction system, for application in supercritical fluid chromatography (SFC). In this system, the mobile phase is split by the differential pressure between two back pressure regulators (BPRs) after full-loop injection suitable for SFC, and this differential pressure determines the introduction rate. Nine compounds with a wide range of characteristics were introduced with high reproducibility and universality, confirming that a robust variable sample injection system was achieved. We also investigated the control factors of our proposed system. Sample introduction was controlled by the ratio between the column-side pressure drops in splitless and split flow, ΔP columnsideinsplitless and ΔP columnsideinsplit , respectively, where ΔP columnsideinsplitless is related to the mobile phase flow rate and composition and the column resistance. When all other conditions are kept constant, increasing the make-up flow induces an additional pressure drop on the column side of the system, which leads to a reduced column-side flow rate, and hence decreased the amount of sample injected, even when the net pressure drop on the column side remains the same. Thus, sample introduction could be highly controlled at low sample introduction rate, regardless of the introduction conditions. This feature is advantageous because, as a control factor, the solvent in the make-up pump is independent of the column-side pressure drop. Copyright © 2017. Published by Elsevier B.V.

  4. Effect of process variables on synthesis of MgB2 by a high energy ball mill

    Directory of Open Access Journals (Sweden)

    Kurama Haldun

    2016-01-01

    Full Text Available The discovery of superconductivity of MgB2 in 2001, with a critical temperature of 39 K, offered the promise of important large-scale applications at around 20 K. Except than the other featured synthesis methods, mechanical activation performed by high energy ball mills, as bulk form synthesis or as a first step of wire and thin film productions, has considered as an effective alternative production route in recent years. The process of mechanical activation (MA starts with mixing the powders in the right proportion and loading the powder mixture into the mill with the grinding media. The milled powder is then consolidated into a bulk shape and heat-treated to obtain desired microstructure and properties. Thus, the important components of the MA process are the raw materials, mill type and process variables. During the MA process, heavy deformation of particles occure. This is manifested by the presence of a variety of crystal defects such as dislocations, vacancies, stacking faults and increased number of particle boundaries. The presence of this defect structure enhances the diffusivity of solute hence the critical currents and magnetic flux pinning ability of MgB2 are improved. The aim of the present study is to determine the effects of process variables such as ball-to-powder mass ratio, size of balls, milling time, annealing temperature and contribution of process control agent (toluene on the product size, morphology and conversion level of precursor powders to MgB2 after subsequent heat treatment. The morphological analyses of the samples were performed by a high vacuum electron microscope ZEISS SUPRA VP 50. The phase compositions of the samples were performed with an Rigaku-Rint 2200 diffractometer, with nickel filtered Cu Kα radiation and conversion level. The MgB2 phase wt % was calculated by the Rietveld refinement method. The obtained results were discussed according to the process variables to find out their affect on the structure

  5. Impacts of High Variable Renewable Energy Futures on Wholesale Electricity Prices, and on Electric-Sector Decision Making

    Energy Technology Data Exchange (ETDEWEB)

    Seel, Joachim [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Mills, Andrew D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wiser, Ryan H. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Deb, Sidart [LCG Consulting, Los Altos, CA (United States); Asokkumar, Aarthi [LCG Consulting, Los Altos, CA (United States); Hassanzadeh, Mohammad [LCG Consulting, Los Altos, CA (United States); Aarabali, Amirsaman [LCG Consulting, Los Altos, CA (United States)

    2018-05-11

    Increasing penetrations of variable renewable energy (VRE) can affect wholesale electricity price patterns and make them meaningfully different from past, traditional price patterns. Many long-lasting decisions for supply- and demand-side electricity infrastructure and programs are based on historical observations or assume a business-as-usual future with low shares of VRE. Our motivating question is whether certain electric-sector decisions that are made based on assumptions reflecting low VRE levels will still achieve their intended objective in a high VRE future. We qualitatively describe how various decisions may change with higher shares of VRE and outline an analytical framework for quantitatively evaluating the impacts of VRE on long-lasting decisions. We then present results from detailed electricity market simulations with capacity expansion and unit commitment models for multiple regions of the U.S. for low and high VRE futures. We find a general decrease in average annual hourly wholesale energy prices with more VRE penetration, increased price volatility and frequency of very low-priced hours, and changing diurnal price patterns. Ancillary service prices rise substantially and peak net-load hours with high capacity value are shifted increasingly into the evening, particularly for high solar futures. While in this report we only highlight qualitatively the possible impact of these altered price patterns on other demand- and supply-side electric sector decisions, the core set of electricity market prices derived here provides a foundation for later planned quantitative evaluations of these decisions in low and high VRE futures.

  6. High-Resolution Experimental Investigation of mass transfer enhancement by chemical oxidation from DNAPL entrapped in variable-aperture fractures

    Science.gov (United States)

    Arshadi, M.; Rajaram, H.; Detwiler, R. L.; Jones, T.

    2012-12-01

    Permanganate oxidation of DNAPL- contaminated fractured rock is an effective remediation technology. Permanganate ion reacts with dissolved DNAPL in a bi-molecular oxidation-reduction reaction. The consumption of dissolved DNAPL in this reaction results in increased concentration gradients away from the free-phase DNAPL, resulting in reaction-enhanced mass transfer, which accelerates contaminant removal. The specific objective of our research was to perform high-resolution non-intrusive experimental studies of permanganate oxidation in a 15.24 × 15.24 cm, transparent, analog, variable-aperture fracture with complex initial TCE entrapped phase geometry. Our experimental system uses light-transmission techniques to accurately measure both fracture aperture and the evolution of individual entrapped DNAPL blobs during the remediation experiments at high resolution (pixel size : 6.2×10-3 cm). Three experiments were performed with different flow rates and permanganate inflow concentrations to observe DNAPL-permanganate interactions across a broader range of conditions. Prior to initiating each experiment, the aperture field within the fracture was measured. The oxidation experiment was initiated by TCE injection into the water saturated fracture till the TCE reached the outflow end, followed by water re-injection through the fracture. The flowing water mobilized some TCE. We continued injection of water till TCE mobilization ceased, leaving behind the residual TCE entrapped within the variable-aperture fracture. Subsequently, permanganate injection through the fracture resulted in propagation of a fingered reaction front into the fracture. We developed image processing algorithms to analyze the evolution of DNAPL phase geometry over the duration of the experiment. The permanganate consumption rate varied significantly within the fracture due to the complex flow and DNAPL concentration fields. Precipitated MnO2 was clearly evident on the downstream side of DNAPL blobs

  7. Diurnal variability and biogeochemical reactivity of mercury species in an extreme high-altitude lake ecosystem of the Bolivian Altiplano.

    Science.gov (United States)

    Alanoca, L; Amouroux, D; Monperrus, M; Tessier, E; Goni, M; Guyoneaud, R; Acha, D; Gassie, C; Audry, S; Garcia, M E; Quintanilla, J; Point, D

    2016-04-01

    Methylation and demethylation represent major transformation pathways regulating the net production of methylmercury (MMHg). Very few studies have documented Hg reactivity and transformation in extreme high-altitude lake ecosystems. Mercury (Hg) species concentrations (IHg, MMHg, Hg°, and DMHg) and in situ Hg methylation (M) and MMHg demethylation (D) potentials were determined in water, sediment, floating organic aggregates, and periphyton compartments of a shallow productive Lake of the Bolivian Altiplano (Uru Uru Lake, 3686 m). Samples were collected during late dry season (October 2010) and late wet season (May 2011) at a north (NS) and a south (SS) site of the lake, respectively. Mercury species concentrations exhibited significant diurnal variability as influenced by the strong diurnal biogeochemical gradients. Particularly high methylated mercury concentrations (0.2 to 4.5 ng L(-1) for MMHgT) were determined in the water column evidencing important Hg methylation in this ecosystem. Methylation and D potentials range were, respectively, production in both water (up to 0.45 ng MMHg L(-1) day(-1)) and sediment compartments (2.0 to 19.7 ng MMHg g(-1) day(-1)). While the sediment compartment appears to represent a major source of MMHg in this shallow ecosystem, floating organic aggregates (dry season, SS) and Totora's periphyton (wet season, NS) were found to act as a significant source (5.8 ng MMHg g(-1) day(-1)) and a sink (-2.1 ng MMHg g(-1) day(-1)) of MMHg, respectively. This work demonstrates that high-altitude productive lake ecosystems can promote MMHg formation in various compartments supporting recent observations of high Hg contents in fish and water birds.

  8. Quantifying small-scale spatio-temporal variability of snow stratigraphy in forests based on high-resolution snow penetrometry

    Science.gov (United States)

    Teich, M.; Hagenmuller, P.; Bebi, P.; Jenkins, M. J.; Giunta, A. D.; Schneebeli, M.

    2017-12-01

    Snow stratigraphy, the characteristic layering within a seasonal snowpack, has important implications for snow remote sensing, hydrology and avalanches. Forests modify snowpack properties through interception, wind speed reduction, and changes to the energy balance. The lack of snowpack observations in forests limits our ability to understand the evolution of snow stratigraphy and its spatio-temporal variability as a function of forest structure and to observe snowpack response to changes in forest cover. We examined the snowpack under canopies of a spruce forest in the central Rocky Mountains, USA, using the SnowMicroPen (SMP), a high resolution digital penetrometer. Weekly-repeated penetration force measurements were recorded along 10 m transects every 0.3 m in winter 2015 and bi-weekly along 20 m transects every 0.5 m in 2016 in three study plots beneath canopies of undisturbed, bark beetle-disturbed and harvested forest stands, and an open meadow. To disentangle information about layer hardness and depth variabilities, and to quantitatively compare the different SMP profiles, we applied a matching algorithm to our dataset, which combines several profiles by automatically adjusting their layer thicknesses. We linked spatial and temporal variabilities of penetration force and depth, and thus snow stratigraphy to forest and meteorological conditions. Throughout the season, snow stratigraphy was more heterogeneous in undisturbed but also beneath bark beetle-disturbed forests. In contrast, and despite remaining small diameter trees and woody debris, snow stratigraphy was rather homogenous at the harvested plot. As expected, layering at the non-forested plot varied only slightly over the small spatial extent sampled. At the open and harvested plots, persistent crusts and ice lenses were clearly present in the snowpack, while such hard layers barely occurred beneath undisturbed and disturbed canopies. Due to settling, hardness significantly increased with depth at

  9. Changes in the Economic Value of Variable Generation at High Penetration Levels: A Pilot Case Study of California

    Energy Technology Data Exchange (ETDEWEB)

    Mills, Andrew [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Wiser, Ryan [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2012-05-18

    We estimate the long-run economic value of variable renewable generation with increasing penetration using a unique investment and dispatch model that captures long-run investment decisions while also incorporating detailed operational constraints and hourly time resolution over a full year. High time resolution and the incorporation of operational constraints are important for estimating the economic value of variable generation, as is the use of a modeling framework that accommodates new investment decisions. The model is herein applied with a case study that is loosely based on California in 2030. Increasing amounts of wind, photovoltaics (PV), and concentrating solar power (CSP) with and without thermal energy storage (TES) are added one at a time. The marginal economic value of these renewable energy sources is estimated and then decomposed into capacity value, energy value, day-ahead forecast error cost, and ancillary services. The marginal economic value, as defined here, is primarily based on the combination of avoided capital investment cost and avoided variable fuel and operations and maintenance costs from other power plants in the power system. Though the model only captures a subset of the benefits and costs of renewable energy, it nonetheless provides unique insights into how the value of that subset changes with technology and penetration level. Specifically, in this case study implementation of the model, the marginal economic value of all three solar options is found to exceed the value of a flat-block of power (as well as wind energy) by \\$20--30/MWh at low penetration levels, largely due to the high capacity value of solar at low penetration. Because the value of CSP per unit of energy is found to be high with or without thermal energy storage at low penetration, we find little apparent incremental value to thermal storage at low solar penetration in the present case study analysis. The marginal economic value of PV and CSP without thermal

  10. Transport critical current measurement apparatus using liquid nitrogen cooled high-T(c) superconducting magnet with variable temperature insert.

    Science.gov (United States)

    Nishijima, G; Kitaguchi, H; Tshuchiya, Y; Nishimura, T; Kato, T

    2013-01-01

    We have developed an apparatus to investigate transport critical current (I(c)) as a function of magnetic field and temperature using only liquid nitrogen. The apparatus consists of a (Bi,Pb)(2)Sr(2)Ca(2)Cu(3)O(10) (Bi-2223) superconducting magnet, an outer dewar, and a variable temperature insert (VTI). The magnet, which is operated in depressurized liquid nitrogen, generates magnetic field up to 1.26 T. The sample is also immersed in liquid nitrogen. The pressure in the VTI is controlled from 0.02 to 0.3 MPa, which corresponds to temperature ranging from 66 to 88 K. We have confirmed the long-term stable operation of the Bi-2223 magnet at 1 T. The temperature stability of the sample at high transport current was also demonstrated. The apparatus provides easy-operating I(c) measurement environment for a high-T(c) superconductor up to 500 A in magnetic fields up to 1 T and in temperatures ranging from 66 to 88 K.

  11. Signal enhancement due to high-Z nanofilm electrodes in parallel plate ionization chambers with variable microgaps.

    Science.gov (United States)

    Brivio, Davide; Sajo, Erno; Zygmanski, Piotr

    2017-12-01

    We developed a method for measuring signal enhancement produced by high-Z nanofilm electrodes in parallel plate ionization chambers with variable thickness microgaps. We used a laboratory-made variable gap parallel plate ionization chamber with nanofilm electrodes made of aluminum-aluminum (Al-Al) and aluminum-tantalum (Al-Ta). The electrodes were evaporated on 1 mm thick glass substrates. The interelectrode air gap was varied from 3 μm to 1 cm. The gap size was measured using a digital micrometer and it was confirmed by capacitance measurements. The electric field in the chamber was kept between 0.1 kV/cm and 1 kV/cm for all the gap sizes by applying appropriate compensating voltages. The chamber was exposed to 120 kVp X-rays. The current was measured using a commercial data acquisition system with temporal resolution of 600 Hz. In addition, radiation transport simulations were carried out to characterize the dose, D(x), high-energy electron current, J(x), and deposited charge, Q(x), as a function of distance, x, from the electrodes. A deterministic method was selected over Monte Carlo due to its ability to produce results with 10 nm spatial resolution without stochastic uncertainties. Experimental signal enhancement ratio, SER(G) which we defined as the ratio of signal for Al-air-Ta to signal for Al-air-Al for each gap size, was compared to computations. The individual contributions of dose, electron current, and charge deposition to the signal enhancement were determined. Experimental signals matched computed data for all gap sizes after accounting for several contributions to the signal: (a) charge carrier generated via ionization due to the energy deposited in the air gap, D(x); (b) high-energy electron current, J(x), leaking from high-Z electrode (Ta) toward low-Z electrode (Al); (c) deposited charge in the air gap, Q(x); and (d) the decreased collection efficiency for large gaps (>~500 μm). Q(x) accounts for the electrons below 100 eV, which are

  12. Population-Specific Resequencing Associates the ATP-Binding Cassette Subfamily C Member 4 Gene With Gout in New Zealand Māori and Pacific Men.

    Science.gov (United States)

    Tanner, Callum; Boocock, James; Stahl, Eli A; Dobbyn, Amanda; Mandal, Asim K; Cadzow, Murray; Phipps-Green, Amanda J; Topless, Ruth K; Hindmarsh, Jennie Harré; Stamp, Lisa K; Dalbeth, Nicola; Choi, Hyon K; Mount, David B; Merriman, Tony R

    2017-07-01

    There is no evidence for a genetic association between organic anion transporters 1-3 (SLC22A6, SLC22A7, and SLC22A8) and multidrug resistance protein 4 (MRP4; encoded by ABCC4) with the levels of serum urate or gout. The Māori and Pacific (Polynesian) population of New Zealand has the highest prevalence of gout worldwide. The aim of this study was to determine whether any Polynesian population-specific genetic variants in SLC22A6-8 and ABCC4 are associated with gout. All participants had ≥3 self-reported Māori and/or Pacific grandparents. Among the total sample set of 1,808 participants, 191 hyperuricemic and 202 normouricemic individuals were resequenced over the 4 genes, and the remaining 1,415 individuals were used for replication. Regression analyses were performed, adjusting for age, sex, and Polynesian ancestry. To study the functional effect of nonsynonymous variants of ABCC4, transport assays were performed in Xenopus laevis oocytes. A total of 39 common variants were detected, with an ABCC4 variant (rs4148500) significantly associated with hyperuricemia and gout. This variant was monomorphic for the urate-lowering allele in Europeans. There was evidence for an association of rs4148500 with gout in the resequenced samples (odds ratio [OR] 1.62 [P = 0.012]) that was replicated (OR 1.25 [P = 0.033]) and restricted to men (OR 1.43 [P = 0.001] versus OR 0.98 [P = 0.89] in women). The gout risk allele was associated with fractional excretion of uric acid in male individuals (β = -0.570 [P = 0.01]). A rare population-specific allele (P1036L) with predicted strong functional consequence reduced the uric acid transport activity of ABCC4 by 30%. An association between ABCC4 and gout and fractional excretion of uric acid is consistent with the established role of MRP4 as a unidirectional renal uric acid efflux pump. © 2017, American College of Rheumatology.

  13. Possible Noise Nature of Elsässer Variable z- in Highly Alfvénic Solar Wind Fluctuations

    Science.gov (United States)

    Wang, X.; Tu, C.-Y.; He, J.-S.; Wang, L.-H.; Yao, S.; Zhang, L.

    2018-01-01

    It has been a long-standing debate on the nature of Elsässer variable z- observed in the solar wind fluctuations. It is widely believed that z- represents inward propagating Alfvén waves and interacts nonlinearly with z+ (outward propagating Alfvén waves) to generate energy cascade. However, z- variations sometimes show a feature of convective structures. Here we present a new data analysis on autocorrelation functions of z- in order to get some definite information on its nature. We find that there is usually a large drop on the z- autocorrelation function when the solar wind fluctuations are highly Alfvénic. The large drop observed by Helios 2 spacecraft near 0.3 AU appears at the first nonzero time lag τ = 81 s, where the value of the autocorrelation coefficient drops to 25%-65% of that at τ = 0 s. Beyond the first nonzero time lag, the autocorrelation coefficient decreases gradually to zero. The drop of z- correlation function also appears in the Wind observations near 1 AU. These features of the z- correlation function may suggest that z- fluctuations consist of two components: high-frequency white noise and low-frequency pseudo structures, which correspond to flat and steep parts of z- power spectrum, respectively. This explanation is confirmed by doing a simple test on an artificial time series, which is obtained from the superposition of a random data series on its smoothed sequence. Our results suggest that in highly Alfvénic fluctuations, z- may not contribute importantly to the interactions with z+ to produce energy cascade.

  14. Determining the high variability of pCO2 and pO2 in the littoral zone of a subtropical coastal lake

    Directory of Open Access Journals (Sweden)

    Denise Tonetta

    2014-09-01

    Full Text Available The aquatic metabolism comprises production and mineralization of organic matter through biological processes, such as primary production and respiration that can be estimated by gases concentration in the water column. AIM: The study aimed to assess the temporal variability of pCO2 and pO2 in the littoral zone of a subtropical coastal lake. Our hypotheses are i high variability in meteorological conditions, such as temperature and light, drive the high variability in pCO2 and pO2, and ii the lake is permanently heterotrophic due to the low phosphorus concentration. METHODS: We estimated pCO2 from pH-alkalinity method, and pO2 from dissolved oxygen concentration and water temperature measured in free-water during 24 hours in the autumn, winter, spring and summer. RESULTS: Our findings showed that limnological variables had low temporal variability, while the meteorological variables and pCO2 presented a high coefficient of variation, which is representative of each climatic season. In autumn and winter, it was recorded that the lake was supersaturated in CO2 relative to the atmosphere, while in spring and summer CO2 concentration was below the concentration found in the atmosphere. Over 24 hours, pCO2 also showed high variability, with autumn presenting higher concentration during the night when compared to daytime. Water temperature and chlorophyll a were negatively correlated with pCO2, while pO2 was positively correlated with wind and light. CONCLUSION: Agreeing with our first hypothesis, pCO2 showed an expressive temporal variation in a subtropical lake associated to the high variability in meteorological conditions. On the other hand, our second hypothesis was not confirmed, since Peri Lake exported CO2 to the atmosphere in some periods and in others, CO2 was removed from the atmosphere.

  15. Highly variable penetrance of abnormal phenotypes in embryonic lethal knockout mice [version 2; referees: 1 approved, 2 approved with reservations

    Directory of Open Access Journals (Sweden)

    Robert Wilson

    2017-02-01

    Full Text Available Background: Identifying genes that are essential for mouse embryonic development and survival through term is a powerful and unbiased way to discover possible genetic determinants of human developmental disorders. Characterising the changes in mouse embryos that result from ablation of lethal genes is a necessary first step towards uncovering their role in normal embryonic development and establishing any correlates amongst human congenital abnormalities. Methods: Here we present results gathered to date in the Deciphering the Mechanisms of Developmental Disorders (DMDD programme, cataloguing the morphological defects identified from comprehensive imaging of 220 homozygous mutant and 114 wild type embryos from 42 lethal and subviable lines, analysed at E14.5. Results: Virtually all mutant embryos show multiple abnormal phenotypes and amongst the 42 lines these affect most organ systems. Within each mutant line, the phenotypes of individual embryos form distinct but overlapping sets. Subcutaneous edema, malformations of the heart or great vessels, abnormalities in forebrain morphology and the musculature of the eyes are all prevalent phenotypes, as is loss or abnormal size of the hypoglossal nerve. Conclusions: Overall, the most striking finding is that no matter how profound the malformation, each phenotype shows highly variable penetrance within a mutant line. These findings have challenging implications for efforts to identify human disease correlates.

  16. Phytoremediation potential of Pityrogramma calomelanos var. austroamericana and Pteris vittata L. grown at a highly variable arsenic contaminated site.

    Science.gov (United States)

    Niazi, Nabeel Khan; Singh, Balwant; Van Zwieten, Lukas; Kachenko, Anthony George

    2011-10-01

    This study examined the phytoextraction potential of two arsenic (As) hyperaccumulators, Pteris vittata L. and Pityrogramma calomelanos var. austroamericana at a historical As-contaminated cattle dip site in northern New South Wales (NSW), Australia. Total As concentration in the surface soil (0-20 cm) showed a better spatial structure than phosphate-extractable As in the surface and sub-surface soil at this site. P. calomelanos var. austroamericana produced greater frond dry biomass (mean = 130 g plant(-1)) than P. vittata (mean = 81 g plant(-1)) after 10 months of growth. Arsenic concentration and uptake in fronds were also significantly higher in P. calomelanos var. austroamericana (means = 887 mg kg(-1) and 124 mg plant(-1)) than in P. vittata (means = 674 mg kg(-1) and 57 mg plant(-1)). Our results showed that under the field conditions and highly variable soil As at the site, P. calomelanos var. austroamericana performed better than P. vittata. We predict that P. calomelanos var. austroamericana would take approximately 100 years to reduce the total As to below 20 mg kg(-1) at the site compared to > or =200 years estimated for P. vittata. However, long-term data are required to confirm these observations under field conditions.

  17. Low to high frequency ratio of heart rate variability spectra fails to describe sympatho-vagal balance in cardiac patients.

    Science.gov (United States)

    Milicević, Goran

    2005-06-01

    Heart rate variability (HRV) reflects an influence of autonomic nervous system on heart work. In healthy subjects, ratio between low and high frequency components (LF/HF ratio) of HRV spectra represents a measure of sympatho-vagal balance. The ratio was defined by the authorities as an useful clinical tool, but it seems that it fails to summarise sympatho-vagal balance in a clinical setting. Value of the method was re-evaluated in several categories of cardiac patients. HRV was analysed from 24-hour Holter ECGs in 132 healthy subjects, and 2159 cardiac patients dichotomised by gender, median of age, diagnosis of myocardial infarction or coronary artery surgery, left ventricular systolic function and divided by overall HRV into several categories. In healthy subjects, LF/HF ratio correlated with overall HRV negatively, as expected. The paradoxical finding was obtained in cardiac patients; the lower the overall HRV and the time-domain indices of vagal modulation activity were the lower the LF/HF ratio was. If used as a measure of sympatho-vagal balance, long-term recordings of LF/HF ratio contradict to clinical finding and time-domain HRV indices in cardiac patients. The ratio cannot therefore be used as a reliable marker of autonomic activity in a clinical setting.

  18. High production of llama variable heavy-chain antibody fragment (VHH) fused to various reader proteins by Aspergillus oryzae.

    Science.gov (United States)

    Hisada, Hiromoto; Tsutsumi, Hiroko; Ishida, Hiroki; Hata, Yoji

    2013-01-01

    Llama variable heavy-chain antibody fragment (VHH) fused to four different reader proteins was produced and secreted in culture medium by Aspergillus oryzae. These fusion proteins consisted of N-terminal reader proteins, VHH, and a C-terminal his-tag sequence which facilitated purification using one-step his-tag affinity chromatography. SDS-PAGE analysis of the deglycosylated purified fusion proteins confirmed that the molecular weight of each corresponded to the expected sum of VHH and the respective reader proteins. The apparent high molecular weight reader protein glucoamylase (GlaB) was found to be suitable for efficient VHH production. The GlaB-VHH-His protein bound its antigen, human chorionic gonadotropin, and was detectable by a new ELISA-based method using a coupled assay with glucoamylase, glucose oxidase, peroxidase, maltose, and 3,3',5,5'-tetramethylbenzidine as substrates. Addition of potassium phosphate to the culture medium induced secretion of 0.61 mg GlaB-VHH-His protein/ml culture medium in 5 days.

  19. High mutation rates explain low population genetic divergence at copy-number-variable loci in Homo sapiens.

    Science.gov (United States)

    Hu, Xin-Sheng; Yeh, Francis C; Hu, Yang; Deng, Li-Ting; Ennos, Richard A; Chen, Xiaoyang

    2017-02-22

    Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites. Populations generally exhibit very small genetic divergence (G st  = 0.05 ± 0.049). The smallest divergence is among African populations (G st  = 0.0081 ± 0.0025), with increased divergence among non-African populations (G st  = 0.0217 ± 0.0109) and then among African and non-African populations (G st  = 0.0324 ± 0.0064). Genetic diversity is high in African populations (~0.13), low in Asian populations (~0.11), and intermediate in the remaining 11 populations. Few significant linkage disequilibria (LDs) occur between the genome-wide CNV loci. Patterns of gametic and zygotic LDs indicate the absence of epistasis among CNV loci. Mutation rate is about twice as large as the migration rate in the non-African populations, suggesting that the high mutation rates play dominant roles in producing the low population genetic divergence at CNV loci.

  20. THE LONGEST TIMESCALE X-RAY VARIABILITY REVEALS EVIDENCE FOR ACTIVE GALACTIC NUCLEI IN THE HIGH ACCRETION STATE

    International Nuclear Information System (INIS)

    Zhang Youhong

    2011-01-01

    The All Sky Monitor (ASM) on board the Rossi X-ray Timing Explorer has continuously monitored a number of active galactic nuclei (AGNs) with similar sampling rates for 14 years, from 1996 January to 2009 December. Utilizing the archival ASM data of 27 AGNs, we calculate the normalized excess variances of the 300-day binned X-ray light curves on the longest timescale (between 300 days and 14 years) explored so far. The observed variance appears to be independent of AGN black-hole mass and bolometric luminosity. According to the scaling relation of black-hole mass (and bolometric luminosity) from galactic black hole X-ray binaries (GBHs) to AGNs, the break timescales that correspond to the break frequencies detected in the power spectral density (PSD) of our AGNs are larger than the binsize (300 days) of the ASM light curves. As a result, the singly broken power-law (soft-state) PSD predicts the variance to be independent of mass and luminosity. Nevertheless, the doubly broken power-law (hard-state) PSD predicts, with the widely accepted ratio of the two break frequencies, that the variance increases with increasing mass and decreases with increasing luminosity. Therefore, the independence of the observed variance on mass and luminosity suggests that AGNs should have soft-state PSDs. Taking into account the scaling of the break timescale with mass and luminosity synchronously, the observed variances are also more consistent with the soft-state than the hard-state PSD predictions. With the averaged variance of AGNs and the soft-state PSD assumption, we obtain a universal PSD amplitude of 0.030 ± 0.022. By analogy with the GBH PSDs in the high/soft state, the longest timescale variability supports the standpoint that AGNs are scaled-up GBHs in the high accretion state, as already implied by the direct PSD analysis.

  1. Spatiotemporal Co-variability of Surface Climate for Renewable Energy across the Contiguous United States: Role of the North Atlantic Subtropical High

    Science.gov (United States)

    Doering, K.; Steinschneider, S.

    2017-12-01

    The variability of renewable energy supply and drivers of demand across space and time largely determines the energy balance within power systems with a high penetration of renewable technologies. This study examines the joint spatiotemporal variability of summertime climate linked to renewable energy production (precipitation, wind speeds, insolation) and energy demand (temperature) across the contiguous United States (CONUS) between 1948 and 2015. Canonical correlation analysis is used to identify the major modes of joint variability between summer wind speeds and precipitation and related patterns of insolation and temperature. Canonical variates are then related to circulation anomalies to identify common drivers of the joint modes of climate variability. Results show that the first two modes of joint variability between summer wind speeds and precipitation exhibit pan-US dipole patterns with centers of action located in the eastern and central CONUS. Temperature and insolation also exhibit related US-wide dipoles. The relationship between canonical variates and lower-tropospheric geopotential height indicates that these modes are related to variability in the North Atlantic subtropical high (NASH). This insight can inform optimal strategies for siting renewables in an interconnected electric grid, and has implications for the impacts of climate variability and change on renewable energy systems.

  2. Targeted Resequencing and Functional Testing Identifies Low-Frequency Missense Variants in the Gene Encoding GARP as Significant Contributors to Atopic Dermatitis Risk.

    Science.gov (United States)

    Manz, Judith; Rodríguez, Elke; ElSharawy, Abdou; Oesau, Eva-Maria; Petersen, Britt-Sabina; Baurecht, Hansjörg; Mayr, Gabriele; Weber, Susanne; Harder, Jürgen; Reischl, Eva; Schwarz, Agatha; Novak, Natalija; Franke, Andre; Weidinger, Stephan

    2016-12-01

    Gene-mapping studies have consistently identified a susceptibility locus for atopic dermatitis and other inflammatory diseases on chromosome band 11q13.5, with the strongest association observed for a common variant located in an intergenic region between the two annotated genes C11orf30 and LRRC32. Using a targeted resequencing approach we identified low-frequency and rare missense mutations within the LRRC32 gene encoding the protein GARP, a receptor on activated regulatory T cells that binds latent transforming growth factor-β. Subsequent association testing in more than 2,000 atopic dermatitis patients and 2,000 control subjects showed a significant excess of these LRRC32 variants in individuals with atopic dermatitis. Structural protein modeling and bioinformatic analysis predicted a disruption of protein transport upon these variants, and overexpression assays in CD4 + CD25 - T cells showed a significant reduction in surface expression of the mutated protein. Consistently, flow cytometric (FACS) analyses of different T-cell subtypes obtained from atopic dermatitis patients showed a significantly reduced surface expression of GARP and a reduced conversion of CD4 + CD25 - T cells into regulatory T cells, along with lower expression of latency-associated protein upon stimulation in carriers of the LRRC32 A407T variant. These results link inherited disturbances of transforming growth factor-β signaling with atopic dermatitis risk. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  3. Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger.

    Science.gov (United States)

    Reilly, Morgann C; Kim, Joonhoon; Lynn, Jed; Simmons, Blake A; Gladden, John M; Magnuson, Jon K; Baker, Scott E

    2018-02-01

    Plant biomass, once reduced to its composite sugars, can be converted to fuel substitutes. One means of overcoming the recalcitrance of lignocellulose is pretreatment followed by enzymatic hydrolysis. However, currently available commercial enzyme cocktails are inhibited in the presence of residual pretreatment chemicals. Recent studies have identified a number of cellulolytic enzymes from bacteria that are tolerant to pretreatment chemicals such as ionic liquids. The challenge now is generation of these enzymes in copious amounts, an arena where fungal organisms such as Aspergillus niger have proven efficient. Fungal host strains still need to be engineered to increase production titers of heterologous protein over native enzymes, which has been a difficult task. Here, we developed a forward genetics screen coupled with whole-genome resequencing to identify specific lesions responsible for a protein hyper-production phenotype in A. niger. This strategy successfully identified novel targets, including a low-affinity glucose transporter, MstC, whose deletion significantly improved secretion of recombinant proteins driven by a glucoamylase promoter.

  4. Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger

    Energy Technology Data Exchange (ETDEWEB)

    Reilly, Morgann C. [Joint BioEnergy Institute, Emeryville, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kim, Joonhoon [Joint BioEnergy Institute, Emeryville, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lynn, Jed [Joint BioEnergy Institute, Emeryville, CA (United States); Wright-Patterson Air Force Base, Dayton, OH (United States); Simmons, Blake A. [Joint BioEnergy Institute, Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Gladden, John M. [Joint BioEnergy Institute, Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States); Magnuson, Jon K. [Joint BioEnergy Institute, Emeryville, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Joint BioEnergy Institute, Emeryville, CA (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2018-01-06

    Plant biomass, once reduced to its composite sugars, can be converted to fuel substitutes. One means of overcoming the recalcitrance of lignocellulose is pretreatment followed by enzymatic hydrolysis. However, currently available commercial enzyme cocktails are inhibited in the presence of residual pretreatment chemicals. Recent studies have identified a number of cellulolytic enzymes from bacteria that are tolerant to pretreatment chemicals such as ionic liquids. The challenge now is generation of these enzymes in copious amounts, an arena where fungal organisms such as Aspergillus niger have proven efficient. Fungal host strains still need to be engineered to increase production titers of heterologous protein over native enzymes, which has been a difficult task. Here, we developed a forward genetics screen coupled with whole-genome resequencing to identify specific lesions responsible for a protein hyper-production phenotype in A. niger. This strategy successfully identified novel targets, including a low-affinity glucose transporter, MstC, whose deletion significantly improved secretion of recombinant proteins driven by a glucoamylase promoter.

  5. Effect of task-oriented training and high-variability practice on gross motor performance and activities of daily living in children with spastic diplegia.

    Science.gov (United States)

    Kwon, Hae-Yeon; Ahn, So-Yoon

    2016-10-01

    [Purpose] This study investigates how a task-oriented training and high-variability practice program can affect the gross motor performance and activities of daily living for children with spastic diplegia and provides an effective and reliable clinical database for future improvement of motor performances skills. [Subjects and Methods] This study randomly assigned seven children with spastic diplegia to each intervention group including that of a control group, task-oriented training group, and a high-variability practice group. The control group only received neurodevelopmental treatment for 40 minutes, while the other two intervention groups additionally implemented a task-oriented training and high-variability practice program for 8 weeks (twice a week, 60 min per session). To compare intra and inter-relationships of the three intervention groups, this study measured gross motor performance measure (GMPM) and functional independence measure for children (WeeFIM) before and after 8 weeks of training. [Results] There were statistically significant differences in the amount of change before and after the training among the three intervention groups for the gross motor performance measure and functional independence measure. [Conclusion] Applying high-variability practice in a task-oriented training course may be considered an efficient intervention method to improve motor performance skills that can tune to movement necessary for daily livelihood through motor experience and learning of new skills as well as change of tasks learned in a complex environment or similar situations to high-variability practice.

  6. First report of the mutational and phenotypic spectrum of Hereditary Spherocytosis in Indian patients by targeted resequencing

    Directory of Open Access Journals (Sweden)

    Anu Aggarwal

    2017-10-01

    This first ever study on the molecular spectrum of HS from India revealed predominantly sporadic and dominantly-inherited defects in ANK1 and SPTB in patients. Most of the cases (70% presented at an early age with jaundice and anemia. Co-inherited G6PD deficiency and Gilbert’s syndrome led to phenotypic variability. NGS provided a sensitive, cost-effective and rapid tool for understanding the molecular pathology of HS patients.

  7. The Effect of Nitriding Treatment Variables on the Fatigue Limit of Alloy Steel (34crnimo6) Under High Cycle Fatigue

    International Nuclear Information System (INIS)

    Mohamed, J.; Al-Alkawi, H.; Salameh, M.

    2009-01-01

    The aim of this research is to improve the fatigue limit for alloy steel (34CrNiMo6) by salt bath nitriding process. This property is more effective to increase the fatigue life for parts which are used in continuous cyclic loading. All the fatigue tests were implemented before and after nitriding process under rotating bending. Constant and variable capacity stresses were applied before and after nitriding processes. The nitriding process were implemented in salt bath component at three different times (1, 2, 3) hr when temperature was constant at (555 degree centigrade). The depth of the nitride layer reached (0.24, 0.37, 0.5) mm. The nitriding process repeated of another specimens at the same times but the temperature was (600 degree centigrade), the layer depth reached (0.28, 0.41, 0.55) mm. The formation of a high nitrogen iron phases were detected with a layer of the hard chrome nitrides on the surface. The nitriding process is forming the barriers on the surface that resist the initiation and propagation of cracks, as well as generating the compressive residual stresses which delay the progress of fatigue crack. This research deduced that the nitriding processes increased the fatigue limit and this limit is proportional to the time of the nitriding process. When the time increased, the depth of nitride layer is increased, but decreased when the temperature increased to (600 degree centigrade) because of the formation of brittle phase,in spite of the increase in layer depth. (author)

  8. Resting state connectivity of the medial prefrontal cortex covaries with individual differences in high-frequency heart rate variability.

    Science.gov (United States)

    Jennings, J Richard; Sheu, Lei K; Kuan, Dora C-H; Manuck, Stephen B; Gianaros, Peter J

    2016-04-01

    Resting high-frequency heart rate variability (HF-HRV) relates to cardiac vagal control and predicts individual differences in health and longevity, but its functional neural correlates are not well defined. The medial prefrontal cortex (mPFC) encompasses visceral control regions that are components of intrinsic networks of the brain, particularly the default mode network (DMN) and the salience network (SN). Might individual differences in resting HF-HRV covary with resting state neural activity in the DMN and SN, particularly within the mPFC? This question was addressed using fMRI data from an eyes-open, 5-min rest period during which echoplanar brain imaging yielded BOLD time series. Independent component analysis yielded functional connectivity estimates defining the DMN and SN. HF-HRV was measured in a rest period outside of the scanner. Midlife (52% female) adults were assessed in two studies (Study 1, N = 107; Study 2, N = 112). Neither overall DMN nor SN connectivity strength was related to HF-HRV. However, HF-HRV related to connectivity of one region within mPFC shared by the DMN and SN, namely, the perigenual anterior cingulate cortex, an area with connectivity to other regions involved in autonomic control. In sum, HF-HRV does not seem directly related to global resting state activity of intrinsic brain networks, but rather to more localized connectivity. A mPFC region was of particular interest as connectivity related to HF-HRV was shared by the DMN and SN. These findings may indicate a functional basis for the coordination of autonomic cardiac control with engagement and disengagement from the environment. © 2015 Society for Psychophysiological Research.

  9. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project

    Science.gov (United States)

    Frampton, Dan; Gallo Cassarino, Tiziano; Raffle, Jade; Hubb, Jonathan; Ferns, R. Bridget; Waters, Laura; Tong, C. Y. William; Kozlakidis, Zisis; Hayward, Andrew; Kellam, Paul; Pillay, Deenan; Clark, Duncan; Nastouli, Eleni; Leigh Brown, Andrew J.

    2018-01-01

    Background & methods The ICONIC project has developed an automated high-throughput pipeline to generate HIV nearly full-length genomes (NFLG, i.e. from gag to nef) from next-generation sequencing (NGS) data. The pipeline was applied to 420 HIV samples collected at University College London Hospitals NHS Trust and Barts Health NHS Trust (London) and sequenced using an Illumina MiSeq at the Wellcome Trust Sanger Institute (Cambridge). Consensus genomes were generated and subtyped using COMET, and unique recombinants were studied with jpHMM and SimPlot. Maximum-likelihood phylogenetic trees were constructed using RAxML to identify transmission networks using the Cluster Picker. Results The pipeline generated sequences of at least 1Kb of length (median = 7.46Kb, IQR = 4.01Kb) for 375 out of the 420 samples (89%), with 174 (46.4%) being NFLG. A total of 365 sequences (169 of them NFLG) corresponded to unique subjects and were included in the down-stream analyses. The most frequent HIV subtypes were B (n = 149, 40.8%) and C (n = 77, 21.1%) and the circulating recombinant form CRF02_AG (n = 32, 8.8%). We found 14 different CRFs (n = 66, 18.1%) and multiple URFs (n = 32, 8.8%) that involved recombination between 12 different subtypes/CRFs. The most frequent URFs were B/CRF01_AE (4 cases) and A1/D, B/C, and B/CRF02_AG (3 cases each). Most URFs (19/26, 73%) lacked breakpoints in the PR+RT pol region, rendering them undetectable if only that was sequenced. Twelve (37.5%) of the URFs could have emerged within the UK, whereas the rest were probably imported from sub-Saharan Africa, South East Asia and South America. For 2 URFs we found highly similar pol sequences circulating in the UK. We detected 31 phylogenetic clusters using the full dataset: 25 pairs (mostly subtypes B and C), 4 triplets and 2 quadruplets. Some of these were not consistent across different genes due to inter- and intra-subtype recombination. Clusters involved 70 sequences, 19.2% of the dataset. Conclusions

  10. Effects of high spatial and temporal resolution Earth observations on simulated hydrometeorological variables in a cropland (southwestern France

    Directory of Open Access Journals (Sweden)

    J. Etchanchu

    2017-11-01

    Full Text Available Agricultural landscapes are often constituted by a patchwork of crop fields whose seasonal evolution is dependent on specific crop rotation patterns and phenologies. This temporal and spatial heterogeneity affects surface hydrometeorological processes and must be taken into account in simulations of land surface and distributed hydrological models. The Sentinel-2 mission allows for the monitoring of land cover and vegetation dynamics at unprecedented spatial resolutions and revisit frequencies (20 m and 5 days, respectively that are fully compatible with such heterogeneous agricultural landscapes. Here, we evaluate the impact of Sentinel-2-like remote sensing data on the simulation of surface water and energy fluxes via the Interactions between the Surface Biosphere Atmosphere (ISBA land surface model included in the EXternalized SURface (SURFEX modeling platform. The study focuses on the effect of the leaf area index (LAI spatial and temporal variability on these fluxes. We compare the use of the LAI climatology from ECOCLIMAP-II, used by default in SURFEX-ISBA, and time series of LAI derived from the high-resolution Formosat-2 satellite data (8 m. The study area is an agricultural zone in southwestern France covering 576 km2 (24 km  ×  24 km. An innovative plot-scale approach is used, in which each computational unit has a homogeneous vegetation type. Evaluation of the simulations quality is done by comparing model outputs with in situ eddy covariance measurements of latent heat flux (LE. Our results show that the use of LAI derived from high-resolution remote sensing significantly improves simulated evapotranspiration with respect to ECOCLIMAP-II, especially when the surface is covered with summer crops. The comparison with in situ measurements shows an improvement of roughly 0.3 in the correlation coefficient and a decrease of around 30 % of the root mean square error (RMSE in the simulated evapotranspiration. This

  11. Variability and population genetic structure in Achyrocline flaccida (Weinm. DC., a species with high value in folk medicine in South America.

    Directory of Open Access Journals (Sweden)

    Juliana da Rosa

    Full Text Available Better knowledge of medicinal plant species and their conservation is an urgent need worldwide. Decision making for conservation strategies can be based on the knowledge of the variability and population genetic structure of the species and on the events that may influence these genetic parameters. Achyrocline flaccida (Weinm. DC. is a native plant from the grassy fields of South America with high value in folk medicine. In spite of its importance, no genetic and conservation studies are available for the species. In this work, microsatellite and ISSR (inter-simple sequence repeat markers were used to estimate the genetic variability and structure of seven populations of A. flaccida from southern Brazil. The microsatellite markers were inefficient in A. flaccida owing to a high number of null alleles. After the evaluation of 42 ISSR primers on one population, 10 were selected for further analysis of seven A. flaccida populations. The results of ISSR showed that the high number of exclusive absence of loci might contribute to the inter-population differentiation. Genetic variability of the species was high (Nei's diversity of 0.23 and Shannon diversity of 0.37. AMOVA indicated higher genetic variability within (64.7% than among (33.96% populations, and the variability was unevenly distributed (FST 0.33. Gene flow among populations ranged from 1.68 to 5.2 migrants per generation, with an average of 1.39. The results of PCoA and Bayesian analyses corroborated and indicated that the populations are structured. The observed genetic variability and population structure of A. flaccida are discussed in the context of the vegetation formation history in southern Brazil, as well as the possible anthropogenic effects. Additionally, we discuss the implications of the results in the conservation of the species.

  12. Mean-Level Change and Intraindividual Variability in Self-Esteem and Depression among High-Risk Children

    Science.gov (United States)

    Kim, Jungmeen; Cicchetti, Dante

    2009-01-01

    This study investigated mean-level changes and intraindividual variability of self-esteem among maltreated (N = 142) and nonmaltreated (N = 109) school-aged children from low-income families. Longitudinal factor analysis revealed higher temporal stability of self-esteem among maltreated children compared to nonmaltreated children. Cross-domain…

  13. High-Rate Pacing Reduces Variability of Repolarization and Prevents Repolarization-Dependent Arrhythmias in Dogs With Chronic AV Block

    DEFF Research Database (Denmark)

    Oosterhoff, Peter; Thomsen, Morten Bækgaard; Maas, Joep N

    2010-01-01

    -term variability of repolarization (STV) as a feedback parameter of arrhythmic risk. Methods and Results: The minimal signal sampling frequency required for measuring STV was determined through computer simulation. Arrhythmogenic response to dofetilide (25 µg/kg/5minutes) was tested at two different paced heart...

  14. Single nucleotide variants and InDels identified from whole-genome re-sequencing of Guzerat, Gyr, Girolando and Holstein cattle breeds.

    Directory of Open Access Journals (Sweden)

    Nedenia Bonvino Stafuzza

    Full Text Available Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose, Gyr, Girolando and Holstein (dairy production. A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs and 3,828,041 insertions/deletions (InDels were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs.

  15. Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing.

    Science.gov (United States)

    Fu, Chong-Yun; Liu, Wu-Ge; Liu, Di-Lin; Li, Ji-Hua; Zhu, Man-Shan; Liao, Yi-Long; Liu, Zhen-Rong; Zeng, Xue-Qin; Wang, Feng

    2016-03-01

    Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791 SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

  16. Impacts of High Variable Renewable Energy Futures on Wholesale Electricity Prices, and on Electric-Sector Decision Making

    OpenAIRE

    Seel, J; Mills, AD; Wiser, RH

    2018-01-01

    Increasing penetrations of variable renewable energy (VRE) can affect wholesale electricity price patterns and make them meaningfully different from past, traditional price patterns. Many long-lasting decisions for supply- and demand-side electricity infrastructure and programs are based on historical observations or assume a business-as-usual future with low shares of VRE. Our motivating question is whether certain electric-sector decisions that are made based on assumptions reflecting low V...

  17. High-resolution spatial databases of monthly climate variables (1961-2010) over a complex terrain region in southwestern China

    Science.gov (United States)

    Wu, Wei; Xu, An-Ding; Liu, Hong-Bin

    2015-01-01

    Climate data in gridded format are critical for understanding climate change and its impact on eco-environment. The aim of the current study is to develop spatial databases for three climate variables (maximum, minimum temperatures, and relative humidity) over a large region with complex topography in southwestern China. Five widely used approaches including inverse distance weighting, ordinary kriging, universal kriging, co-kriging, and thin-plate smoothing spline were tested. Root mean square error (RMSE), mean absolute error (MAE), and mean absolute percentage error (MAPE) showed that thin-plate smoothing spline with latitude, longitude, and elevation outperformed other models. Average RMSE, MAE, and MAPE of the best models were 1.16 °C, 0.74 °C, and 7.38 % for maximum temperature; 0.826 °C, 0.58 °C, and 6.41 % for minimum temperature; and 3.44, 2.28, and 3.21 % for relative humidity, respectively. Spatial datasets of annual and monthly climate variables with 1-km resolution covering the period 1961-2010 were then obtained using the best performance methods. Comparative study showed that the current outcomes were in well agreement with public datasets. Based on the gridded datasets, changes in temperature variables were investigated across the study area. Future study might be needed to capture the uncertainty induced by environmental conditions through remote sensing and knowledge-based methods.

  18. Fixed-speed and Variable-speed Pumped Storage Dispatch Model in Power Systems with High Renewable Penetration

    Directory of Open Access Journals (Sweden)

    Yuan Bo

    2018-01-01

    Full Text Available According to different operating characteristics of pumped storage fixed speed unit and variable speed unit, a joint dispatching model of pumped storage unit and other types of units based on mixed integer linear optimization is constructed. The model takes into account the operating conditions, reservoir capacity, cycle type and other pumped storage unit constraints, but also consider the frequent start and stop and the stability of the operation of the unit caused by the loss. Using the Cplex solver to solve the model, the empirical example of the provincial power grid shows that the model can effectively arrange the pumping storage speed and the dispatching operation of the variable speed unit under the precondition of economic life of the unit, and give full play to the function of peak shaving and accommodating new energy. Because of its more flexible regulation characteristics of power generation and pumping conditions, the variable speed unit can better improve the operating conditions of other units in the system and promote the new energy dissipation.

  19. Fixed-speed and Variable-speed Pumped Storage Dispatch Model in Power Systems with High Renewable Penetration

    Science.gov (United States)

    Yuan, Bo; Zong, Jin; Xu, Zhicheng

    2018-06-01

    According to different operating characteristics of pumped storage fixed speed unit and variable speed unit, a joint dispatching model of pumped storage unit and other types of units based on mixed integer linear optimization is constructed. The model takes into account the operating conditions, reservoir capacity, cycle type and other pumped storage unit constraints, but also consider the frequent start and stop and the stability of the operation of the unit caused by the loss. Using the Cplex solver to solve the model, the empirical example of the provincial power grid shows that the model can effectively arrange the pumping storage speed and the dispatching operation of the variable speed unit under the precondition of economic life of the unit, and give full play to the function of peak shaving and accommodating new energy. Because of its more flexible regulation characteristics of power generation and pumping conditions, the variable speed unit can better improve the operating conditions of other units in the system and promote the new energy dissipation.

  20. The application of k-Nearest Neighbour in the identification of high potential archers based on relative psychological coping skills variables

    Science.gov (United States)

    Taha, Zahari; Muazu Musa, Rabiu; Majeed, Anwar P. P. Abdul; Razali Abdullah, Mohamad; Muaz Alim, Muhammad; Nasir, Ahmad Fakhri Ab

    2018-04-01

    The present study aims at classifying and predicting high and low potential archers from a collection of psychological coping skills variables trained on different k-Nearest Neighbour (k-NN) kernels. 50 youth archers with the average age and standard deviation of (17.0 ±.056) gathered from various archery programmes completed a one end shooting score test. Psychological coping skills inventory which evaluates the archers level of related coping skills were filled out by the archers prior to their shooting tests. k-means cluster analysis was applied to cluster the archers based on their scores on variables assessed k-NN models, i.e. fine, medium, coarse, cosine, cubic and weighted kernel functions, were trained on the psychological variables. The k-means clustered the archers into high psychologically prepared archers (HPPA) and low psychologically prepared archers (LPPA), respectively. It was demonstrated that the cosine k-NN model exhibited good accuracy and precision throughout the exercise with an accuracy of 94% and considerably fewer error rate for the prediction of the HPPA and the LPPA as compared to the rest of the models. The findings of this investigation can be valuable to coaches and sports managers to recognise high potential athletes from the selected psychological coping skills variables examined which would consequently save time and energy during talent identification and development programme.

  1. Variability Bugs:

    DEFF Research Database (Denmark)

    Melo, Jean

    . Although many researchers suggest that preprocessor-based variability amplifies maintenance problems, there is little to no hard evidence on how actually variability affects programs and programmers. Specifically, how does variability affect programmers during maintenance tasks (bug finding in particular......)? How much harder is it to debug a program as variability increases? How do developers debug programs with variability? In what ways does variability affect bugs? In this Ph.D. thesis, I set off to address such issues through different perspectives using empirical research (based on controlled...... experiments) in order to understand quantitatively and qualitatively the impact of variability on programmers at bug finding and on buggy programs. From the program (and bug) perspective, the results show that variability is ubiquitous. There appears to be no specific nature of variability bugs that could...

  2. The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

    DEFF Research Database (Denmark)

    Guo, Shaogui; Zhang, Jianguo; Sun, Honghe

    2013-01-01

    Watermelon, Citrullus lanatus, is an important cucurbit crop grown throughout the world. Here we report a high-quality draft genome sequence of the east Asia watermelon cultivar 97103 (2n = 2× = 22) containing 23,440 predicted protein-coding genes. Comparative genomics analysis provided an evolut...

  3. Spatial variability in the density, distribution and vectorial capacity of anopheline species in a high transmission village (Equatorial Guinea

    Directory of Open Access Journals (Sweden)

    Buatiche Jesús N

    2006-03-01

    Full Text Available Abstract Background Malaria transmission varies from one country to another and there are also local differences in time and space. An important variable when explaining the variability in transmission is the breeding behaviour of the different vector species and the availability of breeding sites. The aim of this study was to determine the geographical variability of certain entomological parameters: human biting rate (HBR, sporozoitic index (SI for Plasmodium falciparum and entomological inoculation rate (EIR. Methods The study was carried out in a small village in the mainland region of Equatorial Guinea. Adult mosquitoes were collected by CDC light traps. Polymerase Chain Reaction was employed to identify the species within the Anopheles gambiae complex and to detect P. falciparum sporozoites. The geographical position of all the dwellings in the village were taken using a global positioning system receiver unit. Data relating to the dwelling, occupants, use of bednets and the mosquitoes collection data were used to generate a geographical information system (GIS. This GIS allowed the minimum distance of the dwellings to the closest water point (potential breeding sites to be determined. Results A total of 1,173 anophelines were caught: 279 A. gambiae s.l. (217 A. gambiae s.s. and one Anopheles melas, 777 Anopheles moucheti and 117 Anopheles carnevalei. A. moucheti proved to be the main vector species and was responsible for 52.38 [95% IC: 33.7–71] night infective bites during this period. The highest SI was found in A. carnevalei (24%, even though the HBR was the lowest for this species. A significant association was found between the distance from the dwellings to the closest water point (River Ntem or secondary streams and the total HBR. Conclusion A clear association has been observed between the distance to potential breeding sites and the variability in the anopheline density, while the other parameters measured do not seem to

  4. Targeted deep resequencing identifies coding variants in the PEAR1 gene that play a role in platelet aggregation.

    Directory of Open Access Journals (Sweden)

    Yoonhee Kim

    Full Text Available Platelet aggregation is heritable, and genome-wide association studies have detected strong associations with a common intronic variant of the platelet endothelial aggregation receptor1 (PEAR1 gene both in African American and European American individuals. In this study, we used a sequencing approach to identify additional exonic variants in PEAR1 that may also determine variability in platelet aggregation in the GeneSTAR Study. A 0.3 Mb targeted region on chromosome 1q23.1 including the entire PEAR1 gene was Sanger sequenced in 104 subjects (45% male, 49% African American, age = 52±13 selected on the basis of hyper- and hypo- aggregation across three different agonists (collagen, epinephrine, and adenosine diphosphate. Single-variant and multi-variant burden tests for association were performed. Of the 235 variants identified through sequencing, 61 were novel, and three of these were missense variants. More rare variants (MAF<5% were noted in African Americans compared to European Americans (108 vs. 45. The common intronic GWAS-identified variant (rs12041331 demonstrated the most significant association signal in African Americans (p = 4.020×10(-4; no association was seen for additional exonic variants in this group. In contrast, multi-variant burden tests indicated that exonic variants play a more significant role in European Americans (p = 0.0099 for the collective coding variants compared to p = 0.0565 for intronic variant rs12041331. Imputation of the individual exonic variants in the rest of the GeneSTAR European American cohort (N = 1,965 supports the results noted in the sequenced discovery sample: p = 3.56×10(-4, 2.27×10(-7, 5.20×10(-5 for coding synonymous variant rs56260937 and collagen, epinephrine and adenosine diphosphate induced platelet aggregation, respectively. Sequencing approaches confirm that a common intronic variant has the strongest association with platelet aggregation in African Americans

  5. The Sterilization Effect of Cooperative Treatment of High Voltage Electrostatic Field and Variable Frequency Pulsed Electromagnetic Field on Heterotrophic Bacteria in Circulating Cooling Water

    Science.gov (United States)

    Gao, Xuetong; Liu, Zhian; Zhao, Judong

    2018-01-01

    Compared to other treatment of industrial circulating cooling water in the field of industrial water treatment, high-voltage electrostatic field and variable frequency pulsed electromagnetic field co-sterilization technology, an advanced technology, is widely used because of its special characteristics--low energy consumption, nonpoisonous and environmentally friendly. In order to get a better cooling water sterilization effect under the premise of not polluting the environment, some experiments about sterilization of heterotrophic bacteria in industrial circulating cooling water by cooperative treatment of high voltage electrostatic field and variable frequency pulsed electromagnetic field were carried out. The comparison experiment on the sterilization effect of high-voltage electrostatic field and variable frequency pulsed electromagnetic field co-sterilization on heterotrophic bacteria in industrial circulating cooling water was carried out by change electric field strength and pulse frequency. The results show that the bactericidal rate is selective to the frequency and output voltage, and the heterotrophic bacterium can only kill under the condition of sweep frequency range and output voltage. When the voltage of the high voltage power supply is 4000V, the pulse frequency is 1000Hz and the water temperature is 30°C, the sterilization rate is 48.7%, the sterilization rate is over 90%. Results of this study have important guiding significance for future application of magnetic field sterilization.

  6. Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing

    Directory of Open Access Journals (Sweden)

    Doori Park

    2015-09-01

    Full Text Available Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF in genetically modified rice cells. A total of 29.3 Gb (~72× coverage was sequenced with a 2 × 150 bp paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.

  7. Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

    Directory of Open Access Journals (Sweden)

    Jie Qiu

    Full Text Available Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou and a wild line (Lanxi 1 collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1 no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2 besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3 high heterozygous rates (0.19-0.49 were observed in several semi-wild lines; and (4 over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.

  8. A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar

    Directory of Open Access Journals (Sweden)

    Jamie A. O'Rourke

    2013-06-01

    Full Text Available A small fast neutron mutant population has been established from Phaseolus vulgaris cv. Red Hawk. We leveraged the available P. vulgaris genome sequence and high throughput next generation DNA sequencing to examine the genomic structure of five Phaseolus vulgaris cv. Red Hawk fast neutron mutants with striking visual phenotypes. Analysis of these genomes identified three classes of structural variation; between cultivar variation, natural variation within the fast neutron mutant population, and fast neutron induced mutagenesis. Our analyses focused on the latter two classes. We identified 23 large deletions (>40 bp common to multiple individuals, illustrating residual heterogeneity and regions of structural variation within the common bean cv. Red Hawk. An additional 18 large deletions were identified in individual mutant plants. These deletions, ranging in size from 40 bp to 43,000 bp, are potentially the result of fast neutron mutagenesis. Six of the 18 deletions lie near or within gene coding regions, identifying potential candidate genes causing the mutant phenotype.

  9. Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly.

    Science.gov (United States)

    Wragg, David; Marti-Marimon, Maria; Basso, Benjamin; Bidanel, Jean-Pierre; Labarthe, Emmanuelle; Bouchez, Olivier; Le Conte, Yves; Vignal, Alain

    2016-06-03

    Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail.

  10. HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.

    Science.gov (United States)

    Moens, Lotte N J; Falk-Sörqvist, Elin; Ljungström, Viktor; Mattsson, Johanna; Sundström, Magnus; La Fleur, Linnéa; Mathot, Lucy; Micke, Patrick; Nilsson, Mats; Botling, Johan

    2015-11-01

    In recent years, the advent of massively parallel next-generation sequencing technologies has enabled substantial advances in the study of human diseases. Combined with targeted DNA enrichment methods, high sequence coverage can be obtained for different genes simultaneously at a reduced cost per sample, creating unique opportunities for clinical cancer diagnostics. However, the formalin-fixed, paraffin-embedded (FFPE) process of tissue samples, routinely used in pathology departments, results in DNA fragmentation and nucleotide modifications that introduce a number of technical challenges for downstream biomolecular analyses. We evaluated the HaloPlex target enrichment system for somatic mutation detection in 80 tissue fractions derived from 20 clinical cancer cases with paired tumor and normal tissue available in both FFPE and fresh-frozen format. Several modifications to the standard method were introduced, including a reduced target fragment length and two strand capturing. We found that FFPE material can be used for HaloPlex-based target enrichment and next-generation sequencing, even when starting from small amounts of DNA. By specifically capturing both strands for each target fragment, we were able to reduce the number of false-positive errors caused by FFPE-induced artifacts and lower the detection limit for somatic mutations. We believe that the HaloPlex method presented here will be broadly applicable as a tool for somatic mutation detection in clinical cancer settings. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  11. Power variables and bilateral force differences during unloaded and loaded squat jumps in high performance alpine ski racers.

    Science.gov (United States)

    Patterson, Carson; Raschner, Christian; Platzer, Hans-Peter

    2009-05-01

    The purpose of this paper was to investigate the power-load relationship and to compare power variables and bilateral force imbalances between sexes with squat jumps. Twenty men and 17 women, all members of the Austrian alpine ski team (junior and European Cup), performed unloaded and loaded (barbell loads equal to 25, 50, 75, and 100% body weight [BW]) squat jumps with free weights using a specially designed spotting system. Ground reaction force records from 2 force platforms were used to calculate relative average power (P), relative average power in the first 100 ms of the jump (P01), relative average power in the first 200 ms of the jump (P02), jump height, percentage of best jump height (%Jump), and maximal force difference between dominant and nondominant leg (Fmaxdiff). The men displayed significantly higher values at all loads for P and jump height (p free weights.

  12. An Adaptive Frequency Strategy for Variable Speed Wind Turbines: Application to High Wind Integration Into Power Systems

    Directory of Open Access Journals (Sweden)

    Ana Fernández-Guillamón

    2018-06-01

    Full Text Available This paper presents a new frequency controller for variable speed wind turbines connected to the grid under power imbalance conditions. It is based on the fast power reserve emulation technique, having two different operation modes: overproduction and recovery mode. In the first mode, the active power provided by wind turbines is set over the mechanical power, reducing their rotational speed. This overproduction power is estimated according to the frequency excursion. In the second mode, the active power is established under the mechanical power to recover the initial rotational speed through a smooth trajectory. The power system considered for simulation purposes includes thermal, hydro-power and wind-power plants. The controller proposed has been evaluated under different mix-generation scenarios implemented in Matlab/Simulink. Extensive results and comparison to previous proposals are also included in the paper.

  13. Systematic Multi-variable H-infinity Control Design for Primary Frequency Regulation in Stand-alone Microgrids with High Penetration of Renewable Energy Sources

    OpenAIRE

    Lam , Quang Linh; Bratcu , Antoneta Iuliana; Riu , Delphine

    2016-01-01

    International audience; In this paper, a systematic design of a robust multi-variable control structure for primary frequency regulation in microgrids with high rate of renewable source penetration is proposed. The considered microgrid represents a diesel-photovoltaic-supercapacitor hybrid power generation system operating in stand-alone mode. The proposed control structure relies on a two-level architecture: classical PI-based current tracking controllers are placed on the low control level ...

  14. The Effect of Biological Movement Variability on the Performance of the Golf Swing in High- and Low-Handicapped Players

    Science.gov (United States)

    Bradshaw, Elizabeth J.; Keogh, Justin W. L.; Hume, Patria A.; Maulder, Peter S.; Nortje, Jacques; Marnewick, Michel

    2009-01-01

    The purpose of this study was to examine the role of neuromotor noise on golf swing performance in high- and low-handicap players. Selected two-dimensional kinematic measures of 20 male golfers (n = 10 per high- or low-handicap group) performing 10 golf swings with a 5-iron club was obtained through video analysis. Neuromotor noise was calculated…

  15. Resequencing of IRS2 reveals rare variants for obesity but not fasting glucose homeostasis in Hispanic children.

    Science.gov (United States)

    Butte, Nancy F; Voruganti, V Saroja; Cole, Shelley A; Haack, Karin; Comuzzie, Anthony G; Muzny, Donna M; Wheeler, David A; Chang, Kyle; Hawes, Alicia; Gibbs, Richard A

    2011-09-22

    Our objective was to resequence insulin receptor substrate 2 (IRS2) to identify variants associated with obesity- and diabetes-related traits in Hispanic children. Exonic and intronic segments, 5' and 3' flanking regions of IRS2 (∼14.5 kb), were bidirectionally sequenced for single nucleotide polymorphism (SNP) discovery in 934 Hispanic children using 3730XL DNA Sequencers. Additionally, 15 SNPs derived from Illumina HumanOmni1-Quad BeadChips were analyzed. Measured genotype analysis tested associations between SNPs and obesity and diabetes-related traits. Bayesian quantitative trait nucleotide analysis was used to statistically infer the most likely functional polymorphisms. A total of 140 SNPs were identified with minor allele frequencies (MAF) ranging from 0.001 to 0.47. Forty-two of the 70 coding SNPs result in nonsynonymous amino acid substitutions relative to the consensus sequence; 28 SNPs were detected in the promoter, 12 in introns, 28 in the 3'-UTR, and 2 in the 5'-UTR. Two insertion/deletions (indels) were detected. Ten independent rare SNPs (MAF = 0.001-0.009) were associated with obesity-related traits (P = 0.01-0.00002). SNP 10510452_139 in the promoter region was shown to have a high posterior probability (P = 0.77-0.86) of influencing BMI, fat mass, and waist circumference in Hispanic children. SNP 10510452_139 contributed between 2 and 4% of the population variance in body weight and composition. None of the SNPs or indels were associated with diabetes-related traits or accounted for a previously identified quantitative trait locus on chromosome 13 for fasting serum glucose. Rare but not common IRS2 variants may play a role in the regulation of body weight but not an essential role in fasting glucose homeostasis in Hispanic children.

  16. Hierarchical high-pressure hydraulic system for a continuously variable transmission; Mudan hensokuki no kaisoshiki koyuatsu system no kaihatsu

    Energy Technology Data Exchange (ETDEWEB)

    Tominaga, M; Wakahara, T; Hiraoka, Y; Ishimori, Y [Nissan Motor Co. Ltd., Tokyo (Japan)

    1997-10-01

    A belt CVT system requires a large oil flow during shifts compared with a conventional automatic transmission. And the hydraulic pressure is higher for high-powered engines. As a result the oil pump is bigger and efficiency is lower(fuel consumption is higher). This system develops high pressure in three stages first reducing the hydraulic control system so that a small oil pump is attained. 8 figs.

  17. Propagation and forcing of high-frequency sea level variability along the west coast of South America

    Science.gov (United States)

    del Pilar Cornejo-Rodriguez, Maria; Enfield, David B.

    1987-12-01

    Tide and wind data from coastal and island stations from Buenaventura, Colombia (4°N), to Callao, Peru (12°S), have been analyzed for the 1979-1984 time period to determine the propagation and forcing characteristics of coastal sea level variability at periods of days to weeks, as well as how they vary either with season or between the 1982-1983 El Niño-Southern Oscillation (ENSO) period and non-ENSO years. During four non-ENSO years, the ensemble averaged cross spectra between coastal sea level height (SLH) and local winds show weak evidence of local forcing during the whole year without significant differences between the austral summer and winter seasons, other than a greater energy in the wind fluctuations at Talara during summer. Cross spectra between SLH series from neighboring stations show evidence of poleward phase propagation during winter seasons at speeds of about 2.0 m s-1 between La Libertad and Talara at periods of a week or more, and about 2.7 m s-1 between Talara and Callao at periods of 5-11 days, but no propagation is found during summers. During the 1982-1983 ENSO there is a large increase in SLH energy at most frequencies at all coastal stations, but especially in the 8-to-11-day band, where energies are enhanced by as much as an order of magnitude above non-ENSO levels. The cross spectra between adjacent SLH stations indicate a nondispersive poleward propagation of events during the 1982-1983 ENSO with phase speeds of 2.2-3.5 m s-1 from La Libertad to Talara (periods of a week or more) and 3.4-3.6 m s-1 from Talara to Callao (3.5 days or more). As with the SLH energy, the coherence and phase propagation were much stronger along the Peru coast in 1982-1983 than during non-ENSO periods, especially in the 8-to-11-day band. The one-third increase in phase speeds during the ENSO over the non-ENSO speeds is found to be consistent with the anomalous depressions of the density structure during El Niño. Comparisons between coastal SLH and the local

  18. Assessing the seasonal variability of ephemeral gully erosion using high-frequency monitoring: case study in a fully cultivated catchment (The Pommeroye, Northern France)

    Science.gov (United States)

    Patault, E.; Alary, C.; Franke, C.; Gauthier, A.; Abriak, N. E.

    2017-12-01

    Gully erosion results in on-site and off-site problems including the loss of cultivated soils, the silting of riverbeds and dams as well as infrastructure and property damage by muddy floods. Regions of intensive agricultural production situated on the European loess belt are particularly affected. Recently a growing interest has focused on ephemeral gullies since there have been recognized as a major contributor to the sediment yield in small agricultural catchment in this area. The aims of this case study are (i) to quantify the sediment yield transported by ephemeral gullies, (ii) to identify parameters that control the function of the hydro-sedimentary response and (iii) to evaluate the influence of seasonal variability on the ephemeral gully erosion. For this study a high-frequency monitoring station was implemented. For each flood event, 8 variables related to hydro-sedimentary and rainfall dynamics are calculated and the relationships between these variables are analyzed using the Pearson correlation matrix and Principal Component Analysis. During the first year of monitoring (03/2016-03/2017), 22 flood events were recorded of which 75% occurred in spring and winter. The specific sediment yield was evaluated to 30 t km-2 yr-1 which is conventional for the study region but the results show a highly variable seasonal distribution; 90% of the sedimentary transfer occurred in winter and autumn. The main reasons were a high cumulative rainfall and a long duration for the events. The maximum suspended sediment concentration at the catchment outlet was observed in spring, likely due to maximum rainfall intensities in that season. Also, a huge variability between the events is observed; e.g. one exceptional rain storm in 11/2016 represents 45% of the total sediment yield of the study period. For the monitored 22 events, 2 different types of hysteresis behavior were observed: (i) clockwise and (ii) complex. In winter, only clockwise hysteresis was observed. These

  19. Pulsating variables

    International Nuclear Information System (INIS)

    1989-01-01

    The study of stellar pulsations is a major route to the understanding of stellar structure and evolution. At the South African Astronomical Observatory (SAAO) the following stellar pulsation studies were undertaken: rapidly oscillating Ap stars; solar-like oscillations in stars; 8-Scuti type variability in a classical Am star; Beta Cephei variables; a pulsating white dwarf and its companion; RR Lyrae variables and galactic Cepheids. 4 figs

  20. Molecular technique reveals high variability of 18S rDNA distribution in harvestmen (Opiliones, Phalangiidae) from South Africa.

    Science.gov (United States)

    Šťáhlavský, František; Opatova, Vera; Just, Pavel; Lotz, Leon N; Haddad, Charles R

    2018-01-01

    The knowledge of cytogenetics in the harvestmen family Phalangiidae has been based on taxa from the Northern Hemisphere. We performed cytogenetic analysis on Guruia africana (Karsch, 1878) (2n=24) and four species of the genus Rhampsinitus Simon, 1879 (2n=24, 26, 34) from South Africa. Fluorescence in situ hybridization with an 18S rDNA probe was used to analyze the number and the distribution of this cluster in the family Phalangiidae for the first time. The results support the cytogenetic characteristics typical for the majority of harvestmen taxa, i.e. the predominance of small biarmed chromosomes and the absence of morphologically well-differentiated sex chromosomes as an ancestral state. We identified the number of 18S rDNA sites ranging from two in R. qachasneki Kauri, 1962 to seven in one population of R. leighi Pocock, 1903. Moreover, we found differences in the number and localization of 18S rDNA sites in R. leighi between populations from two localities and between sexes of R. capensis (Loman, 1898). The heterozygous states of the 18S rDNA sites in these species may indicate the presence of XX/XY and ZZ/ZW sex chromosomes, and the possible existence of these systems in harvestmen is discussed. The variability of the 18S rDNA sites indicates intensive chromosomal changes during the differentiation of the karyotypes, which is in contrast to the usual uniformity in chromosomal morphology known from harvestmen so far.

  1. High resolution LiDAR measurements reveal fine internal structure and variability of sediment-carrying coastal plume

    Science.gov (United States)

    Zavialov, P. O.; Pelevin, V. V.; Belyaev, N. A.; Izhitskiy, A. S.; Konovalov, B. V.; Krementskiy, V. V.; Goncharenko, I. V.; Osadchiev, A. A.; Soloviev, D. M.; Garcia, C. A. E.; Pereira, E. S.; Sartorato, L.; Moller, O. O.

    2018-05-01

    We report results of a field survey conducted in the buoyant, sediment-carrying coastal plume generated by the discharge from the Patos Lagoon, the World's largest choked lagoon. The concentration of total suspended matter (TSM) and organic matter (as represented by total organic carbon, TOC) were mapped using an ultraviolet fluorescent LiDAR, which allowed for extensive data coverage (total of 79,387 simultaneous determinations of TSM and TOC) during 3 consecutive days. These observations were accompanied by hydrographic measurements from the ship and at a mooring station. We first describe synoptic variability of the plume, which responded energetically to wind forcing. We then analyze the TSM, TOC and hydrographic data jointly and develop a simple approach to estimate the rates of suspended matter removal from the upper layer due to gravitational settling and turbulent mixing based on relative changes in TSM and TOC concentrations. Four distinct regions within the plume exhibiting different dynamics of suspended and dissolved constituents were identified on this basis.

  2. Population structure, fluctuating asymmetry and genetic variability in an endemic and highly isolated Astyanax fish population (Characidae

    Directory of Open Access Journals (Sweden)

    Maria Claudia Gross

    2004-01-01

    Full Text Available Morphological and chromosomal markers were used to infer the structure and genetic variability of a population of fish of the genus Astyanax, geographically isolated at sinkhole 2 of Vila Velha State Park, Paraná, Brazil. Two morphotypes types were observed, the standard phenotype I and phenotype II which showed an anatomical alteration probably due to an inbreeding process. Fluctuating asymmetry (FA analysis of different characters showed low levels of morphological variation among the population from sinkhole 2 and in another population from the Tibagi river (Paraná, Brazil. The Astyanax karyotype was characterized in terms of chromosomal morphology, constitutive heterochromatin and nucleolar organizer regions. Males and females presented similar karyotypes (2n=48, 6M+18SM+14ST+10A with no evidence of a sex chromosome system. One female from sinkhole 2 was a natural triploid with 2n=3x=72 chromosomes (9M+27SM+21ST+15A. The data are discussed regarding the maintenance of population structure and their evolutionary importance, our data suggesting that Astyanax from the Vila Velha State Park sinkhole 2 is a recently isolated population.

  3. Variable responses of benthic communities to anomalously warm sea temperatures on a high-latitude coral reef.

    Science.gov (United States)

    Bridge, Tom C L; Ferrari, Renata; Bryson, Mitch; Hovey, Renae; Figueira, Will F; Williams, Stefan B; Pizarro, Oscar; Harborne, Alastair R; Byrne, Maria

    2014-01-01

    High-latitude reefs support unique ecological communities occurring at the biogeographic boundaries between tropical and temperate marine ecosystems. Due to their lower ambient temperatures, they are regarded as potential refugia for tropical species shifting poleward due to rising sea temperatures. However, acute warming events can cause rapid shifts in the composition of high-latitude reef communities, including range contractions of temperate macroalgae and bleaching-induced mortality in corals. While bleaching has been reported on numerous high-latitude reefs, post-bleaching trajectories of benthic communities are poorly described. Consequently, the longer-term effects of thermal anomalies on high-latitude reefs are difficult to predict. Here, we use an autonomous underwater vehicle to conduct repeated surveys of three 625 m(2) plots on a coral-dominated high-latitude reef in the Houtman Abrolhos Islands, Western Australia, over a four-year period spanning a large-magnitude thermal anomaly. Quantification of benthic communities revealed high coral cover (>70%, comprising three main morphospecies) prior to the bleaching event. Plating Montipora was most susceptible to bleaching, but in the plot where it was most abundant, coral cover did not change significantly because of post-bleaching increases in branching Acropora. In the other two plots, coral cover decreased while macroalgal cover increased markedly. Overall, coral cover declined from 73% to 59% over the course of the study, while macroalgal cover increased from 11% to 24%. The significant differences in impacts and post-bleaching trajectories among plots underline the importance of understanding the underlying causes of such variation to improve predictions of how climate change will affect reefs, especially at high-latitudes.

  4. Variable responses of benthic communities to anomalously warm sea temperatures on a high-latitude coral reef.

    Directory of Open Access Journals (Sweden)

    Tom C L Bridge

    Full Text Available High-latitude reefs support unique ecological communities occurring at the biogeographic boundaries between tropical and temperate marine ecosystems. Due to their lower ambient temperatures, they are regarded as potential refugia for tropical species shifting poleward due to rising sea temperatures. However, acute warming events can cause rapid shifts in the composition of high-latitude reef communities, including range contractions of temperate macroalgae and bleaching-induced mortality in corals. While bleaching has been reported on numerous high-latitude reefs, post-bleaching trajectories of benthic communities are poorly described. Consequently, the longer-term effects of thermal anomalies on high-latitude reefs are difficult to predict. Here, we use an autonomous underwater vehicle to conduct repeated surveys of three 625 m(2 plots on a coral-dominated high-latitude reef in the Houtman Abrolhos Islands, Western Australia, over a four-year period spanning a large-magnitude thermal anomaly. Quantification of benthic communities revealed high coral cover (>70%, comprising three main morphospecies prior to the bleaching event. Plating Montipora was most susceptible to bleaching, but in the plot where it was most abundant, coral cover did not change significantly because of post-bleaching increases in branching Acropora. In the other two plots, coral cover decreased while macroalgal cover increased markedly. Overall, coral cover declined from 73% to 59% over the course of the study, while macroalgal cover increased from 11% to 24%. The significant differences in impacts and post-bleaching trajectories among plots underline the importance of understanding the underlying causes of such variation to improve predictions of how climate change will affect reefs, especially at high-latitudes.

  5. Rotor-dynamic design aspects for a variable frequency drive based high speed cryogenic centrifugal pump in fusion devices

    International Nuclear Information System (INIS)

    Das, Jotirmoy; Vaghela, Hitensinh; Bhattacharya, Ritendra; Patel, Pratik; Shukla, Vinit; Shah, Nitin; Sarkar, Biswanath

    2015-01-01

    Superconducting magnets of large size are inevitable for fusion devices due to high magnetic field requirements. Forced flow cooling of the superconducting magnets with high mass flowrate of the order ∼3 kg/s is required to keep superconducting magnets within its safe operational boundaries during various plasma scenarios. This important requirement can be efficiently fulfilled by employing high capacity and high efficiency cryogenic centrifugal pumps. The efficiency > 70% will ensure overall lower heat load to the cryoplant. Thermo-hydraulic design of cryogenic centrifugal pump revealed that to achieve the operational regime with high efficiency, the speed should be ∼ 10,000 revolutions per minute. In this regard, the rotor-dynamic design aspect is quite critical from the operational stability point of view. The rotor shaft design of the cryogenic pump is primarily an outcome of optimization between thermal heat-in leak at cryogenic temperature level from ambient, cryogenic fluid impedance and designed rotation speed of the impeller wheel. The paper describes the basic design related to critical speed of the rotor shaft, rotor whirl and system instability prediction to explore the ideal operational range of the pump from the system stability point of view. In the rotor-dynamic analysis, the paper also describes the Campbell plots to ensure that the pump is not disturbed by any of the critical speeds, especially while operating near the nominal and enhanced operating modes. (author)

  6. Redesign of a Variable-Gain Output Feedback Longitudinal Controller Flown on the High-Alpha Research Vehicle (HARV)

    Science.gov (United States)

    Ostroff, Aaron J.

    1998-01-01

    This paper describes a redesigned longitudinal controller that flew on the High-Alpha Research Vehicle (HARV) during calendar years (CY) 1995 and 1996. Linear models are developed for both the modified controller and a baseline controller that was flown in CY 1994. The modified controller was developed with three gain sets for flight evaluation, and several linear analysis results are shown comparing the gain sets. A Neal-Smith flying qualities analysis shows that performance for the low- and medium-gain sets is near the level 1 boundary, depending upon the bandwidth assumed, whereas the high-gain set indicates a sensitivity problem. A newly developed high-alpha Bode envelope criterion indicates that the control system gains may be slightly high, even for the low-gain set. A large motion-base simulator in the United Kingdom was used to evaluate the various controllers. Desired performance, which appeared to be satisfactory for flight, was generally met with both the low- and medium-gain sets. Both the high-gain set and the baseline controller were very sensitive, and it was easy to generate pilot-induced oscillation (PIO) in some of the target-tracking maneuvers. Flight target-tracking results varied from level 1 to level 3 and from no sensitivity to PIO. These results were related to pilot technique and whether actuator rate saturation was encountered.

  7. Climate SPHINX: High-resolution present-day and future climate simulations with an improved representation of small-scale variability

    Science.gov (United States)

    Davini, Paolo; von Hardenberg, Jost; Corti, Susanna; Subramanian, Aneesh; Weisheimer, Antje; Christensen, Hannah; Juricke, Stephan; Palmer, Tim

    2016-04-01

    The PRACE Climate SPHINX project investigates the sensitivity of climate simulations to model resolution and stochastic parameterization. The EC-Earth Earth-System Model is used to explore the impact of stochastic physics in 30-years climate integrations as a function of model resolution (from 80km up to 16km for the atmosphere). The experiments include more than 70 simulations in both a historical scenario (1979-2008) and a climate change projection (2039-2068), using RCP8.5 CMIP5 forcing. A total amount of 20 million core hours will be used at end of the project (March 2016) and about 150 TBytes of post-processed data will be available to the climate community. Preliminary results show a clear improvement in the representation of climate variability over the Euro-Atlantic following resolution increase. More specifically, the well-known atmospheric blocking negative bias over Europe is definitely resolved. High resolution runs also show improved fidelity in representation of tropical variability - such as the MJO and its propagation - over the low resolution simulations. It is shown that including stochastic parameterization in the low resolution runs help to improve some of the aspects of the MJO propagation further. These findings show the importance of representing the impact of small scale processes on the large scale climate variability either explicitly (with high resolution simulations) or stochastically (in low resolution simulations).

  8. High accuracy subwavelength distance measurements: A variable-angle standing-wave total-internal-reflection optical microscope

    International Nuclear Information System (INIS)

    Haynie, A.; Min, T.-J.; Luan, L.; Mu, W.; Ketterson, J. B.

    2009-01-01

    We describe an extension of the total-internal-reflection microscopy technique that permits direct in-plane distance measurements with high accuracy (<10 nm) over a wide range of separations. This high position accuracy arises from the creation of a standing evanescent wave and the ability to sweep the nodal positions (intensity minima of the standing wave) in a controlled manner via both the incident angle and the relative phase of the incoming laser beams. Some control over the vertical resolution is available through the ability to scan the incoming angle and with it the evanescent penetration depth.

  9. Mechanisms of decadal variability in the Labrador Sea and the wider North Atlantic in a high-resolution climate model

    Science.gov (United States)

    Ortega, Pablo; Robson, Jon; Sutton, Rowan T.; Andrews, Martin B.

    2017-10-01

    A necessary step before assessing the performance of decadal predictions is the evaluation of the processes that bring memory to the climate system, both in climate models and observations. These mechanisms are particularly relevant in the North Atlantic, where the ocean circulation, related to both the Subpolar Gyre and the Meridional Overturning Circulation (AMOC), is thought to be important for driving significant heat content anomalies. Recently, a rapid decline in observed densities in the deep Labrador Sea has pointed to an ongoing slowdown of the AMOC strength taking place since the mid 90s, a decline also hinted by in-situ observations from the RAPID array. This study explores the use of Labrador Sea densities as a precursor of the ocean circulation changes, by analysing a 300-year long simulation with the state-of-the-art coupled model HadGEM3-GC2. The major drivers of Labrador Sea density variability are investigated, and are characterised by three major contributions. First, the integrated effect of local surface heat fluxes, mainly driven by year-to-year changes in the North Atlantic Oscillation, which accounts for 62% of the total variance. Additionally, two multidecadal-to-centennial contributions from the Greenland-Scotland Ridge outflows are quantified; the first associated with freshwater exports via the East Greenland Current, and the second with density changes in the Denmark Strait Overflow. Finally, evidence is shown that decadal trends in Labrador Sea densities are followed by important atmospheric impacts. In particular, a positive winter NAO response appears to follow the negative Labrador Sea density trends, and provides a phase reversal mechanism.

  10. Assessment of high precision, high accuracy Inductively Coupled Plasma-Optical Emission Spectroscopy to obtain concentration uncertainties less than 0.2% with variable matrix concentrations

    International Nuclear Information System (INIS)

    Rabb, Savelas A.; Olesik, John W.

    2008-01-01

    The ability to obtain high precision, high accuracy measurements in samples with complex matrices using High Performance Inductively Coupled Plasma-Optical Emission Spectroscopy (HP-ICP-OES) was investigated. The Common Analyte Internal Standard (CAIS) procedure was incorporated into the High Performance Inductively Coupled Plasma-Optical Emission Spectroscopy method to correct for matrix-induced changes in emission intensity ratios. Matrix matching and standard addition approaches to minimize matrix-induced errors when using High Performance Inductively Coupled Plasma-Optical Emission Spectroscopy were also assessed. The High Performance Inductively Coupled Plasma-Optical Emission Spectroscopy method was tested with synthetic solutions in a variety of matrices, alloy standard reference materials and geological reference materials

  11. Variable epidemiology of the three outbreaks of unrelated highly pathogenic avian influenza viruses in the United States, 2014-2017

    Science.gov (United States)

    Three unrelated highly pathogenic avian influenza (HPAI) outbreaks have occurred in the United States (US) during 2014-2017. Late in 2014, Canada reported the first outbreak of an H5N2 reassortment virus between the A/goose/Guangdong/1/1996 (Gs/GD)-lineage H5Nx clade 2.3.4.4A HPAI and North American...

  12. Sea ice and wind variability during the Holocene in East Antarctica: Insight on middle high latitude coupling

    NARCIS (Netherlands)

    Denis, D.; Crosta, X.; Barbera, L.; Masse, G.; Renssen, H.; Ther, O.; Giraudeau, J.

    2010-01-01

    Micropaleontological and biomarker data from two high-accumulation marine sites from the Coastal and Continental Shelf Zone (CCSZ) off East Antarctica (Adélie Land at ∼140°E and eastern Prydz Bay at ∼77°E) are used to reconstruct Holocene changes in sea ice and wind stress at the basin-wide scale.

  13. School Variables as Mediators of Personal and Family Factors on School Violence in Taiwanese Junior High Schools

    Science.gov (United States)

    Chen, Ji-Kang; Astor, Ron Avi

    2012-01-01

    Using a nationally representative sample of 3,058 junior high school students in Taiwan, this study examines a model of how personal traits, family factors, and school dynamics influence school violence committed by students against students and teachers. This model proposed that school violence is directly influenced by personal traits,…

  14. Genotype and year variability of the chemical composition of walnut oil of Moroccan seedlings from the high Atlas Mountains

    Energy Technology Data Exchange (ETDEWEB)

    Kodad, O.; EstopaNan, G.; Juan, T.; Socias i Company, R.; Sindic, M.

    2016-07-01

    Protein and oil content, fatty acid composition and tocopherol concentration were determined for two years in the kernel of ten candidate walnut selections from the high Atlas Mountains in Morocco. Considerable variation between genotypes was found for all parameters. The ranges of protein content (11.58–14.5% of kernel dry weight, DW), oil content (54.4–67.48% of kernel DW), oleic (12.47–22.01% of total oil), linoleic (55.03–60.01%), linolenic (9.3–15.87%), palmitic (6.84–9.12%), and stearic (1.7–2.92%) acid percentages, ?-tocopherol (188.1–230.7 mg·kg-1 of oil), d-tocopherol (23.3–43.4 mg·kg-1), and a-tocopherol (8.9–16.57 mg·kg-1) contents agreed with previous results obtained from other commercial walnut cultivars. The effect of year was significant for all the chemical components, except for oil content and palmitic acid percentage. Some genotypes showed high oil contents and consistently high values of ?-tocopherol in both years of study. The introduction of these genotypes as new cultivars by vegetative propagation may result in a an increase in quality of the walnuts from the high Atlas Mountains of Morocco, and as a seed source for forest walnut propagation in the same region. (Author)

  15. Seasonal variability in physicochemical characteristics of small water bodies across a High Arctic wetland, Polar Bear Pass, Bathurst Island, Nunavut, Canada

    Science.gov (United States)

    Abnizova, A.; Miller, E.; Shakil, S.; Young, K. L.

    2012-12-01

    Small water bodies (lakes, ponds) in permafrost environments make up roughly half of the total area of surface water, but their relevance to nutrient and carbon fluxes on a landscape scale still remains largely unknown. Small variations in pond water balance as a result of seasonal changes in precipitation, evaporation, or drainage processes have the potential to produce considerable changes in the carbon and nutrient budgets as small changes in the water level can have a major effect on volumes and surface areas of ponds. The aims of this study were (1) to identify the main characteristics in pond hydrology both seasonally and between years; (2) to identify factors controlling variation in measured physicochemical variables; and (3) to detect seasonal trends in the hydrological and chemical characteristics of ponds located in an extensive low-gradient High Arctic wetland. We conducted detailed limnological surveys of 50 wetland ponds located at Polar Bear Pass (PBP), Bathurst Island, Nunavut, Canada during 2007-2010. The results indicate large seasonal variability in physicochemical parameters that is associated with pond water budget changes, especially for ponds with steady water levels vs. dynamic ponds (fluctuating water levels). Principal component analysis (PCA) of the datasets indicated that major ion content, specifically calcium (Ca2+), was responsible for much of the variability among the ponds in both 2008 and 2009. Additionally in 2009 most of the variability was also due to specific conductivity in the summer and magnesium (Mg2+) in the fall. These trends are typically identified as a result of dilution or evapo-concentration processes in small water bodies. In 2007, a warm and dry year, pH and potassium (K+) were responsible for much of variation between ponds. This is attributed to high vegetation growth in ponds and a longer growing season. While no trend was identified in 2010 (PCA analysis), calculations of greenhouse gas (GHG) emissions from 50

  16. High-frequency (8 to 16 kHz) reference thresholds and intrasubject threshold variability relative to ototoxicity criteria using a Sennheiser HDA 200 earphone.

    Science.gov (United States)

    Frank, T

    2001-04-01

    The first purpose of this study was to determine high-frequency (8 to 16 kHz) thresholds for standardizing reference equivalent threshold sound pressure levels (RETSPLs) for a Sennheiser HDA 200 earphone. The second and perhaps more important purpose of this study was to determine whether repeated high-frequency thresholds using a Sennheiser HDA 200 earphone had a lower intrasubject threshold variability than the ASHA 1994 significant threshold shift criteria for ototoxicity. High-frequency thresholds (8 to 16 kHz) were obtained for 100 (50 male, 50 female) normally hearing (0.25 to 8 kHz) young adults (mean age of 21.2 yr) in four separate test sessions using a Sennheiser HDA 200 earphone. The mean and median high-frequency thresholds were similar for each test session and increased as frequency increased. At each frequency, the high-frequency thresholds were not significantly (p > 0.05) different for gender, test ear, or test session. The median thresholds at each frequency were similar to the 1998 interim ISO RETSPLs; however, large standard deviations and wide threshold distributions indicated very high intersubject threshold variability, especially at 14 and 16 kHz. Threshold repeatability was determined by finding the threshold differences between each possible test session comparison (N = 6). About 98% of all of the threshold differences were within a clinically acceptable range of +/-10 dB from 8 to 14 kHz. The threshold differences between each subject's second, third, and fourth minus their first test session were also found to determine whether intrasubject threshold variability was less than the ASHA 1994 criteria for determining a significant threshold shift due to ototoxicity. The results indicated a false-positive rate of 0% for a threshold shift > or = 20 dB at any frequency and a false-positive rate of 2% for a threshold shift >10 dB at two consecutive frequencies. This study verified that the output of high-frequency audiometers at 0 dB HL using

  17. Day and Night Variability of CO2 Fluxes and Priming Effects under zea Mays Measured in High Resolution

    Science.gov (United States)

    Splettstoesser, Thomas; Pausch, Johanna

    2017-04-01

    Plant induced increase of soil organic matter turnover rates contribute to carbon emissions in agricultural land use systems. In order to better understand these rhizosphere priming effects, we conducted an experiment which enabled us to monitor CO2 fluxes under Zea mays plants in high resolution. The experiment was conducted in a climate chamber where the plants were grown in tightly sealed boxes for 40 days and CO2 efflux from soil was measured twice a day. Continuous 13C-CO2 label was used to allow differentiation between plant- and soil-derived CO2.This enabled us to monitor root respiration and soil organic matter turnover in the early stages of plant growth and to highlight changes in soil CO2 emissions and priming effects between day and night. The measurements were conducted with a PICARRO G2131-I C high-precision isotopic CO2 Analyzer (PICARRO INC.) utilizing an automated valve system governed by a CR1000 data logger (Campbell Scientific). After harvest roots and shoots were analyzed for 13C content. Microbial biomass, root length density and enzymatic activities in soil were measured and linked to soil organic matter turnover rates. Results show an increased soil CO2 efflux at day time periods and an overall increase with increasing plant biomass. No difference in chloroform fumigation extractable microbial biomass has been found but a strong negative priming effect was measured in the short experimental period, suggesting that the microbes shifted to the utilization of plant exudates without actual microbial growth triggered by the new labile C input. This is coherent with the observed shift in enzyme kinetics. With this experimental setup we show that measurement of priming effects in high resolution can be achieved.

  18. Streak-Camera Measurements with High Currents in PEP-II and Variable Optics in SPEAR3

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Weixeng; Fisher, Alan, a Corbett, Jeff; /SLAC

    2008-06-05

    A dual-axis, synchroscan streak camera was used to measure longitudinal bunch profiles in three storage rings at SLAC: the PEP-II low- and high-energy rings, and SPEAR3. At high currents, both PEP rings exhibit a transient synchronous-phase shift along the bunch train due to RF-cavity beam loading. Bunch length and profile asymmetry were measured along the train for a range of beam currents. To avoid the noise inherent in a dual-axis sweep, we accumulated single-axis synchroscan images while applying a 50-ns gate to the microchannel plate. To improve the extinction ratio, an upstream mirror pivoting at 1 kHz was synchronized with the 2kHz MCP gate to deflect light from other bunches off the photocathode. Bunch length was also measured on the HER as a function of beam energy. For SPEAR3 we measured bunch length as a function of single-bunch current for several lattices: achromatic, low-emittance and low momentum compaction. In the first two cases, resistive and reactive impedance components can be extracted from the longitudinal bunch profiles. In the low-alpha configurations, we observed natural bunch lengths approaching the camera resolution, requiring special care to remove instrumental effects, and saw evidence of periodic bursting.

  19. Factors Determining the Inter-observer Variability and Diagnostic Accuracy of High-resolution Manometry for Esophageal Motility Disorders.

    Science.gov (United States)

    Kim, Ji Hyun; Kim, Sung Eun; Cho, Yu Kyung; Lim, Chul-Hyun; Park, Moo In; Hwang, Jin Won; Jang, Jae-Sik; Oh, Minkyung

    2018-01-30

    Although high-resolution manometry (HRM) has the advantage of visual intuitiveness, its diagnostic validity remains under debate. The aim of this study was to evaluate the diagnostic accuracy of HRM for esophageal motility disorders. Six staff members and 8 trainees were recruited for the study. In total, 40 patients enrolled in manometry studies at 3 institutes were selected. Captured images of 10 representative swallows and a single swallow in analyzing mode in both high-resolution pressure topography (HRPT) and conventional line tracing formats were provided with calculated metrics. Assessments of esophageal motility disorders showed fair agreement for HRPT and moderate agreement for conventional line tracing (κ = 0.40 and 0.58, respectively). With the HRPT format, the k value was higher in category A (esophagogastric junction [EGJ] relaxation abnormality) than in categories B (major body peristalsis abnormalities with intact EGJ relaxation) and C (minor body peristalsis abnormalities or normal body peristalsis with intact EGJ relaxation). The overall exact diagnostic accuracy for the HRPT format was 58.8% and rater's position was an independent factor for exact diagnostic accuracy. The diagnostic accuracy for major disorders was 63.4% with the HRPT format. The frequency of major discrepancies was higher for category B disorders than for category A disorders (38.4% vs 15.4%; P < 0.001). The interpreter's experience significantly affected the exact diagnostic accuracy of HRM for esophageal motility disorders. The diagnostic accuracy for major disorders was higher for achalasia than distal esophageal spasm and jackhammer esophagus.

  20. Long-term creep behavior of high-temperature gas turbine materials under constant and variable stress

    International Nuclear Information System (INIS)

    Granacher, J.; Preussler, T.

    1987-01-01

    Within the framework of the documented research project, extensive creep rupture tests were carried out with characteristic, high-temperature gas turbine materials for establishment of improved design data. In the range of the main application temperatures and in stress ranges down to application-relevant values the tests extended over a period of about 40,000 hours. In addition, long-term annealing tests were carried out in the most important temperature ranges for the measurement of the density-dependent straim, which almost always manifested itself as a material contraction. Furthermore, hot tensile tests were carried out for the description of the elastoplastic short-term behavior. Several creep curves were derived from the results of the different tests with a differentiated evaluation method. On the basis of these creep curves, creep equations were set up for a series of materials which are valid in the entire examined temperature range and stress range and up to the end of the secondary creep range. Also, equations for the time-temperature-dependent description of the material contraction behavior were derived. With these equations, the high-temperature deformation behavior of the examined materials under constant creep stress can be described simply and application-oriented. (orig.) With 109 figs., 19 tabs., 77 refs [de

  1. Spatial Variability of Geriatric Depression Risk in a High-Density City: A Data-Driven Socio-Environmental Vulnerability Mapping Approach.

    Science.gov (United States)

    Ho, Hung Chak; Lau, Kevin Ka-Lun; Yu, Ruby; Wang, Dan; Woo, Jean; Kwok, Timothy Chi Yui; Ng, Edward

    2017-08-31

    Previous studies found a relationship between geriatric depression and social deprivation. However, most studies did not include environmental factors in the statistical models, introducing a bias to estimate geriatric depression risk because the urban environment was found to have significant associations with mental health. We developed a cross-sectional study with a binomial logistic regression to examine the geriatric depression risk of a high-density city based on five social vulnerability factors and four environmental measures. We constructed a socio-environmental vulnerability index by including the significant variables to map the geriatric depression risk in Hong Kong, a high-density city characterized by compact urban environment and high-rise buildings. Crude and adjusted odds ratios (ORs) of the variables were significantly different, indicating that both social and environmental variables should be included as confounding factors. For the comprehensive model controlled by all confounding factors, older adults who were of lower education had the highest geriatric depression risks (OR: 1.60 (1.21, 2.12)). Higher percentage of residential area and greater variation in building height within the neighborhood also contributed to geriatric depression risk in Hong Kong, while average building height had negative association with geriatric depression risk. In addition, the socio-environmental vulnerability index showed that higher scores were associated with higher geriatric depression risk at neighborhood scale. The results of mapping and cross-section model suggested that geriatric depression risk was associated with a compact living environment with low socio-economic conditions in historical urban areas in Hong Kong. In conclusion, our study found a significant difference in geriatric depression risk between unadjusted and adjusted models, suggesting the importance of including environmental factors in estimating geriatric depression risk. We also

  2. Spatial Variability of Geriatric Depression Risk in a High-Density City: A Data-Driven Socio-Environmental Vulnerability Mapping Approach

    Directory of Open Access Journals (Sweden)

    Hung Chak Ho

    2017-08-01

    Full Text Available Previous studies found a relationship between geriatric depression and social deprivation. However, most studies did not include environmental factors in the statistical models, introducing a bias to estimate geriatric depression risk because the urban environment was found to have significant associations with mental health. We developed a cross-sectional study with a binomial logistic regression to examine the geriatric depression risk of a high-density city based on five social vulnerability factors and four environmental measures. We constructed a socio-environmental vulnerability index by including the significant variables to map the geriatric depression risk in Hong Kong, a high-density city characterized by compact urban environment and high-rise buildings. Crude and adjusted odds ratios (ORs of the variables were significantly different, indicating that both social and environmental variables should be included as confounding factors. For the comprehensive model controlled by all confounding factors, older adults who were of lower education had the highest geriatric depression risks (OR: 1.60 (1.21, 2.12. Higher percentage of residential area and greater variation in building height within the neighborhood also contributed to geriatric depression risk in Hong Kong, while average building height had negative association with geriatric depression risk. In addition, the socio-environmental vulnerability index showed that higher scores were associated with higher geriatric depression risk at neighborhood scale. The results of mapping and cross-section model suggested that geriatric depression risk was associated with a compact living environment with low socio-economic conditions in historical urban areas in Hong Kong. In conclusion, our study found a significant difference in geriatric depression risk between unadjusted and adjusted models, suggesting the importance of including environmental factors in estimating geriatric depression risk

  3. The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau.

    Science.gov (United States)

    Zeng, Xingquan; Long, Hai; Wang, Zhuo; Zhao, Shancen; Tang, Yawei; Huang, Zhiyong; Wang, Yulin; Xu, Qijun; Mao, Likai; Deng, Guangbing; Yao, Xiaoming; Li, Xiangfeng; Bai, Lijun; Yuan, Hongjun; Pan, Zhifen; Liu, Renjian; Chen, Xin; WangMu, QiMei; Chen, Ming; Yu, Lili; Liang, Junjun; DunZhu, DaWa; Zheng, Yuan; Yu, Shuiyang; LuoBu, ZhaXi; Guang, Xuanmin; Li, Jiang; Deng, Cao; Hu, Wushu; Chen, Chunhai; TaBa, XiongNu; Gao, Liyun; Lv, Xiaodan; Abu, Yuval Ben; Fang, Xiaodong; Nevo, Eviatar; Yu, Maoqun; Wang, Jun; Tashi, Nyima

    2015-01-27

    The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called "Qingke" in Chinese and "Ne" in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.

  4. Variable wide range of lens power and its improvement in a liquid-crystal lens using highly resistive films divided into two regions with different diameters

    Science.gov (United States)

    Kawamura, Marenori; Sato, Susumu

    2018-05-01

    The variable range of lens power of a liquid-crystal (LC) lens driven by two voltages is discussed on the basis of calculated and experimental results. The LC lens has two electrodes, which are a circularly hole-patterned electrode and a circular electrode, in addition to a common electrode, and highly resistive transparent films. The variable range of lens power increases with increasing driving voltage applied across the circularly hole-patterned electrode and the common electrode, and with decreasing diameter of highly resistive films. However, the optical-phase retardation profile tends to deviate from a parabolic curve in these cases. As a method to improve the trade-off properties, the highly resistive film is divided into two regions with different diameters, where the sheet resistance of an outer film is larger than that of an inner one. The improved LC lens has a lens power that varies in a wide range, and it exhibits a good parabolic phase retardation profile.

  5. Design considerations for high current regulated DC power supplies with reference to 600 kW variable DC power supply

    International Nuclear Information System (INIS)

    Ushakumari; Garud, A.N.; Nadkarni, S.S.

    1980-01-01

    High current regulated dc power supplies find increasing applications in industry and research. The power rating of these supplies vary from few killowatts to megawatts. The general requirements of these supplies for various applications and the techniques used to achieve the desired performance are presented. The design and selection of various circuit blocks namely the rectifier transformer, multiphase rectifier arrangement, SCR paralleling and current sensing techniques, are discussed in detail for a 600 killowatt current controlled supply developed in the Bhabha Atomic Research Centre, Bombay, and used for the thermal studies of reactor components. The power supply incorporates paralleled phase controlled thyristors with a closed loop feedback circuitary to achieve a current stability of 0.1% and smooth output variation from 10 to 100%. (auth.)

  6. Genotype and year variability of the chemical composition of walnut oil of Moroccan seedlings from the high Atlas Mountains

    Directory of Open Access Journals (Sweden)

    Kodad, O.

    2016-03-01

    Full Text Available Protein and oil content, fatty acid composition and tocopherol concentration were determined for two years in the kernel of ten candidate walnut selections from the high Atlas Mountains in Morocco. Considerable variation between genotypes was found for all parameters. The ranges of protein content (11.58–14.5% of kernel dry weight, DW, oil content (54.4–67.48% of kernel DW, oleic (12.47–22.01% of total oil, linoleic (55.03–60.01%, linolenic (9.3–15.87%, palmitic (6.84–9.12%, and stearic (1.7–2.92% acid percentages, γ-tocopherol (188.1–230.7 mg·kg-1 of oil, δ-tocopherol (23.3–43.4 mg·kg-1, and α-tocopherol (8.9–16.57 mg·kg-1 contents agreed with previous results obtained from other commercial walnut cultivars. The effect of year was significant for all the chemical components, except for oil content and palmitic acid percentage. Some genotypes showed high oil contents and consistently high values of γ-tocopherol in both years of study. The introduction of these genotypes as new cultivars by vegetative propagation may result in a an increase in quality of the walnuts from the high Atlas Mountains of Morocco, and as a seed source for forest walnut propagation in the same region.Se determinó durante dos años el contenido en proteína y aceite, la composición en ácidos grasos y la concentración en tocoferoles en la pepita de diez plantones de nogal seleccionados en el Alto Atlas de Marruecos, encontrándose una considerable variación entre genotipos para todos los parámetros. Los rangos del contenido en proteína (11.58–14.5 % del peso seco, PS, contenido en aceite (54.4–67.48 % PS, porcentaje de ácido oleico (12.47–22.01% del aceite total, linoleico (55.03–60.01 %, linolénico (9.3–15.87 %, palmítico (6.84–9.12 %, y esteárico (1.7–2.92 %, contenido en γ-tocoferol (188.1–230.7 mg·kg−1 de aceite, δ-tocoferol (23.3–43.4 mg·kg−1 y α-tocoferol (8.9–16.57 mg·kg−1, coincidieron con

  7. The variability of the isotopic signal during the last Glacial as seen from the ultra-high resolution NEEM and NorthGRIP ice cores.

    Science.gov (United States)

    Gkinis, Vasileios; Møllesøe Vinther, Bo; Terkelsen Holme, Christian; Capron, Emilie; Popp, Trevor James; Olander Rasmussen, Sune

    2017-04-01

    The continuity and high resolution available in polar ice core records constitutes them an excellent tool for the study of the stadial-interstadial transitions, notably through the study of the water isotopic composition of polar precipitation (δ18O, δD ). The quest for the highest resolution possible has resulted in experimental sampling and analysis techniques that have yielded data sets with a potential to change the current picture on the climatic signals of the last Glacial. Specifically, the ultra-high resolution δ18O signals from the NorthGRIP and NEEM ice cores, present a variability at multi-annual and decadal time scales, whose interpretation gives rise to further puzzling though interesting questions and an obvious paradox. By means of simple firn isotope diffusion and densification calculations, we firstly demonstrate that the variability of observed signals is unlikely to be due to post depositional effects that are known to occur on the surface of the Greenland ice cap and alter the δ18O composition of the precipitated snow. Assuming specific values for the δ18O sensitivity to temperature (commonly referred to as the δ18O slope), we estimate that the temperature signal during the stadials has a variability that extents from interstadial to extremely cold levels with peak-to-peak fluctuations of almost 35 K occurring in a few years. Similarly, during interstadial phases the temperature varies rapidly from stadial to Holocene levels while the signal variability shows a maximum during the LGM, with magnitudes of up to 15‰ that translate to ≈ 50 K when a δ18O slope of 0.3‰K-1 is used. We assess the validity of these results and comment on the stability of the δ18O slope. Driven by a simple logical queue, we conclude that the observed δ18O variability reflects a climatic signal although not necessarily attributed 100% to temperature changes. From this we can assume that there occur climatic mechanisms during the previously thought stable

  8. High-resolution lake sediment archives of midcontinental atmospheric and hydroclimate variability during the Medieval Climate Anomaly and Little Ice Age

    Science.gov (United States)

    Bird, B. W.; Wilson, J. J.; Gilhooly, W., III; Steinman, B. A.; Stamps, L. G.; Ahmed, M. N.; Abbott, M. B.; Pompeani, D. P.; Hillman, A. L.; Finkenbinder, M. S.

    2017-12-01

    Hydroclimate variability in the midcontinental United States (US) during the last 2000 years is not well characterized because there are few high-resolution paleoclimate records from the region. The majority of information about late Holocene midcontinental hydroclimate variability comes from scattered lake and bog sediment archives (primarily north of 42˚N) and gridded Palmer Drought Severity Index (PDSI) data calculated from a network of tree-ring records. The density of tree-ring records is lowest in the midcontinent, however, and decreases precipitously with time. In order to address this midcontinental paleoclimate data gap, we are developing a series of new lake-sediment-based hydroclimate records spanning 85˚ to 98˚W and 38˚ to 45˚N. New results from the eastern and central portions of the study area indicate large hydroclimate changes during the last 2000 years. Specifically, the Ohio and central Mississippi River valleys were wetter during the Medieval Climate Anomaly (MCA; 950-1250 CE), but drier during the Little Ice Age (LIA; 1350-1850 CE) with an especially severe, multi-decadal drought between 1350-1450 CE. Comparison with western (west of 96˚W) drought and fire records supports the existence of a hydroclimate dipole, with opposite hydroclimate conditions west and east of 96˚W. Isotopic changes in precipitation during the MCA and LIA suggest hydroclimate anomalies during these events were associated with mean state atmospheric circulation changes that resemble modern Pacific North American Mode (PNA) variability. Midcontinental Native American populations appear to have responded to MCA and LIA hydroclimate variability, with the latter event contributing to midcontinental depopulation between 1350-1500 CE.

  9. High Resolution Measurement of Rhizosphere Priming Effects and Temporal Variability of CO2 Fluxes under Zea Mays

    Science.gov (United States)

    Splettstößer, T.; Pausch, J.

    2016-12-01

    Plant induced increase of soil organic matter turnover rates contribute to carbon emissions in agricultural land use systems. In order to better understand these rhizosphere priming effects, we conducted an experiment, which enabled us to monitor CO2 fluxes under zea mays plants with high resolution. The experiment was conducted in a climate chamber where the plants were grown in thin, tightly sealed boxes for 40 days and CO2 efflux from soil was measured twice a day. 13C-CO2 was introduced to allow differentiation between plant and soil derived CO2.This enabled us to monitor root respiration and soil organic matter turnover in the early stages of plant growth and to highlight changes in soil CO2 emissions and priming effects between day and night. The measurements were conducted with a PICARRO G2131-I δ13C high-precision isotopic CO2 Analyzer (PICARRO INC.) utilizing an automated valve system governed by a CR1000 data logger (Campbell Scientific). After harvest roots and shoots were analyzed for 13C content. Microbial biomass, root length density and enzymatic activities in soil were measured and linked to soil organic matter turnover rates. In order to visualize the spatial distribution of carbon allocation to the root system a few plants were additionally labeled with 14C and 14C distribution was monitored by 14C imaging of the root systems over 4 days. Based on the 14C distribution a grid was chosen and the soil was sampled from each square of the grid to investigate the impact of carbon allocation hotspots on enzymatic activities and microbial biomass. First initial results show an increase of soil CO2 efflux in the night periods, whereby the contribution of priming is not fully analyzed yet. Additionally, root tips were identified as hotspots of short term carbon allocation via 14C imaging and an in increase in microbial biomass could be measured in this regions. The full results will be shown at AGU 2016.

  10. Interobserver Variability and Accuracy of High-Definition Endoscopic Diagnosis for Gastric Intestinal Metaplasia among Experienced and Inexperienced Endoscopists

    Science.gov (United States)

    Hyun, Yil Sik; Bae, Joong Ho; Park, Hye Sun; Eun, Chang Soo

    2013-01-01

    Accurate diagnosis of gastric intestinal metaplasia is important; however, conventional endoscopy is known to be an unreliable modality for diagnosing gastric intestinal metaplasia (IM). The aims of the study were to evaluate the interobserver variation in diagnosing IM by high-definition (HD) endoscopy and the diagnostic accuracy of this modality for IM among experienced and inexperienced endoscopists. Selected 50 cases, taken with HD endoscopy, were sent for a diagnostic inquiry of gastric IM through visual inspection to five experienced and five inexperienced endoscopists. The interobserver agreement between endoscopists was evaluated to verify the diagnostic reliability of HD endoscopy in diagnosing IM, and the diagnostic accuracy, sensitivity, and specificity were evaluated for validity of HD endoscopy in diagnosing IM. Interobserver agreement among the experienced endoscopists was "poor" (κ = 0.38) and it was also "poor" (κ = 0.33) among the inexperienced endoscopists. The diagnostic accuracy of the experienced endoscopists was superior to that of the inexperienced endoscopists (P = 0.003). Since diagnosis through visual inspection is unreliable in the diagnosis of IM, all suspicious areas for gastric IM should be considered to be biopsied. Furthermore, endoscopic experience and education are needed to raise the diagnostic accuracy of gastric IM. PMID:23678267

  11. Enzymatic Synthesis of Highly Fluorescent 8-Azapurine Ribosides Using a Purine Nucleoside Phosphorylase Reverse Reaction: Variable Ribosylation Sites

    Directory of Open Access Journals (Sweden)

    Goran Mikleušević

    2013-10-01

    Full Text Available Various forms of purine-nucleoside phosphorylase (PNP were used as catalysts of enzymatic ribosylation of selected fluorescent 8-azapurines. It was found that the recombinant calf PNP catalyzes ribosylation of 2,6-diamino-8-azapurine in a phosphate-free medium, with ribose-1-phosphate as ribose donor, but the ribosylation site is predominantly N7 and N8, with the proportion of N8/N7 ribosylated products markedly dependent on the reaction conditions. Both products are fluorescent. Application of the E. coli PNP gave a mixture of N8 and N9-substituted ribosides. Fluorescence of the ribosylated 2,6-diamino-8-azapurine has been briefly characterized. The highest quantum yield, ~0.9, was obtained for N9-β-d-riboside (λmax 365 nm, while for N8-β-d-riboside, emitting at ~430 nm, the fluorescence quantum yield was found to be close to 0.4. Ribosylation of 8-azaguanine with calf PNP as a catalyst goes exclusively to N9. By contrast, the E. coli PNP ribosylates 8-azaGua predominantly at N9, with minor, but highly fluorescent products ribosylated at N8/N7.

  12. Satellite observations of high northern latitude vegetation productivity changes between 1982 and 2008: ecological variability and regional differences

    Energy Technology Data Exchange (ETDEWEB)

    Beck, Pieter S A; Goetz, Scott J, E-mail: pbeck@whrc.org [Woods Hole Research Center, 149 Woods Hole Road, Falmouth, MA 02540 (United States)

    2011-10-15

    To assess ongoing changes in high latitude vegetation productivity we compared spatiotemporal patterns in remotely sensed vegetation productivity in the tundra and boreal zones of North America and Eurasia. We compared the long-term GIMMS (Global Inventory Modeling and Mapping Studies) NDVI (Normalized Difference Vegetation Index) to the more recent and advanced MODIS (Moderate Resolution Imaging Spectroradiometer) NDVI data set, and mapped circumpolar trends in a gross productivity metric derived from the former. We then analyzed how temporal changes in productivity differed along an evergreen-deciduous gradient in boreal Alaska, along a shrub cover gradient in Arctic Alaska, and during succession after fire in boreal North America and northern Eurasia. We find that the earlier reported contrast between trends of increasing tundra and decreasing boreal forest productivity has amplified in recent years, particularly in North America. Decreases in boreal forest productivity are most prominent in areas of denser tree cover and, particularly in Alaska, evergreen forest stands. On the North Slope of Alaska, however, increases in tundra productivity do not appear restricted to areas of higher shrub cover, which suggests enhanced productivity across functional vegetation types. Differences in the recovery of post-disturbance vegetation productivity between North America and Eurasia are described using burn chronosequences, and the potential factors driving regional differences are discussed.

  13. Satellite observations of high northern latitude vegetation productivity changes between 1982 and 2008: ecological variability and regional differences

    International Nuclear Information System (INIS)

    Beck, Pieter S A; Goetz, Scott J

    2011-01-01

    To assess ongoing changes in high latitude vegetation productivity we compared spatiotemporal patterns in remotely sensed vegetation productivity in the tundra and boreal zones of North America and Eurasia. We compared the long-term GIMMS (Global Inventory Modeling and Mapping Studies) NDVI (Normalized Difference Vegetation Index) to the more recent and advanced MODIS (Moderate Resolution Imaging Spectroradiometer) NDVI data set, and mapped circumpolar trends in a gross productivity metric derived from the former. We then analyzed how temporal changes in productivity differed along an evergreen-deciduous gradient in boreal Alaska, along a shrub cover gradient in Arctic Alaska, and during succession after fire in boreal North America and northern Eurasia. We find that the earlier reported contrast between trends of increasing tundra and decreasing boreal forest productivity has amplified in recent years, particularly in North America. Decreases in boreal forest productivity are most prominent in areas of denser tree cover and, particularly in Alaska, evergreen forest stands. On the North Slope of Alaska, however, increases in tundra productivity do not appear restricted to areas of higher shrub cover, which suggests enhanced productivity across functional vegetation types. Differences in the recovery of post-disturbance vegetation productivity between North America and Eurasia are described using burn chronosequences, and the potential factors driving regional differences are discussed.

  14. Estimating the abundance of airborne pollen and fungal spores at variable elevations using an aircraft: how high can they fly?

    Science.gov (United States)

    Damialis, Athanasios; Kaimakamis, Evangelos; Konoglou, Maria; Akritidis, Ioannis; Traidl-Hoffmann, Claudia; Gioulekas, Dimitrios

    2017-03-16

    Airborne pollen and fungal spores are monitored mainly in highly populated, urban environments, for allergy prevention purposes. However, their sources can frequently be located outside cities' fringes with more vegetation. So as to shed light to this paradox, we investigated the diversity and abundance of airborne pollen and fungal spores at various environmental regimes. We monitored pollen and spores using an aircraft and a car, at elevations from sea level to 2,000 m above ground, in the region of Thesssaloniki, Greece. We found a total of 24 pollen types and more than 15 spore types. Pollen and spores were detected throughout the elevational transect. Lower elevations exhibited higher pollen concentrations in only half of plant taxa and higher fungal spore concentrations in only Ustilago. Pinaceae and Quercus pollen were the most abundant recorded by airplane (>54% of the total). Poaceae pollen were the most abundant via car measurements (>77% of the total). Cladosporium and Alternaria spores were the most abundant in all cases (aircraft: >69% and >17%, car: >45% and >27%, respectively). We conclude that pollen and fungal spores can be diverse and abundant even outside the main source area, evidently because of long-distance transport incidents.

  15. Interobserver variability and accuracy of high-definition endoscopic diagnosis for gastric intestinal metaplasia among experienced and inexperienced endoscopists.

    Science.gov (United States)

    Hyun, Yil Sik; Han, Dong Soo; Bae, Joong Ho; Park, Hye Sun; Eun, Chang Soo

    2013-05-01

    Accurate diagnosis of gastric intestinal metaplasia is important; however, conventional endoscopy is known to be an unreliable modality for diagnosing gastric intestinal metaplasia (IM). The aims of the study were to evaluate the interobserver variation in diagnosing IM by high-definition (HD) endoscopy and the diagnostic accuracy of this modality for IM among experienced and inexperienced endoscopists. Selected 50 cases, taken with HD endoscopy, were sent for a diagnostic inquiry of gastric IM through visual inspection to five experienced and five inexperienced endoscopists. The interobserver agreement between endoscopists was evaluated to verify the diagnostic reliability of HD endoscopy in diagnosing IM, and the diagnostic accuracy, sensitivity, and specificity were evaluated for validity of HD endoscopy in diagnosing IM. Interobserver agreement among the experienced endoscopists was "poor" (κ = 0.38) and it was also "poor" (κ = 0.33) among the inexperienced endoscopists. The diagnostic accuracy of the experienced endoscopists was superior to that of the inexperienced endoscopists (P = 0.003). Since diagnosis through visual inspection is unreliable in the diagnosis of IM, all suspicious areas for gastric IM should be considered to be biopsied. Furthermore, endoscopic experience and education are needed to raise the diagnostic accuracy of gastric IM.

  16. The rate of nonallelic homologous recombination in males is highly variable, correlated between monozygotic twins and independent of age.

    Directory of Open Access Journals (Sweden)

    Jacqueline A L MacArthur

    2014-03-01

    Full Text Available Nonallelic homologous recombination (NAHR between highly similar duplicated sequences generates chromosomal deletions, duplications and inversions, which can cause diverse genetic disorders. Little is known about interindividual variation in NAHR rates and the factors that influence this. We estimated the rate of deletion at the CMT1A-REP NAHR hotspot in sperm DNA from 34 male donors, including 16 monozygotic (MZ co-twins (8 twin pairs aged 24 to 67 years old. The average NAHR rate was 3.5 × 10(-5 with a seven-fold variation across individuals. Despite good statistical power to detect even a subtle correlation, we observed no relationship between age of unrelated individuals and the rate of NAHR in their sperm, likely reflecting the meiotic-specific origin of these events. We then estimated the heritability of deletion rate by calculating the intraclass correlation (ICC within MZ co-twins, revealing a significant correlation between MZ co-twins (ICC = 0.784, p = 0.0039, with MZ co-twins being significantly more correlated than unrelated pairs. We showed that this heritability cannot be explained by variation in PRDM9, a known regulator of NAHR, or variation within the NAHR hotspot itself. We also did not detect any correlation between Body Mass Index (BMI, smoking status or alcohol intake and rate of NAHR. Our results suggest that other, as yet unidentified, genetic or environmental factors play a significant role in the regulation of NAHR and are responsible for the extensive variation in the population for the probability of fathering a child with a genomic disorder resulting from a pathogenic deletion.

  17. Sphagnum-dominated bog systems are highly effective yet variable sources of bio-available iron to marine waters.

    Science.gov (United States)

    Krachler, Regina; Krachler, Rudolf F; Wallner, Gabriele; Steier, Peter; El Abiead, Yasin; Wiesinger, Hubert; Jirsa, Franz; Keppler, Bernhard K

    2016-06-15

    Iron is a micronutrient of particular interest as low levels of iron limit primary production of phytoplankton and carbon fluxes in extended regions of the world's oceans. Sphagnum-peatland runoff is extraordinarily rich in dissolved humic-bound iron. Given that several of the world's largest wetlands are Sphagnum-dominated peatlands, this ecosystem type may serve as one of the major sources of iron to the ocean. Here, we studied five near-coastal creeks in North Scotland using freshwater/seawater mixing experiments of natural creek water and synthetic seawater based on a (59)Fe radiotracer technique combined with isotopic characterization of dissolved organic carbon by Accelerator Mass Spectrometry. Three of the creeks meander through healthy Sphagnum-dominated peat bogs and the two others through modified peatlands which have been subject to artificial drainage for centuries. The results revealed that, at the time of sampling (August 16-24, 2014), the creeks that run through modified peatlands delivered 11-15μg iron per liter creek water to seawater, whereas the creeks that run through intact peatlands delivered 350-470μg iron per liter creek water to seawater. To find out whether this humic-bound iron is bio-available to marine algae, we performed algal growth tests using the unicellular flagellated marine prymnesiophyte Diacronema lutheri and the unicellular marine green alga Chlorella salina, respectively. In both cases, the riverine humic material provided a highly bio-available source of iron to the marine algae. These results add a new item to the list of ecosystem services of Sphagnum-peatlands. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  18. Are anthropometric, flexibility, muscular strength, and endurance variables related to clubhead velocity in low- and high-handicap golfers?

    Science.gov (United States)

    Keogh, Justin W L; Marnewick, Michel C; Maulder, Peter S; Nortje, Jacques P; Hume, Patria A; Bradshaw, Elizabeth J

    2009-09-01

    The present study assessed the anthropometric profile (International Society for the Advancement of Kinanthropometry protocol), flexibility, muscular strength, and endurance of 20 male golfers. These data were collected in order to determine: a) the relationship between these kinanthropometric measures and clubhead velocity; and b) if these measures could distinguish low-handicap (LHG) and high-handicap (HHG) golfers. Ten LHG (handicap of 0.3 +/- 0.5) and 10 HHG (handicap of 20.3 +/- 2.4) performed 10 swings for maximum velocity and accuracy with their own 5-iron golf club at a wall-mounted target. LHG hit the target significantly more (115%) and had a 12% faster clubhead velocity than HHG (p bench press strength and longer (5%) upper am and total arm (4%) length and less (24%) right hip internal rotation than HHG (0.01 velocity (p bench press and hack squat strength as well as upper arm and total arm length also approaching significance (0.01 bench press strength and longer arms may therefore be at a competitive advantage, as these characteristics allow the production of greater clubhead velocity and resulting ball displacement. Such results have implications for golf talent identification programs and for the prescription and monitoring of golf conditioning programs. While golf conditioning programs may have many aims, specific trunk rotation exercises need to be included if increased clubhead velocity is the goal. Muscular hypertrophy development may not need to be emphasized as it could reduce golf performance by limiting range of motion and/or increasing moment of inertia.

  19. Structural analysis of GaN using high-resolution X-ray diffraction at variable temperatures; Analyse struktureller Eigenschaften von GaN mittels hochaufloesender Roentgenbeugung bei variabler Messtemperatur

    Energy Technology Data Exchange (ETDEWEB)

    Roder, C.

    2007-02-26

    The main topic of this thesis was the study of stress phenomena in GaN layers by application of high-resolution X-ray diffractometry at variable measurement temperature. For this a broad spectrum of different GaN samples was studied, which extended from bulk GaN crystals as well as thick c-plane oriented HVPE-GaN layers on c-plane sapphire over laterlaly overgrown c-plane GaN Layers on Si(111) substrates toon-polar a-plnae GaN layers on r-plane sapphire. The main topic of the measurements was the determination of the lattice parameters. Supplementarily the curvature of the waver as well as the excitonic resosance energies were studied by means of photoluminescence respectively photoreflection spectroscopy. By the measurement of the temperature-dependent lattice parameters of different GaN bulk crystals for the first time a closed set of thermal-expansion coefficients of GaN was determined from 12 to 1205 K with large accuracy. Analoguously the thermal-expansion coefficents of the substrate material sapphire were determinde over a temperature range from 10 to 1166 K.

  20. Seasonal variability of water transport through the Straits of Gibraltar, Sicily and Corsica, derived from a high-resolution model of the Mediterranean circulation

    Science.gov (United States)

    Béranger, K.; Mortier, L.; Crépon, M.

    2005-08-01

    The variability of the water transport through three major straits of the Mediterranean Sea (Gibraltar, Sicily and Corsica) was investigated using a high-resolution model. This model of the Mediterranean circulation was developed in the context of the Mercator project. The region of interest is the western Mediterranean between the Strait of Gibraltar and the Strait of Sicily. The major water masses and the winter convection in the Gulf of Lions were simulated. The model reproduced the meso-scale and large-scale patterns of the circulation in very good agreement with recent observations. The western and the eastern gyres of the Alboran Sea were observed but high interannual variability was noticed. The Algerian Current splits into several branches at the longitude of the Strait of Sicily level, forming the Tyrrhenian branch, and, the Atlantic Ionian Stream and the Atlantic Tunisian Current in the eastern Mediterranean. The North Current retroflexed north of the Balearic Islands and a dome structure was observed in the Gulf of Lions. The cyclonic barotropic Algerian gyre, which was recently observed during the MATER and ELISA experiment, was evidenced in the simulation. From time-series of 10-day mean transport, the three straits presented a high variability at short time-scales. The transport was generally maximum, in April for the Strait of Gibraltar, in November for the Strait of Sicily, and in January for the Strait of Corsica. The amplitudes of the transport through the Straits of Gibraltar (0.11 Sv) and Sicily (0.30 Sv) presented a weaker seasonal variability than that of the Strait of Corsica (0.70 Sv). The study of the relation between transport and wind forcing showed that the transport through the Strait of Gibraltar is dependent on local zonal wind over short time-scales (70%), which was not the case for the other straits (less than 30%). The maximum (minimum) of the transport occurred for an eastward (westward) wind stress in the strait. An interannual

  1. Objectively Assessed Sleep Variability as an Acute Warning Sign of Suicidal Ideation in a Longitudinal Evaluation of Young Adults at High Suicide Risk.

    Science.gov (United States)

    Bernert, Rebecca A; Hom, Melanie A; Iwata, Naomi G; Joiner, Thomas E

    2017-06-01

    Young adults attempt suicide at disproportionately high rates relative to other groups and demonstrate high rates of sleep disturbance. No study has yet prospectively evaluated disturbed sleep as an acute indicator of risk using an objective index of sleep. We investigated objective and subjective parameters of disturbed sleep as a warning sign of suicidal ideation among young adults over an acute period. A longitudinal study across a 21-day observation period and 3 time points. Fifty of 4,847 participants (aged 18-23 years) were prescreened from a university undergraduate research pool (February 2007-June 2008) on the basis of suicide attempt history and recent suicidal ideation. Actigraphic and subjective sleep parameters were evaluated as acute predictors of suicidal ideation (Beck Scale for Suicide Ideation), with adjustment for baseline symptoms. Hierarchical regression analyses were employed to predict residual change scores. Ninety-six percent of participants (n = 48) endorsed a suicide attempt history. Mean actigraphy values revealed objectively disturbed sleep parameters; 78% (n = 39) and 36% (n = 18) endorsed clinically significant insomnia and nightmares, respectively. When results were controlled for baseline suicidal and depressive symptoms, actigraphic and subjective sleep parameters predicted suicidal ideation residual change scores at 7- and 21-day follow-ups (P defined variability in sleep timing, insomnia, and nightmares predicted increases in suicidal ideation (P < .05). In a test of competing risk factors, sleep variability outperformed depressive symptoms in the longitudinal prediction of suicidal ideation across time points (P < .05). Objectively and subjectively measured sleep disturbances predicted acute suicidal ideation increases in this population, independent of depressed mood. Self-reported