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Sample records for high depth resequencing

  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

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    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. Layered compression for high-precision depth data.

    Science.gov (United States)

    Miao, Dan; Fu, Jingjing; Lu, Yan; Li, Shipeng; Chen, Chang Wen

    2015-12-01

    With the development of depth data acquisition technologies, access to high-precision depth with more than 8-b depths has become much easier and determining how to efficiently represent and compress high-precision depth is essential for practical depth storage and transmission systems. In this paper, we propose a layered high-precision depth compression framework based on an 8-b image/video encoder to achieve efficient compression with low complexity. Within this framework, considering the characteristics of the high-precision depth, a depth map is partitioned into two layers: 1) the most significant bits (MSBs) layer and 2) the least significant bits (LSBs) layer. The MSBs layer provides rough depth value distribution, while the LSBs layer records the details of the depth value variation. For the MSBs layer, an error-controllable pixel domain encoding scheme is proposed to exploit the data correlation of the general depth information with sharp edges and to guarantee the data format of LSBs layer is 8 b after taking the quantization error from MSBs layer. For the LSBs layer, standard 8-b image/video codec is leveraged to perform the compression. The experimental results demonstrate that the proposed coding scheme can achieve real-time depth compression with satisfactory reconstruction quality. Moreover, the compressed depth data generated from this scheme can achieve better performance in view synthesis and gesture recognition applications compared with the conventional coding schemes because of the error control algorithm.

  11. 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.

  12. 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...

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

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    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.

  14. Scanning Auger microscopy for high lateral and depth elemental sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Martinez, E., E-mail: eugenie.martinez@cea.fr [CEA, LETI, MINATEC Campus, 17 rue des Martyrs, 38054 Grenoble Cedex 9 (France); Yadav, P. [CEA, LETI, MINATEC Campus, 17 rue des Martyrs, 38054 Grenoble Cedex 9 (France); Bouttemy, M. [Institut Lavoisier de Versailles, 45 av. des Etats-Unis, 78035 Versailles Cedex (France); Renault, O.; Borowik, Ł.; Bertin, F. [CEA, LETI, MINATEC Campus, 17 rue des Martyrs, 38054 Grenoble Cedex 9 (France); Etcheberry, A. [Institut Lavoisier de Versailles, 45 av. des Etats-Unis, 78035 Versailles Cedex (France); Chabli, A. [CEA, LETI, MINATEC Campus, 17 rue des Martyrs, 38054 Grenoble Cedex 9 (France)

    2013-12-15

    Highlights: •SAM performances and limitations are illustrated on real practical cases such as the analysis of nanowires and nanodots. •High spatial elemental resolution is shown with the analysis of reference semiconducting Al{sub 0.7}Ga{sub 0.3}As/GaAs multilayers. •High in-depth elemental resolution is also illustrated. Auger depth profiling with low energy ion beams allows revealing ultra-thin layers (∼1 nm). •Analysis of cross-sectional samples is another effective approach to obtain in-depth elemental information. -- Abstract: Scanning Auger microscopy is currently gaining interest for investigating nanostructures or thin multilayers stacks developed for nanotechnologies. New generation Auger nanoprobes combine high lateral (∼10 nm), energy (0.1%) and depth (∼2 nm) resolutions thus offering the possibility to analyze the elemental composition as well as the chemical state, at the nanometre scale. We report here on the performances and limitations on practical examples from nanotechnology research. The spatial elemental sensitivity is illustrated with the analysis of Al{sub 0.7}Ga{sub 0.3}As/GaAs heterostructures, Si nanowires and SiC nanodots. Regarding the elemental in-depth composition, two effective approaches are presented: low energy depth profiling to reveal ultra-thin layers (∼1 nm) and analysis of cross-sectional samples.

  15. 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.

  16. Definition of novel GP6 polymorphisms and major difference in haplotype frequencies between populations by a combination of in-depth exon resequencing and genotyping with tag single nucleotide polymorphisms.

    Science.gov (United States)

    Watkins, N A; O'Connor, M N; Rankin, A; Jennings, N; Wilson, E; Harmer, I J; Davies, L; Smethurst, P A; Dudbridge, F; Farndale, R W; Ouwehand, W H

    2006-06-01

    Common genetic variants of cell surface receptors contribute to differences in functional responses and disease susceptibility. We have previously shown that single nucleotide polymorphisms (SNPs) in platelet glycoprotein VI (GP6) determine the extent of response to agonist. In addition, SNPs in the GP6 gene have been proposed as risk factors for coronary artery disease. To completely characterize genetic variation in the GP6 gene we generated a high-resolution SNP map by sequencing the promoter, exons and consensus splice sequences in 94 non-related Caucasoids. In addition, we sequenced DNA encoding the ligand-binding domains of GP6 from non-human primates to determine the level of evolutionary conservation. Eighteen SNPs were identified, six of which encoded amino acid substitutions in the mature form of the protein. The single non-synonymous SNP identified in the exons encoding the ligand-binding domains, encoding for a 103Leu > Val substitution, resulted in reduced ligand binding. Two common protein isoforms were confirmed in Caucasoid with frequencies of 0.82 and 0.15. Variation at the GP6 locus was characterized further by determining SNP frequency in over 2000 individuals from different ethnic backgrounds. The SNPs were polymorphic in all populations studied although significant differences in allele frequencies were observed. Twelve additional GP6 protein isoforms were identified from the genotyping results and, despite extensive variation in GP6, the sequence of the ligand-binding domains is conserved. Sequences from non-human primates confirmed this observation. These data provide valuable information for the optimal selection of genetic variants for use in future association studies.

  17. High bit depth infrared image compression via low bit depth codecs

    DEFF Research Database (Denmark)

    Belyaev, Evgeny; Mantel, Claire; Forchhammer, Søren

    2017-01-01

    images via 8 bit depth codecs in the following way. First, an input 16 bit depth image is mapped into 8 bit depth images, e.g., the first image contains only the most significant bytes (MSB image) and the second one contains only the least significant bytes (LSB image). Then each image is compressed.......264/AVC codecs, which are usually available in efficient implementations, and compare their rate-distortion performance with JPEG2000, JPEG-XT and H.265/HEVC codecs supporting direct compression of infrared images in 16 bit depth format. A preliminary result shows that two 8 bit H.264/AVC codecs can...

  18. High bit depth infrared image compression via low bit depth codecs

    Science.gov (United States)

    Belyaev, Evgeny; Mantel, Claire; Forchhammer, Søren

    2017-08-01

    Future infrared remote sensing systems, such as monitoring of the Earth's environment by satellites, infrastructure inspection by unmanned airborne vehicles etc., will require 16 bit depth infrared images to be compressed and stored or transmitted for further analysis. Such systems are equipped with low power embedded platforms where image or video data is compressed by a hardware block called the video processing unit (VPU). However, in many cases using two 8-bit VPUs can provide advantages compared with using higher bit depth image compression directly. We propose to compress 16 bit depth images via 8 bit depth codecs in the following way. First, an input 16 bit depth image is mapped into 8 bit depth images, e.g., the first image contains only the most significant bytes (MSB image) and the second one contains only the least significant bytes (LSB image). Then each image is compressed by an image or video codec with 8 bits per pixel input format. We analyze how the compression parameters for both MSB and LSB images should be chosen to provide the maximum objective quality for a given compression ratio. Finally, we apply the proposed infrared image compression method utilizing JPEG and H.264/AVC codecs, which are usually available in efficient implementations, and compare their rate-distortion performance with JPEG2000, JPEG-XT and H.265/HEVC codecs supporting direct compression of infrared images in 16 bit depth format. A preliminary result shows that two 8 bit H.264/AVC codecs can achieve similar result as 16 bit HEVC codec.

  19. 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

  20. High bit depth infrared image compression via low bit depth codecs

    DEFF Research Database (Denmark)

    Belyaev, Evgeny; Mantel, Claire; Forchhammer, Søren

    .264/AVC codecs, which are usually available in efficient implementations, and compare their rate-distortion performance with JPEG2000, JPEG-XT and H.265/HEVC codecs supporting direct compression of infrared images in 16 bit depth format. A preliminary result shows that two 8 bit H.264/AVC codecs can...

  1. 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 ...

  2. High Bit-Depth Medical Image Compression With HEVC.

    Science.gov (United States)

    Parikh, Saurin S; Ruiz, Damian; Kalva, Hari; Fernandez-Escribano, Gerardo; Adzic, Velibor

    2018-03-01

    Efficient storing and retrieval of medical images has direct impact on reducing costs and improving access in cloud-based health care services. JPEG 2000 is currently the commonly used compression format for medical images shared using the DICOM standard. However, new formats such as high efficiency video coding (HEVC) can provide better compression efficiency compared to JPEG 2000. Furthermore, JPEG 2000 is not suitable for efficiently storing image series and 3-D imagery. Using HEVC, a single format can support all forms of medical images. This paper presents the use of HEVC for diagnostically acceptable medical image compression, focusing on compression efficiency compared to JPEG 2000. Diagnostically acceptable lossy compression and complexity of high bit-depth medical image compression are studied. Based on an established medically acceptable compression range for JPEG 2000, this paper establishes acceptable HEVC compression range for medical imaging applications. Experimental results show that using HEVC can increase the compression performance, compared to JPEG 2000, by over 54%. Along with this, a new method for reducing computational complexity of HEVC encoding for medical images is proposed. Results show that HEVC intra encoding complexity can be reduced by over 55% with negligible increase in file size.

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

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    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.

  4. Soil gas measurements at high permeabilities and below foundation depth

    International Nuclear Information System (INIS)

    Johner, H.U; Surbeck, H.

    2000-01-01

    We started a project of soil gas measurements beneath houses. Since the foundations of houses often lie deeper than 0.5 to 1 m - the depth where soil gas measurements are often made - the first approach was to apply the method developed previously to deeper soil layers. The radon availability index (RAI), which was defined empirically, proved to be a reliable indicator for radon problems in nearby houses. The extreme values of permeability, non-Darcy flow and scale dependence of permeability stimulated the development of a multi-probe method. A hydrological model was applied to model the soil gas transport. The soil gas measurements below foundation depth provided a wealth of new information. A good classification of soil properties could be achieved. If soil gas measurements are to be made, the low permeability layer has to be traversed. A minimum depth of 1 .5 m is suggested, profiles to below the foundation depth are preferable. There are also implications for mitigation works. A sub-slab suction system should reach the permeable layer to function well. This also holds for radon wells. If a house is located on a slope, it is most convenient to install the sub-slab suction system on the hillside, as the foundation reaches the deepest levels there

  5. 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

  6. 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.

  7. 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

  8. High resolution depth reconstruction from monocular images and sparse point clouds using deep convolutional neural network

    Science.gov (United States)

    Dimitrievski, Martin; Goossens, Bart; Veelaert, Peter; Philips, Wilfried

    2017-09-01

    Understanding the 3D structure of the environment is advantageous for many tasks in the field of robotics and autonomous vehicles. From the robot's point of view, 3D perception is often formulated as a depth image reconstruction problem. In the literature, dense depth images are often recovered deterministically from stereo image disparities. Other systems use an expensive LiDAR sensor to produce accurate, but semi-sparse depth images. With the advent of deep learning there have also been attempts to estimate depth by only using monocular images. In this paper we combine the best of the two worlds, focusing on a combination of monocular images and low cost LiDAR point clouds. We explore the idea that very sparse depth information accurately captures the global scene structure while variations in image patches can be used to reconstruct local depth to a high resolution. The main contribution of this paper is a supervised learning depth reconstruction system based on a deep convolutional neural network. The network is trained on RGB image patches reinforced with sparse depth information and the output is a depth estimate for each pixel. Using image and point cloud data from the KITTI vision dataset we are able to learn a correspondence between local RGB information and local depth, while at the same time preserving the global scene structure. Our results are evaluated on sequences from the KITTI dataset and our own recordings using a low cost camera and LiDAR setup.

  9. High-level fusion of depth and intensity for pedestrian classification

    NARCIS (Netherlands)

    Rohrbach, M.; Enzweiler, M.; Gavrila, D.M.

    2009-01-01

    This paper presents a novel approach to pedestrian classification which involves a high-level fusion of depth and intensity cues. Instead of utilizing depth information only in a pre-processing step, we propose to extract discriminative spatial features (gradient orientation histograms and local

  10. Direct depth distribution measurement of deuterium in bulk tungsten exposed to high-flux plasma

    Directory of Open Access Journals (Sweden)

    C. N. Taylor

    2017-05-01

    Full Text Available Understanding tritium retention and permeation in plasma-facing components is critical for fusion safety and fuel cycle control. Glow discharge optical emission spectroscopy (GD-OES is shown to be an effective tool to reveal the depth profile of deuterium in tungsten. Results confirm the detection of deuterium. A ∼46 μm depth profile revealed that the deuterium content decreased precipitously in the first 7 μm, and detectable amounts were observed to depths in excess of 20 μm. The large probing depth of GD-OES (up to 100s of μm enables studies not previously accessible to the more conventional techniques for investigating deuterium retention. Of particular applicability is the use of GD-OES to measure the depth profile for experiments where high deuterium concentration in the bulk material is expected: deuterium retention in neutron irradiated materials, and ultra-high deuterium fluences in burning plasma environment.

  11. Estimated Depth Maps of the Northwestern Hawaiian Islands Derived from High Resolution IKONOS Satellite Imagery (Draft)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Estimated shallow-water, depth maps were produced using rule-based, semi-automated image analysis of high-resolution satellite imagery for nine locations in the...

  12. 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.

  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. 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

  15. Limitations to depth resolution in high-energy, heavy-ion elastic recoil detection analysis

    International Nuclear Information System (INIS)

    Elliman, R.G.; Palmer, G.R.; Ophel, T.R.; Timmers, H.

    1998-01-01

    The depth resolution of heavy-ion elastic recoil detection analysis was examined for Al and Co thin films ranging in thickness from 100 to 400 nm. Measurements were performed with 154 MeV Au ions as the incident beam, and recoils were detected using a gas ionisation detector. Energy spectra were extracted for the Al and Co recoils and the depth resolution determined as a function of film thickness from the width of the high- and low- energy edges. These results were compared with theoretical estimates calculated using the computer program DEPTH. (authors)

  16. 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

  17. 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.

  18. 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

  19. Depth-resolved incoherent and coherent wide-field high-content imaging (Conference Presentation)

    Science.gov (United States)

    So, Peter T.

    2016-03-01

    Recent advances in depth-resolved wide-field imaging technique has enabled many high throughput applications in biology and medicine. Depth resolved imaging of incoherent signals can be readily accomplished with structured light illumination or nonlinear temporal focusing. The integration of these high throughput systems with novel spectroscopic resolving elements further enable high-content information extraction. We will introduce a novel near common-path interferometer and demonstrate its uses in toxicology and cancer biology applications. The extension of incoherent depth-resolved wide-field imaging to coherent modality is non-trivial. Here, we will cover recent advances in wide-field 3D resolved mapping of refractive index, absorbance, and vibronic components in biological specimens.

  20. 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

  1. 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.

  2. BH5047 type depth sand moisture-meter of high sensitivity

    International Nuclear Information System (INIS)

    Ji Changsong; Xie Liangnian; Zhang Shulan; Zhang Shuheng

    2000-01-01

    A new depth neutron moisture meter BH5047 has been developed. BH5047 neutron moisture meter is characterised by it is high sensitivity and used for sand water content measurement at concrete mixer. Calibration function is obtained by the Method of Least Squares. Linear correlation efficiency is as good as 0.9977

  3. High Resolution Depth-Resolved Imaging From Multi-Focal Images for Medical Ultrasound

    DEFF Research Database (Denmark)

    Diamantis, Konstantinos; Dalgarno, Paul A.; Greenaway, Alan H.

    2015-01-01

    An ultrasound imaging technique providing subdiffraction limit axial resolution for point sources is proposed. It is based on simultaneously acquired multi-focal images of the same object, and on the image metric of sharpness. The sharpness is extracted by image data and presents higher values...... calibration curves combined with the use of a maximum-likelihood algorithm is then able to estimate, with high precision, the depth location of any emitter fron each single image. Estimated values are compared with the ground truth demonstrating that an accuracy of 28.6 µm (0.13λ) is achieved for a 4 mm depth...

  4. Off-Line High-pH Reversed-Phase Fractionation for In-Depth Phosphoproteomics

    DEFF Research Database (Denmark)

    Batth, Tanveer S; Francavilla, Chiara; Olsen, Jesper V

    2014-01-01

    thousands of phosphorylation sites. However, in-depth phosphoproteomics often require off-line enrichment and fractionation techniques. In this study, we provide a detailed analysis of the physicochemical characteristics of phosphopeptides, which have been fractionated by off-line high-pH chromatography (Hp...... phosphorylated peptides over that with SCX. Further optimizations in the pooling and concatenation strategy increased the total number of multiphosphorylated peptides detected after HpH fractionation. In conclusion, we provide a basic framework and resource for performing in-depth phosphoproteome studies...

  5. Depth profiling by Raman spectroscopy of high-energy ion irradiated silicon carbide

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xu; Zhang, Yanwen; Liu, Shiyi; Zhao, Ziqiang, E-mail: zqzhao@pku.edu.cn

    2014-01-15

    Single crystals of 6H–SiC were irradiated at room temperature with 20 MeV carbon ions at fluences of 1.5 × 10{sup 15} and 6.0 × 10{sup 15} cm{sup −2}. Raman measurements were performed to study irradiation induced damage and the in-depth damage profile of SiC. A clear change of damage from the surface down to the stopping region of carbon ions as simulated by SRIM is exhibited. The affected area as detected by Raman is in good agreement with SRIM predictions while a little shallower dpa profile is observed. The partial disorder defined in the present work as a function of depth is demonstrated. A shift of the position of the TO peak towards lower wavenumbers with in-depth damage and then to higher wavenumbers beyond the most damaged region indicates that tensile strain due to defects has a backward V-curve distribution. The damaged layer is subjected to a compressive in-plane stress associated with the out-of-plane strain and the magnitude of this stress also has a backward V-curve depth profile. The evolution of line width of the TO peak with depth clearly shows the density of defects reaches the higher level at the most damaged region. The Raman spectroscopy scanning technique is proved to be a powerful tool for profiling of crystal damage induced by high-energy ion implantation.

  6. Nondestructive strain depth profiling with high energy X-ray diffraction: System capabilities and limitations

    Science.gov (United States)

    Zhang, Zhan; Wendt, Scott; Cosentino, Nicholas; Bond, Leonard J.

    2018-04-01

    Limited by photon energy, and penetration capability, traditional X-ray diffraction (XRD) strain measurements are only capable of achieving a few microns depth due to the use of copper (Cu Kα1) or molybdenum (Mo Kα1) characteristic radiation. For deeper strain depth profiling, destructive methods are commonly necessary to access layers of interest by removing material. To investigate deeper depth profiles nondestructively, a laboratory bench-top high-energy X-ray diffraction (HEXRD) system was previously developed. This HEXRD method uses an industrial 320 kVp X-Ray tube and the Kα1 characteristic peak of tungsten, to produces a higher intensity X-ray beam which enables depth profiling measurement of lattice strain. An aluminum sample was investigated with deformation/load provided using a bending rig. It was shown that the HEXRD method is capable of strain depth profiling to 2.5 mm. The method was validated using an aluminum sample where both the HEXRD method and the traditional X-ray diffraction method gave data compared with that obtained using destructive etching layer removal, performed by a commercial provider. The results demonstrate comparable accuracy up to 0.8 mm depth. Nevertheless, higher attenuation capabilities in heavier metals limit the applications in other materials. Simulations predict that HEXRD works for steel and nickel in material up to 200 µm, but experiment results indicate that the HEXRD strain profile is not practical for steel and nickel material, and the measured diffraction signals are undetectable when compared to the noise.

  7. Depth geological model building: application to the 3D high resolution 'ANDRA' seismic block

    International Nuclear Information System (INIS)

    Mari, J.L.; Yven, B.

    2012-01-01

    Document available in extended abstract form only. 3D seismic blocks and logging data, mainly acoustic and density logs, are often used for geological model building in time. The geological model must be then converted from time to depth. Geostatistical approach for time-to-depth conversion of seismic horizons is often used in many geo-modelling projects. From a geostatistical point of view, the time-to-depth conversion of seismic horizons is a classical estimation problem involving one or more secondary variables. Bayesian approach [1] provides an excellent estimator which is more general than the traditional kriging with external drift(s) and fits very well to the needs for time-to-depth conversion of seismic horizons. The time-to-depth conversion of the selected seismic horizons is used to compute a time-to-depth conversion model at the time sampling rate (1 ms). The 3D depth conversion model allows the computation of an interval velocity block which is compared with the acoustic impedance block to estimate a density block as QC. Non realistic density values are edited and the interval velocity block as well as the depth conversion model is updated. The proposed procedure has been applied on a 3D data set. The dataset comes from a High Resolution 3D seismic survey recorded in France at the boundary of the Meuse and Haute-Marne departments in the vicinity of the Andra Center (National radioactive waste management Agency). The 3D design is a cross spread. The active spread is composed of 12 receiver lines with 120 stations each. The source lines are perpendicular to the receiver lines. The receiver and source line spacings are respectively 80 m and 120 m. The receiver and source point spacings are 20 m. The source is a Vibroseis source generating a signal in the 14 - 140 Hz frequency bandwidth.. The bin size is 10 x 10 m 2 . The nominal fold is 60. A conventional seismic sequence was applied to the data set. It includes amplitude recovery, deconvolution and wave

  8. Highly effective portable beta spectrometer for precise depth selective electron Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    Aldiyarov, N.U.; Kadyrzhanov, K.K.; Seytimbetov, A.M.; Zhdanov, V.S.

    2007-01-01

    Full text: More broad application of the nuclear-physical method of precise Depth Selective Electron Moessbauer Spectroscopy (DS EMS) is limited by insufficient accessibility of highly-effective beta spectrometers with acceptable resolution. It should be mentioned that the method DS EMS is realized at a combined installation that consists of a highly-effective beta spectrometer and a conventional portable nuclear gamma-resonance spectrometer. Yet few available beta spectrometers have sophisticated design and controlling; in most cases they are cumbersome. All the attempts to simplify beta spectrometers resulted in noticeable worsening of depth resolution for the DS EMS method making the measurements non precise. There is currently an obvious need in a highly-effective portable easily controlled beta spectrometer. While developing such portable beta spectrometer, it is more promising to use as basis a simpler spectrometer, which has ratio of sample size to spectrometer size of about five times. The paper presents an equal-arm version of a highly-effective portable beta spectrometer with transverse heterogeneous sector magnetic field that assures double focusing. The spectrometer is equipped with a large-area non-equipotential source (a sample under investigation) and a position-sensitive detector. This portable spectrometer meets all requirements for achievement of the DS EMS depth resolution close to the physical limit and demonstrates the following main characteristics: equilibrium orbit radius ρ 0 = 80 mm, instrumental energy resolution 0.6 % at solid angle 1 % of 4π steradian, area of non-equipotential source ∼ 80 mm 2 , registration by position-sensitive detector of ∼ 10 % of the energy interval. Highly-effective portable beta spectrometer assures obtaining Moessbauer data with depth resolution close to physical limit of the DS EMS method. So in measurements at conversion and Auger electrons with energies of about units of keV and above, the achieved

  9. Mapping the depth to ice-cemented ground in the high elevation Dry Valleys, Antarctica

    Science.gov (United States)

    Marinova, M.; McKay, C. P.; Heldmann, J. L.; Davila, A. F.; Andersen, D. T.; Jackson, A.; Lacelle, D.; Paulsen, G.; Pollard, W. H.; Zacny, K.

    2011-12-01

    The high elevation Dry Valleys of Antarctica provide a unique location for the study of permafrost distribution and stability. In particular, the extremely arid and cold conditions preclude the presence of liquid water, and the exchange of water between the ice-cemented ground and the atmosphere is through vapour transport (diffusion). In addition, the low atmospheric humidity results in the desiccation of the subsurface, forming a dry permafrost layer (i.e., cryotic soils which are dry and not ice-cemented). Weather data suggests that subsurface ice is unstable under current climatic conditions. Yet we do find ice-cemented ground in these valleys. This contradiction provides insight into energy balance modeling, vapour transport, and additional climate effects which stabilize subsurface ice. To study the driving factors in the stability and distribution of ice-cemented ground, we have extensively mapped the depth to ice-cemented ground in University Valley (1730 m; 77°S 51.8', 160°E 43'), and three neighbouring valleys in the Beacon Valley area. We measured the depth to ice-cemented ground at 15-40 locations per valley by digging soil pits and drilling until ice was reached; for each location 3-5 measurements within a ~1 m2 area were averaged (see figure). This high-resolution mapping of the depth to ice-cemented ground provides new insight on the distribution and stability of subsurface ice, and shows significant variability in the depth to ground ice within each valley. We are combining data from mapping the depth to ice-cemented ground with year-round, in situ measurements of the atmospheric and subsurface conditions, such as temperature, humidity, wind, and light, to model the local stability of ice-cemented ground. We are using this dataset to examine the effects of slopes, shading, and soil properties, as well as the suggested importance of snow recurrence, to better understand diffusion-controlled subsurface ice stability.

  10. Failure Assessment for the High-Strength Pipelines with Constant-Depth Circumferential Surface Cracks

    OpenAIRE

    X. Liu; Z. X. Lu; Y. Chen; Y. L. Sui; L. H. Dai

    2018-01-01

    In the oil and gas transportation system over long distance, application of high-strength pipeline steels can efficiently reduce construction and operation cost by increasing operational pressure and reducing the pipe wall thickness. Failure assessment is an important issue in the design, construction, and maintenance of the pipelines. The small circumferential surface cracks with constant depth in the welded pipelines are of practical interest. This work provides an engineering estimation pr...

  11. Failure Assessment for the High-Strength Pipelines with Constant-Depth Circumferential Surface Cracks

    Directory of Open Access Journals (Sweden)

    X. Liu

    2018-01-01

    Full Text Available In the oil and gas transportation system over long distance, application of high-strength pipeline steels can efficiently reduce construction and operation cost by increasing operational pressure and reducing the pipe wall thickness. Failure assessment is an important issue in the design, construction, and maintenance of the pipelines. The small circumferential surface cracks with constant depth in the welded pipelines are of practical interest. This work provides an engineering estimation procedure based upon the GE/EPRI method to determine the J-integral for the thin-walled pipelines with small constant-depth circumferential surface cracks subject to tension and bending loads. The values of elastic influence functions for stress intensity factor and plastic influence functions for fully plastic J-integral estimation are derived in tabulated forms through a series of three-dimensional finite element calculations for different crack geometries and material properties. To check confidence of the J-estimation solution in practical application, J-integral values obtained from detailed finite element (FE analyses are compared with those estimated from the new influence functions. Excellent agreement of FE results with the proposed J-estimation solutions for both tension and bending loads indicates that the new solutions can be applied for accurate structural integrity assessment of high-strength pipelines with constant-depth circumferential surface cracks.

  12. Depth Profiling Analysis of Aluminum Oxidation During Film Deposition in a Conventional High Vacuum System

    Science.gov (United States)

    Kim, Jongmin; Weimer, Jeffrey J.; Zukic, Muamer; Torr, Douglas G.

    1994-01-01

    The oxidation of aluminum thin films deposited in a conventional high vacuum chamber has been investigated using x-ray photoelectron spectroscopy (XPS) and depth profiling. The state of the Al layer was preserved by coating it with a protective MgF2 layer in the deposition chamber. Oxygen concentrations in the film layers were determined as a function of sputter time (depth into the film). The results show that an oxidized layer is formed at the start of Al deposition and that a less extensively oxidized Al layer is deposited if the deposition rate is fast. The top surface of the Al layer oxidizes very quickly. This top oxidized layer may be thicker than has been previously reported by optical methods. Maximum oxygen concentrations measured by XPS at each Al interface are related to pressure to rate ratios determined during the Al layer deposition.

  13. Depth of interaction resolution measurements for a high resolution PET detector using position sensitive avalanche photodiodes

    International Nuclear Information System (INIS)

    Yang Yongfeng; Dokhale, Purushottam A; Silverman, Robert W; Shah, Kanai S; McClish, Mickel A; Farrell, Richard; Entine, Gerald; Cherry, Simon R

    2006-01-01

    We explore dual-ended read out of LSO arrays with two position sensitive avalanche photodiodes (PSAPDs) as a high resolution, high efficiency depth-encoding detector for PET applications. Flood histograms, energy resolution and depth of interaction (DOI) resolution were measured for unpolished LSO arrays with individual crystal sizes of 1.0, 1.3 and 1.5 mm, and for a polished LSO array with 1.3 mm pixels. The thickness of the crystal arrays was 20 mm. Good flood histograms were obtained for all four arrays, and crystals in all four arrays can be clearly resolved. Although the amplitude of each PSAPD signal decreases as the interaction depth moves further from the PSAPD, the sum of the two PSAPD signals is essentially constant with irradiation depth for all four arrays. The energy resolutions were similar for all four arrays, ranging from 14.7% to 15.4%. A DOI resolution of 3-4 mm (including the width of the irradiation band which is ∼2 mm) was obtained for all the unpolished arrays. The best DOI resolution was achieved with the unpolished 1 mm array (average 3.5 mm). The DOI resolution for the 1.3 mm and 1.5 mm unpolished arrays was 3.7 and 4.0 mm respectively. For the polished array, the DOI resolution was only 16.5 mm. Summing the DOI profiles across all crystals for the 1 mm array only degraded the DOI resolution from 3.5 mm to 3.9 mm, indicating that it may not be necessary to calibrate the DOI response separately for each crystal within an array. The DOI response of individual crystals in the array confirms this finding. These results provide a detailed characterization of the DOI response of these PSAPD-based PET detectors which will be important in the design and calibration of a PET scanner making use of this detector approach

  14. 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.

  15. Volume Attenuation and High Frequency Loss as Auditory Depth Cues in Stereoscopic 3D Cinema

    Science.gov (United States)

    Manolas, Christos; Pauletto, Sandra

    2014-09-01

    Assisted by the technological advances of the past decades, stereoscopic 3D (S3D) cinema is currently in the process of being established as a mainstream form of entertainment. The main focus of this collaborative effort is placed on the creation of immersive S3D visuals. However, with few exceptions, little attention has been given so far to the potential effect of the soundtrack on such environments. The potential of sound both as a means to enhance the impact of the S3D visual information and to expand the S3D cinematic world beyond the boundaries of the visuals is large. This article reports on our research into the possibilities of using auditory depth cues within the soundtrack as a means of affecting the perception of depth within cinematic S3D scenes. We study two main distance-related auditory cues: high-end frequency loss and overall volume attenuation. A series of experiments explored the effectiveness of these auditory cues. Results, although not conclusive, indicate that the studied auditory cues can influence the audience judgement of depth in cinematic 3D scenes, sometimes in unexpected ways. We conclude that 3D filmmaking can benefit from further studies on the effectiveness of specific sound design techniques to enhance S3D cinema.

  16. 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.

  17. 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...

  18. 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.

  19. GIOVE: a new detector setup for high sensitivity germanium spectroscopy at shallow depth

    International Nuclear Information System (INIS)

    Heusser, G.; Weber, M.; Hakenmüller, J.; Laubenstein, M.; Lindner, M.; Maneschg, W.; Simgen, H.; Stolzenburg, D.; Strecker, H.

    2015-01-01

    We report on the development and construction of the high-purity germanium spectrometer setup GIOVE (Germanium Inner Outer VEto), recently built and now operated at the shallow underground laboratory of the Max-Planck-Institut für Kernphysik, Heidelberg. Particular attention was paid to the design of a novel passive and active shield, aiming at efficient rejection of environmental and muon induced radiation backgrounds. The achieved sensitivity level of ≤100 μBq kg -1 for primordial radionuclides from U and Th in typical γ ray sample screening measurements is unique among instruments located at comparably shallow depths and can compete with instruments at far deeper underground sites

  20. GIOVE: a new detector setup for high sensitivity germanium spectroscopy at shallow depth

    Energy Technology Data Exchange (ETDEWEB)

    Heusser, G.; Weber, M.; Hakenmueller, J.; Lindner, M.; Maneschg, W.; Simgen, H.; Stolzenburg, D.; Strecker, H. [Max-Planck-Institut fuer Kernphysik, Heidelberg (Germany); Laubenstein, M. [Laboratori Nazionali del Gran Sasso, Assergi (Italy)

    2015-11-15

    We report on the development and construction of the high-purity germanium spectrometer setup GIOVE (Germanium Inner Outer VEto), recently built and now operated at the shallow underground laboratory of the Max-Planck-Institut fuer Kernphysik, Heidelberg. Particular attention was paid to the design of a novel passive and active shield, aiming at efficient rejection of environmental and muon induced radiation backgrounds. The achieved sensitivity level of ≤ 100μBq kg{sup -1} for primordial radionuclides from U and Th in typical γ ray sample screening measurements is unique among instruments located at comparably shallow depths and can compete with instruments at far deeper underground sites. (orig.)

  1. High temperature corrosion under conditions simulating biomass firing: depth-resolved phase identification

    DEFF Research Database (Denmark)

    Okoro, Sunday Chukwudi; Montgomery, Melanie; Jappe Frandsen, Flemming

    2014-01-01

    ) were coated with KCl and is o-thermally exposed at 560 o C for 168 h under a flue gas corresponding to straw firing. Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS), and X-ray Diffraction (XRD) characterization techniques were employed for comprehensive characterization......Both cross-sectional and plan view, ‘top-down’ characterization methods were employed , for a depth-resolved characterization of corrosion products resulting from high temperature corrosion under laboratory conditions simulating biomass firing. Samples of an austenitic stainless steel (TP 347H FG...... of the corrosion product. Results from this comprehensive characterization revealed more details on the morphology and composition of the corrosion product....

  2. High resolution MR imaging of bladder cancer: new criteria for determining depth of wall invasion

    International Nuclear Information System (INIS)

    Suh, Chang Hae; Kressel, Herbert Y

    1993-01-01

    To establish new criteria to determine the depth of bladder cancer as well as to obtain the findings of each stage of bladder cancer we reviewed high resolution MR images of 18 bladder cancer patients including seven cases (26%) with superficial bladder wall invasion. All MR scans were done before biopsy or surgery. Multiple layers of the bladder wall (inner black, middle white, outer black) were demonstrated in 11 cases out of a total 18 cases. Thickening of the middle layer caused by tumor infiltration or edema of lamina propria was seen in 8 of 12 patients with stage T2 or greater, and was suggestive of superficial muscle invasion when multiple layers were demonstrated. Disruption of outer layer (as well as inner layer) and external protrusion of tumor itself were indicative of perivesical invasion. When multiple layers were not demonstrated, the depth of tumor invasion could not be judged. High resolution MR imaging can depict submucosal invasion, muscle invasion, and perivesical invasion secondary to bladder cancer

  3. A terahertz EO detector with large dynamical range, high modulation depth and signal-noise ratio

    Science.gov (United States)

    Pan, Xinjian; Cai, Yi; Zeng, Xuanke; Zheng, Shuiqin; Li, Jingzhen; Xu, Shixiang

    2017-05-01

    The paper presents a novel design for terahertz (THz) free-space time domain electro-optic (EO) detection where the static birefringent phases of the two balanced arms are set close to zero but opposite to each other. Our theoretical and numerical analyses show this design has much stronger ability to cancel the optical background noise than both THz ellipsometer and traditional crossed polarizer geometry (CPG). Its optical modulation depth is about twice as high as that of traditional CPG, but about ten times as high as that of THz ellipsometer. As for the dynamical range, our improved design is comparable to the THz ellipsometer but obviously larger than the traditional CPG. Some experiments for comparing our improved CPG with traditional CPG agree well with the corresponding theoretical predictions. Our experiments also show that the splitting ratio of the used non-polarization beam splitter is critical for the performance of our design.

  4. Very high frame rate volumetric integration of depth images on mobile devices.

    Science.gov (United States)

    Kähler, Olaf; Adrian Prisacariu, Victor; Yuheng Ren, Carl; Sun, Xin; Torr, Philip; Murray, David

    2015-11-01

    Volumetric methods provide efficient, flexible and simple ways of integrating multiple depth images into a full 3D model. They provide dense and photorealistic 3D reconstructions, and parallelised implementations on GPUs achieve real-time performance on modern graphics hardware. To run such methods on mobile devices, providing users with freedom of movement and instantaneous reconstruction feedback, remains challenging however. In this paper we present a range of modifications to existing volumetric integration methods based on voxel block hashing, considerably improving their performance and making them applicable to tablet computer applications. We present (i) optimisations for the basic data structure, and its allocation and integration; (ii) a highly optimised raycasting pipeline; and (iii) extensions to the camera tracker to incorporate IMU data. In total, our system thus achieves frame rates up 47 Hz on a Nvidia Shield Tablet and 910 Hz on a Nvidia GTX Titan XGPU, or even beyond 1.1 kHz without visualisation.

  5. On Statistical Modeling of Sequencing Noise in High Depth Data to Assess Tumor Evolution

    Science.gov (United States)

    Rabadan, Raul; Bhanot, Gyan; Marsilio, Sonia; Chiorazzi, Nicholas; Pasqualucci, Laura; Khiabanian, Hossein

    2017-12-01

    One cause of cancer mortality is tumor evolution to therapy-resistant disease. First line therapy often targets the dominant clone, and drug resistance can emerge from preexisting clones that gain fitness through therapy-induced natural selection. Such mutations may be identified using targeted sequencing assays by analysis of noise in high-depth data. Here, we develop a comprehensive, unbiased model for sequencing error background. We find that noise in sufficiently deep DNA sequencing data can be approximated by aggregating negative binomial distributions. Mutations with frequencies above noise may have prognostic value. We evaluate our model with simulated exponentially expanded populations as well as data from cell line and patient sample dilution experiments, demonstrating its utility in prognosticating tumor progression. Our results may have the potential to identify significant mutations that can cause recurrence. These results are relevant in the pretreatment clinical setting to determine appropriate therapy and prepare for potential recurrence pretreatment.

  6. GIOVE: a new detector setup for high sensitivity germanium spectroscopy at shallow depth

    Energy Technology Data Exchange (ETDEWEB)

    Heusser, G., E-mail: gerd.heusser@mpi-hd.mpg.de; Weber, M., E-mail: marc.weber@mpi-hd.mpg.de; Hakenmüller, J. [Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117, Heidelberg (Germany); Laubenstein, M. [Laboratori Nazionali del Gran Sasso, Via G. Acitelli 22, 67100, Assergi, AQ (Italy); Lindner, M.; Maneschg, W.; Simgen, H.; Stolzenburg, D.; Strecker, H. [Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117, Heidelberg (Germany)

    2015-11-09

    We report on the development and construction of the high-purity germanium spectrometer setup GIOVE (Germanium Inner Outer VEto), recently built and now operated at the shallow underground laboratory of the Max-Planck-Institut für Kernphysik, Heidelberg. Particular attention was paid to the design of a novel passive and active shield, aiming at efficient rejection of environmental and muon induced radiation backgrounds. The achieved sensitivity level of ≤100 μBq kg{sup -1} for primordial radionuclides from U and Th in typical γ ray sample screening measurements is unique among instruments located at comparably shallow depths and can compete with instruments at far deeper underground sites.

  7. Depths to Ice-cemented Soils in High-elevation Quartermain Mountains, Dry Valleys, Antarctica, Version 1

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set is comprised of four surveyed valleys focusing on the depth to ground ice in the high-elevation Quartermain Mountains in the Beacon Valley area:...

  8. High spatial resolution measurement of depth-of-interaction of a PET LSO crystal

    International Nuclear Information System (INIS)

    Simon, A.; Kalinka, G.; Novak, D.; Sipos, A.; Vegh, J.; Molnar, J.

    2004-01-01

    Complete text of publication follows. A new type of experimental technique to investigate the depth-of-interaction (DOI) dependence in small scintillator elements designed for high-resolution animal PET [1] has been introduced at our institute, recently. A lutetium oxyorthosilicate (LSO) crystal (2x2x10 mm 3 ) was irradiated with a highly focused 2 MeV He + beam at the ATOMKI nuclear microprobe laboratory. Pulse height spectra from a photomultiplier (PMT) attached to one end of the LSO crystal were collected in list mode. Sequential scans of 1000x1000 μm 2 areas along the 10 mm long crystal were made to get high lateral resolution images of pulse height spectra at different distances from the window of the PMT. A mean pulse height algorithm was applied to each pixel to generate two dimensional intensity images and the corresponding spectra of 100 μmx1 mm areas. Representative pulse height spectra are shown in Fig. 1 for different distances between the position of irradiation and the PMT. The mean value of the pulse height spectrum describing the position of the full energy peak is a way to measure DOI effects. It is seen that the closer the DOI to the PMT-end of the crystal the higher the energy of the peak. The centre of the detected peak varies about 30 % along the lateral side of the crystal. This effect is due to the increasing number of reflections with associated loss of light when the distance between the DOI position and the light collecting PMT grows. Further these results, no difference in the light intensity was found depending on which position across (perpendicular to the length of) the crystal was irradiated with the microbeam. The obtained results of the overall DOI dependence confirm previous measurements on LSO crystals with similar geometry and wrapping but based on collimated gamma-ray irradiation. Since the present experimental setup allows obtaining data with several orders of magnitude better spatial resolution (from μm up to mm) than with

  9. High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic.

    Science.gov (United States)

    Sealfon, Rachel; Gire, Stephen; Ellis, Crystal; Calderwood, Stephen; Qadri, Firdausi; Hensley, Lisa; Kellis, Manolis; Ryan, Edward T; LaRocque, Regina C; Harris, Jason B; Sabeti, Pardis C

    2012-09-11

    Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x); four of the seven isolates were previously sequenced. Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961), 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways. Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

  10. High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic

    Directory of Open Access Journals (Sweden)

    Sealfon Rachel

    2012-09-01

    Full Text Available Abstract Background Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x; four of the seven isolates were previously sequenced. Results Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961, 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways. Conclusions Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

  11. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.

    Science.gov (United States)

    Peng, Yu; Leung, Henry C M; Yiu, S M; Chin, Francis Y L

    2012-06-01

    Next-generation sequencing allows us to sequence reads from a microbial environment using single-cell sequencing or metagenomic sequencing technologies. However, both technologies suffer from the problem that sequencing depth of different regions of a genome or genomes from different species are highly uneven. Most existing genome assemblers usually have an assumption that sequencing depths are even. These assemblers fail to construct correct long contigs. We introduce the IDBA-UD algorithm that is based on the de Bruijn graph approach for assembling reads from single-cell sequencing or metagenomic sequencing technologies with uneven sequencing depths. Several non-trivial techniques have been employed to tackle the problems. Instead of using a simple threshold, we use multiple depthrelative thresholds to remove erroneous k-mers in both low-depth and high-depth regions. The technique of local assembly with paired-end information is used to solve the branch problem of low-depth short repeat regions. To speed up the process, an error correction step is conducted to correct reads of high-depth regions that can be aligned to highconfident contigs. Comparison of the performances of IDBA-UD and existing assemblers (Velvet, Velvet-SC, SOAPdenovo and Meta-IDBA) for different datasets, shows that IDBA-UD can reconstruct longer contigs with higher accuracy. The IDBA-UD toolkit is available at our website http://www.cs.hku.hk/~alse/idba_ud

  12. Development of high-resolution detector module with depth of interaction identification for positron emission tomography

    International Nuclear Information System (INIS)

    Niknejad, Tahereh; Pizzichemi, Marco; Stringhini, Gianluca; Auffray, Etiennette; Bugalho, Ricardo; Da Silva, Jose Carlos; Di Francesco, Agostino; Ferramacho, Luis; Lecoq, Paul; Leong, Carlos; Paganoni, Marco; Rolo, Manuel; Silva, Rui; Silveira, Miguel; Tavernier, Stefaan; Varela, Joao; Zorraquino, Carlos

    2017-01-01

    We have developed a Time-of-flight high resolution and commercially viable detector module for the application in small PET scanners. A new approach to depth of interaction (DOI) encoding with low complexity for a pixelated crystal array using a single side readout and 4-to-1 coupling between scintillators and photodetectors was investigated. In this method the DOI information is estimated using the light sharing technique. The detector module is a 1.53×1.53×15 mm"3 matrix of 8×8 LYSO scintillator with lateral surfaces optically depolished separated by reflective foils. The crystal array is optically coupled to 4×4 silicon photomultipliers (SiPM) array and readout by a high performance front-end ASIC with TDC capability (50 ps time binning). The results show an excellent crystal identification for all the scintillators in the matrix, a timing resolution of 530 ps, an average DOI resolution of 5.17 mm FWHM and an average energy resolution of 18.29% FWHM. - Highlights: • A new method for DOI encoding for PET detectors based on light sharing is proposed. • A prototype module with LYSO scintillator matrix coupled to SiPMs array is produced. • The module has one side readout and 4-to-1 coupling between scintillators and SiPMs. • A compact TOF front-end ASIC is used. • Excellent performances are shown by the prototype module.

  13. Development of high-resolution detector module with depth of interaction identification for positron emission tomography

    Energy Technology Data Exchange (ETDEWEB)

    Niknejad, Tahereh, E-mail: tniknejad@lip.pt [Laboratory of Instrumentation and Experimental Particles Physics, Lisbon (Portugal); Pizzichemi, Marco [University of Milano-Bicocca (Italy); Stringhini, Gianluca [University of Milano-Bicocca (Italy); CERN, Geneve (Switzerland); Auffray, Etiennette [CERN, Geneve (Switzerland); Bugalho, Ricardo; Da Silva, Jose Carlos; Di Francesco, Agostino [Laboratory of Instrumentation and Experimental Particles Physics, Lisbon (Portugal); Ferramacho, Luis [PETsys Electronics, Oeiras (Portugal); Lecoq, Paul [CERN, Geneve (Switzerland); Leong, Carlos [PETsys Electronics, Oeiras (Portugal); Paganoni, Marco [University of Milano-Bicocca (Italy); Rolo, Manuel [Laboratory of Instrumentation and Experimental Particles Physics, Lisbon (Portugal); INFN, Turin (Italy); Silva, Rui [Laboratory of Instrumentation and Experimental Particles Physics, Lisbon (Portugal); Silveira, Miguel [PETsys Electronics, Oeiras (Portugal); Tavernier, Stefaan [PETsys Electronics, Oeiras (Portugal); Vrije Universiteit Brussel (Belgium); Varela, Joao [Laboratory of Instrumentation and Experimental Particles Physics, Lisbon (Portugal); CERN, Geneve (Switzerland); Zorraquino, Carlos [Biomedical Image Technologies Lab, Universidad Politécnica de Madrid (Spain); CIBER-BBN, Universidad Politécnica de Madrid (Spain)

    2017-02-11

    We have developed a Time-of-flight high resolution and commercially viable detector module for the application in small PET scanners. A new approach to depth of interaction (DOI) encoding with low complexity for a pixelated crystal array using a single side readout and 4-to-1 coupling between scintillators and photodetectors was investigated. In this method the DOI information is estimated using the light sharing technique. The detector module is a 1.53×1.53×15 mm{sup 3} matrix of 8×8 LYSO scintillator with lateral surfaces optically depolished separated by reflective foils. The crystal array is optically coupled to 4×4 silicon photomultipliers (SiPM) array and readout by a high performance front-end ASIC with TDC capability (50 ps time binning). The results show an excellent crystal identification for all the scintillators in the matrix, a timing resolution of 530 ps, an average DOI resolution of 5.17 mm FWHM and an average energy resolution of 18.29% FWHM. - Highlights: • A new method for DOI encoding for PET detectors based on light sharing is proposed. • A prototype module with LYSO scintillator matrix coupled to SiPMs array is produced. • The module has one side readout and 4-to-1 coupling between scintillators and SiPMs. • A compact TOF front-end ASIC is used. • Excellent performances are shown by the prototype module.

  14. Three-layer GSO depth-of-interaction detector for high-energy gamma camera

    International Nuclear Information System (INIS)

    Yamamoto, S.; Watabe, H.; Kawachi, N.; Fujimaki, S.; Kato, K.; Hatazawa, J.

    2014-01-01

    Using Ce-doped Gd 2 SiO 5 (GSO) of different Ce concentrations, three-layer DOI block detectors were developed to reduce the parallax error at the edges of a pinhole gamma camera for high-energy gamma photons. GSOs with Ce concentrations of 1.5 mol% (decay time ∼40 ns), 0.5 mol% crystal (∼60 ns), 0.4 mol% (∼80 ns) were selected for the depth of interaction (DOI) detectors. These three types of GSOs were optically coupled in the depth direction, arranged in a 22×22 matrix and coupled to a flat panel photomultiplier tube (FP-PMT, Hamamatsu H8500). Sizes of these GSO cells were 1.9 mm×1.9 mm×4 mm, 1.9 mm×1.9 mm×5 mm, and 1.9 mm×1.9 mm×6 mm for 1.5 mol%, 0.5 mol%, and 0.4 mol%, respectively. With these combinations of GSOs, all spots corresponding to GSO cells were clearly resolved in the position histogram. Pulse shape spectra showed three peaks for these three decay times of GSOs. The block detector was contained in a 2-cm-thick tungsten shield, and a pinhole collimator with a 0.5-mm aperture was mounted. With pulse shape discrimination, we separated the point source images of the Cs-137 for each DOI layer. The point source image of the lower layer was detected at the most central part of the field-of-view, and the distribution was the smallest. The point source image of the higher layer was detected at the most peripheral part of the field-of-view, and the distribution was widest. With this information, the spatial resolution of the pinhole gamma camera can be improved. We conclude that DOI detection is effective for pinhole gamma cameras for high energy gamma photons

  15. Depth extraction method with high accuracy in integral imaging based on moving array lenslet technique

    Science.gov (United States)

    Wang, Yao-yao; Zhang, Juan; Zhao, Xue-wei; Song, Li-pei; Zhang, Bo; Zhao, Xing

    2018-03-01

    In order to improve depth extraction accuracy, a method using moving array lenslet technique (MALT) in pickup stage is proposed, which can decrease the depth interval caused by pixelation. In this method, the lenslet array is moved along the horizontal and vertical directions simultaneously for N times in a pitch to get N sets of elemental images. Computational integral imaging reconstruction method for MALT is taken to obtain the slice images of the 3D scene, and the sum modulus (SMD) blur metric is taken on these slice images to achieve the depth information of the 3D scene. Simulation and optical experiments are carried out to verify the feasibility of this method.

  16. 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.

  17. 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

  18. In-depth, high-accuracy proteomics of sea urchin tooth organic matrix

    Directory of Open Access Journals (Sweden)

    Mann Matthias

    2008-12-01

    Full Text Available Abstract Background The organic matrix contained in biominerals plays an important role in regulating mineralization and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin tooth, which is an important model for developmental biology and biomineralization, only few matrix components have been identified. The recent publication of the Strongylocentrotus purpuratus genome sequence rendered possible not only the identification of genes potentially coding for matrix proteins, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy proteomic analysis. Results We identified 138 proteins in the matrix of tooth powder. Only 56 of these proteins were previously identified in the matrices of test (shell and spine. Among the novel components was an interesting group of five proteins containing alanine- and proline-rich neutral or basic motifs separated by acidic glycine-rich motifs. In addition, four of the five proteins contained either one or two predicted Kazal protease inhibitor domains. The major components of tooth matrix were however largely identical to the set of spicule matrix proteins and MSP130-related proteins identified in test (shell and spine matrix. Comparison of the matrices of crushed teeth to intact teeth revealed a marked dilution of known intracrystalline matrix proteins and a concomitant increase in some intracellular proteins. Conclusion This report presents the most comprehensive list of sea urchin tooth matrix proteins available at present. The complex mixture of proteins identified may reflect many different aspects of the mineralization process. A comparison between intact tooth matrix, presumably containing odontoblast remnants, and crushed tooth matrix served to differentiate between matrix components and possible contributions of cellular remnants. Because LC-MS/MS-based methods directly

  19. Detection of High Frequency Oscillations by Hybrid Depth Electrodes in Standard Clinical Intracranial EEG Recordings

    Directory of Open Access Journals (Sweden)

    Efstathios D Kondylis

    2014-08-01

    Full Text Available High frequency oscillations (HFOs have been proposed as a novel marker for epileptogenic tissue, spurring tremendous research interest into the characterization of these transient events. A wealth of continuously recorded intracranial electroencephalographic (iEEG data is currently available from patients undergoing invasive monitoring for the surgical treatment of epilepsy. In contrast to data recorded on research-customized recording systems, data from clinical acquisition systems remain an underutilized resource for HFO detection in most centers. The effective and reliable use of this clinically obtained data would be an important advance in the ongoing study of HFOs and their relationship to ictogenesis. The diagnostic utility of HFOs ultimately will be limited by the ability of clinicians to detect these brief, sporadic, and low amplitude events in an electrically noisy clinical environment. Indeed, one of the most significant factors limiting the use of such clinical recordings for research purposes is their low signal to noise ratio, especially in the higher frequency bands. In order to investigate the presence of HFOs in clinical data, we first obtained continuous intracranial recordings in a typical clinical environment using a commercially available, commonly utilized data acquisition system and off the shelf hybrid macro/micro depth electrodes. This data was then inspected for the presence of HFOs using semi-automated methods and expert manual review. With targeted removal of noise frequency content, HFOs were detected on both macro- and micro-contacts, and preferentially localized to seizure onset zones. HFOs detected by the offline, semi-automated method were also validated in the clinical viewer, demonstrating that 1 this clinical system allows for the visualization of HFOs, and 2 with effective signal processing, clinical recordings can yield valuable information for offline analysis.

  20. 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

  1. 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.

  2. High resolution axicon-based endoscopic FD OCT imaging with a large depth range

    Science.gov (United States)

    Lee, Kye-Sung; Hurley, William; Deegan, John; Dean, Scott; Rolland, Jannick P.

    2010-02-01

    Endoscopic imaging in tubular structures, such as the tracheobronchial tree, could benefit from imaging optics with an extended depth of focus (DOF). This optics could accommodate for varying sizes of tubular structures across patients and along the tree within a single patient. In the paper, we demonstrate an extended DOF without sacrificing resolution showing rotational images in biological tubular samples with 2.5 μm axial resolution, 10 ìm lateral resolution, and > 4 mm depth range using a custom designed probe.

  3. 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.

  4. A new chest compression depth feedback algorithm for high-quality CPR based on smartphone.

    Science.gov (United States)

    Song, Yeongtak; Oh, Jaehoon; Chee, Youngjoon

    2015-01-01

    Although many smartphone application (app) programs provide education and guidance for basic life support, they do not commonly provide feedback on the chest compression depth (CCD) and rate. The validation of its accuracy has not been reported to date. This study was a feasibility assessment of use of the smartphone as a CCD feedback device. In this study, we proposed the concept of a new real-time CCD estimation algorithm using a smartphone and evaluated the accuracy of the algorithm. Using the double integration of the acceleration signal, which was obtained from the accelerometer in the smartphone, we estimated the CCD in real time. Based on its periodicity, we removed the bias error from the accelerometer. To evaluate this instrument's accuracy, we used a potentiometer as the reference depth measurement. The evaluation experiments included three levels of CCD (insufficient, adequate, and excessive) and four types of grasping orientations with various compression directions. We used the difference between the reference measurement and the estimated depth as the error. The error was calculated for each compression. When chest compressions were performed with adequate depth for the patient who was lying on a flat floor, the mean (standard deviation) of the errors was 1.43 (1.00) mm. When the patient was lying on an oblique floor, the mean (standard deviation) of the errors was 3.13 (1.88) mm. The error of the CCD estimation was tolerable for the algorithm to be used in the smartphone-based CCD feedback app to compress more than 51 mm, which is the 2010 American Heart Association guideline.

  5. Exploration of depth modeling mode one lossless wedgelets storage strategies for 3D-high efficiency video coding

    Science.gov (United States)

    Sanchez, Gustavo; Marcon, César; Agostini, Luciano Volcan

    2018-01-01

    The 3D-high efficiency video coding has introduced tools to obtain higher efficiency in 3-D video coding, and most of them are related to the depth maps coding. Among these tools, the depth modeling mode-1 (DMM-1) focuses on better encoding edges regions of depth maps. The large memory required for storing all wedgelet patterns is one of the bottlenecks in the DMM-1 hardware design of both encoder and decoder since many patterns must be stored. Three algorithms to reduce the DMM-1 memory requirements and a hardware design targeting the most efficient among these algorithms are presented. Experimental results demonstrate that the proposed solutions surpass related works reducing up to 78.8% of the wedgelet memory, without degrading the encoding efficiency. Synthesis results demonstrate that the proposed algorithm reduces almost 75% of the power dissipation when compared to the standard approach.

  6. An In-Depth Look At the Lunar Crater Copernicus: Exposed Mineralogy by High-Resolution Near-Infrared Spectroscopy

    OpenAIRE

    2011-01-01

    Abstract Highlights ?We present an in-depth study of Copernicus crater. ? First publication based on new NIR data from the SIR-2 mission to the Moon. ? New NIR spectral classification of surface materials within the crater. ? Highly detailed mapping of spectrally-prominent mineral species. Abstract Newly acquired, sequentially spaced, high resolution near-infrared spectra across the central section of crater Copernicus? interior have been analysed using a r...

  7. Assessment of mural invasion depth of gastric carcinoma with high-resolution compound sonographic imaging in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Park, Seong Hoon; Kim, Eun A; Yoon, Kwon Ha; Yun, Ki Jung; Kim, Jeong Ho; Won, Jong Jin [Wonkwang University School of Medicine, Iksan (Korea, Republic of)

    2002-11-01

    To evaluate whether the accuracy of invasion depth assessment in gastric carcinoma in vitro can be improved with high-resolution spatial compound sonographic imaging. In sixteen fresh gastric specimens obtained from patients with preoperatively biopsy proven gastric carcinoma, normal and lesional areas were scanned using conventional and compound imaging technique with a 15-MHz linear transducer. Two radiologists independently compared the sharpness and the contrast of images obtained with two different modes and determined the layers invaded by cancer with consensus. The invasion depths by images were compared with histopathologic results. The sharpness and the contrast in normal and lesional areas were significantly higher in compound imaging (p<0.01) than those in conventional imaging and interobserver agreement was over moderate, with k-value of 0.41 to 0.86. But the accuracy in invasion depth assessment was 68.8% (11/16) on conventional imaging and 75% (12/16) on compound imaging and non different significantly between two modes (p>0305). High-resolution spatial compound sonographic imaging has improved image quality, compared with conventional imaging, but the accuracy of invasion depth assessment in gastric carcinoma was not significantly different.

  8. Geographic differences in vertical connectivity in the Caribbean coral Montastraea cavernosa despite high levels of horizontal connectivity at shallow depths.

    Science.gov (United States)

    Serrano, X; Baums, I B; O'Reilly, K; Smith, T B; Jones, R J; Shearer, T L; Nunes, F L D; Baker, A C

    2014-09-01

    The deep reef refugia hypothesis proposes that deep reefs can act as local recruitment sources for shallow reefs following disturbance. To test this hypothesis, nine polymorphic DNA microsatellite loci were developed and used to assess vertical connectivity in 583 coral colonies of the Caribbean depth-generalist coral Montastraea cavernosa. Samples were collected from three depth zones (≤10, 15-20 and ≥25 m) at sites in Florida (within the Upper Keys, Lower Keys and Dry Tortugas), Bermuda, and the U.S. Virgin Islands. Migration rates were estimated to determine the probability of coral larval migration from shallow to deep and from deep to shallow. Finally, algal symbiont (Symbiodinium spp.) diversity and distribution were assessed in a subset of corals to test whether symbiont depth zonation might indicate limited vertical connectivity. Overall, analyses revealed significant genetic differentiation by depth in Florida, but not in Bermuda or the U.S. Virgin Islands, despite high levels of horizontal connectivity between these geographic locations at shallow depths. Within Florida, greater vertical connectivity was observed in the Dry Tortugas compared to the Lower or Upper Keys. However, at all sites, and regardless of the extent of vertical connectivity, migration occurred asymmetrically, with greater likelihood of migration from shallow to intermediate/deep habitats. Finally, most colonies hosted a single Symbiodinium type (C3), ruling out symbiont depth zonation of the dominant symbiont type as a structuring factor. Together, these findings suggest that the potential for shallow reefs to recover from deep-water refugia in M. cavernosa is location-specific, varying among and within geographic locations likely as a consequence of local hydrology. © 2014 John Wiley & Sons Ltd.

  9. High resolution coherence domain depth-resolved nailfold capillaroscopy based on correlation mapping optical coherence tomography

    Science.gov (United States)

    Subhash, Hrebesh M.; O'Gorman, Sean; Neuhaus, Kai; Leahy, Martin

    2014-03-01

    In this paper we demonstrate a novel application of correlation mapping optical coherence tomography (cm-OCT) for volumetric nailfold capillaroscopy (NFC). NFC is a widely used non-invasive diagnostic method to analyze capillary morphology and microvascular abnormalities of nailfold area for a range of disease conditions. However, the conventional NFC is incapable of providing volumetric imaging, when volumetric quantitative microangiopathic parameters such as plexus morphology, capillary density, and morphologic anomalies of the end row loops most critical. cm-OCT is a recently developed well established coherence domain magnitude based angiographic modality, which takes advantage of the time-varying speckle effect, which is normally dominant in the vicinity of vascular regions compared to static tissue region. It utilizes the correlation coefficient as a direct measurement of decorrelation between two adjacent B-frames to enhance the visibility of depth-resolved microcirculation.

  10. Application of Low-Cost UASs and Digital Photogrammetry for High-Resolution Snow Depth Mapping in the Arctic

    Directory of Open Access Journals (Sweden)

    Emiliano Cimoli

    2017-11-01

    Full Text Available The repeat acquisition of high-resolution snow depth measurements has important research and civil applications in the Arctic. Currently the surveying methods for capturing the high spatial and temporal variability of the snowpack are expensive, in particular for small areal extents. An alternative methodology based on Unmanned Aerial Systems (UASs and digital photogrammetry was tested over varying surveying conditions in the Arctic employing two diverse and low-cost UAS-camera combinations (500 and 1700 USD, respectively. Six areas, two in Svalbard and four in Greenland, were mapped covering from 1386 to 38,410 m2. The sites presented diverse snow surface types, underlying topography and light conditions in order to test the method under potentially limiting conditions. The resulting snow depth maps achieved spatial resolutions between 0.06 and 0.09 m. The average difference between UAS-estimated and measured snow depth, checked with conventional snow probing, ranged from 0.015 to 0.16 m. The impact of image pre-processing was explored, improving point cloud density and accuracy for different image qualities and snow/light conditions. Our UAS photogrammetry results are expected to be scalable to larger areal extents. While further validation is needed, with the inclusion of extra validation points, the study showcases the potential of this cost-effective methodology for high-resolution monitoring of snow dynamics in the Arctic and beyond.

  11. GlobalSoilMap France: High-resolution spatial modelling the soils of France up to two meter depth.

    Science.gov (United States)

    Mulder, V L; Lacoste, M; Richer-de-Forges, A C; Arrouays, D

    2016-12-15

    This work presents the first GlobalSoilMap (GSM) products for France. We developed an automatic procedure for mapping the primary soil properties (clay, silt, sand, coarse elements, pH, soil organic carbon (SOC), cation exchange capacity (CEC) and soil depth). The procedure employed a data-mining technique and a straightforward method for estimating the 90% confidence intervals (CIs). The most accurate models were obtained for pH, sand and silt. Next, CEC, clay and SOC were found reasonably accurate predicted. Coarse elements and soil depth were the least accurate of all models. Overall, all models were considered robust; important indicators for this were 1) the small difference in model diagnostics between the calibration and cross-validation set, 2) the unbiased mean predictions, 3) the smaller spatial structure of the prediction residuals in comparison to the observations and 4) the similar performance compared to other developed GlobalSoilMap products. Nevertheless, the confidence intervals (CIs) were rather wide for all soil properties. The median predictions became less reliable with increasing depth, as indicated by the increase of CIs with depth. In addition, model accuracy and the corresponding CIs varied depending on the soil variable of interest, soil depth and geographic location. These findings indicated that the CIs are as informative as the model diagnostics. In conclusion, the presented method resulted in reasonably accurate predictions for the majority of the soil properties. End users can employ the products for different purposes, as was demonstrated with some practical examples. The mapping routine is flexible for cloud-computing and provides ample opportunity to be further developed when desired by its users. This allows regional and international GSM partners with fewer resources to develop their own products or, otherwise, to improve the current routine and work together towards a robust high-resolution digital soil map of the world

  12. 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.

  13. Depth Probing Soft X-ray Microprobe (DPSXRM) for High Resolution Probing of Earth's Microstructural Samples

    Science.gov (United States)

    Dikedi, P. N.

    2015-12-01

    The Cambrian explosion; occurrence of landslides in very dry weather conditions; rockslides; dead, shriveled-up and crumbled leaves possessing fossil records with the semblance of well preserved, flat leaves; abundance of trilobite tracks in lower and higher rock layers; and sailing stones are enigmas demanding demystifications. These enigmas could be elucidated when data on soil structure, texture and strength are provided by some device with submicrometre accuracy; for these and other reasons, the design of a Depth Probing Soft X-ray Microprobe (DPSXRM), is being proposed; it is expected to deliver soft X-rays, at spatial resolution, ϛ≥600nm and to probe at the depth of 0.5m in 17s. The microprobe is portable compared to a synchrotron radiation facility (Diamond Light Source has land size of 43,300m2); spatial resolution,ϛ , of the DPSXRM surpasses those of the X-ray Fluorescence microanalysis (10µm), electron microprobe (1-3µm) and ion microprobe (5->30µm); the DPSXRM has allowance for multiple targets. Vanadium and Manganese membranes are proposed owing to respective 4.952KeV VKα1 and 5.899KeV MnKα1 X-rays emitted, which best suits micro-probing of Earth's microstructural samples. Compound systems like the Kirk-Patrick and Baez and Wolter optics, aspheric mirrors like elliptical and parabolic optics, small apertures and Abbe sine condition are employed to reduce or remove astigmatism, obliquity, comatic and spherical aberrations—leading to good image quality. Results show that 5.899KeV MnKα1 and 4.952KeV VKα1 soft X-rays will travel a distance of 2.75mm to form circular patches of radii 2.2mm and 2.95mm respectively. Zone plate with nth zone radius of 1.5mm must be positioned 1.5mm and 2mm from the electron gun if circular patches must be formed from 4.952KeV VKα1 and 5.899KeV MnKα1 soft X-rays respectively. The focal lengths of 0.25μm≤ƒ≤1.50μm and 0.04μm≤ƒ≤0.2μm covered by 4.952KeV VKα1 and 5.899KeV Mn Kα1 soft X-Rays, will

  14. 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.

  15. In-depth analysis and discussions of water absorption-typed high power laser calorimeter

    Science.gov (United States)

    Wei, Ji Feng

    2017-02-01

    In high-power and high-energy laser measurement, the absorber materials can be easily destroyed under long-term direct laser irradiation. In order to improve the calorimeter's measuring capacity, a measuring system directly using water flow as the absorber medium was built. The system's basic principles and the designing parameters of major parts were elaborated. The system's measuring capacity, the laser working modes, and the effects of major parameters were analyzed deeply. Moreover, the factors that may affect the accuracy of measurement were analyzed and discussed. The specific control measures and methods were elaborated. The self-calibration and normal calibration experiments show that this calorimeter has very high accuracy. In electrical calibration, the average correction coefficient is only 1.015, with standard deviation of only 0.5%. In calibration experiments, the standard deviation relative to a middle-power standard calorimeter is only 1.9%.

  16. Multimodal adaptive optics for depth-enhanced high-resolution ophthalmic imaging

    Science.gov (United States)

    Hammer, Daniel X.; Mujat, Mircea; Iftimia, Nicusor V.; Lue, Niyom; Ferguson, R. Daniel

    2010-02-01

    We developed a multimodal adaptive optics (AO) retinal imager for diagnosis of retinal diseases, including glaucoma, diabetic retinopathy (DR), age-related macular degeneration (AMD), and retinitis pigmentosa (RP). The development represents the first ever high performance AO system constructed that combines AO-corrected scanning laser ophthalmoscopy (SLO) and swept source Fourier domain optical coherence tomography (SSOCT) imaging modes in a single compact clinical prototype platform. The SSOCT channel operates at a wavelength of 1 μm for increased penetration and visualization of the choriocapillaris and choroid, sites of major disease activity for DR and wet AMD. The system is designed to operate on a broad clinical population with a dual deformable mirror (DM) configuration that allows simultaneous low- and high-order aberration correction. The system also includes a wide field line scanning ophthalmoscope (LSO) for initial screening, target identification, and global orientation; an integrated retinal tracker (RT) to stabilize the SLO, OCT, and LSO imaging fields in the presence of rotational eye motion; and a high-resolution LCD-based fixation target for presentation to the subject of stimuli and other visual cues. The system was tested in a limited number of human subjects without retinal disease for performance optimization and validation. The system was able to resolve and quantify cone photoreceptors across the macula to within ~0.5 deg (~100-150 μm) of the fovea, image and delineate ten retinal layers, and penetrate to resolve targets deep into the choroid. In addition to instrument hardware development, analysis algorithms were developed for efficient information extraction from clinical imaging sessions, with functionality including automated image registration, photoreceptor counting, strip and montage stitching, and segmentation. The system provides clinicians and researchers with high-resolution, high performance adaptive optics imaging to help

  17. 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

  18. Fine Particulate Matter Predictions Using High Resolution Aerosol Optical Depth (AOD) Retrievals

    Science.gov (United States)

    Chudnovsky, Alexandra A.; Koutrakis, Petros; Kloog, Itai; Melly, Steven; Nordio, Francesco; Lyapustin, Alexei; Wang, Jujie; Schwartz, Joel

    2014-01-01

    To date, spatial-temporal patterns of particulate matter (PM) within urban areas have primarily been examined using models. On the other hand, satellites extend spatial coverage but their spatial resolution is too coarse. In order to address this issue, here we report on spatial variability in PM levels derived from high 1 km resolution AOD product of Multi-Angle Implementation of Atmospheric Correction (MAIAC) algorithm developed for MODIS satellite. We apply day-specific calibrations of AOD data to predict PM(sub 2.5) concentrations within the New England area of the United States. To improve the accuracy of our model, land use and meteorological variables were incorporated. We used inverse probability weighting (IPW) to account for nonrandom missingness of AOD and nested regions within days to capture spatial variation. With this approach we can control for the inherent day-to-day variability in the AOD-PM(sub 2.5) relationship, which depends on time-varying parameters such as particle optical properties, vertical and diurnal concentration profiles and ground surface reflectance among others. Out-of-sample "ten-fold" cross-validation was used to quantify the accuracy of model predictions. Our results show that the model-predicted PM(sub 2.5) mass concentrations are highly correlated with the actual observations, with out-of- sample R(sub 2) of 0.89. Furthermore, our study shows that the model captures the pollution levels along highways and many urban locations thereby extending our ability to investigate the spatial patterns of urban air quality, such as examining exposures in areas with high traffic. Our results also show high accuracy within the cities of Boston and New Haven thereby indicating that MAIAC data can be used to examine intra-urban exposure contrasts in PM(sub 2.5) levels.

  19. Evidence of weak pair coupling in the penetration depth of bi-based high-Tc superconductors

    International Nuclear Information System (INIS)

    Thompson, J.R.; Sun, Yang Ren; Ossandon, J.G.; Christen, D.K.; Chakoumakos, B.C.; Sales, B.C.; Kerchner, H.R.; Sonder, E.

    1990-01-01

    The magnetic penetration depth λ(T) has been investigated in Bi(Pb)SrCaCuO high-T c compounds having 2- and 3-layers of copper-oxygen per unit cell. Studies of the magnetization in the vortex state were employed and the results were compared with weak and strong coupling calculations. The temperature dependence of λ is described well by BCS theory in the clean limit, giving evidence for weak pair coupling in this family of materials. For the short component of the λ tensor, we obtain values of 292 and 220 nm (T = 0) for Bi-2212 and (BiPb)-2223, respectively

  20. Application of Low-Cost UASs and Digital Photogrammetry for High-Resolution Snow Depth Mapping in the Arctic

    DEFF Research Database (Denmark)

    Cimoli, Emiliano; Marcer, Marco; Vandecrux, Baptiste Robert Marcel

    2017-01-01

    The repeat acquisition of high-resolution snow depth measurements has important research and civil applications in the Arctic. Currently the surveying methods for capturing the high spatial and temporal variability of the snowpack are expensive, in particular for small areal extents. An alternati...... areal extents. While further validation is needed, with the inclusion of extra validation points, the study showcases the potential of this cost-effective methodology for high-resolution monitoring of snow dynamics in the Arctic and beyond....... methodology based on Unmanned Aerial Systems (UASs) and digital photogrammetry was tested over varying surveying conditions in the Arctic employing two diverse and low-cost UAS-camera combinations (500 and 1700 USD, respectively). Six areas, two in Svalbard and four in Greenland, were mapped covering from......-estimated and measured snow depth, checked with conventional snow probing, ranged from 0.015 to 0.16 m. The impact of image pre-processing was explored, improving point cloud density and accuracy for different image qualities and snow/light conditions. Our UAS photogrammetry results are expected to be scalable to larger...

  1. Effects of prescription depth, cylinder size, treatment length, tip space, and curved end on doses in high-dose-rate vaginal brachytherapy

    International Nuclear Information System (INIS)

    Li Shidong; Aref, Ibrahim; Walker, Eleanor; Movsas, Benjamin

    2007-01-01

    Purpose: To determine the effects of the prescription depth, cylinder size, treatment length, tip space, and curved end on high-dose-rate vaginal brachytherapy (HDR-VBT) of endometrial cancer. Methods and Materials: Treatment plans were prescribed and optimized based on points at the cylinder surface or at 0.5-cm depth. Cylinder sizes ranging from 2 to 4 cm in diameter, and treatment lengths ranging from 3 to 8 cm were used. Dose points in various depths were precisely defined along the cylinder dome. The given dose and dose uniformity to a depth of interest were measured by the mean dose (MD) and standard deviation (SD), respectively, among the dose points belonging to the depth. Dose fall-off beyond the 0.5 cm treatment depth was determined by the ratio of MD at 0.75-cm depth to MD at 0.5-cm depth. Results: Dose distribution varies significantly with different prescriptions. The surface prescription provides more uniform doses at all depths in the target volume, whereas the 0.5-cm depth prescription creates larger dose variations at the cylinder surface. Dosimetric uncertainty increases significantly (>30%) with shorter tip space. Extreme hot (>150%) and cold spots (<60%) occur if no optimization points were placed at the curved end. Conclusions: Instead of prescribing to a depth of 0.5 cm, increasing the dose per fraction and prescribing to the surface with the exact surface points around the cylinder dome appears to be the optimal approach

  2. High-Resolution Assimilation of GRACE Terrestrial Water Storage Observations to Represent Local-Scale Water Table Depths

    Science.gov (United States)

    Stampoulis, D.; Reager, J. T., II; David, C. H.; Famiglietti, J. S.; Andreadis, K.

    2017-12-01

    Despite the numerous advances in hydrologic modeling and improvements in Land Surface Models, an accurate representation of the water table depth (WTD) still does not exist. Data assimilation of observations of the joint NASA and DLR mission, Gravity Recovery and Climate Experiment (GRACE) leads to statistically significant improvements in the accuracy of hydrologic models, ultimately resulting in more reliable estimates of water storage. However, the usually shallow groundwater compartment of the models presents a problem with GRACE assimilation techniques, as these satellite observations account for much deeper aquifers. To improve the accuracy of groundwater estimates and allow the representation of the WTD at fine spatial scales we implemented a novel approach that enables a large-scale data integration system to assimilate GRACE data. This was achieved by augmenting the Variable Infiltration Capacity (VIC) hydrologic model, which is the core component of the Regional Hydrologic Extremes Assessment System (RHEAS), a high-resolution modeling framework developed at the Jet Propulsion Laboratory (JPL) for hydrologic modeling and data assimilation. The model has insufficient subsurface characterization and therefore, to reproduce groundwater variability not only in shallow depths but also in deep aquifers, as well as to allow GRACE assimilation, a fourth soil layer of varying depth ( 1000 meters) was added in VIC as the bottom layer. To initialize a water table in the model we used gridded global WTD data at 1 km resolution which were spatially aggregated to match the model's resolution. Simulations were then performed to test the augmented model's ability to capture seasonal and inter-annual trends of groundwater. The 4-layer version of VIC was run with and without assimilating GRACE Total Water Storage anomalies (TWSA) over the Central Valley in California. This is the first-ever assimilation of GRACE TWSA for the determination of realistic water table depths, at

  3. High temperature corrosion during biomass firing: improved understanding by depth resolved characterisation of corrosion products

    DEFF Research Database (Denmark)

    Okoro, Sunday Chukwudi; Montgomery, Melanie; Jappe Frandsen, Flemming

    2015-01-01

    changes within the near surface region (covering both the deposit and the steel surface). Such cross-section analysis was further complemented by plan view investigations (additionally involving X-ray diffraction) combined with removal of the corrosion products. Improved insights into the nature......The high temperature corrosion of an austenitic stainless steel (TP 347H FG), widely utilised as a superheater tube material in Danish power stations, was investigated to verify the corrosion mechanisms related to biomass firing. KCl coated samples were exposed isothermally to 560 degrees C...... of the corrosion products as a function of distance from the deposit surface were revealed through this comprehensive characterisation. Corrosion attack during simulated straw-firing conditions was observed to occur through both active oxidation and sulphidation mechanisms....

  4. Depth-kymography: high-speed calibrated 3D imaging of human vocal fold vibration dynamics

    International Nuclear Information System (INIS)

    George, Nibu A; Mul, Frits F M de; Qiu Qingjun; Rakhorst, Gerhard; Schutte, Harm K

    2008-01-01

    We designed and developed a laser line-triangulation endoscope compatible with any standard high-speed camera for a complete three-dimensional profiling of human vocal fold vibration dynamics. With this novel device we are able to measure absolute values of vertical and horizontal vibration amplitudes, length and width of vocal folds as well as the opening and closing velocities from a single in vivo measurement. We have studied, for the first time, the generation and propagation of mucosal waves by locating the position of its maximum vertical position and the propagation velocity. Precise knowledge about the absolute dimensions of human vocal folds and their vibration parameters has significant importance in clinical diagnosis and treatment as well as in fundamental research in voice. The new device can be used to investigate different kinds of pathological conditions including periodic or aperiodic vibrations. Consequently, the new device has significant importance in investigating vocal fold paralysis and in phonosurgical applications

  5. Depth-kymography: high-speed calibrated 3D imaging of human vocal fold vibration dynamics

    Energy Technology Data Exchange (ETDEWEB)

    George, Nibu A; Mul, Frits F M de; Qiu Qingjun; Rakhorst, Gerhard; Schutte, Harm K [Groningen Voice Research Lab, Department of Biomedical Engineering, University Medical Center Groningen and University of Groningen, 9700 AD Groningen (Netherlands)

    2008-05-21

    We designed and developed a laser line-triangulation endoscope compatible with any standard high-speed camera for a complete three-dimensional profiling of human vocal fold vibration dynamics. With this novel device we are able to measure absolute values of vertical and horizontal vibration amplitudes, length and width of vocal folds as well as the opening and closing velocities from a single in vivo measurement. We have studied, for the first time, the generation and propagation of mucosal waves by locating the position of its maximum vertical position and the propagation velocity. Precise knowledge about the absolute dimensions of human vocal folds and their vibration parameters has significant importance in clinical diagnosis and treatment as well as in fundamental research in voice. The new device can be used to investigate different kinds of pathological conditions including periodic or aperiodic vibrations. Consequently, the new device has significant importance in investigating vocal fold paralysis and in phonosurgical applications.

  6. 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.

  7. An experimental investigation on bending stiffness and neutral axis depth variation of over-reinforced high strength concrete beams

    International Nuclear Information System (INIS)

    Mohammadhassani, Mohammad; Bin Jumaat, Mohd Zamin; Chemrouk, Mohamed; Akbar Maghsoudi, Ali; Jameel, Mohammed; Akib, Shatirah

    2011-01-01

    Highlights: → Improvement of the assessment of correspond stress for calculation of modules of elasticity → better evaluation of cracked moment of inertia. → Low distinction of neutral axis depth → low bending stiffness variation. → Rate of slope in the line connecting the origin of first crack to yield point of N.A.D-LOAD graph → rate of ductility of beam section. - Abstract: The present work is an attempt to study the neutral axis variation and the evolution of the moment inertia with the loading of over reinforced high strength concrete sections in conjunction with ACI 318-05. In this sense, four high strength concrete beams, having different tension reinforcement quantities expressed as proportions of the balanced steel ratio (0.75ρ b , 0.85ρ b , ρ b , 1.2ρ b ) were tested. Measurements of the deflection and the reinforcement and concrete strains of all specimens were made during the loading process. The load-neutral axis depth variation and the load-section stiffness curves were drawn. The slope of the line connecting the origin of the first crack to the initial yielding of the failure point in the neutral axis depth-load graphs shows the rate of ductility; ductile behaviour in the beam increases as the slope becomes steeper. Based on the results of this study, it is recommended that the modulus of elasticity of concrete E c be reviewed and evaluated at a stress higher than 0.5f ' c for the determination of the cracked moment of inertia.

  8. In-depth glycoproteomic characterization of γ-conglutin by high-resolution accurate mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Silvia Schiarea

    Full Text Available The molecular characterization of bioactive food components is necessary for understanding the mechanisms of their beneficial or detrimental effects on human health. This study focused on γ-conglutin, a well-known lupin seed N-glycoprotein with health-promoting properties and controversial allergenic potential. Given the importance of N-glycosylation for the functional and structural characteristics of proteins, we studied the purified protein by a mass spectrometry-based glycoproteomic approach able to identify the structure, micro-heterogeneity and attachment site of the bound N-glycan(s, and to provide extensive coverage of the protein sequence. The peptide/N-glycopeptide mixtures generated by enzymatic digestion (with or without N-deglycosylation were analyzed by high-resolution accurate mass liquid chromatography-multi-stage mass spectrometry. The four main micro-heterogeneous variants of the single N-glycan bound to γ-conglutin were identified as Man2(Xyl (Fuc GlcNAc2, Man3(Xyl (Fuc GlcNAc2, GlcNAcMan3(Xyl (Fuc GlcNAc2 and GlcNAc 2Man3(Xyl (Fuc GlcNAc2. These carry both core β1,2-xylose and core α1-3-fucose (well known Cross-Reactive Carbohydrate Determinants, but corresponding fucose-free variants were also identified as minor components. The N-glycan was proven to reside on Asn131, one of the two potential N-glycosylation sites. The extensive coverage of the γ-conglutin amino acid sequence suggested three alternative N-termini of the small subunit, that were later confirmed by direct-infusion Orbitrap mass spectrometry analysis of the intact subunit.

  9. 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.

  10. High Resolution Trajectory-Based Smoke Forecasts Using VIIRS Aerosol Optical Depth and NUCAPS Carbon Monoxide Retrievals

    Science.gov (United States)

    Pierce, R. B.; Smith, N.; Barnet, C.; Barnet, C. D.; Kondragunta, S.; Davies, J. E.; Strabala, K.

    2016-12-01

    We use Suomi National Polar-orbiting Partnership (S-NPP) Visible Infrared Imaging Radiometer Suite (VIIRS) Aerosol Optical Depth (AOD) and combined Cross-track Infrared Sounder (CrIS) and Advanced Technology Microwave Sounder (ATMS) NOAA-Unique CrIS-ATMS Processing System (NUCAPS) carbon monoxide (CO) retrievals to initialize trajectory-based, high spatial resolution North American smoke dispersion forecasts during the May 2016 Fort McMurray wildfire in northern Alberta and the July 2016 Soberanes Fire in Northern California. These two case studies illustrate how long range transport of wild fire smoke can adversely impact surface air quality thousands of kilometers downwind and how local topographic flow can lead to complex transport patterns near the wildfire source region. The NUCAPS CO retrievals are shown to complement the high resolution VIIRS AOD retrievals by providing retrievals in partially cloudy scenes and also providing information on the vertical distribution of the wildfire smoke. This work addresses the need for low latency, web-based, high resolution forecasts of smoke dispersion for use by NWS Incident Meteorologists (IMET) to support on-site decision support services for fire incident management teams. The primary user community for the IDEA-I smoke forecasts is the Western regions of the NWS and US EPA due to the significant impacts of wildfires in these regions. Secondary users include Alaskan NWS offices and Western State and Local air quality management agencies such as the Western Regional Air Partnership (WRAP).

  11. Influence of heat treatment and indenter tip material on depth sensing hardness tests at high temperatures of fusion relevant materials

    International Nuclear Information System (INIS)

    Bredl, Julian; Dany, Manuel; Albinski, Bartlomiej; Schneider, Hans-Christian; Kraft, Oliver

    2015-01-01

    Highlights: • Operation of a custom-made indentation device designed for test temperatures up to 650 °C and a remote handled operation in a Hot Cell. • Instrumented indentation and conventional hardness testing of unirradiated MANET II and EUROFER. • Comparison of diamond and sapphire as indenter tip materials. - Abstract: The instrumented indentation is a suitable method for testing of even small neutron-irradiated specimens. From the continuously recorded indentation depth and the indentation force, it is possible to deduce mechanical parameters of the tested material. In this paper, a brief description of the high temperature device is given and representative results are presented. In the study, unirradiated steels are investigated by instrumented indentation at temperatures up to 500 °C. It is shown that the hardness is highly depending on the testing-temperature and can be correlated to the results of conventional tensile testing experiments. A not negligible influence of the indenter tip material is observed. The results show the functionality of the high-temperature indentation device.

  12. Influence of heat treatment and indenter tip material on depth sensing hardness tests at high temperatures of fusion relevant materials

    Energy Technology Data Exchange (ETDEWEB)

    Bredl, Julian, E-mail: julian.bredl@kit.edu; Dany, Manuel; Albinski, Bartlomiej; Schneider, Hans-Christian; Kraft, Oliver

    2015-10-15

    Highlights: • Operation of a custom-made indentation device designed for test temperatures up to 650 °C and a remote handled operation in a Hot Cell. • Instrumented indentation and conventional hardness testing of unirradiated MANET II and EUROFER. • Comparison of diamond and sapphire as indenter tip materials. - Abstract: The instrumented indentation is a suitable method for testing of even small neutron-irradiated specimens. From the continuously recorded indentation depth and the indentation force, it is possible to deduce mechanical parameters of the tested material. In this paper, a brief description of the high temperature device is given and representative results are presented. In the study, unirradiated steels are investigated by instrumented indentation at temperatures up to 500 °C. It is shown that the hardness is highly depending on the testing-temperature and can be correlated to the results of conventional tensile testing experiments. A not negligible influence of the indenter tip material is observed. The results show the functionality of the high-temperature indentation device.

  13. Performance of a high-resolution depth-encoding PET detector module using linearly-graded SiPM arrays

    Science.gov (United States)

    Du, Junwei; Bai, Xiaowei; Gola, Alberto; Acerbi, Fabio; Ferri, Alessandro; Piemonte, Claudio; Yang, Yongfeng; Cherry, Simon R.

    2018-02-01

    The goal of this study was to exploit the excellent spatial resolution characteristics of a position-sensitive silicon photomultiplier (SiPM) and develop a high-resolution depth-of-interaction (DOI) encoding positron emission tomography (PET) detector module. The detector consists of a 30  ×  30 array of 0.445  ×  0.445  ×  20 mm3 polished LYSO crystals coupled to two 15.5  ×  15.5 mm2 linearly-graded SiPM (LG-SiPM) arrays at both ends. The flood histograms show that all the crystals in the LYSO array can be resolved. The energy resolution, the coincidence timing resolution and the DOI resolution were 21.8  ±  5.8%, 1.23  ±  0.10 ns and 3.8  ±  1.2 mm, respectively, at a temperature of -10 °C and a bias voltage of 35.0 V. The performance did not degrade significantly for event rates of up to 130 000 counts s-1. This detector represents an attractive option for small-bore PET scanner designs that simultaneously emphasize high spatial resolution and high detection efficiency, important, for example, in preclinical imaging of the rodent brain with neuroreceptor ligands.

  14. Depth and breadth: Bridging the gap between scientific inquiry and high-stakes testing with diverse junior high school students

    Science.gov (United States)

    Kang, Jee Sun Emily

    This study explored how inquiry-based teaching and learning processes occurred in two teachers' diverse 8th grade Physical Science classrooms in a Program Improvement junior high school within the context of high-stakes standardized testing. Instructors for the courses examined included not only the two 8th grade science teachers, but also graduate fellows from a nearby university. Research was drawn from inquiry-based instruction in science education, the achievement gap, and the high stakes testing movement, as well as situated learning theory to understand how opportunities for inquiry were negotiated within the diverse classroom context. Transcripts of taped class sessions; student work samples; interviews of teachers and students; and scores from the California Standards Test in science were collected and analyzed. Findings indicated that the teachers provided structured inquiry in order to support their students in learning about forces and to prepare them for the standardized test. Teachers also supported students in generating evidence-based explanations, connecting inquiry-based investigations with content on forces, proficiently using science vocabulary, and connecting concepts about forces to their daily lives. Findings from classroom data revealed constraints to student learning: students' limited language proficiency, peer counter culture, and limited time. Supports were evidenced as well: graduate fellows' support during investigations, teachers' guided questioning, standardized test preparation, literacy support, and home-school connections. There was no statistical difference in achievement on the Forces Unit test or science standardized test between classes with graduate fellows and without fellows. There was also no statistical difference in student performance between the two teachers' classrooms, even though their teaching styles were very different. However, there was a strong correlation between students' achievement on the chapter test and

  15. Experimental validation of a 2D overland flow model using high resolution water depth and velocity data

    Science.gov (United States)

    Cea, L.; Legout, C.; Darboux, F.; Esteves, M.; Nord, G.

    2014-05-01

    This paper presents a validation of a two-dimensional overland flow model using empirical laboratory data. Unlike previous publications in which model performance is evaluated as the ability to predict an outlet hydrograph, we use high resolution 2D water depth and velocity data to analyze to what degree the model is able to reproduce the spatial distribution of these variables. Several overland flow conditions over two impervious surfaces of the order of one square meter with different micro and macro-roughness characteristics are studied. The first surface is a simplified representation of a sinusoidal terrain with three crests and furrows, while the second one is a mould of a real agricultural seedbed terrain. We analyze four different bed friction parameterizations and we show that the performance of formulations which consider the transition between laminar, smooth turbulent and rough turbulent flow do not improve the results obtained with Manning or Keulegan formulas for rough turbulent flow. The simulations performed show that using Keulegan formula with a physically-based definition of the bed roughness coefficient, a two-dimensional shallow water model is able to reproduce satisfactorily the flow hydrodynamics. It is shown that, even if the resolution of the topography data and numerical mesh are high enough to include all the small scale features of the bed surface, the roughness coefficient must account for the macro-roughness characteristics of the terrain in order to correctly reproduce the flow hydrodynamics.

  16. Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing.

    Directory of Open Access Journals (Sweden)

    Alexander C Outhred

    Full Text Available Improved tuberculosis control and the need to contain the spread of drug-resistant strains provide a strong rationale for exploring tuberculosis transmission dynamics at the population level. Whole-genome sequencing provides optimal strain resolution, facilitating detailed mapping of potential transmission pathways.We sequenced 22 isolates from a Mycobacterium tuberculosis cluster in New South Wales, Australia, identified during routine 24-locus mycobacterial interspersed repetitive unit typing. Following high-depth paired-end sequencing using the Illumina HiSeq 2000 platform, two independent pipelines were employed for analysis, both employing read mapping onto reference genomes as well as de novo assembly, to control biases in variant detection. In addition to single-nucleotide polymorphisms, the analyses also sought to identify insertions, deletions and structural variants.Isolates were highly similar, with a distance of 13 variants between the most distant members of the cluster. The most sensitive analysis classified the 22 isolates into 18 groups. Four of the isolates did not appear to share a recent common ancestor with the largest clade; another four isolates had an uncertain ancestral relationship with the largest clade.Whole genome sequencing, with analysis of single-nucleotide polymorphisms, insertions, deletions, structural variants and subpopulations, enabled the highest possible level of discrimination between cluster members, clarifying likely transmission pathways and exposing the complexity of strain origin. The analysis provides a basis for targeted public health intervention and enhanced classification of future isolates linked to the cluster.

  17. Determination of penetration depth at high velocity impact using finite element method and artificial neural network tools

    Directory of Open Access Journals (Sweden)

    Namık KılıÇ

    2015-06-01

    Full Text Available Determination of ballistic performance of an armor solution is a complicated task and evolved significantly with the application of finite element methods (FEM in this research field. The traditional armor design studies performed with FEM requires sophisticated procedures and intensive computational effort, therefore simpler and accurate numerical approaches are always worthwhile to decrease armor development time. This study aims to apply a hybrid method using FEM simulation and artificial neural network (ANN analysis to approximate ballistic limit thickness for armor steels. To achieve this objective, a predictive model based on the artificial neural networks is developed to determine ballistic resistance of high hardness armor steels against 7.62 mm armor piercing ammunition. In this methodology, the FEM simulations are used to create training cases for Multilayer Perceptron (MLP three layer networks. In order to validate FE simulation methodology, ballistic shot tests on 20 mm thickness target were performed according to standard Stanag 4569. Afterwards, the successfully trained ANN(s is used to predict the ballistic limit thickness of 500 HB high hardness steel armor. Results show that even with limited number of data, FEM-ANN approach can be used to predict ballistic penetration depth with adequate accuracy.

  18. 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...

  19. 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.

  20. Long range surface plasmon resonance with ultra-high penetration depth for self-referenced sensing and ultra-low detection limit using diverging beam approach

    Energy Technology Data Exchange (ETDEWEB)

    Isaacs, Sivan, E-mail: sivan.isaacs@gmail.com; Abdulhalim, Ibrahim [Department of Electro-Optical Engineering and TheIlse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva 84105 (Israel); NEW CREATE Programme, School of Materials Science and Engineering, 1 CREATE Way, Research Wing, #02-06/08, Singapore 138602 (Singapore)

    2015-05-11

    Using an insulator-metal-insulator structure with dielectric having refractive index (RI) larger than the analyte, long range surface plasmon (SP) resonance exhibiting ultra-high penetration depth is demonstrated for sensing applications of large bioentities at wavelengths in the visible range. Based on the diverging beam approach in Kretschmann-Raether configuration, one of the SP resonances is shown to shift in response to changes in the analyte RI while the other is fixed; thus, it can be used as a built in reference. The combination of the high sensitivity, high penetration depth and self-reference using the diverging beam approach in which a dark line is detected of the high sensitivity, high penetration depth, self-reference, and the diverging beam approach in which a dark line is detected using large number of camera pixels with a smart algorithm for sub-pixel resolution, a sensor with ultra-low detection limit is demonstrated suitable for large bioentities.

  1. 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.

  2. Development of a novel depth of interaction PET detector using highly multiplexed G-APD cross-strip encoding

    Energy Technology Data Exchange (ETDEWEB)

    Kolb, A., E-mail: armin.kolb@med.uni-tuebingen.de; Parl, C.; Liu, C. C.; Pichler, B. J. [Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University, 72076 Tübingen (Germany); Mantlik, F. [Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University, 72076 Tübingen, Germany and Department of Empirical Inference, Max Planck Institute for Intelligent Systems, 72076 Tübingen (Germany); Lorenz, E. [Max Planck Institute for Physics, Föhringer Ring 6, 80805 München (Germany); Renker, D. [Department of Physics, Technische Universität München, 85748 Garching (Germany)

    2014-08-15

    Purpose: The aim of this study was to develop a prototype PET detector module for a combined small animal positron emission tomography and magnetic resonance imaging (PET/MRI) system. The most important factor for small animal imaging applications is the detection sensitivity of the PET camera, which can be optimized by utilizing longer scintillation crystals. At the same time, small animal PET systems must yield a high spatial resolution. The measured object is very close to the PET detector because the bore diameter of a high field animal MR scanner is limited. When used in combination with long scintillation crystals, these small-bore PET systems generate parallax errors that ultimately lead to a decreased spatial resolution. Thus, we developed a depth of interaction (DoI) encoding PET detector module that has a uniform spatial resolution across the whole field of view (FOV), high detection sensitivity, compactness, and insensitivity to magnetic fields. Methods: The approach was based on Geiger mode avalanche photodiode (G-APD) detectors with cross-strip encoding. The number of readout channels was reduced by a factor of 36 for the chosen block elements. Two 12 × 2 G-APD strip arrays (25μm cells) were placed perpendicular on each face of a 12 × 12 lutetium oxyorthosilicate crystal block with a crystal size of 1.55 × 1.55 × 20 mm. The strip arrays were multiplexed into two channels and used to calculate the x, y coordinates for each array and the deposited energy. The DoI was measured in step sizes of 1.8 mm by a collimated {sup 18}F source. The coincident resolved time (CRT) was analyzed at all DoI positions by acquiring the waveform for each event and applying a digital leading edge discriminator. Results: All 144 crystals were well resolved in the crystal flood map. The average full width half maximum (FWHM) energy resolution of the detector was 12.8% ± 1.5% with a FWHM CRT of 1.14 ± 0.02 ns. The average FWHM DoI resolution over 12 crystals was 2.90

  3. 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.

  4. 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).

  5. [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.

  6. 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.

  7. Corneal ablation depth readout of the MEL 80 excimer laser compared to Artemis three-dimensional very high-frequency digital ultrasound stromal measurements.

    Science.gov (United States)

    Reinstein, Dan Z; Archer, Timothy J; Gobbe, Marine

    2010-12-01

    To evaluate the accuracy of the ablation depth readout for the MEL 80 excimer laser (Carl Zeiss Meditec). Artemis 1 very high-frequency digital ultrasound measurements were obtained before and at least 3 months after LASIK in 121 eyes (65 patients). The Artemis-measured ablation depth was calculated as the maximum difference in stromal thickness before and after treatment. Laser in situ keratomileusis was performed using the MEL 80 excimer laser and the Hansatome microkeratome (Bausch & Lomb). The Aberration Smart Ablation profile was used in 56 eyes and the Tissue Saving Ablation profile was used in 65 eyes. All ablations were centered on the corneal vertex. Comparative statistics and linear regression analysis were performed between the laser readout ablation depth and Artemis-measured ablation depth. The mean maximum myopic meridian was -6.66±2.40 diopters (D) (range: -1.50 to -10.00 D) for Aberration Smart Ablation-treated eyes and -6.50±2.56 D (range: -1.34 to -11.50 D) for Tissue Saving Ablation-treated eyes. The MEL 80 readout was found to overestimate the Artemis-measured ablation depth by 20±12 μm for Aberration Smart Ablation and by 21±12 μm for Tissue Saving Ablation profiles. The accuracy of ablation depth measurement was improved by using the Artemis stromal thickness profile measurements before and after surgery to exclude epithelial changes. The MEL 80 readout was found to overestimate the achieved ablation depth. The linear regression equations could be used by MEL 80 users to adjust the ablation depth for predicted residual stromal thickness calculations without increasing the risk of ectasia due to excessive keratectomy depth as long as a suitable flap thickness bias is included. Copyright 2010, SLACK Incorporated.

  8. Assessment of nocturnal aerosol optical depth from lunar photometry at the Izaña high mountain observatory

    Directory of Open Access Journals (Sweden)

    Á. Barreto

    2017-08-01

    Full Text Available This work is a first approach to correct the systematic errors observed in the aerosol optical depth (AOD retrieved at nighttime using lunar photometry and calibration techniques dependent on the lunar irradiance model. To this end, nocturnal AOD measurements were performed in 2014 using the CE318-T master Sun–sky–lunar photometer (lunar Langley calibrated at the Izaña high mountain observatory. This information has been restricted to 59 nights characterized as clean and stable according to lidar vertical profiles. A phase angle dependence as well as an asymmetry within the Moon's cycle of the Robotic Lunar Observatory (ROLO model could be deduced from the comparison in this 59-night period of the CE318-T calibration performed by means of the lunar Langley calibration and the calibration performed every single night by means of the common Langley technique. Nocturnal AOD has also been compared in the same period with a reference AOD based on daylight AOD extracted from the AErosol RObotic NETwork (AERONET at the same station. Considering stable conditions, the difference ΔAODfit, between AOD from lunar observations and the linearly interpolated AOD (the reference from daylight data, has been calculated. The results show that ΔAODfit values are strongly affected by the Moon phase and zenith angles. This dependency has been parameterized using an empirical model with two independent variables (Moon phase and zenith angles in order to correct the AOD for these residual dependencies. The correction of this parameterized dependency has been checked at four stations with quite different environmental conditions (Izaña, Lille, Carpentras and Dakar showing a significant reduction of the AOD dependence on phase and zenith angles and an improved agreement with daylight reference data. After the correction, absolute AOD differences for day–night–day clean and stable transitions remain below 0.01 for all wavelengths.

  9. Complexity and Dynamical Depth

    Directory of Open Access Journals (Sweden)

    Terrence Deacon

    2014-07-01

    Full Text Available We argue that a critical difference distinguishing machines from organisms and computers from brains is not complexity in a structural sense, but a difference in dynamical organization that is not well accounted for by current complexity measures. We propose a measure of the complexity of a system that is largely orthogonal to computational, information theoretic, or thermodynamic conceptions of structural complexity. What we call a system’s dynamical depth is a separate dimension of system complexity that measures the degree to which it exhibits discrete levels of nonlinear dynamical organization in which successive levels are distinguished by local entropy reduction and constraint generation. A system with greater dynamical depth than another consists of a greater number of such nested dynamical levels. Thus, a mechanical or linear thermodynamic system has less dynamical depth than an inorganic self-organized system, which has less dynamical depth than a living system. Including an assessment of dynamical depth can provide a more precise and systematic account of the fundamental difference between inorganic systems (low dynamical depth and living systems (high dynamical depth, irrespective of the number of their parts and the causal relations between them.

  10. 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.

  11. Variation of Pressure with Depth of Water: Working with High-Tech and Low-Cost Materials

    Science.gov (United States)

    Ornek, Funda; Zziwa, Byansi Jude; Taganahan, Teresita D.

    2013-01-01

    When you dive underwater, you feel the pressure on your ears and, as you dive deeper, more pressure is felt. This article presents an activity that teachers might find useful for demonstrating the relationship between water depth and pressure. (Contains 5 figures and 1 table.)

  12. Using high-resolution satellite aerosol optical depth to estimate daily PM2.5 geographical distribution in Mexico City

    OpenAIRE

    Just, Allan C.; Wright, Robert O.; Schwartz, Joel; Coull, Brent A.; Baccarelli, Andrea A.; Tellez-Rojo, Martha María; Moody, Emily; Wang, Yujie; Lyapustin, Alexei; Kloog, Itai

    2015-01-01

    Recent advances in estimating fine particle (PM2.5) ambient concentrations use daily satellite measurements of aerosol optical depth (AOD) for spatially and temporally resolved exposure estimates. Mexico City is a dense megacity that differs from other previously modeled regions in several ways: it has bright land surfaces, a distinctive climatological cycle, and an elevated semi-enclosed air basin with a unique planetary boundary layer dynamic. We extend our previous satellite methodology to...

  13. Linking carbon and nitrogen metabolism to depth distribution of submersed macrophytes using high ammonium dosing tests and a lake survey.

    Science.gov (United States)

    Yuan, Guixiang; Cao, Te; Fu, Hui; Ni, Leyi; Zhang, Xiaolin; Li, Wei; Song, Xin; Xie, Ping; Jeppesen, Erik

    2013-12-01

    Strategies of carbon (C) and nitrogen (N) utilisation are among the factors determining plant distribution. It has been argued that submersed macrophytes adapted to lower light environments are more efficient in maintaining C metabolic homeostasis due to their conservative C strategy and ability to balance C shortage. We studied how depth distributions of 12 submersed macrophytes in Lake Erhai, China, were linked to their C-N metabolic strategies when facing acute [Formula: see text] dosing.[Formula: see text] dosing changed C-N metabolism significantly by decreasing the soluble carbohydrate (SC) content and increasing the [Formula: see text]-N and free amino acid (FAA) content of plant tissues.The proportional changes in SC contents in the leaves and FAA contents in the stems induced by [Formula: see text] dosing were closely correlated (positive for SC and negative for FAA) with the colonising water depths of the plants in Lake Erhai, the plants adapted to lower light regimes being more efficient in maintaining SC and FAA homeostasis.These results indicate that conservative carbohydrate metabolism of submersed macrophytes allowed the plants to colonise greater water depths in eutrophic lakes, where low light availability in the water column diminishes carbohydrate production by the plants.

  14. 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.

  15. 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

  16. Correlation of Foreshock Occurrence with Mainshock Depth, Rake, and Magnitude from the High Precision Catalog for Northern California

    Science.gov (United States)

    Schaff, D. P.; Waldhauser, F.; Lerner-Lam, A.

    2010-12-01

    Foreshocks are perhaps the best-documented and most undisputed precursors to some large earthquakes. The question remains, however, if foreshocks have any more predictive power for future mainshocks than any other earthquake. Several researchers argue for a single unifying triggering law for foreshocks, mainshocks, and aftershocks. An alternate model is that foreshocks are the byproduct of an aseismic pre-slip phase that scales with mainshock magnitude. In this case foreshocks are different than other earthquakes and have predictive value for the mainshock location, origin time, and magnitude. We examine 612 mainshocks with M ≥ 4 from the cross-correlation double-difference catalog for northern California. 235 (44%) of these had foreshock sequences, providing us with a data set more than an order of magnitude larger than those used in previous studies. We are able to confirm with improved accuracy correlations of foreshock occurrence and characteristics with depth. The proportion of mainshocks with associated foreshocks, the number of foreshocks in the sequence, the foreshock duration, and the foreshock radius in map view all decrease with increasing depth, all with statistical significance above 95%. This supports models where increasing normal stress due to lithostatic load inhibits foreshock occurrence. Other M ≥ 4 events that were classified as aftershocks of larger events did not show the depth dependence. However, our analysis does not confirm a previous observation that increased normal stress due to tectonic loading appears to inhibit foreshock occurrence. We observe a negative correlation of foreshock magnitude with foreshock duration which is consistent with a model of mainshocks triggered by increased pore pressure. We observe a statistically significant relationship between foreshock magnitude and mainshock magnitude, lending support to the pre-slip model.

  17. Out of their depth? Isolated deep populations of the cosmopolitan coral Desmophyllum dianthus may be highly vulnerable to environmental change.

    Directory of Open Access Journals (Sweden)

    Karen J Miller

    Full Text Available Deep sea scleractinian corals will be particularly vulnerable to the effects of climate change, facing loss of up to 70% of their habitat as the Aragonite Saturation Horizon (below which corals are unable to form calcium carbonate skeletons rises. Persistence of deep sea scleractinian corals will therefore rely on the ability of larvae to disperse to, and colonise, suitable shallow-water habitat. We used DNA sequence data of the internal transcribed spacer (ITS, the mitochondrial ribosomal subunit (16S and mitochondrial control region (MtC to determine levels of gene flow both within and among populations of the deep sea coral Desmophyllum dianthus in SE Australia, New Zealand and Chile to assess the ability of corals to disperse into different regions and habitats. We found significant genetic subdivision among the three widely separated geographic regions consistent with isolation and limited contemporary gene flow. Furthermore, corals from different depth strata (shallow 1500 m even on the same or nearby seamounts were strongly differentiated, indicating limited vertical larval dispersal. Genetic differentiation with depth is consistent with the stratification of the Subantarctic Mode Water, Antarctic Intermediate Water, the Circumpolar Deep and North Pacific Deep Waters in the Southern Ocean, and we propose that coral larvae will be retained within, and rarely migrate among, these water masses. The apparent absence of vertical larval dispersal suggests deep populations of D. dianthus are unlikely to colonise shallow water as the aragonite saturation horizon rises and deep waters become uninhabitable. Similarly, assumptions that deep populations will act as refuges for shallow populations that are impacted by activities such as fishing or mining are also unlikely to hold true. Clearly future environmental management strategies must consider both regional and depth-related isolation of deep-sea coral populations.

  18. Out of their depth? Isolated deep populations of the cosmopolitan coral Desmophyllum dianthus may be highly vulnerable to environmental change.

    Science.gov (United States)

    Miller, Karen J; Rowden, Ashley A; Williams, Alan; Häussermann, Vreni

    2011-01-01

    Deep sea scleractinian corals will be particularly vulnerable to the effects of climate change, facing loss of up to 70% of their habitat as the Aragonite Saturation Horizon (below which corals are unable to form calcium carbonate skeletons) rises. Persistence of deep sea scleractinian corals will therefore rely on the ability of larvae to disperse to, and colonise, suitable shallow-water habitat. We used DNA sequence data of the internal transcribed spacer (ITS), the mitochondrial ribosomal subunit (16S) and mitochondrial control region (MtC) to determine levels of gene flow both within and among populations of the deep sea coral Desmophyllum dianthus in SE Australia, New Zealand and Chile to assess the ability of corals to disperse into different regions and habitats. We found significant genetic subdivision among the three widely separated geographic regions consistent with isolation and limited contemporary gene flow. Furthermore, corals from different depth strata (shallow 1500 m) even on the same or nearby seamounts were strongly differentiated, indicating limited vertical larval dispersal. Genetic differentiation with depth is consistent with the stratification of the Subantarctic Mode Water, Antarctic Intermediate Water, the Circumpolar Deep and North Pacific Deep Waters in the Southern Ocean, and we propose that coral larvae will be retained within, and rarely migrate among, these water masses. The apparent absence of vertical larval dispersal suggests deep populations of D. dianthus are unlikely to colonise shallow water as the aragonite saturation horizon rises and deep waters become uninhabitable. Similarly, assumptions that deep populations will act as refuges for shallow populations that are impacted by activities such as fishing or mining are also unlikely to hold true. Clearly future environmental management strategies must consider both regional and depth-related isolation of deep-sea coral populations.

  19. Deepest Depth of Seismogenic Layer Within the Crust Beneath Japanese Islands on the Japan Sea Side Using High Resolved Earthquake Catalog and Heat Flux Data

    Science.gov (United States)

    Matsubara, M.; Yano, T. E.

    2017-12-01

    Understanding the deepest depth of seismogenic layer is important parameter for the earthquake hazard assessment because this relates to the size of earthquakes caused by the active fault. Using the indexes D90 and D95, defined as the depth above which 90% and 95 % of the whole crustal earthquakes occurred from the surface, as the lower limits of the seismogenic layer. We verified the seismogenic depth for particular earthquakes on the Japan Sea side occurred after the year of 2001. We compared with the actual main shock hypocenter depth, their aftershocks, main slip region on the fault, and depth where the temperature estimated to be 250, 300, and 450 degrees. For D90 and D95, we used two different earthquake catalogs. First, the catalog in which we relocated hypocenters for 12 years between 2001 and 2012 from the NIED Hi-net catalog (JUICE catalog, Yano et al. 2017) for high resolution hypocenter locations (Depth 0.0). This catalog is used to get D95 values. Second, the earthquake catalog redetermined with the 3D velocity structure (Matsubara and Obara, 2011) particularly for getting the D90 value around the costal region. In order to satisfy Gutenberg-Richter magnitude-frequency relation, we chose events M>1.5. We then calculated the D90 and D95 using the same method as Matsubara and Sato (2015). For depths where the temperatures are 250, 300, and 450 degrees are estimated from heat flux measured at Hi-net boreholes (Matsumoto, 2007) and other additional data Sakagawa et al. (2005). Depths are calculated using the steady-state, one-dimensional, heat conduction equation with an exponential decrease in the radioactivity heat generation introduced in Tanaka (2004). The general pattern of our results is consistent with previous studies of D90 as very deep D95 beneath the northern Hokkaido and northern Honshu and very shallow D95 along the volcanic front. We found that our D90/D95 showed the deepest boundary of hypocenter of mainshock, majority of aftershocks, main

  20. Prestack depth migration

    International Nuclear Information System (INIS)

    Postma, R.W.

    1991-01-01

    Two lines form the southern North Sea, with known velocity inhomogeneities in the overburden, have been pre-stack depth migrated. The pre-stack depth migrations are compared with conventional processing, one with severe distortions and one with subtle distortions on the conventionally processed sections. The line with subtle distortions is also compared with post-stack depth migration. The results on both lines were very successful. Both have already influenced drilling decisions, and have caused a modification of structural interpretation in the respective areas. Wells have been drilled on each of the lines, and well tops confirm the results. In fact, conventional processing led to incorrect locations for the wells, both of which were dry holes. The depth migrated sections indicate the incorrect placement, and on one line reveals a much better drilling location. This paper reports that even though processing costs are high for pre-stack depth migration, appropriate use can save millions of dollars in dry-hole expense

  1. Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic

    DEFF Research Database (Denmark)

    Mundra, Sunil; Halvorsen, Rune; Kauserud, Håvard

    2016-01-01

    on the variation in species richness and community structure of ectomycorrhizal (ECM) and saprotrophic fungi. Soil samples were collected weekly from mid-July to mid-September in both control and deep snow plots. Richness of ECM fungi was lower, while saprotrophic fungi was higher in increased snow depth plots...... relative to controls. [Correction added on 23 September 2016 after first online publication: In the preceding sentence, the richness of ECM and saprotrophic fungi were wrongly interchanged and have been fixed in this current version.] ECM fungal richness was related to soil NO3-N, NH4-N, and K......; and saprotrophic fungi to NO3-N and pH. Small but significant changes in the composition of saprotrophic fungi could be attributed to snow treatment and sampling time, but not so for the ECM fungi. Delayed snow melt did not influence the temporal variation in fungal communities between the treatments. Results...

  2. Combining target enrichment with barcode multiplexing for high throughput SNP discovery

    Directory of Open Access Journals (Sweden)

    Lunke Sebastian

    2010-11-01

    Full Text Available Abstract Background The primary goal of genetic linkage analysis is to identify genes affecting a phenotypic trait. After localisation of the linkage region, efficient genetic dissection of the disease linked loci requires that functional variants are identified across the loci. These functional variations are difficult to detect due to extent of genetic diversity and, to date, incomplete cataloguing of the large number of variants present both within and between populations. Massively parallel sequencing platforms offer unprecedented capacity for variant discovery, however the number of samples analysed are still limited by cost per sample. Some progress has been made in reducing the cost of resequencing using either multiplexing methodologies or through the utilisation of targeted enrichment technologies which provide the ability to resequence genomic areas of interest rather that full genome sequencing. Results We developed a method that combines current multiplexing methodologies with a solution-based target enrichment method to further reduce the cost of resequencing where region-specific sequencing is required. Our multiplex/enrichment strategy produced high quality data with nominal reduction of sequencing depth. We undertook a genotyping study and were successful in the discovery of novel SNP alleles in all samples at uniplex, duplex and pentaplex levels. Conclusion Our work describes the successful combination of a targeted enrichment method and index barcode multiplexing to reduce costs, time and labour associated with processing large sample sets. Furthermore, we have shown that the sequencing depth obtained is adequate for credible SNP genotyping analysis at uniplex, duplex and pentaplex levels.

  3. Toward improved prediction of the bedrock depth underneath hillslopes: Bayesian inference of the bottom-up control hypothesis using high-resolution topographic data

    Science.gov (United States)

    Gomes, Guilherme J. C.; Vrugt, Jasper A.; Vargas, Eurípedes A.

    2016-04-01

    The depth to bedrock controls a myriad of processes by influencing subsurface flow paths, erosion rates, soil moisture, and water uptake by plant roots. As hillslope interiors are very difficult and costly to illuminate and access, the topography of the bedrock surface is largely unknown. This essay is concerned with the prediction of spatial patterns in the depth to bedrock (DTB) using high-resolution topographic data, numerical modeling, and Bayesian analysis. Our DTB model builds on the bottom-up control on fresh-bedrock topography hypothesis of Rempe and Dietrich (2014) and includes a mass movement and bedrock-valley morphology term to extent the usefulness and general applicability of the model. We reconcile the DTB model with field observations using Bayesian analysis with the DREAM algorithm. We investigate explicitly the benefits of using spatially distributed parameter values to account implicitly, and in a relatively simple way, for rock mass heterogeneities that are very difficult, if not impossible, to characterize adequately in the field. We illustrate our method using an artificial data set of bedrock depth observations and then evaluate our DTB model with real-world data collected at the Papagaio river basin in Rio de Janeiro, Brazil. Our results demonstrate that the DTB model predicts accurately the observed bedrock depth data. The posterior mean DTB simulation is shown to be in good agreement with the measured data. The posterior prediction uncertainty of the DTB model can be propagated forward through hydromechanical models to derive probabilistic estimates of factors of safety.

  4. Breaking the Crowther limit: Combining depth-sectioning and tilt tomography for high-resolution, wide-field 3D reconstructions

    Energy Technology Data Exchange (ETDEWEB)

    Hovden, Robert, E-mail: rmh244@cornell.edu [School of Applied and Engineering Physics and Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 (United States); Ercius, Peter [National Center for Electron Microscopy, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Jiang, Yi [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Wang, Deli; Yu, Yingchao; Abruña, Héctor D. [Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (United States); Elser, Veit [Department of Physics, Cornell University, Ithaca, NY 14853 (United States); Muller, David A. [School of Applied and Engineering Physics and Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853 (United States)

    2014-05-01

    To date, high-resolution (<1 nm) imaging of extended objects in three-dimensions (3D) has not been possible. A restriction known as the Crowther criterion forces a tradeoff between object size and resolution for 3D reconstructions by tomography. Further, the sub-Angstrom resolution of aberration-corrected electron microscopes is accompanied by a greatly diminished depth of field, causing regions of larger specimens (>6 nm) to appear blurred or missing. Here we demonstrate a three-dimensional imaging method that overcomes both these limits by combining through-focal depth sectioning and traditional tilt-series tomography to reconstruct extended objects, with high-resolution, in all three dimensions. The large convergence angle in aberration corrected instruments now becomes a benefit and not a hindrance to higher quality reconstructions. A through-focal reconstruction over a 390 nm 3D carbon support containing over 100 dealloyed and nanoporous PtCu catalyst particles revealed with sub-nanometer detail the extensive and connected interior pore structure that is created by the dealloying instability. - Highlights: • Develop tomography technique for high-resolution and large field of view. • We combine depth sectioning with traditional tilt tomography. • Through-focal tomography reduces tilts and improves resolution. • Through-focal tomography overcomes the fundamental Crowther limit. • Aberration-corrected becomes a benefit and not a hindrance for tomography.

  5. Using High-Resolution Satellite Aerosol Optical Depth To Estimate Daily PM2.5 Geographical Distribution in Mexico City.

    Science.gov (United States)

    Just, Allan C; Wright, Robert O; Schwartz, Joel; Coull, Brent A; Baccarelli, Andrea A; Tellez-Rojo, Martha María; Moody, Emily; Wang, Yujie; Lyapustin, Alexei; Kloog, Itai

    2015-07-21

    Recent advances in estimating fine particle (PM2.5) ambient concentrations use daily satellite measurements of aerosol optical depth (AOD) for spatially and temporally resolved exposure estimates. Mexico City is a dense megacity that differs from other previously modeled regions in several ways: it has bright land surfaces, a distinctive climatological cycle, and an elevated semi-enclosed air basin with a unique planetary boundary layer dynamic. We extend our previous satellite methodology to the Mexico City area, a region with higher PM2.5 than most U.S. and European urban areas. Using a novel 1 km resolution AOD product from the MODIS instrument, we constructed daily predictions across the greater Mexico City area for 2004-2014. We calibrated the association of AOD to PM2.5 daily using municipal ground monitors, land use, and meteorological features. Predictions used spatial and temporal smoothing to estimate AOD when satellite data were missing. Our model performed well, resulting in an out-of-sample cross-validation R(2) of 0.724. Cross-validated root-mean-squared prediction error (RMSPE) of the model was 5.55 μg/m(3). This novel model reconstructs long- and short-term spatially resolved exposure to PM2.5 for epidemiological studies in Mexico City.

  6. Nutrients, High Light and Shallow Depths Favor the Expansion of the Brown Macroalgae Turbinaria ornata in the Coral Reefs of Mo'orea, French Polynesia

    Science.gov (United States)

    Nieves, M.; Cordoba, G.; Rogers, J.

    2016-02-01

    Coral reefs provide food, recreation and economic resources for billions of people. Despite this importance, anthropogenic stressors including climate change and nutrification threaten coral reefs globally, causing phase-shifts to algal dominated ecosystems and loss of coral habitats. Throughout the tropical South Pacific, the brown macroalgae Turbinaria ornata is expanding its range and now dominates areas where corals used to thrive, especially shallow areas on fringing reefs of French Polynesia. Abiotic factors like light and nutrient availability could enhance the expansion of T. ornata by promoting its growth or by making it physically tougher, which could reduce herbivory pressure and enhance its survival in high energy zones. To understand the abiotic factors favoring growth and survival of T. ornata in Mo'orea, French Polynesia, we conducted a field experiment testing the effect of nutrients (+/- fertilizer), depth (1m within Turbinaria zone, 1.5m at border, 2m below depth distribution), and light (+/- shade) on the growth and toughness of T. ornata. Three-factor ANOVA showed that an interaction between nutrients and light favored T. ornata biomass accumulation (p=0.04). In addition, T. ornata from shallow depths were significantly tougher than those at intermediate depths (p=0.01). These results imply that nutrient enrichment combined with high light levels common in shallow coral reefs may promote growth and expansion of T. ornata to near-shore reef environments. Increased survival and population growth is likely further enhanced by increased toughness of T. ornata in shallow areas, which may limit herbivore grazing and improve survival in strong wave action or currents. Future research should examine whether reducing nutrient loading to coastal waters may limit the expansion of T. ornata in the South Pacific.

  7. 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.

  8. All-fiber probe for optical coherence tomography with an extended depth of focus by a high-efficient fiber-based filter

    Science.gov (United States)

    Qiu, Jianrong; Shen, Yi; Shangguan, Ziwei; Bao, Wen; Yang, Shanshan; Li, Peng; Ding, Zhihua

    2018-04-01

    Although methods have been proposed to maintain high transverse resolution over an increased depth range, it is not straightforward to scale down the bulk-optic solutions to minimized probes of optical coherence tomography (OCT). In this paper, we propose a high-efficient fiber-based filter in an all-fiber OCT probe to realize an extended depth of focus (DOF) while maintaining a high transverse resolution. Mode interference in the probe is exploited to modulate the complex field with controllable radial distribution. The principle of DOF extension by the fiber-based filter is theoretically analyzed. Numerical simulations are conducted to evaluate the performances of the designed probes. A DOF extension ratio of 2.6 over conventional Gaussian beam is obtainable in one proposed probe under a focused beam diameter of 4 . 6 μm. Coupling efficiencies of internal interfaces of the proposed probe are below -40 dB except the last probe-air interface, which can also be depressed to be -44 dB after minor modification in lengths for the filter. Length tolerance of the proposed probe is determined to be - 28 / + 20 μm, which is readily satisfied in fabrication. With the merits of extended-DOF, high-resolution, high-efficiency and easy-fabrication, the proposed probe is promising in endoscopic applications.

  9. Construction of System for Seismic Observation in Deep Borehole (SODB) - Development of Multi-depth, High-temperature/pressure resistance seismometer

    International Nuclear Information System (INIS)

    Mamada, Yutaka

    2014-01-01

    The development of a high quality system for seismic observation in deep boreholes, the installation process at the NIIT site, and the data sharing plan for this observation were explained. The key points of the development were high temperature resistance (150 degrees Celsius), high pressure resistance (30 MPa), and a high dynamic/wide frequency range seismometer which allows for observation of micro-tremor to strong motions as well as a cascade-connection-type borehole seismometer, which allows multiple probes to be set at several depths in a single borehole. The developed system consists of broadband (0.1-50 Hz) and high dynamic range (up to 1000 gal) seismometer with electronic parts on the ground and only the pendulum part in the borehole (it became a servo-type seismometer). Durability and maintenance may be issues in the future. (author)

  10. Measurement and modeling of the low-temperature penetration-depth anomaly in high-quality MgB{sub 2} thin films

    Energy Technology Data Exchange (ETDEWEB)

    Agassi, Y.D. [Naval Surface Warfare Center, Carderock Division, Bethesda, MD 20817 (United States); Oates, D.E., E-mail: OATES@LL.MIT.EDU [MIT-Lincoln Laboratory, Lexington, MA 02420 (United States); Moeckly, B.H. [STI, Inc. Santa Barbara, CA 93111 (United States)

    2012-10-15

    Based on our measurements of intermodulation distortion in MgB{sub 2}, we have previously proposed that the {pi} energy-gap in MgB{sub 2} entails six nodal lines [Y.D. Agassi, D.E. Oates, and B.H. Moeckly, Phys. Rev. B 80 (2009) 174522]. Here we report high-precision measurements in MgB{sub 2} stripline resonators that show an increase of the penetration depth as the temperature is decreased below 5 K. This increase is consistent with the Script-Small-L = 6 symmetry of the {pi} energy gap that we have proposed. We interpret the increase as a manifestation of Andreev surface-attached states that are associated with the nodal lines of the {pi} energy gap. Penetration-depth calculations are in good agreement with our data. To reconcile the present interpretation with existing literature, we review other penetration-depth data, magnetic-impurity and tunneling experiments, and data on the paramagnetic Meissner effect. We conclude that these data do not rule out the interpretation of our experimental data based on a nodal {pi} energy gap.

  11. 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.

  12. Combined UHV/high-pressure catalysis setup for depth-resolved near-surface spectroscopic characterization and catalytic testing of model catalysts

    International Nuclear Information System (INIS)

    Mayr, Lukas; Klötzer, Bernhard; Penner, Simon; Rameshan, Raffael; Rameshan, Christoph

    2014-01-01

    An ultra-high vacuum (UHV) setup for “real” and “inverse” model catalyst preparation, depth-resolved near-surface spectroscopic characterization, and quantification of catalytic activity and selectivity under technologically relevant conditions is described. Due to the all-quartz reactor attached directly to the UHV-chamber, transfer of the catalyst for in situ testing without intermediate contact to the ambient is possible. The design of the UHV-compatible re-circulating batch reactor setup allows the study of reaction kinetics under close to technically relevant catalytic conditions up to 1273 K without contact to metallic surfaces except those of the catalyst itself. With the attached differentially pumped exchangeable evaporators and the quartz-microbalance thickness monitoring equipment, a reproducible, versatile, and standardised sample preparation is possible. For three-dimensional near-surface sample characterization, the system is equipped with a hemispherical analyser for X-ray photoelectron spectroscopy (XPS), electron-beam or X-ray-excited Auger-electron spectroscopy, and low-energy ion scattering measurements. Due the dedicated geometry of the X-ray gun (54.7°, “magic angle”) and the rotatable sample holder, depth analysis by angle-resolved XPS measurements can be performed. Thus, by the combination of characterisation methods with different information depths, a detailed three-dimensional picture of the electronic and geometric structure of the model catalyst can be obtained. To demonstrate the capability of the described system, comparative results for depth-resolved sample characterization and catalytic testing in methanol steam reforming on PdGa and PdZn near-surface intermetallic phases are shown

  13. Combined UHV/high-pressure catalysis setup for depth-resolved near-surface spectroscopic characterization and catalytic testing of model catalysts

    Science.gov (United States)

    Mayr, Lukas; Rameshan, Raffael; Klötzer, Bernhard; Penner, Simon; Rameshan, Christoph

    2014-05-01

    An ultra-high vacuum (UHV) setup for "real" and "inverse" model catalyst preparation, depth-resolved near-surface spectroscopic characterization, and quantification of catalytic activity and selectivity under technologically relevant conditions is described. Due to the all-quartz reactor attached directly to the UHV-chamber, transfer of the catalyst for in situ testing without intermediate contact to the ambient is possible. The design of the UHV-compatible re-circulating batch reactor setup allows the study of reaction kinetics under close to technically relevant catalytic conditions up to 1273 K without contact to metallic surfaces except those of the catalyst itself. With the attached differentially pumped exchangeable evaporators and the quartz-microbalance thickness monitoring equipment, a reproducible, versatile, and standardised sample preparation is possible. For three-dimensional near-surface sample characterization, the system is equipped with a hemispherical analyser for X-ray photoelectron spectroscopy (XPS), electron-beam or X-ray-excited Auger-electron spectroscopy, and low-energy ion scattering measurements. Due the dedicated geometry of the X-ray gun (54.7°, "magic angle") and the rotatable sample holder, depth analysis by angle-resolved XPS measurements can be performed. Thus, by the combination of characterisation methods with different information depths, a detailed three-dimensional picture of the electronic and geometric structure of the model catalyst can be obtained. To demonstrate the capability of the described system, comparative results for depth-resolved sample characterization and catalytic testing in methanol steam reforming on PdGa and PdZn near-surface intermetallic phases are shown.

  14. Validation of calculated tissue maximum ratio obtained from measured percentage depth dose (PPD) data for high energy photon beam ( 6 MV and 15 MV)

    International Nuclear Information System (INIS)

    Osei, J.E.

    2014-07-01

    During external beam radiotherapy treatments, high doses are delivered to the cancerous cell. Accuracy and precision of dose delivery are primary requirements for effective and efficiency in treatment. This leads to the consideration of treatment parameters such as percentage depth dose (PDD), tissue air ratio (TAR) and tissue phantom ratio (TPR), which show the dose distribution in the patient. Nevertheless, tissue air ratio (TAR) for treatment time calculation, calls for the need to measure in-air-dose rate. For lower energies, measurement is not a problem but for higher energies, in-air measurement is not attainable due to the large build-up material required for the measurement. Tissue maximum ratio (TMR) is the quantity required to replace tissue air ratio (TAR) for high energy photon beam. It is known that tissue maximum ratio (TMR) is an important dosimetric function in radiotherapy treatment. As the calculation methods used to determine tissue maximum ratio (TMR) from percentage depth dose (PDD) were derived by considering the differences between TMR and PDD such as geometry and field size, where phantom scatter or peak scatter factors are used to correct dosimetric variation due to field size difference. The purpose of this study is to examine the accuracy of calculated tissue maximum ratio (TMR) data with measured TMR values for 6 MV and 15 MV photon beam at Sweden Ghana Medical Centre. With the help of the Blue motorize water phantom and the Omni pro-Accept software, Pdd values from which TMRs are calculated were measured at 100 cm source-to-surface distance (SSD) for various square field sizes from 5x5 cm to 40x40 cm and depth of 1.5 cm to 25 cm for 6 MV and 15 MV x-ray beam. With the same field sizes, depths and energies, the TMR values were measured. The validity of the calculated data was determined by making a comparison with values measured experimentally at some selected field sizes and depths. The results show that; the reference depth of maximum

  15. 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

  16. An in-depth look at the lunar crater Copernicus: Exposed mineralogy by high-resolution near-infrared spectroscopy

    Science.gov (United States)

    Bugiolacchi, Roberto; Mall, Urs; Bhatt, Megha; McKenna-Lawlor, Susan; Banaszkiewicz, Marek; Brønstad, Kjell; Nathues, Andreas; Søraas, Finn; Ullaland, Kjetil; Pedersen, Rolf B.

    2011-05-01

    Newly acquired, sequentially spaced, high-resolution near-infrared spectra across the central section of crater Copernicus' interior have been analyzed using a range of complementary techniques and indexes. We have developed a new interpretative method based on a multiple stage normalization process that appears to both confirm and expand on previous mineralogical estimations and mapping. In broad terms, the interpreted distribution of the principle mafic species suggests an overall composition of surface materials dominated by calcium-poor pyroxenes and minor olivine but with notable exceptions: the southern rim displays strong ca-rich pyroxene absorption features and five other locations, the uppermost northern crater wall, opposite rim sections facing the crater floor, and the central peak Pk1 and at the foot of Pk3, show instead strong olivine signatures. We also propose impact glass an alternative interpretation to the source of the weak but widespread olivine-like spectral signature found in low-reflectance samples, since it probably represents a major regolith constituent and component in large craters such as Copernicus. The high quality and performance of the SIR-2 data allows for the detection of diagnostic key mineral species even when investigating spectral samples with very subdued absorption features, confirming the intrinsic high-quality value of the returned data.

  17. Radiation production and absorption in human spacecraft shielding systems under high charge and energy Galactic Cosmic Rays: Material medium, shielding depth, and byproduct aspects

    Science.gov (United States)

    Barthel, Joseph; Sarigul-Klijn, Nesrin

    2018-03-01

    Deep space missions such as the planned 2025 mission to asteroids require spacecraft shields to protect electronics and humans from adverse effects caused by the space radiation environment, primarily Galactic Cosmic Rays. This paper first reviews the theory on how these rays of charged particles interact with matter, and then presents a simulation for a 500 day Mars flyby mission using a deterministic based computer code. High density polyethylene and aluminum shielding materials at a solar minimum are considered. Plots of effective dose with varying shield depth, charged particle flux, and dose in silicon and human tissue behind shielding are presented.

  18. Breaking the Crowther limit: Combining depth-sectioning and tilt tomography for high-resolution, wide-field 3D reconstructions

    International Nuclear Information System (INIS)

    Hovden, Robert; Ercius, Peter; Jiang, Yi; Wang, Deli; Yu, Yingchao; Abruña, Héctor D.; Elser, Veit; Muller, David A.

    2014-01-01

    To date, high-resolution ( 6 nm) to appear blurred or missing. Here we demonstrate a three-dimensional imaging method that overcomes both these limits by combining through-focal depth sectioning and traditional tilt-series tomography to reconstruct extended objects, with high-resolution, in all three dimensions. The large convergence angle in aberration corrected instruments now becomes a benefit and not a hindrance to higher quality reconstructions. A through-focal reconstruction over a 390 nm 3D carbon support containing over 100 dealloyed and nanoporous PtCu catalyst particles revealed with sub-nanometer detail the extensive and connected interior pore structure that is created by the dealloying instability. - Highlights: • Develop tomography technique for high-resolution and large field of view. • We combine depth sectioning with traditional tilt tomography. • Through-focal tomography reduces tilts and improves resolution. • Through-focal tomography overcomes the fundamental Crowther limit. • Aberration-corrected becomes a benefit and not a hindrance for tomography

  19. Non-contrast magnetic resonance imaging for bladder cancer: fused high b value diffusion-weighted imaging and T2-weighted imaging helps evaluate depth of invasion

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Minsu; Oh, Young Taik; Jung, Dae Chul; Park, Sung Yoon [Yonsei University College of Medicine, Department of Radiology, Seoul (Korea, Republic of); Shin, Su-Jin [Yonsei University College of Medicine, Department of Pathology, Seoul (Korea, Republic of); Hanyang University College of Medicine, Department of Pathology, Seoul (Korea, Republic of); Cho, Nam Hoon [Yonsei University College of Medicine, Department of Pathology, Seoul (Korea, Republic of); Choi, Young Deuk [Yonsei University College of Medicine, Department of Urology, Seoul (Korea, Republic of)

    2017-09-15

    To investigate the utility of fused high b value diffusion-weighted imaging (DWI) and T2-weighted imaging (T2WI) for evaluating depth of invasion in bladder cancer. We included 62 patients with magnetic resonance imaging (MRI) and surgically confirmed urothelial carcinoma in the urinary bladder. An experienced genitourinary radiologist analysed the depth of invasion (T stage <2 or ≥2) using T2WI, DWI, T2WI plus DWI, and fused DWI and T2WI (fusion MRI). Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy were investigated. Area under the curve (AUC) was analysed to identify T stage ≥2. The rate of patients with surgically confirmed T stage ≥2 was 41.9% (26/62). Sensitivity, specificity, PPV, NPV and accuracy were 50.0%, 55.6%, 44.8%, 60.6% and 53.2%, respectively, with T2WI; 57.7%, 77.8%, 65.2%, 71.8% and 69.4%, respectively, with DWI; 65.4%, 80.6%, 70.8%, 76.3% and 74.2%, respectively, with T2WI plus DWI and 80.8%, 77.8%, 72.4%, 84.9% and 79.0%, respectively, with fusion MRI. AUC was 0.528 with T2WI, 0.677 with DWI, 0.730 with T2WI plus DWI and 0.793 with fusion MRI for T stage ≥2. Fused high b value DWI and T2WI may be a promising non-contrast MRI technique for assessing depth of invasion in bladder cancer. (orig.)

  20. Non-contrast magnetic resonance imaging for bladder cancer: fused high b value diffusion-weighted imaging and T2-weighted imaging helps evaluate depth of invasion

    International Nuclear Information System (INIS)

    Lee, Minsu; Oh, Young Taik; Jung, Dae Chul; Park, Sung Yoon; Shin, Su-Jin; Cho, Nam Hoon; Choi, Young Deuk

    2017-01-01

    To investigate the utility of fused high b value diffusion-weighted imaging (DWI) and T2-weighted imaging (T2WI) for evaluating depth of invasion in bladder cancer. We included 62 patients with magnetic resonance imaging (MRI) and surgically confirmed urothelial carcinoma in the urinary bladder. An experienced genitourinary radiologist analysed the depth of invasion (T stage <2 or ≥2) using T2WI, DWI, T2WI plus DWI, and fused DWI and T2WI (fusion MRI). Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy were investigated. Area under the curve (AUC) was analysed to identify T stage ≥2. The rate of patients with surgically confirmed T stage ≥2 was 41.9% (26/62). Sensitivity, specificity, PPV, NPV and accuracy were 50.0%, 55.6%, 44.8%, 60.6% and 53.2%, respectively, with T2WI; 57.7%, 77.8%, 65.2%, 71.8% and 69.4%, respectively, with DWI; 65.4%, 80.6%, 70.8%, 76.3% and 74.2%, respectively, with T2WI plus DWI and 80.8%, 77.8%, 72.4%, 84.9% and 79.0%, respectively, with fusion MRI. AUC was 0.528 with T2WI, 0.677 with DWI, 0.730 with T2WI plus DWI and 0.793 with fusion MRI for T stage ≥2. Fused high b value DWI and T2WI may be a promising non-contrast MRI technique for assessing depth of invasion in bladder cancer. (orig.)

  1. 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.

  2. 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.

  3. 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.

  4. International program: Feasibility of the evacuation of high-level radioactive wastes under the ocean depths. (Seabed Program)

    International Nuclear Information System (INIS)

    Barbreau, A.

    1990-01-01

    The Seabed feasibility program is an international scientific program of research on the feasibility of the disposal of high-level radioactive wastes into the geological formations making up the floor of the great abyssal plains of the oceans. Decided in 1977, the program is aimed at answering the three following questions: 1) are there potentially favourable sites. 2) is the disposal of wastes possible. 3) does the operation present safety guarantees. First initiated by four countries (USA, UK, Japan and France), the program sponsored by the OECD nuclear energy agency was gathering ten countries and the Commission of the European communities in 1988. The techniques of waste disposal by means of drilling in consolidated sediments and penetrators in loose sediments have been studied. The penetrator technique has been the most thoroughly studied, especially through in situ experiments in the Atlantic ocean. The various factors affecting safety have been studied and the radiological consequences of a burial operation assessed through models. It has been concluded that such an operation could be carried out technically under quite satisfying conditions [fr

  5. Evaluation of Depth of Field for depth perception in DVR

    KAUST Repository

    Grosset, A.V.Pascal; Schott, Mathias; Bonneau, Georges-Pierre; Hansen, Charles D.

    2013-01-01

    In this paper we present a user study on the use of Depth of Field for depth perception in Direct Volume Rendering. Direct Volume Rendering with Phong shading and perspective projection is used as the baseline. Depth of Field is then added to see its impact on the correct perception of ordinal depth. Accuracy and response time are used as the metrics to evaluate the usefulness of Depth of Field. The onsite user study has two parts: static and dynamic. Eye tracking is used to monitor the gaze of the subjects. From our results we see that though Depth of Field does not act as a proper depth cue in all conditions, it can be used to reinforce the perception of which feature is in front of the other. The best results (high accuracy & fast response time) for correct perception of ordinal depth occurs when the front feature (out of the two features users were to choose from) is in focus and perspective projection is used. © 2013 IEEE.

  6. Evaluation of Depth of Field for depth perception in DVR

    KAUST Repository

    Grosset, A.V.Pascal

    2013-02-01

    In this paper we present a user study on the use of Depth of Field for depth perception in Direct Volume Rendering. Direct Volume Rendering with Phong shading and perspective projection is used as the baseline. Depth of Field is then added to see its impact on the correct perception of ordinal depth. Accuracy and response time are used as the metrics to evaluate the usefulness of Depth of Field. The onsite user study has two parts: static and dynamic. Eye tracking is used to monitor the gaze of the subjects. From our results we see that though Depth of Field does not act as a proper depth cue in all conditions, it can be used to reinforce the perception of which feature is in front of the other. The best results (high accuracy & fast response time) for correct perception of ordinal depth occurs when the front feature (out of the two features users were to choose from) is in focus and perspective projection is used. © 2013 IEEE.

  7. Final deposition of high-level nuclear waste in very deep boreholes. An evaluation based on recent research of bedrock conditions at great depths

    International Nuclear Information System (INIS)

    Aahaell, Karl-Inge

    2007-01-01

    This report evaluates the feasibility of very deep borehole disposal of high-level nuclear waste, e.g., spent nuclear fuel, in the light of recent technological developments and research on the characteristics of bedrock at extreme depths. The evaluation finds that new knowledge in the field of hydrogeology and technical advances in drilling technology have advanced the possibility of using very deep boreholes (3-5 km) for disposal of the Swedish nuclear waste. Decisive factors are (1) that the repository can be located in stable bedrock at a level where the groundwater is isolated from the biosphere, and (2) that the waste can be deposited and the boreholes permanently sealed without causing long-term disturbances in the density-stratification of the groundwater that surrounds the repository. Very deep borehole disposal might offer important advantage compared to the relatively more shallow KBS approach that is presently planned to be used by the Swedish nuclear industry in Sweden, in that it has the potential of being more robust. The reason for this is that very deep borehole disposal appears to permit emplacement of the waste at depths where the entire repository zone would be surrounded by stable, density-stratified groundwater having no contact with the surface, whereas a KBS-3 repository would be surrounded by upwardly mobile groundwater. This hydro-geological difference is a major safety factor, which is particularly apparent in all scenarios that envisage leakage of radioactive substances. Another advantage of a repository at a depth of 3 to 5 km is that it is less vulnerable to impacts from expected events (e.g., changes in groundwater conditions during future ice ages) as well as undesired events (e.g. such as terrorist actions, technical malfunction and major local earthquakes). Decisive for the feasibility of a repository based on the very deep borehole concept is, however, the ability to emplace the waste without failures. In order to achieve this

  8. A 20 Mfps high frame-depth CMOS burst-mode imager with low power in-pixel NMOS-only passive amplifier

    Science.gov (United States)

    Wu, L.; San Segundo Bello, D.; Coppejans, P.; Craninckx, J.; Wambacq, P.; Borremans, J.

    2017-02-01

    This paper presents a 20 Mfps 32 × 84 pixels CMOS burst-mode imager featuring high frame depth with a passive in-pixel amplifier. Compared to the CCD alternatives, CMOS burst-mode imagers are attractive for their low power consumption and integration of circuitry such as ADCs. Due to storage capacitor size and its noise limitations, CMOS burst-mode imagers usually suffer from a lower frame depth than CCD implementations. In order to capture fast transitions over a longer time span, an in-pixel CDS technique has been adopted to reduce the required memory cells for each frame by half. Moreover, integrated with in-pixel CDS, an in-pixel NMOS-only passive amplifier alleviates the kTC noise requirements of the memory bank allowing the usage of smaller capacitors. Specifically, a dense 108-cell MOS memory bank (10fF/cell) has been implemented inside a 30μm pitch pixel, with an area of 25 × 30μm2 occupied by the memory bank. There is an improvement of about 4x in terms of frame depth per pixel area by applying in-pixel CDS and amplification. With the amplifier's gain of 3.3, an FD input-referred RMS noise of 1mV is achieved at 20 Mfps operation. While the amplification is done without burning DC current, including the pixel source follower biasing, the full pixel consumes 10μA at 3.3V supply voltage at full speed. The chip has been fabricated in imec's 130nm CMOS CIS technology.

  9. Percentage depth dose calculation accuracy of model based algorithms in high energy photon small fields through heterogeneous media and comparison with plastic scintillator dosimetry.

    Science.gov (United States)

    Alagar, Ananda Giri Babu; Mani, Ganesh Kadirampatti; Karunakaran, Kaviarasu

    2016-01-08

    Small fields smaller than 4 × 4 cm2 are used in stereotactic and conformal treatments where heterogeneity is normally present. Since dose calculation accuracy in both small fields and heterogeneity often involves more discrepancy, algorithms used by treatment planning systems (TPS) should be evaluated for achieving better treatment results. This report aims at evaluating accuracy of four model-based algorithms, X-ray Voxel Monte Carlo (XVMC) from Monaco, Superposition (SP) from CMS-Xio, AcurosXB (AXB) and analytical anisotropic algorithm (AAA) from Eclipse are tested against the measurement. Measurements are done using Exradin W1 plastic scintillator in Solid Water phantom with heterogeneities like air, lung, bone, and aluminum, irradiated with 6 and 15 MV photons of square field size ranging from 1 to 4 cm2. Each heterogeneity is introduced individually at two different depths from depth-of-dose maximum (Dmax), one setup being nearer and another farther from the Dmax. The central axis percentage depth-dose (CADD) curve for each setup is measured separately and compared with the TPS algorithm calculated for the same setup. The percentage normalized root mean squared deviation (%NRMSD) is calculated, which represents the whole CADD curve's deviation against the measured. It is found that for air and lung heterogeneity, for both 6 and 15 MV, all algorithms show maximum deviation for field size 1 × 1 cm2 and gradually reduce when field size increases, except for AAA. For aluminum and bone, all algorithms' deviations are less for 15 MV irrespective of setup. In all heterogeneity setups, 1 × 1 cm2 field showed maximum deviation, except in 6MV bone setup. All algorithms in the study, irrespective of energy and field size, when any heterogeneity is nearer to Dmax, the dose deviation is higher compared to the same heterogeneity far from the Dmax. Also, all algorithms show maximum deviation in lower-density materials compared to high-density materials.

  10. High-resolution delineation of chlorinated volatile organic compounds in a dipping, fractured mudstone: depth- and strata-dependent spatial variability from rock-core sampling

    Science.gov (United States)

    Goode, Daniel J.; Imbrigiotta, Thomas E.; Lacombe, Pierre J.

    2014-01-01

    Synthesis of rock-core sampling and chlorinated volatile organic compound (CVOC) analysis at five coreholes, with hydraulic and water-quality monitoring and a detailed hydrogeologic framework, was used to characterize the fine-scale distribution of CVOCs in dipping, fractured mudstones of the Lockatong Formation of Triassic age, of the Newark Basin in West Trenton, New Jersey. From these results, a refined conceptual model for more than 55 years of migration of CVOCs and depth- and strata-dependent rock-matrix contamination was developed. Industrial use of trichloroethene (TCE) at the former Naval Air Warfare Center (NAWC) from 1953 to 1995 resulted in dense non-aqueous phase liquid (DNAPL) TCE and dissolved TCE and related breakdown products, including other CVOCs, in underlying mudstones. Shallow highly weathered and fractured strata overlie unweathered, gently dipping, fractured strata that become progressively less fractured with depth. The unweathered lithology includes black highly fractured (fissile) carbon-rich strata, gray mildly fractured thinly layered (laminated) strata, and light-gray weakly fractured massive strata. CVOC concentrations in water samples pumped from the shallow weathered and highly fractured strata remain elevated near residual DNAPL TCE, but dilution by uncontaminated recharge, and other natural and engineered attenuation processes, have substantially reduced concentrations along flow paths removed from sources and residual DNAPL. CVOCs also were detected in most rock-core samples in source areas in shallow wells. In many locations, lower aqueous concentrations, compared to rock core concentrations, suggest that CVOCs are presently back-diffusing from the rock matrix. Below the weathered and highly fractured strata, and to depths of at least 50 meters (m), groundwater flow and contaminant transport is primarily in bedding-plane-oriented fractures in thin fissile high-carbon strata, and in fractured, laminated strata of the gently

  11. Application of the high-temperature ratio method for evaluation of the depth distribution of dose equivalent in a water-filled phantom on board space station Mir

    International Nuclear Information System (INIS)

    Berger, T.; Hajek, M.; Schoener, W.; Fugger, M.; Vana, N.; Akatov, Y.; Shurshakov, V.; Arkhangelsky, V.; Kartashov, D.

    2002-01-01

    A water-filled tissue equivalent phantom with a diameter of 35 cm was developed at the Institute for Biomedical Problems, Moscow, Russia. It contains four channels perpendicular to each other, where dosemeters can be exposed at different depths. Between May 1997 and February 1999 the phantom was installed at three different locations on board the Mir space station. Thermoluminescence dosemeters (TLDs) were exposed at various depths inside the phantom either parallel or perpendicular to the hull of the spacecraft. The high-temperature ratio (HTR) method was used for the evaluation of the TLDs. The method was developed at the Atominstitute of the Austrian Universities, Vienna, Austria, and has already been used for measurements in mixed radiation fields on earth and in space with great success. It uses the changes of peak height ratios in LiF:Mg,Ti glow curves in dependence on the linear energy transfer (LET), and therefore allows determination of an 'averaged' LET as well as measurement of the absorbed dose. A mean quality factor and, subsequently, the dose equivalent can be calculated according to the Q(LET ( ) relationship proposed by the ICRP. The small size of the LiF dosemeters means that the HTR method can be used to determine the gradient of absorbed dose and dose equivalent inside the tissue equivalent body. (author)

  12. High-resolution cellular MRI: gadolinium and iron oxide nanoparticles for in-depth dual-cell imaging of engineered tissue constructs.

    Science.gov (United States)

    Di Corato, Riccardo; Gazeau, Florence; Le Visage, Catherine; Fayol, Delphine; Levitz, Pierre; Lux, François; Letourneur, Didier; Luciani, Nathalie; Tillement, Olivier; Wilhelm, Claire

    2013-09-24

    Recent advances in cell therapy and tissue engineering opened new windows for regenerative medicine, but still necessitate innovative noninvasive imaging technologies. We demonstrate that high-resolution magnetic resonance imaging (MRI) allows combining cellular-scale resolution with the ability to detect two cell types simultaneously at any tissue depth. Two contrast agents, based on iron oxide and gadolinium oxide rigid nanoplatforms, were used to "tattoo" endothelial cells and stem cells, respectively, with no impact on cell functions, including their capacity for differentiation. The labeled cells' contrast properties were optimized for simultaneous MRI detection: endothelial cells and stem cells seeded together in a polysaccharide-based scaffold material for tissue engineering appeared respectively in black and white and could be tracked, at the cellular level, both in vitro and in vivo. In addition, endothelial cells labeled with iron oxide nanoparticles could be remotely manipulated by applying a magnetic field, allowing the creation of vessel substitutes with in-depth detection of individual cellular components.

  13. RBS and ERDA determinations of depth distributions of high-dose carbon ions implanted in silicon for silicon-carbide synthesis study

    International Nuclear Information System (INIS)

    Intarasiri, S.; Kamwanna, T.; Hallen, A.; Yu, L.D.; Janson, M.S.; Thongleum, C.; Possnert, G.; Singkarat, S.

    2006-01-01

    For ion beam synthesis of silicon carbide (SiC), a knowledge of the depth distribution of implanted carbon ions in silicon is crucial for successful development. Based on its simplicity and availability, we selected Rutherford backscattering spectrometry (RBS) as an analysis technique for this purpose. A self-developed computer program dedicated to extract depth profiles of lighter impurities in heavier matrix is established. For control, calculated results are compared with an other ion beam analysis (IBA) technique superior for studying lighter impurity in heavier substrate i.e. elastic recoil detection analysis (ERDA). The RBS was performed with a 1.7-MV Tandetron accelerator using He 2+ as the probe ions. The ERDA was performed with a 5-MV Pelletron accelerator using I 8+ as the probe ions. This work shows that the RBS-extracted data had no significant deviations from those of ERDA and simulations by SRIM2003 and SIIMPL computer codes. We also found that annealing at temperatures as high as 1000 deg. C had quite limited effect on the redistribution of carbon in silicon

  14. Training a Chest Compression of 6-7 cm Depth for High Quality Cardiopulmonary Resuscitation in Hospital Setting: A Randomised Controlled Trial.

    Science.gov (United States)

    Oh, Jaehoon; Lim, Tae Ho; Cho, Youngsuk; Kang, Hyunggoo; Kim, Wonhee; Chee, Youngjoon; Song, Yeongtak; Kim, In Young; Lee, Juncheol

    2016-03-01

    During cardiopulmonary resuscitation (CPR), chest compression (CC) depth is influenced by the surface on which the patient is placed. We hypothesized that training healthcare providers to perform a CC depth of 6-7 cm (instead of 5-6 cm) on a manikin placed on a mattress during CPR in the hospital might improve their proper CC depth. This prospective randomised controlled study involved 66 premedical students without CPR training. The control group was trained to use a CC depth of 5-6 cm (G 5-6), while the experimental group was taught to use a CC depth of 6-7 cm (G 6-7) with a manikin on the floor. All participants performed CCs for 2 min on a manikin that was placed on a bed 1 hour and then again 4 weeks after the training without a feedback. The parameters of CC quality (depth, rate, % of accurate depth) were assessed and compared between the 2 groups. Four students were excluded due to loss to follow-up and recording errors, and data of 62 were analysed. CC depth and % of accurate depth were significantly higher among students in the G 6-7 than G 5-6 both 1 hour and 4 weeks after the training (p0.05). Training healthcare providers to perform a CC depth of 6-7 cm could improve quality CC depth when performing CCs on patients who are placed on a mattress during CPR in a hospital setting.

  15. Sugammadex at both high and low doses does not affect the depth of anesthesia or hemodynamics: a randomized double blind trial.

    Science.gov (United States)

    Fassoulaki, Argyro; Chondrogiannis, Konstantinos; Staikou, Chryssoula

    2017-04-01

    Previous studies have shown that sugammadex decreases the anesthetic depth when administered to reverse the neuromuscular blockade produced by rocuronium/vecuronium. The aim of the present study was to investigate the effect of sugammadex alone on anesthetic depth and hemodynamics. Sixty patients scheduled for abdominal surgery participated in the study. Anesthesia was induced with thiopental/fentanyl and maintained with N 2 O/oxygen and sevoflurane concentrations adjusted to maintain Entropy and Bispectral Index (BIS) values between 40 and 50. Cis-atracurium 0.2 mg/kg was administered for neuromuscular blockade which was monitored with a TOF-Watch ® SX acceleromyograph. State entropy (SE), response entropy (RE), Bispectral Index (BIS), systolic (SAP) and diastolic blood pressure (DAP), heart rate (HR), SpO 2 , end-tidal CO 2 and sevoflurane concentrations were recorded every 3 min intraoperatively. Sugammadex 2 mg/kg (Group-2), 4 mg/kg (Group-4) or 16 mg/kg (Group-16) was given intravenously when a count of two responses of the train-of-four (TOF) or a post-tetanic count (PTC) 1-3 appeared or when no response at all (PTC = 0) was observed, respectively. The overall SE values, thus the primary outcome of the study, were 44 ± 11, 43 ± 10 and 43 ± 11 for Group-2, Group-4 and Group-16, respectively (p = 0.812). Also, the secondary endpoints, namely RE, BIS, SAP and DAP, HR and SpO 2 did not differ between the three groups. Comparisons between Group-2 versus Group-4, Group-2 versus Group-16 and Group-4 versus Group-16 showed no differences (p > 0.05) for all the studied variables. Sugammadex alone at low, medium or high clinical doses has no effect on anesthetic depth as assessed by Entropy and BIS or on hemodynamics.

  16. Influence of structural disorder on low-temperature behavior of penetration depth in electron-doped high-TC thin films

    International Nuclear Information System (INIS)

    Lanfredi, A.J.C.; Sergeenkov, S.; Araujo-Moreira, F.M.

    2006-01-01

    To probe the influence of structural disorder on low-temperature behavior of magnetic penetration depth, λ(T), in electron-doped high-T C superconductors, a comparative study of high-quality Pr 1.85 Ce 0.15 CuO 4 (PCCO) and Sm 1.85 Ce 0.15 CuO 4 (SCCO) thin films is presented. The λ(T) profiles are extracted from conductance-voltage data using a highly-sensitive home-made mutual-inductance technique. The obtained results confirm a d-wave pairing mechanism in both samples (with nodal gap parameter Δ 0 /k B T C =2.0 and 2.1 for PCCO and SCCO films, respectively), substantially modified by impurity scattering (which is more noticeable in less homogeneous SCCO films) at the lowest temperatures. More precisely, Δλ(T)=λ(T)-λ(0) is found to follow the Goldenfeld-Hirschfeld interpolation formulae Δλ(T)/λ(0)=AT 2 /(T+T 0 ) with T 0 =ln(2)k B Γ 1/2 Δ 0 1/2 being the crossover temperature which demarcates pure and impure scattering processes (T 0 /T C =0.13 and 0.26 for PCCO and SCCO films, respectively). The value of the extracted impurity scattering rate Γ correlates with the quality of our samples and is found to be much higher in less homogeneous films with lower T C

  17. Highly Resolved Mg/Ca Depth Profiles of Planktic Foraminifer test Walls Using Single shot Measurements of fs-LA-ICPMS

    Science.gov (United States)

    Jochum, K. P.; Schiebel, R.; Stoll, B.; Weis, U.; Haug, G. H.

    2017-12-01

    Foraminifers are sensitive archives of changes in climate and marine environment. It has been shown that the Mg/Ca signal is a suitable proxy of seawater temperature, because the incorporation of Mg depends on ambient water temperature. In contrast to most former studies, where this ratio is determined by solution-based bulk analysis of 20 - 30 specimens, we have investigated Mg/Ca in single specimens and single chambers at high resolution. A new fs-200 nm-LA-ICPMS technique was developed for the µm-sized layered calcite shells. To generate depth profiles with a resolution of about 50 nm/shot, we chose a low fluence of about 0.3 Jcm-2 and performed single shot measurements of the double charged 44Ca++ and the single charged 25Mg+ ions together. Precision (RSD) of the Mg/Ca data is about 5 %. Calibration was performed with the carbonate reference material MACS-3 from the USGS. Our results for different species from the Arabian Sea and Caribbean Sea demonstrate that Mg/Ca of different chambers vary and indicate that the foraminifer individuals built their chambers in different water depths and/or experienced seasonal changes in seawater temperature caused, for example, by upwelling (cold) versus stratified (warm) conditions. Typically, the Mg/Ca ratios of the final two chambers of the planktic foraminifer Globorotalia menardii from a sediment core of the Arabian Sea differ by about 5 mmol/mol from earlier chambers (2 mmol/mol) corresponding to seawater temperatures of 28 °C and 18 °C, respectively. In addition, mass fractions of other elements like Sr, Mn, Fe, Ba, and U have been determined with fs-LA-ICPMS using fast line scans, and thus provide further insights in the ecology of foraminifers.

  18. 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

  19. Weighted halfspace depth

    Czech Academy of Sciences Publication Activity Database

    Kotík, Lukáš; Hlubinka, D.; Vencálek, O.

    Vol. 46, č. 1 (2010), s. 125-148 ISSN 0023-5954 Institutional research plan: CEZ:AV0Z10750506 Keywords : data depth * nonparametric multivariate analysis * strong consistency of depth * mixture of distributions Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 0.461, year: 2010 http://library.utia.cas.cz/separaty/2010/SI/kotik-weighted halfspace depth.pdf

  20. 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.

  1. Final disposal of high-level radioactive waste in deep boreholes. An evaluation based on recent research on the bedrock at great depths

    International Nuclear Information System (INIS)

    Aahaell, Karl-Inge

    2006-05-01

    New knowledge in hydrogeology and boring technology have opened the possibility to use deep boreholes as a repository for the Swedish high-level radioactive wastes. The determining property is that the repository can be housed in the stable bedrock at levels where the ground water has no contact with the biosphere and disposal and sealing can take place without disturbing the ground water stratification outside the disposal area. An advantage compared to a shallow repository of KBS-3 type, that is now being planned in Sweden, is that a borehole repository is likely to be technologically more robust, since the concept 'deep boreholes' seems to admit such a deep disposal that the entire disposal area would be surrounded by stable density-layered ground water, while a KBS-3 repository would be surrounded by moving ground water in contact with level close to the surface. This hydrological difference is of great importance for the safety in scenarios with leaching of radioactive substances. A deep repository is also less vulnerable for effects from natural events such as glaciation and earthquakes as well as from technological mishaps and terrorist actions. A crucial factor is, however, that the radioactive waste can be disposed of, in a secure way, at the intended depth, which will require new research and technology development

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Comparison of publically available Moho depth and crustal thickness grids with newly derived grids by 3D gravity inversion for the High Arctic region.

    Science.gov (United States)

    Lebedeva-Ivanova, Nina; Gaina, Carmen; Minakov, Alexander; Kashubin, Sergey

    2016-04-01

    We derived Moho depth and crustal thickness for the High Arctic region by 3D forward and inverse gravity modelling method in the spectral domain (Minakov et al. 2012) using lithosphere thermal gravity anomaly correction (Alvey et al., 2008); a vertical density variation for the sedimentary layer and lateral crustal variation density. Recently updated grids of bathymetry (Jakobsson et al., 2012), gravity anomaly (Gaina et al, 2011) and dynamic topography (Spasojevic & Gurnis, 2012) were used as input data for the algorithm. TeMAr sedimentary thickness grid (Petrov et al., 2013) was modified according to the most recently published seismic data, and was re-gridded and utilized as input data. Other input parameters for the algorithm were calibrated using seismic crustal scale profiles. The results are numerically compared with publically available grids of the Moho depth and crustal thickness for the High Arctic region (CRUST 1 and GEMMA global grids; the deep Arctic Ocean grids by Glebovsky et al., 2013) and seismic crustal scale profiles. The global grids provide coarser resolution of 0.5-1.0 geographic degrees and not focused on the High Arctic region. Our grids better capture all main features of the region and show smaller error in relation to the seismic crustal profiles compare to CRUST 1 and GEMMA grids. Results of 3D gravity modelling by Glebovsky et al. (2013) with separated geostructures approach show also good fit with seismic profiles; however these grids cover the deep part of the Arctic Ocean only. Alvey A, Gaina C, Kusznir NJ, Torsvik TH (2008). Integrated crustal thickness mapping and plate recon-structions for the high Arctic. Earth Planet Sci Lett 274:310-321. Gaina C, Werner SC, Saltus R, Maus S (2011). Circum-Arctic mapping project: new magnetic and gravity anomaly maps of the Arctic. Geol Soc Lond Mem 35, 39-48. Glebovsky V.Yu., Astafurova E.G., Chernykh A.A., Korneva M.A., Kaminsky V.D., Poselov V.A. (2013). Thickness of the Earth's crust in the

  8. Consistently high sports/exercise activity is associated with better sleep quality, continuity and depth in midlife women: the SWAN sleep study.

    Science.gov (United States)

    Kline, Christopher E; Irish, Leah A; Krafty, Robert T; Sternfeld, Barbara; Kravitz, Howard M; Buysse, Daniel J; Bromberger, Joyce T; Dugan, Sheila A; Hall, Martica H

    2013-09-01

    To examine relationships between different physical activity (PA) domains and sleep, and the influence of consistent PA on sleep, in midlife women. Cross-sectional. Community-based. 339 women in the Study of Women's Health Across the Nation Sleep Study (52.1 ± 2.1 y). None. Sleep was examined using questionnaires, diaries and in-home polysomnography (PSG). PA was assessed in three domains (Active Living, Household/Caregiving, Sports/Exercise) using the Kaiser Physical Activity Survey (KPAS) up to 4 times over 6 years preceding the sleep assessments. The association between recent PA and sleep was evaluated using KPAS scores immediately preceding the sleep assessments. The association between the historical PA pattern and sleep was examined by categorizing PA in each KPAS domain according to its pattern over the 6 years preceding sleep assessments (consistently low, inconsistent/consistently moderate, or consistently high). Greater recent Sports/Exercise activity was associated with better sleep quality (diary "restedness" [P sleep continuity (diary sleep efficiency [SE; P = 0.02]) and depth (higher NREM delta electroencephalographic [EEG] power [P = 0.04], lower NREM beta EEG power [P Sports/Exercise activity was also associated with better Pittsburgh Sleep Quality Index scores (P = 0.02) and higher PSG-assessed SE (P sleep and Active Living or Household/Caregiving activity (either recent or historical pattern) were noted. Consistently high levels of recreational physical activity, but not lifestyle- or household-related activity, are associated with better sleep in midlife women. Increasing recreational physical activity early in midlife may protect against sleep disturbance in this population.

  9. Precise age for the Permian-Triassic boundary in South China from high-precision U-Pb geochronology and Bayesian age-depth modeling

    Science.gov (United States)

    Baresel, Björn; Bucher, Hugo; Brosse, Morgane; Cordey, Fabrice; Guodun, Kuang; Schaltegger, Urs

    2017-03-01

    This study is based on zircon U-Pb ages of 12 volcanic ash layers and volcanogenic sandstones from two deep water sections with conformable and continuous formational Permian-Triassic boundaries (PTBs) in the Nanpanjiang Basin (South China). Our dates of single, thermally annealed and chemically abraded zircons bracket the PTB in Dongpan and Penglaitan and provide the basis for a first proof-of-concept study utilizing a Bayesian chronology model comparing the three sections of Dongpan, Penglaitan and the Global Stratotype Section and Point (GSSP) at Meishan. Our Bayesian modeling demonstrates that the formational boundaries in Dongpan (251.939 ± 0.030 Ma), Penglaitan (251.984 ± 0.031 Ma) and Meishan (251.956 ± 0.035 Ma) are synchronous within analytical uncertainty of ˜ 40 ka. It also provides quantitative evidence that the ages of the paleontologically defined boundaries, based on conodont unitary association zones in Meishan and on macrofaunas in Dongpan, are identical and coincide with the age of the formational boundaries. The age model also confirms the extreme condensation around the PTB in Meishan, which distorts the projection of any stratigraphic points or intervals onto other more expanded sections by means of Bayesian age-depth models. Dongpan and Penglaitan possess significantly higher sediment accumulation rates and thus offer a greater potential for high-resolution studies of environmental proxies and correlations around the PTB than Meishan. This study highlights the power of high-resolution radio-isotopic ages that allow a robust intercalibration of patterns of biotic changes and fluctuating environmental proxies and will help recognizing their global, regional or local significance.

  10. 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.

  11. 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.

  12. Citizen-Enabled Aerosol Measurements for Satellites (CEAMS): A Network for High-Resolution Measurements of PM2.5 and Aerosol Optical Depth

    Science.gov (United States)

    Pierce, J. R.; Volckens, J.; Ford, B.; Jathar, S.; Long, M.; Quinn, C.; Van Zyl, L.; Wendt, E.

    2017-12-01

    Atmospheric particulate matter with diameter smaller than 2.5 μm (PM2.5) is a pollutant that contributes to the development of human disease. Satellite-derived estimates of surface-level PM2.5 concentrations have the potential to contribute greatly to our understanding of how particulate matter affects health globally. However, these satellite-derived PM2.5 estimates are often uncertain due to a lack of information about the ratio of surface PM2.5 to aerosol optical depth (AOD), which is the primary aerosol retrieval made by satellite instruments. While modelling and statistical analyses have improved estimates of PM2.5:AOD, large uncertainties remain in situations of high PM2.5 exposure (such as urban areas and in wildfire-smoke plumes) where the health impacts of PM2.5 may be the greatest. Surface monitoring networks for co-incident PM2.5 and AOD measurements are extremely rare, even in the North America. To provide constraints for the PM2.5:AOD relationship, we have developed a relatively low-cost (application (iOS and Android). Sun photometry is performed across 4 discrete wavelengths that match those reported by the Aerosol Robotic Network (AERONET). Aerosol concentration is reported using both time-integrated filter mass (analyzed in an academic laboratory and reported as a 24-48hr average) and a continuous PM sensor within the instrument. Citizen scientists use the device to report daily AOD and PM2.5 measurements made in their backyards to a central server for data display and download. In this presentation, we provide an overview of (1) AOD and PM2.5 measurement calibration; (2) citizen recruiting and training efforts; and (3) results from our pilot citizen-science measurement campaign.

  13. A New Hybrid Spatio-temporal Model for Estimating Daily Multi-year PM2.5 Concentrations Across Northeastern USA Using High Resolution Aerosol Optical Depth Data

    Science.gov (United States)

    Kloog, Itai; Chudnovsky, Alexandra A.; Just, Allan C.; Nordio, Francesco; Koutrakis, Petros; Coull, Brent A.; Lyapustin, Alexei; Wang, Yujie; Schwartz, Joel

    2014-01-01

    The use of satellite-based aerosol optical depth (AOD) to estimate fine particulate matter PM(sub 2.5) for epidemiology studies has increased substantially over the past few years. These recent studies often report moderate predictive power, which can generate downward bias in effect estimates. In addition, AOD measurements have only moderate spatial resolution, and have substantial missing data. We make use of recent advances in MODIS satellite data processing algorithms (Multi-Angle Implementation of Atmospheric Correction (MAIAC), which allow us to use 1 km (versus currently available 10 km) resolution AOD data.We developed and cross validated models to predict daily PM(sub 2.5) at a 1X 1 km resolution across the northeastern USA (New England, New York and New Jersey) for the years 2003-2011, allowing us to better differentiate daily and long term exposure between urban, suburban, and rural areas. Additionally, we developed an approach that allows us to generate daily high-resolution 200 m localized predictions representing deviations from the area 1 X 1 km grid predictions. We used mixed models regressing PM(sub 2.5) measurements against day-specific random intercepts, and fixed and random AOD and temperature slopes. We then use generalized additive mixed models with spatial smoothing to generate grid cell predictions when AOD was missing. Finally, to get 200 m localized predictions, we regressed the residuals from the final model for each monitor against the local spatial and temporal variables at each monitoring site. Our model performance was excellent (mean out-of-sample R(sup 2) = 0.88). The spatial and temporal components of the out-of-sample results also presented very good fits to the withheld data (R(sup 2) = 0.87, R(sup)2 = 0.87). In addition, our results revealed very little bias in the predicted concentrations (Slope of predictions versus withheld observations = 0.99). Our daily model results show high predictive accuracy at high spatial resolutions

  14. Institutional Strength in Depth

    International Nuclear Information System (INIS)

    Weightman, M.

    2016-01-01

    Much work has been undertaken in order to identify, learn and implement the lessons from the TEPCO Fukushima Daiichi nuclear accident. These have mainly targeted on engineering or operational lessons. Less attention has been paid to the institutional lessons, although there have been some measures to improve individual peer reviews, particularly by the World Association of Nuclear Operators, and the authoritative IAEA report published in 2015 brought forward several important lessons for regulators and advocated a system approach. The report noted that one of the contributing factors the accident was the tendency of stakeholders not to challenge. Additionally, it reported deficiencies in the regulatory authority and system. Earlier, the root cause of the accident was identified by a Japanese independent parliamentary report as being cultural and institutional. The sum total of the institutions, the safety system, was ineffective. While it is important to address the many technical and operational lessons these may not necessary address this more fundamental lesson, and may not serve to provide robust defences against human or institutional failings over a wide variety of possible events and combinations. The overall lesson is that we can have rigorous and comprehensive safety standards and other tools in place to deliver high levels of safety, but ultimately what is important is the ability of the nuclear safety system to ensure that the relevant institutions diligently and effectively apply those standards and tools — to be robust and resilient. This has led to the consideration of applying the principles of the strength in depth philosophy to a nuclear safety system as a way of providing a framework for developing, assessing, reviewing and improving the system. At an IAEA conference in October 2013, a model was presented for a robust national nuclear safety system based on strength in depth philosophy. The model highlighted three main layers: industry, the

  15. Motivation with Depth.

    Science.gov (United States)

    DiSpezio, Michael A.

    2000-01-01

    Presents an illusional arena by offering experience in optical illusions in which students must apply critical analysis to their innate information gathering systems. Introduces different types of depth illusions for students to experience. (ASK)

  16. Thermohydromechanical stability analysis upon joint characteristics and depth variations in the region of an underground repository for the study of a disposal concept of high level radioactive wastes

    International Nuclear Information System (INIS)

    Kim, Jhin Wung; Bae, Dae Suk; Kang, Chul Hyung; Choi, Jong Won

    2003-02-01

    The objective of the present study is to understand a long term(500 years) thermohydromechanical interaction behavior in the vicinity of a repository cavern upon joint location and repository depth variations, and then, to contribute to the development of a disposal concept. The model includes a saturated rock mass, PWR spent fuels in a disposal canister surrounded by compacted bentonite inside a deposition hole, and mixed bentonite backfilled in the rest of the space within a cavern. It is assumed that two joint sets exist within a model. A joint set 1 includes 56 .deg. dip joints, 20m spaced, and a joint set 2 is in the direction perpendicular to a joint set 1 and includes 34 .deg. dip joints, 20m spaced. In order to understand the behavior change upon joint location variations, 5 different models of 500m depth are analyzed, and additional 3 different models of 1km depth are analyzed to understand the effect of a depth variation. The two dimensional distinct element code, UDEC is used for the analysis. To understand the joint behavior adjacent to a repository cavern, Barton-Bandis joint model is used. Effect of the decay heat for PWR spent fuels on a repository model is analyzed, and a steady state algorithm is used for a hydraulic analysis. According to the thermohydromechanical interaction behavior of a repository model upon variations of joint locations and a repository depth, during the period of 500 years from waste emplacement, the effect of a depth variation on the stress and displacement behavior of a model is comparatively smaller than the effect of decay heat from radioactive materials. From the study of the joint location variation effect, it is advisable not to locate an underground opening in the region very close to the joint crossings

  17. Glider and satellite high resolution monitoring of a mesoscale eddy in the Algerian basin: effects on the mixed layer depth and biochemistry

    Science.gov (United States)

    Cotroneo, Yuri; Aulicino, Giuseppe; Ruiz, Simón; Pascual, Ananda; Budillon, Giorgio; Fusco, Giannetta; Tintoré, Joaquin

    2016-04-01

    Despite of the extensive bibliography about the circulation of the Mediterranean Sea and its sub-basins, the debate on mesoscale dynamics and its impacts on biochemical processes is still open because of their intrinsic time scales and of the difficulties in sampling. In order to clarify some of these processes, the "Algerian BAsin Circulation Unmanned Survey - ABACUS" project was proposed and realized through access to JERICO Trans National Access (TNA) infrastructures between September and December 2014. In this framework, a deep glider cruise was carried out in the area between Balearic Islands and Algerian coasts to establish an endurance line for monitoring the basin circulation. During the mission, a mesoscale eddy, identified on satellite altimetry maps, was sampled at high-spatial horizontal resolution (4 km) along its main axes and from surface to 1000 m depth. Data were collected by a Slocum glider equipped with a pumped CTD and biochemical sensors that collected about 100 complete casts inside the eddy. In order to describe the structure of the eddy, in situ data were merged with new generation remotely sensed data as daily synoptic sea surface temperature (SST) and chlorophyll concentration (Chl-a) images from MODIS satellites as well as sea surface height and geostrophic velocities from AVISO. From its origin along the Algerian coast in the eastern part of the basin, the eddy propagated to north-west at a mean speed of about 4 km/day with a mean diameter of 112/130 km, a mean elevation of 15.7 cm and clearly distinguished by the surrounding waters thanks to its higher SST and Chl-a values. Temperature and salinity values along the water column confirm the origin of the eddy from the AC showing the presence of recent Atlantic water in the surface layer and Levantine Intermediate Water (LIW) in the deeper layer. Eddy footprint is clearly evident in the multiparametric vertical sections conducted along its main axes. Deepening of temperature, salinity and

  18. Experimental study of the crack depth ratio threshold to analyze the slow crack growth by creep of high density polyethylene pipes

    International Nuclear Information System (INIS)

    Laiarinandrasana, Lucien; Devilliers, Clémence; Lucatelli, Jean Marc; Gaudichet-Maurin, Emmanuelle; Brossard, Jean Michel

    2014-01-01

    To assess the durability of drinking water connection pipes subjected to oxidation and slow crack growth, a comprehensive database was constructed on a novel specimen geometry: the pre-cracked NOL ring. 135 tests were carried out consisting of initial crack depth ratio ranging from 0.08 to 0.6; single or double longitudinal cracks: tensile with steady strain rate and creep loading. A threshold value of the crack depth ratio of 0.2, induced by the oxidation was determined by analyzing several mechanical parameters. This threshold value was shown to be independent on the strain rate effects, single or double crack configuration and the kind of loading: tensile or creep. Creep test results with crack depth ratio larger than 0.2 were then utilized to establish a failure assessment diagram. A methodology allowing the prediction of residual lifetime of in-service pipes was proposed, using this diagram. - Highlights: • Experimental data on pre-cracked rings featuring a longitudinally cracked HDPE pipe. • Crack depth ratio threshold for slow crack growth study consecutive to oxidation. • Investigation of the effects of the single/double notch(es) and of the strain rate. • Original results obtained from tests performed with tensile and creep loadings. • Correlation between creep initiation time and C* with DENT and ring specimens

  19. Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II

    Directory of Open Access Journals (Sweden)

    Archer John

    2012-03-01

    Full Text Available Abstract Background Next generation sequencing provides detailed insight into the variation present within viral populations, introducing the possibility of treatment strategies that are both reactive and predictive. Current software tools, however, need to be scaled up to accommodate for high-depth viral data sets, which are often temporally or spatially linked. In addition, due to the development of novel sequencing platforms and chemistries, each with implicit strengths and weaknesses, it will be helpful for researchers to be able to routinely compare and combine data sets from different platforms/chemistries. In particular, error associated with a specific sequencing process must be quantified so that true biological variation may be identified. Results Segminator II was developed to allow for the efficient comparison of data sets derived from different sources. We demonstrate its usage by comparing large data sets from 12 influenza H1N1 samples sequenced on both the 454 Life Sciences and Illumina platforms, permitting quantification of platform error. For mismatches median error rates at 0.10 and 0.12%, respectively, suggested that both platforms performed similarly. For insertions and deletions median error rates within the 454 data (at 0.3 and 0.2%, respectively were significantly higher than those within the Illumina data (0.004 and 0.006%, respectively. In agreement with previous observations these higher rates were strongly associated with homopolymeric stretches on the 454 platform. Outside of such regions both platforms had similar indel error profiles. Additionally, we apply our software to the identification of low frequency variants. Conclusion We have demonstrated, using Segminator II, that it is possible to distinguish platform specific error from biological variation using data derived from two different platforms. We have used this approach to quantify the amount of error present within the 454 and Illumina platforms in

  20. Radon depth migration

    International Nuclear Information System (INIS)

    Hildebrand, S.T.; Carroll, R.J.

    1993-01-01

    A depth migration method is presented that used Radon-transformed common-source seismograms as input. It is shown that the Radon depth migration method can be extended to spatially varying velocity depth models by using asymptotic ray theory (ART) to construct wavefield continuation operators. These operators downward continue an incident receiver-array plane wave and an assumed point-source wavefield into the subsurface. The migration velocity model is constrain to have longer characteristic wavelengths than the dominant source wavelength such that the ART approximations for the continuation operators are valid. This method is used successfully to migrate two synthetic data examples: (1) a point diffractor, and (2) a dipping layer and syncline interface model. It is shown that the Radon migration method has a computational advantage over the standard Kirchhoff migration method in that fewer rays are computed in a main memory implementation

  1. Measuring depth in boreholes

    International Nuclear Information System (INIS)

    Hodson, G.M.

    1979-01-01

    This invention relates to a method of determining the depth of rock strata and other features of a borehole. It may be employed with particular advantage when access to the top of the borehole is difficult, for example in underwater operations. A radioactive marker, such as a source of gamma rays, is positioned near the top of the riser of a sub-sea wellhead structure. A radiation detector is lowered between the marker and a radioactive stratum and the length of line supplied is measured on the floating platform. This enables the depth of the stratum to be measured irrespective of tidal variations of the height of the platform. (U.K.)

  2. Using Water Depth Sensors and High-resolution Topographic Mapping to Inform Wetland Management at a Globally Important Stopover Site for Migratory Shorebirds

    Science.gov (United States)

    Schaffer-Smith, D.; Swenson, J. J.; Reiter, M. E.; Isola, J. E.

    2017-12-01

    Over 50% of western hemisphere shorebird species are in decline due to ongoing habitat loss and habitat degradation. Wetland dependent shorebirds prefer shallowly flooded habitats (water depth managed to optimize shallow areas. In-situ water depth measurements and microtopography data coupled with satellite image analysis can assist in understanding habitat suitability patterns at broad spatial scales. We generated detailed bathymetry, and estimated spatial daily water depths, the proportion of wetland area providing flooded habitat within the optimal depth range, and the volume of water present in 23 managed wetlands in the Sacramento Valley of California, a globally important shorebird stopover site. Using 30 years of satellite imagery, we estimated suitable habitat extent across the landscape under a range of climate conditions. While spring shorebird abundance has historically peaked in early April, we found that maximum optimal habitat extent occurred after mid-April. More than 50% of monitored wetlands provided limited optimal habitat (fleeting; only 4 wetlands provided at least 10 consecutive days with >5% optimal habitat during the peak of migration. Wetlands with a higher percent clay content and lower topographic variability were more likely to provide a greater extent and duration of suitable habitat. We estimated that even in a relatively wet El-Nino year as little as 0.01%, to 10.72% of managed herbaceous wetlands in the Sacramento Valley provided optimal habitat for shorebirds at the peak of migration in early April. In an extreme drought year, optimal habitat decreased by 80% compared to a wet year Changes in the timing of wetland irrigation and drawdown schedules and the design of future wetland restoration projects could increase the extent and duration of optimal flooded habitat for migratory shorebirds, without significant increases in overall water use requirements.

  3. SRBreak: A read-depth and split-read framework to identify breakpoints of different events inside simple copy-number variable regions

    Directory of Open Access Journals (Sweden)

    HOANG T NGUYEN

    2016-09-01

    Full Text Available Copy-number variation (CNV has been associated with increased risk of complex diseases. High throughput sequencing (HTS technologies facilitate the detection of copy-number variable regions (CNVRs and their breakpoints. This helps in understanding genome structures of genomes as well as their evolution process. Various approaches have been proposed for detecting CNV breakpoints, but currently it is still challenging for tools based on a single analysis method to identify breakpoints of CNVs. It has been shown, however, that pipelines which integrate multiple approaches are able to report more reliable breakpoints. Here, based on HTS data, we have developed a pipeline to identify approximate breakpoints (±10 bp relating to different ancestral events within a specific CNVR. The pipeline combines read-depth and split-read information to infer breakpoints, using information from multiple samples to allow an imputation approach to be taken. The main steps involve using a normal mixture model to cluster samples into different groups, followed by simple kernel-based approaches to maximise information obtained from read-depth and split-read approaches, after which common breakpoints of groups are inferred. The pipeline uses split-read information directly from CIGAR strings of BAM files, without using a re-alignment step. On simulated data sets, it was able to report breakpoints for very low-coverage samples including those for which only single-end reads were available. When applied to three loci from existing human resequencing data sets (NEGR1, LCE3, IRGM the pipeline obtained good concordance with results from the 1000 Genomes Project (92%, 100% and 82%, respectively.The package is available at https://github.com/hoangtn/SRBreak, and also as a docker-based application at https://registry.hub.docker.com/u/hoangtn/srbreak/.

  4. Why bother about depth?

    DEFF Research Database (Denmark)

    Stæhr, Peter A.; Obrador, Biel; Christensen, Jesper Philip

    We present results from a newly developed method to determine depth specific rates of GPP, NEP and R using frequent automated profiles of DO and temperature. Metabolic rate calculations were made for three lakes of different trophic status using a diel DO methodology that integrates rates across...

  5. Defining depth of anesthesia.

    Science.gov (United States)

    Shafer, S L; Stanski, D R

    2008-01-01

    In this chapter, drawn largely from the synthesis of material that we first presented in the sixth edition of Miller's Anesthesia, Chap 31 (Stanski and Shafer 2005; used by permission of the publisher), we have defined anesthetic depth as the probability of non-response to stimulation, calibrated against the strength of the stimulus, the difficulty of suppressing the response, and the drug-induced probability of non-responsiveness at defined effect site concentrations. This definition requires measurement of multiple different stimuli and responses at well-defined drug concentrations. There is no one stimulus and response measurement that will capture depth of anesthesia in a clinically or scientifically meaningful manner. The "clinical art" of anesthesia requires calibration of these observations of stimuli and responses (verbal responses, movement, tachycardia) against the dose and concentration of anesthetic drugs used to reduce the probability of response, constantly adjusting the administered dose to achieve the desired anesthetic depth. In our definition of "depth of anesthesia" we define the need for two components to create the anesthetic state: hypnosis created with drugs such as propofol or the inhalational anesthetics and analgesia created with the opioids or nitrous oxide. We demonstrate the scientific evidence that profound degrees of hypnosis in the absence of analgesia will not prevent the hemodynamic responses to profoundly noxious stimuli. Also, profound degrees of analgesia do not guarantee unconsciousness. However, the combination of hypnosis and analgesia suppresses hemodynamic response to noxious stimuli and guarantees unconsciousness.

  6. High-throughput screening of Si-Ni flux for SiC solution growth using a high-temperature laser microscope observation and secondary ion mass spectroscopy depth profiling.

    Science.gov (United States)

    Maruyama, Shingo; Onuma, Aomi; Kurashige, Kazuhisa; Kato, Tomohisa; Okumura, Hajime; Matsumoto, Yuji

    2013-06-10

    Screening of Si-based flux materials for solution growth of SiC single crystals was demonstrated using a thin film composition-spread technique. The reactivity and diffusion of carbon in a composition spread of the flux was investigated by secondary ion mass spectroscopy depth profiling of the annealed flux thin film spread on a graphite substrate. The composition dependence of the chemical interaction between a seed crystal and flux materials was revealed by high-temperature thermal behavior observation of the flux and the subsequent morphological study of the surface after removing the flux using atomic force microscopy. Our new screening approach is shown to be an efficient process for understanding flux materials for SiC solution growth.

  7. Depth-resolved ultra-violet spectroscopic photo current-voltage measurements for the analysis of AlGaN/GaN high electron mobility transistor epilayer deposited on Si

    International Nuclear Information System (INIS)

    Ozden, Burcu; Yang, Chungman; Tong, Fei; Khanal, Min P.; Mirkhani, Vahid; Sk, Mobbassar Hassan; Ahyi, Ayayi Claude; Park, Minseo

    2014-01-01

    We have demonstrated that the depth-dependent defect distribution of the deep level traps in the AlGaN/GaN high electron mobility transistor (HEMT) epi-structures can be analyzed by using the depth-resolved ultra-violet (UV) spectroscopic photo current-voltage (IV) (DR-UV-SPIV). It is of great importance to analyze deep level defects in the AlGaN/GaN HEMT structure, since it is recognized that deep level defects are the main source for causing current collapse phenomena leading to reduced device reliability. The AlGaN/GaN HEMT epi-layers were grown on a 6 in. Si wafer by metal-organic chemical vapor deposition. The DR-UV-SPIV measurement was performed using a monochromatized UV light illumination from a Xe lamp. The key strength of the DR-UV-SPIV is its ability to provide information on the depth-dependent electrically active defect distribution along the epi-layer growth direction. The DR-UV-SPIV data showed variations in the depth-dependent defect distribution across the wafer. As a result, rapid feedback on the depth-dependent electrical homogeneity of the electrically active defect distribution in the AlGaN/GaN HEMT epi-structure grown on a Si wafer with minimal sample preparation can be elucidated from the DR-UV-SPIV in combination with our previously demonstrated spectroscopic photo-IV measurement with the sub-bandgap excitation.

  8. Depth-resolved ultra-violet spectroscopic photo current-voltage measurements for the analysis of AlGaN/GaN high electron mobility transistor epilayer deposited on Si

    Energy Technology Data Exchange (ETDEWEB)

    Ozden, Burcu; Yang, Chungman; Tong, Fei; Khanal, Min P.; Mirkhani, Vahid; Sk, Mobbassar Hassan; Ahyi, Ayayi Claude; Park, Minseo, E-mail: park@physics.auburn.edu [Department of Physics, Auburn University, Auburn, Alabama 36849 (United States)

    2014-10-27

    We have demonstrated that the depth-dependent defect distribution of the deep level traps in the AlGaN/GaN high electron mobility transistor (HEMT) epi-structures can be analyzed by using the depth-resolved ultra-violet (UV) spectroscopic photo current-voltage (IV) (DR-UV-SPIV). It is of great importance to analyze deep level defects in the AlGaN/GaN HEMT structure, since it is recognized that deep level defects are the main source for causing current collapse phenomena leading to reduced device reliability. The AlGaN/GaN HEMT epi-layers were grown on a 6 in. Si wafer by metal-organic chemical vapor deposition. The DR-UV-SPIV measurement was performed using a monochromatized UV light illumination from a Xe lamp. The key strength of the DR-UV-SPIV is its ability to provide information on the depth-dependent electrically active defect distribution along the epi-layer growth direction. The DR-UV-SPIV data showed variations in the depth-dependent defect distribution across the wafer. As a result, rapid feedback on the depth-dependent electrical homogeneity of the electrically active defect distribution in the AlGaN/GaN HEMT epi-structure grown on a Si wafer with minimal sample preparation can be elucidated from the DR-UV-SPIV in combination with our previously demonstrated spectroscopic photo-IV measurement with the sub-bandgap excitation.

  9. Depth image enhancement using perceptual texture priors

    Science.gov (United States)

    Bang, Duhyeon; Shim, Hyunjung

    2015-03-01

    A depth camera is widely used in various applications because it provides a depth image of the scene in real time. However, due to the limited power consumption, the depth camera presents severe noises, incapable of providing the high quality 3D data. Although the smoothness prior is often employed to subside the depth noise, it discards the geometric details so to degrade the distance resolution and hinder achieving the realism in 3D contents. In this paper, we propose a perceptual-based depth image enhancement technique that automatically recovers the depth details of various textures, using a statistical framework inspired by human mechanism of perceiving surface details by texture priors. We construct the database composed of the high quality normals. Based on the recent studies in human visual perception (HVP), we select the pattern density as a primary feature to classify textures. Upon the classification results, we match and substitute the noisy input normals with high quality normals in the database. As a result, our method provides the high quality depth image preserving the surface details. We expect that our work is effective to enhance the details of depth image from 3D sensors and to provide a high-fidelity virtual reality experience.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Depth determination of low-energy photon emitter deposits in tissue by means of high-resolution X-ray spectrometry

    International Nuclear Information System (INIS)

    Schlueter, W.

    1982-01-01

    A method has been developed for ascertaining the depth of low-energy photon emitters deposited in wounds. It is based on the determination of the energy-dependent absorption of the emitted photons by the tissue separating source and detector. The method is applicable to counting for low-energy photon-emitting nuclides that can be characterized by more than one quantum energy. Attenuation coefficients were given for lard, beef, and five tissue- equivalent materials. For spectrometry, a planar Ge(Li) detector proved most suitable. (author)

  15. The characteristic and influence factors of extinction depth of shallow groundwater on the high-latitude region: a case study on the Sanjiang Plain, northeast China.

    Science.gov (United States)

    Wang, Xihua

    2018-03-01

    Accurate estimation of extinction depth of shallow groundwater (EDSG) and identification of its influence factors are important for sustainable management of groundwater resources, ecological protection, and human health in intensively irrigated region. In this study, the ratio of actual groundwater depth and EDSG (RAE) method was used to understand the spatial variability of EDSG in the Sanjiang Plain, one of China's largest grain production bases and China's largest inland freshwater wetland region. The study showed a large spatial variation of EDSG in the region. Spatially, the sites, which were in the northeast and center had the deepest and the shallowest EDSG, whereby, indicate that it has higher and lower pumping potential capacity. Many factors including climate, soil parameters, vegetation and topography affected the EDSG. We also identified an area of 3.86 × 10 10  m 2 , which accounting for 35.3% of the entire Sanjiang Plain, has exceeded the ESGD by over exploited for years. Knowledge of the variation and influence factors of EDSG for a certain plant system and the current shallow groundwater condition in the higher latitude region can be a key to the development of preventive actions for large quantity pumping groundwater and protection regional and sustainable development of irrigated agriculture.

  16. 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

  17. 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.

  18. Four-layer depth-of-interaction PET detector for high resolution PET using a multi-pixel S8550 avalanche photodiode

    International Nuclear Information System (INIS)

    Nishikido, Fumihiko; Inadama, Naoko; Oda, Ichiro; Shibuya, Kengo; Yoshida, Eiji; Yamaya, Taiga; Kitamura, Keishi; Murayama, Hideo

    2010-01-01

    Avalanche photodiodes (APDs) are being used as photodetectors in positron emission tomography (PET) because they have many advantages over photomultipliers (PMTs) typically used in PET detectors. We have developed a PET detector that consists of a multi-pixel APD and a 6x6x4 array of 1.46x1.46 mm 2 x4.5 m LYSO crystals for a small animal PET scanner. The detector can identify four-layer depth of interaction (DOI) with a position-sensitive APD coupled to the backside of a crystal array by just an optimized reflector arrangement. Since scintillation lights are shared among many pixels by the method, weaker signals in APD pixels far from the interacting crystals are affected by noise. To evaluate the performance of the four-layer DOI detector with the APD and the influence of electrical noise on our method, we constructed a prototype DOI detector and tested its performance. We found, except for crystal elements on the edge of the crystal array, all crystal elements could be identified from the 2D position histogram. An energy resolution of 16.9% was obtained for the whole crystal array of the APD detector. The results of noise dependence of detector performances indicated that the DOI detector using the APD could achieve sufficient performance even when using application-specific integrated circuits.

  19. Four-layer depth-of-interaction PET detector for high resolution PET using a multi-pixel S8550 avalanche photodiode

    Energy Technology Data Exchange (ETDEWEB)

    Nishikido, Fumihiko, E-mail: funis@nirs.go.j [Molecular Imaging Center, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Inadama, Naoko [Molecular Imaging Center, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Oda, Ichiro [Shimadzu Corporation, Nishinokyo Kuwabaracho 1 Nakagyo-ku, Kyoto-shi, Kyoto 604-8511 (Japan); Shibuya, Kengo; Yoshida, Eiji; Yamaya, Taiga [Molecular Imaging Center, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan); Kitamura, Keishi [Shimadzu Corporation, Nishinokyo Kuwabaracho 1 Nakagyo-ku, Kyoto-shi, Kyoto 604-8511 (Japan); Murayama, Hideo [Molecular Imaging Center, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan)

    2010-09-21

    Avalanche photodiodes (APDs) are being used as photodetectors in positron emission tomography (PET) because they have many advantages over photomultipliers (PMTs) typically used in PET detectors. We have developed a PET detector that consists of a multi-pixel APD and a 6x6x4 array of 1.46x1.46 mm{sup 2}x4.5 m LYSO crystals for a small animal PET scanner. The detector can identify four-layer depth of interaction (DOI) with a position-sensitive APD coupled to the backside of a crystal array by just an optimized reflector arrangement. Since scintillation lights are shared among many pixels by the method, weaker signals in APD pixels far from the interacting crystals are affected by noise. To evaluate the performance of the four-layer DOI detector with the APD and the influence of electrical noise on our method, we constructed a prototype DOI detector and tested its performance. We found, except for crystal elements on the edge of the crystal array, all crystal elements could be identified from the 2D position histogram. An energy resolution of 16.9% was obtained for the whole crystal array of the APD detector. The results of noise dependence of detector performances indicated that the DOI detector using the APD could achieve sufficient performance even when using application-specific integrated circuits.

  20. Shave-off depth profiling: Depth profiling with an absolute depth scale

    International Nuclear Information System (INIS)

    Nojima, M.; Maekawa, A.; Yamamoto, T.; Tomiyasu, B.; Sakamoto, T.; Owari, M.; Nihei, Y.

    2006-01-01

    Shave-off depth profiling provides profiling with an absolute depth scale. This method uses a focused ion beam (FIB) micro-machining process to provide the depth profile. We show that the shave-off depth profile of a particle reflected the spherical shape of the sample and signal intensities had no relationship to the depth. Through the introduction of FIB micro-sampling, the shave-off depth profiling of a dynamic random access memory (DRAM) tip was carried out. The shave-off profile agreed with a blue print from the manufacturing process. Finally, shave-off depth profiling is discussed with respect to resolutions and future directions

  1. High-resolution orientation and depth of insertion of the voltage-sensing S4 helix of a potassium channel in lipid bilayers.

    Science.gov (United States)

    Doherty, Tim; Su, Yongchao; Hong, Mei

    2010-08-27

    The opening and closing of voltage-gated potassium (Kv) channels are controlled by several conserved Arg residues in the S4 helix of the voltage-sensing domain. The interaction of these positively charged Arg residues with the lipid membrane has been of intense interest for understanding how membrane proteins fold to allow charged residues to insert into lipid bilayers against free-energy barriers. Using solid-state NMR, we have now determined the orientation and insertion depth of the S4 peptide of the KvAP channel in lipid bilayers. Two-dimensional (15)N correlation experiments of macroscopically oriented S4 peptide in phospholipid bilayers revealed a tilt angle of 40 degrees and two possible rotation angles differing by 180 degrees around the helix axis. Remarkably, the tilt angle and one of the two rotation angles are identical to those of the S4 helix in the intact voltage-sensing domain, suggesting that interactions between the S4 segment and other helices of the voltage-sensing domain are not essential for the membrane topology of the S4 helix. (13)C-(31)P distances between the S4 backbone and the lipid (31)P indicate a approximately 9 A local thinning and 2 A average thinning of the DMPC (1,2-dimyristoyl-sn-glycero-3-phosphochloline)/DMPG (1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol) bilayer, consistent with neutron diffraction data. Moreover, a short distance of 4.6 A from the guanidinium C(zeta) of the second Arg to (31)P indicates the existence of guanidinium phosphate hydrogen bonding and salt bridges. These data suggest that the structure of the Kv gating helix is mainly determined by protein-lipid interactions instead of interhelical protein-protein interactions, and the S4 amino acid sequence encodes sufficient information for the membrane topology of this crucial gating helix. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  2. Offshore Wind Technology Depth Zones

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Coastal bathymetric depth, measured in meters at depth values of: -30, -60, -900 Shallow Zone (0-30m): Technology has been demonstrated on a commercial scale at...

  3. Zooplankton community composition of high mountain lakes in the Tatra Mts., the Alps in North Tyrol, and Scotland: relationship to pH, depth, organic carbon, and chlorophyll-a concentration

    Directory of Open Access Journals (Sweden)

    Skála Ivan

    2015-10-01

    Full Text Available The European EMERGE (European Mountain lake Ecosystems: Regionalisation, diaGnostic & socio-economic Evaluation project was a survey of high mountain lakes (above treeline across Europe using unified methods of sampling and analysis. The sampling was carried out in summer or autumn 2000, and comprised biological samples, and samples for chemical analysis. Data from three lake districts are used in this paper: the Tatra Mts. in Slovakia and Poland (45 lakes, the Alps in Tyrol in Austria (22 lakes, and Scotland (30 lakes. As it is shown by multiple regression analysis, DTOC (dissolved or total organic carbon is the key variable for most groups of zooplankton. With increasing DTOC and mostly with chlorophyll-a decreasing, pH increasing and depth decreasing, macrofitrators with coarse filter meshes are replaced by microfiltrators with fine filter meshes. Higher DTOC may increase bacterioplankton production and advantage species able to consume bacteria (microfiltrators. Other zooplankton species also differ in their preference for DTOC, chlorophyll-a, pH and depth, but DTOC being positively correlated with chlorophyll-a and pH positively correlated with depth. It may be caused by their different preference for food quality in terms of C:P ratio.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Synthesis and in-depth analysis of highly ordered yttrium doped hydroxyapatite nanorods prepared by hydrothermal method and its mechanical analysis

    International Nuclear Information System (INIS)

    Nathanael, A. Joseph; Mangalaraj, D.; Hong, S.I.; Masuda, Y.

    2011-01-01

    In this study, undoped and yttrium (Y) doped nanocrystalline hydroxyapatite crystals were synthesized by the hydrothermal method at 180 °C for 24 h. Highly ordered and oriented hydroxyapatite (HAp) nanorods were prepared by yttrium doping and their nanostructure and physical properties were compared with those of undoped HAp rods. FESEM images showed that the doping with Y ions reduced the diameter (from 25 nm to 15 nm) and increased the length (from 95 nm to 115 nm) of the synthesized rods. The aspect ratio of the undoped and Y-doped nanorods were calculated to be 4.303 (SD = 0.0959) and 7.61 (SD = 0.0355), respectively. Specific surface area (SSA) analysis showed that SSA also increased from 66.74 m 2 /g to 68.57 m 2 /g with the addition of yttrium. Y-doped HAp nanorod reinforced HMWPE composites displayed the better mechanical performance than those reinforced with pure HAp nanorods. The possible strengthening of nanorods and the increase of SSA due to the reduction in the size of nanorods in the presence of yttrium may have contributed to the strengthening of Y-doped HAp/HMWPE composites. - Graphical Abstract: Highly ordered and oriented yttrium doped hydroxyapatite (HAp) nanorods were prepared by hydrothermal method. For undoped HAp the average length of the nanorod is 95 nm with mean diameter of 24 nm and for a Y doped nanorod the average length is ∼ 115 nm and the mean diameter is 15 nm. Mechanical analysis was carried out by polymer/nanoparticle composite method. Highlights: ► Yttrium doped hydroxyapatite nanorods were prepared by hydrothermal method. ► The nanorods have highly uniform size distribution. ► Yttrium substitution and nanostructure formation was confirmed by careful analysis. ► Mechanical strength was analyzed by polymer nanoparticle reinforcement method.

  9. Mass composition studies of Ultra High Energy cosmic rays through the measurement of the Muon Production Depths at the Pierre Auger Observatory

    Energy Technology Data Exchange (ETDEWEB)

    Collica, Laura [Univ. of Milan (Italy); Paris Diderot Univ. (France)

    2014-01-01

    The Pierre Auger Observatory (Auger) in Argentina studies Ultra High Energy Cosmic Rays (UHECRs) physics. The flux of cosmic rays at these energies (above 1018 eV) is very low (less than 100 particle/km2-year) and UHECR properties must be inferred from the measurements of the secondary particles that the cosmic ray primary produces in the atmosphere. These particles cascades are called Extensive Air Showers (EAS) and can be studied at ground by deploying detectors covering large areas. The EAS physics is complex, and the properties of secondary particles depend strongly on the first interaction, which takes place at an energy beyond the ones reached at accelerators. As a consequence, the analysis of UHECRs is subject to large uncertainties and hence many of their properties, in particular their composition, are still unclear. Two complementary techniques are used at Auger to detect EAS initiated by UHE- CRs: a 3000 km2 surface detector (SD) array of water Cherenkov tanks which samples particles at ground level and fluorescence detectors (FD) which collect the ultraviolet light emitted by the de-excitation of nitrogen nuclei in the atmosphere, and can operate only in clear, moonless nights. Auger is the largest cosmic rays detector ever built and it provides high-quality data together with unprecedented statistics. The main goal of this thesis is the measurement of UHECR mass composition using data from the SD of the Pierre Auger Observatory. Measuring the cosmic ray composition at the highest energies is of fundamental importance from the astrophysical point of view, since it could discriminate between different scenarios of origin and propagation of cosmic rays. Moreover, mass composition studies are of utmost importance for particle physics. As a matter of fact, knowing the composition helps in exploring the hadronic interactions at ultra-high energies, inaccessible to present accelerator experiments.

  10. Hydrologic regulation of plant rooting depth.

    Science.gov (United States)

    Fan, Ying; Miguez-Macho, Gonzalo; Jobbágy, Esteban G; Jackson, Robert B; Otero-Casal, Carlos

    2017-10-03

    Plant rooting depth affects ecosystem resilience to environmental stress such as drought. Deep roots connect deep soil/groundwater to the atmosphere, thus influencing the hydrologic cycle and climate. Deep roots enhance bedrock weathering, thus regulating the long-term carbon cycle. However, we know little about how deep roots go and why. Here, we present a global synthesis of 2,200 root observations of >1,000 species along biotic (life form, genus) and abiotic (precipitation, soil, drainage) gradients. Results reveal strong sensitivities of rooting depth to local soil water profiles determined by precipitation infiltration depth from the top (reflecting climate and soil), and groundwater table depth from below (reflecting topography-driven land drainage). In well-drained uplands, rooting depth follows infiltration depth; in waterlogged lowlands, roots stay shallow, avoiding oxygen stress below the water table; in between, high productivity and drought can send roots many meters down to the groundwater capillary fringe. This framework explains the contrasting rooting depths observed under the same climate for the same species but at distinct topographic positions. We assess the global significance of these hydrologic mechanisms by estimating root water-uptake depths using an inverse model, based on observed productivity and atmosphere, at 30″ (∼1-km) global grids to capture the topography critical to soil hydrology. The resulting patterns of plant rooting depth bear a strong topographic and hydrologic signature at landscape to global scales. They underscore a fundamental plant-water feedback pathway that may be critical to understanding plant-mediated global change.

  11. Hydrologic regulation of plant rooting depth

    Science.gov (United States)

    Fan, Ying; Miguez-Macho, Gonzalo; Jobbágy, Esteban G.; Jackson, Robert B.; Otero-Casal, Carlos

    2017-10-01

    Plant rooting depth affects ecosystem resilience to environmental stress such as drought. Deep roots connect deep soil/groundwater to the atmosphere, thus influencing the hydrologic cycle and climate. Deep roots enhance bedrock weathering, thus regulating the long-term carbon cycle. However, we know little about how deep roots go and why. Here, we present a global synthesis of 2,200 root observations of >1,000 species along biotic (life form, genus) and abiotic (precipitation, soil, drainage) gradients. Results reveal strong sensitivities of rooting depth to local soil water profiles determined by precipitation infiltration depth from the top (reflecting climate and soil), and groundwater table depth from below (reflecting topography-driven land drainage). In well-drained uplands, rooting depth follows infiltration depth; in waterlogged lowlands, roots stay shallow, avoiding oxygen stress below the water table; in between, high productivity and drought can send roots many meters down to the groundwater capillary fringe. This framework explains the contrasting rooting depths observed under the same climate for the same species but at distinct topographic positions. We assess the global significance of these hydrologic mechanisms by estimating root water-uptake depths using an inverse model, based on observed productivity and atmosphere, at 30″ (˜1-km) global grids to capture the topography critical to soil hydrology. The resulting patterns of plant rooting depth bear a strong topographic and hydrologic signature at landscape to global scales. They underscore a fundamental plant-water feedback pathway that may be critical to understanding plant-mediated global change.

  12. FINANCIAL DEPTH AND FINANCIAL ACCESS IN INDONESIA

    Directory of Open Access Journals (Sweden)

    Sigit Setiawan

    2015-05-01

    Full Text Available This study is intended to analyze the current levels of financial depth and financial access in Indonesia and to analyze the factors affecting them. The analysis method used was a combination of descriptive quantitative, benchmarking, and literature reviews. The conclusion is that the financial depth in Indonesia has not shown a satisfactory level since it was the lowest, or the second lowest ranked country among the sampled countries. Meanwhile, the financial access in Indonesia is relatively better than its financial depth, especially for financial markets, in which Indonesia ranks in the lower average group. From literature reviews, it can be inferred that the main factor driving the poor financial depth in Indonesia is non-competitiveness of the institutions; whereas the driving force of poor financial access in Indonesia are geographical constraints, poverty, a high income gap, and a less than effective national financial development policy.

  13. Defence in depth perspectives

    International Nuclear Information System (INIS)

    Veneau, Tania; Ferrier, Agnes; Barbaud, Jean

    2017-01-01

    The Defence in Depth (DiD) concept was introduced to the field of nuclear safety in the sixties and early seventies. Even though it was not well developed at the beginning, the principles rapidly became close to those currently used. The concept was then composed of 3 levels, and was already associated with operating conditions. These principles have progressed over time and now there are five levels, including progressively situations issued from design extension conditions, to cope with severe accidents and dealing with accident management off-site. Indeed, human and organizational features are considered as a part of the safety provisions at all levels in an integrated approach that is not just related to reactor design. That's the current vision from IAEA, addressed first in INSAG 3 then in INSAG 10, and in the IAEA standards requirements currently addressed by SSR-2/1 superseding NS-R-1). These five levels of DiD are also referred to in other texts including WENRA documents in Europe, but also in the national requirements from different countries. Thus, the application of DiD principle has become a recognized international practice. The 2011 Fukushima Daiichi accidents, even if they raised many questions on nuclear safety issues, confirmed the merits of the DiD concept. Indeed, lessons learned from the accidents have reinforced the use of the DiD concept to ensure adequate safety. The discussions focused more on the implementation of the concept (how it has been or can be used in practice) than the concept itself, and in particular on the following subjects: the notion of level robustness, generally addressed separately from the levels definition, but playing an important role for the efficiency of the concept; the notion of levels independence and the need for strengthening them; the role of diversity to achieve levels independence. However, a prescription of additional diversity and independence across all safety levels could result in inappropriately

  14. Water Pressure in Depth

    Science.gov (United States)

    Lynch, Mary Jean; Zenchak, John

    2011-01-01

    How can a science concept be taught in a way that generates interest, gives students the opportunity to consider other possibilities, does not lock them into one way of doing or seeing things, and gives them some ownership of their learning? These authors searched high and low for the perfect activity to illustrate a key concept for their partner…

  15. In-depth investigation of high-energy arcing faults (HEAF) of electrical components with possible induced fires; Vertiefte Untersuchungen zum hochenergetischen Versagen elektrischer Komponenten (HEAF) mit moeglicher Brandfolge

    Energy Technology Data Exchange (ETDEWEB)

    Roewekamp, Marina

    2015-11-15

    Main objective of the project 3611R01301 performed on behalf of the Federal Ministry for the Environment, Nature Conservation, Building and Nuclear Safety (BMUB) is an in-depth investigation of fires at electrical components induced by high energy arcing faults (HEAF) according to their non-negligible significance to nuclear safety. This report provides an overview on the insights with respect to high energy arcing faults at electrical components mainly gained from investigations of the national as well as international operating experience from nuclear installations. Moreover, the insights from the international operating experience have resulted in an experimental program carried out in the frame of a task by the OECD Nuclear Energy Agency (NEA) in order to investigate failures of electrical components, e. g. breakers, switchgears or transformers, installed in nuclear power plants of the member countries due to HEAF and potential consequential fires. The results of the in-depth analyses and experimental investigations shall be used for identifying potential areas of damage in a suitable manner. The results based on inter-national research shall also be checked with respect to their applicability to the situation in German nuclear power plants.

  16. 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.

  17. 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.

  18. Improved depth estimation with the light field camera

    Science.gov (United States)

    Wang, Huachun; Sang, Xinzhu; Chen, Duo; Guo, Nan; Wang, Peng; Yu, Xunbo; Yan, Binbin; Wang, Kuiru; Yu, Chongxiu

    2017-10-01

    Light-field cameras are used in consumer and industrial applications. An array of micro-lenses captures enough information that one can refocus images after acquisition, as well as shift one's viewpoint within the sub-apertures of the main lens, effectively obtaining multiple views. Thus, depth estimation from both defocus and correspondence are now available in a single capture. And Lytro.Inc also provides a depth estimation from a single-shot capture with light field camera, like Lytro Illum. This Lytro depth estimation containing many correct depth information can be used for higher quality estimation. In this paper, we present a novel simple and principled algorithm that computes dense depth estimation by combining defocus, correspondence and Lytro depth estimations. We analyze 2D epipolar image (EPI) to get defocus and correspondence depth maps. Defocus depth is obtained by computing the spatial gradient after angular integration and correspondence depth by computing the angular variance from EPIs. Lytro depth can be extracted from Lyrto Illum with software. We then show how to combine the three cues into a high quality depth map. Our method for depth estimation is suitable for computer vision applications such as matting, full control of depth-of-field, and surface reconstruction, as well as light filed display

  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. Gaspe hole sets depth record

    Energy Technology Data Exchange (ETDEWEB)

    1970-03-09

    The deepest diamond-cored hole in the Western Hemisphere, Gulf Sunnybank No. 1 on the Gaspe Peninsula of Quebec, has been completed at a depth of 11,600 ft. This is the deepest cored hole to be drilled anywhere in search of oil and gas production, and the deepest to be drilled using a wire-line core recovery technique. The well was completed in 183 days, and was cored continuously below the surface casing which was set and cemented at 1,004 ft. After underreaming a portion of the bottom of the hole, intermediate casing was set and cemented at 8,000 ft as a safety precaution against possible high oil or gas-fluid pressure. Actual coring time, after deducting time for underreaming and casing operations, was 152 days. Because of the cost of transporting a conventional oil-drilling rig to the E. location, the 89-ft mining rig was modified for the project. The contractor was Heath and Sherwood Drilling (Western) Ltd.

  1. ISLSCP II Ecosystem Rooting Depths

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of this study was to predict the global distribution of plant rooting depths based on data about global aboveground vegetation structure and climate....

  2. ISLSCP II Ecosystem Rooting Depths

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: The goal of this study was to predict the global distribution of plant rooting depths based on data about global aboveground vegetation structure and...

  3. Color image guided depth image super resolution using fusion filter

    Science.gov (United States)

    He, Jin; Liang, Bin; He, Ying; Yang, Jun

    2018-04-01

    Depth cameras are currently playing an important role in many areas. However, most of them can only obtain lowresolution (LR) depth images. Color cameras can easily provide high-resolution (HR) color images. Using color image as a guide image is an efficient way to get a HR depth image. In this paper, we propose a depth image super resolution (SR) algorithm, which uses a HR color image as a guide image and a LR depth image as input. We use the fusion filter of guided filter and edge based joint bilateral filter to get HR depth image. Our experimental results on Middlebury 2005 datasets show that our method can provide better quality in HR depth images both numerically and visually.

  4. Λ and Σ well depth

    International Nuclear Information System (INIS)

    Satoh, Eiji

    1982-01-01

    The Λ well depth was calculated by taking into account the effect of the ΛΣ conversion. Takahashi et al. obtained the separate type of potentials which described the hyperon-nucleon interaction up to p waves. Two types of the potentials among several types they obtained were used to calculate the Λ well depth. The G matrix was easily calculated, and the Λ well depth was obtained by integrating the G matrix in momentum space up to the Fermi surface. The effect of the ΛΣ conversion was given by an equation. The total Λ well depth was estimated to be 9.13 MeV and 49.36 MeV for each type of potential, respectively. It was concluded that the argument by Bodmer et al. was not correct. The Σ well depth was also calculated using the potential obtained by Takahashi et al. for I = 1/2 and the one obtained by Σ + p → Σ + p scattering data for I = 3/2. The obtained value 35.30 MeV may be overestimated, and the experimental value is expected to be in the range from 20 MeV to 30 MeV. (Ito, K.)

  5. Spectrometric kidney depth measurement method

    International Nuclear Information System (INIS)

    George, P.; Soussaline, F.; Raynaud, C.

    1976-01-01

    The method proposed uses the single posterior surface measurement of the kidney radioactivity distribution. The ratio C/P of the number of scattered photons to the number of primary photons, which is a function of the tissue depth penetrated, is calculated for a given region. The parameters on which the C/P value depends are determined from studies on phantoms. On the basis of these results the kidney depth was measured on a series of 13 patients and a correlation was established between the value thus calculated and that obtained by the profile method. The reproducibility of the method is satisfactory [fr

  6. Heat flow of standard depth

    International Nuclear Information System (INIS)

    Cull, J.P.

    1981-01-01

    Secular and long-term periodic changes in surface temperature cause perturbations to the geothermal gradient which may be significant to depths of at least 1000 m, and major corrections are required to determine absolute values of heat flow from the Earth's interior. However, detailed climatic models remain contentious and estimates of error in geothermal gradients differ widely. Consequently, regions of anomalous heat flow which could contain geothermal resources may be more easily resolved by measuring relative values at a standard depth (e.g. 100 m) so that all data are subject to similar corrections. (orig./ME)

  7. 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.

  8. Impact of prior treatment and depth of response on survival in MM-003, a randomized phase 3 study comparing pomalidomide plus low-dose dexamethasone versus high-dose dexamethasone in relapsed/refractory multiple myeloma

    Science.gov (United States)

    San Miguel, Jesus F.; Weisel, Katja C.; Song, Kevin W.; Delforge, Michel; Karlin, Lionel; Goldschmidt, Hartmut; Moreau, Philippe; Banos, Anne; Oriol, Albert; Garderet, Laurent; Cavo, Michele; Ivanova, Valentina; Alegre, Adrian; Martinez-Lopez, Joaquin; Chen, Christine; Renner, Christoph; Bahlis, Nizar Jacques; Yu, Xin; Teasdale, Terri; Sternas, Lars; Jacques, Christian; Zaki, Mohamed H.; Dimopoulos, Meletios A.

    2015-01-01

    Pomalidomide is a distinct oral IMiD® immunomodulatory agent with direct antimyeloma, stromal-support inhibitory, and immunomodulatory effects. The pivotal, multicenter, open-label, randomized phase 3 trial MM-003 compared pomalidomide + low-dose dexamethasone vs high-dose dexamethasone in 455 patients with refractory or relapsed and refractory multiple myeloma after failure of bortezomib and lenalidomide treatment. Initial results demonstrated significantly longer progression-free survival and overall survival with an acceptable tolerability profile for pomalidomide + low-dose dexamethasone vs high-dose dexamethasone. This secondary analysis describes patient outcomes by treatment history and depth of response. Pomalidomide + low-dose dexamethasone significantly prolonged progression-free survival and favored overall survival vs high-dose dexamethasone for all subgroups analyzed, regardless of prior treatments or refractory status. Both univariate and multivariate analyses showed that no variable relating to either the number (≤ or > 3) or type of prior treatment was a significant predictor of progression-free survival or overall survival. No cross-resistance with prior lenalidomide or thalidomide treatment was observed. Patients achieving a minimal response or better to pomalidomide + low-dose dexamethasone treatment experienced a survival benefit, which was even higher in those achieving at least a partial response (17.2 and 19.9 months, respectively, as compared with 7.5 months for patients with less than minimal response). These data suggest that pomalidomide + low-dose dexamethasone should be considered a standard of care in patients with refractory or relapsed and refractory multiple myeloma regardless of prior treatment. ClinicalTrials.gov: NCT01311687; EudraCT: 2010-019820-30. PMID:26160879

  9. Depth of Ultra High Energy Cosmic Ray Induced Air Shower Maxima Measured by the Telescope Array Black Rock and Long Ridge FADC Fluorescence Detectors and Surface Array in Hybrid Mode

    Science.gov (United States)

    Abbasi, R. U.; Abe, M.; Abu-Zayyad, T.; Allen, M.; Azuma, R.; Barcikowski, E.; Belz, J. W.; Bergman, D. R.; Blake, S. A.; Cady, R.; Cheon, B. G.; Chiba, J.; Chikawa, M.; di Matteo, A.; Fujii, T.; Fujita, K.; Fukushima, M.; Furlich, G.; Goto, T.; Hanlon, W.; Hayashi, M.; Hayashi, Y.; Hayashida, N.; Hibino, K.; Honda, K.; Ikeda, D.; Inoue, N.; Ishii, T.; Ishimori, R.; Ito, H.; Ivanov, D.; Jeong, H. M.; Jeong, S. M.; Jui, C. C. H.; Kadota, K.; Kakimoto, F.; Kalashev, O.; Kasahara, K.; Kawai, H.; Kawakami, S.; Kawana, S.; Kawata, K.; Kido, E.; Kim, H. B.; Kim, J. H.; Kim, J. H.; Kishigami, S.; Kitamura, S.; Kitamura, Y.; Kuzmin, V.; Kuznetsov, M.; Kwon, Y. J.; Lee, K. H.; Lubsandorzhiev, B.; Lundquist, J. P.; Machida, K.; Martens, K.; Matsuyama, T.; Matthews, J. N.; Mayta, R.; Minamino, M.; Mukai, K.; Myers, I.; Nagasawa, K.; Nagataki, S.; Nakamura, R.; Nakamura, T.; Nonaka, T.; Oda, H.; Ogio, S.; Ogura, J.; Ohnishi, M.; Ohoka, H.; Okuda, T.; Omura, Y.; Ono, M.; Onogi, R.; Oshima, A.; Ozawa, S.; Park, I. H.; Pshirkov, M. S.; Rodriguez, D. C.; Rubtsov, G.; Ryu, D.; Sagawa, H.; Sahara, R.; Saito, K.; Saito, Y.; Sakaki, N.; Sakurai, N.; Scott, L. M.; Seki, T.; Sekino, K.; Shah, P. D.; Shibata, F.; Shibata, T.; Shimodaira, H.; Shin, B. K.; Shin, H. S.; Smith, J. D.; Sokolsky, P.; Stokes, B. T.; Stratton, S. R.; Stroman, T. A.; Suzawa, T.; Takagi, Y.; Takahashi, Y.; Takamura, M.; Takeda, M.; Takeishi, R.; Taketa, A.; Takita, M.; Tameda, Y.; Tanaka, H.; Tanaka, K.; Tanaka, M.; Thomas, S. B.; Thomson, G. B.; Tinyakov, P.; Tkachev, I.; Tokuno, H.; Tomida, T.; Troitsky, S.; Tsunesada, Y.; Tsutsumi, K.; Uchihori, Y.; Udo, S.; Urban, F.; Wong, T.; Yamamoto, M.; Yamane, R.; Yamaoka, H.; Yamazaki, K.; Yang, J.; Yashiro, K.; Yoneda, Y.; Yoshida, S.; Yoshii, H.; Zhezher, Y.; Zundel, Z.; Telescope Array Collaboration

    2018-05-01

    The Telescope Array (TA) observatory utilizes fluorescence detectors and surface detectors (SDs) to observe air showers produced by ultra high energy cosmic rays in Earth’s atmosphere. Cosmic-ray events observed in this way are termed hybrid data. The depth of air shower maximum is related to the mass of the primary particle that generates the shower. This paper reports on shower maxima data collected over 8.5 yr using the Black Rock Mesa and Long Ridge fluorescence detectors in conjunction with the array of SDs. We compare the means and standard deviations of the observed {X}\\max distributions with Monte Carlo {X}\\max distributions of unmixed protons, helium, nitrogen, and iron, all generated using the QGSJet II-04 hadronic model. We also perform an unbinned maximum likelihood test of the observed data, which is subjected to variable systematic shifting of the data {X}\\max distributions to allow us to test the full distributions, and compare them to the Monte Carlo to see which elements are not compatible with the observed data. For all energy bins, QGSJet II-04 protons are found to be compatible with TA hybrid data at the 95% confidence level after some systematic {X}\\max shifting of the data. Three other QGSJet II-04 elements are found to be compatible using the same test procedure in an energy range limited to the highest energies where data statistics are sparse.

  10. Pursuing the Depths of Knowledge

    Science.gov (United States)

    Boyles, Nancy

    2016-01-01

    Today's state literacy standards and assessments demand deeper levels of knowledge from students. But many teachers ask, "What does depth of knowledge look like on these new, more rigorous assessments? How do we prepare students for this kind of thinking?" In this article, Nancy Boyles uses a sampling of questions from the PARCC and SBAC…

  11. Fluence dependence of disorder depth profiles in Pb implanted Si

    International Nuclear Information System (INIS)

    Christodoulides, C.E.; Kadhim, N.J.; Carter, G.

    1980-01-01

    The total, depth integrated disorder, induced by Pb implantation into Si at room temperature, initially increases rapidly with implantation fluence and then reaches a quasi saturation level where the increase with fluence is slow. Measurements of the depth distributions of the disorder, using high resolution low angle exit Rutherford Backscattering/Channelling analysis, suggest that the quasi saturation results from overlapping of disordered zones generated deep in the tail of the disorder-depth profiles. The depth of the disordered solid-crystal boundary, xsub(D), increases with ion fluence PHI, according to the relation xsub(D) = x bar + f(PHI).σ, where x bar is the most probable projected depth and σ the projected standard deviation of disorder generation. It is shown that this relationship is consistent with an approximately Gaussian depth distribution of disorder production. (author)

  12. 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.

  13. 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.

  14. 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.

  15. Chemotoxic materials in a final repository for high-level radioactive wastes. CHEMOTOX concept for defence in depth concerning ground water protection from chemotoxic materials in a final high-level waste repository

    International Nuclear Information System (INIS)

    Alt, Stefan; Sailer, Michael; Schmidt, Gerhard; Herbert, Horst-Juergen; Krone, Juergen; Tholen, Marion

    2009-01-01

    The disposal of high-level radioactive wastes in a final repository includes chemotoxic materials. The chemotoxic materials are either part of the radioactive material or part of the packaging material, or the structures within the repository. In the frame of the licensing procedure it has to be demonstrated that no hazardous pollution of the ground water or other disadvantageous changes can occur. The report describes the common project of the Oeko-Institut e.V., the DBE Technology GmbH and the GRS mbH concerning the possible demonstration of a systematic protection of the groundwater against chemotoxic materials in case of a final high-level-radioactive waste repository in the host materials salt and clay stone.

  16. Intercomparison On Depth Dose Measurement

    International Nuclear Information System (INIS)

    Rohmah, N; Akhadi, M

    1996-01-01

    Intercomparation on personal dose evaluation system has been carried out between CSRSR-NAEA of Indonesia toward Standard Laboratory of JAERI (Japan) and ARL (Australia). The intercomparison was in 10 amm depth dose measurement , Hp (10), from the intercomparison result could be stated that personal depth dose measurement conducted by CSRSR was sufficiently good. Deviation of dose measurement result using personal dosemeter of TLD BG-1 type which were used by CSRSR in the intercomparison and routine photon personal dose monitoring was still in internationally agreed limit. Maximum deviation of reported doses by CSRSR compared to delivered doses for dosemeter irradiation by JAERI was -10.0 percent and by ARL was +29 percent. Maximum deviation permitted in personal dose monitoring is ± 50 percent

  17. Applications of positron depth profiling

    International Nuclear Information System (INIS)

    Hakvoort, R.A.

    1993-01-01

    In this thesis some contributions of the positron-depth profiling technique to materials science have been described. Following studies are carried out: Positron-annihilation measurements on neon-implanted steel; Void creation in silicon by helium implantation; Density of vacancy-type defects present in amorphous silicon prepared by ion implantation; Measurements of other types of amorphous silicon; Epitaxial cobalt disilicide prepared by cobalt outdiffusion. Positron-annihilation experiments on low-pressure CVD silicon-nitride films. (orig./MM)

  18. Applications of positron depth profiling

    Energy Technology Data Exchange (ETDEWEB)

    Hakvoort, R A

    1993-12-23

    In this thesis some contributions of the positron-depth profiling technique to materials science have been described. Following studies are carried out: Positron-annihilation measurements on neon-implanted steel; Void creation in silicon by helium implantation; Density of vacancy-type defects present in amorphous silicon prepared by ion implantation; Measurements of other types of amorphous silicon; Epitaxial cobalt disilicide prepared by cobalt outdiffusion. Positron-annihilation experiments on low-pressure CVD silicon-nitride films. (orig./MM).

  19. Weak layer fracture: facets and depth hoar

    Directory of Open Access Journals (Sweden)

    I. Reiweger

    2013-09-01

    Full Text Available Understanding failure initiation within weak snow layers is essential for modeling and predicting dry-snow slab avalanches. We therefore performed laboratory experiments with snow samples containing a weak layer consisting of either faceted crystals or depth hoar. During these experiments the samples were loaded with different loading rates and at various tilt angles until fracture. The strength of the samples decreased with increasing loading rate and increasing tilt angle. Additionally, we took pictures of the side of four samples with a high-speed video camera and calculated the displacement using a particle image velocimetry (PIV algorithm. The fracture process within the weak layer could thus be observed in detail. Catastrophic failure started due to a shear fracture just above the interface between the depth hoar layer and the underlying crust.

  20. Double Compressions of Atmospheric Depth by Geopotential Tendency, Vorticity, and Atmospheric Boundary Layer Affected Abrupt High Particulate Matter Concentrations at a Coastal City for a Yellow Dust Period in October

    Directory of Open Access Journals (Sweden)

    Hyo Choi

    2014-01-01

    Full Text Available Using GRIMM-aerosol sampler, NOAA-HYSPLIT model, and 3D-WRF-3.3 model, the transportation of dusts from Gobi Desert toward Gangneung city, Korea was investigated from 09:00 LST October 27 to 04:00 LST October 28, 2003. Maximum PM10 (PM2.5, PM1 concentration was detected with 3.8 (3.4, 14.1 times higher magnitude than one in non-Yellow Dust period. The combination of dusts transported from the desert under westerly wind with particulate matters and gases from vehicles on the road of the city caused high PM concentrations near the ground surface at 09:00 LST and their maxima at 17:00 LST near sunset with further pollutants from heating boilers in the resident area. Positive geopotential tendency at the 500 hPa level of the city (∂Φ/∂t; m day−1 corresponding to negative vorticity of -4×10-5 sec−1 (-2.5×10-5 sec−1 at 0900 LST (21:00 LST; at night was +83 m day−1 (+30 m day−1 and it caused atmospheric depth between 500 hPa level and the ground surface to be vertically expanded. However, its net reduction to −53 m/12 hrs until 21:00 LST indicated synoptic-scale atmospheric layer to be vertical shrunken, resulting in the increase of PM concentrations at 17:00 LST. Simultaneously, much shallower microscale stable nocturnal surface inversion layer (NSIL than daytime thermal internal boundary layer induced particulate matters to be merged inside the NSIL, resulting in maximum PM concentrations at 17:00 LST.

  1. The effect of glenoid cavity depth on rotator cuff tendinitis.

    Science.gov (United States)

    Malkoc, Melih; Korkmaz, Ozgur; Ormeci, Tugrul; Sever, Cem; Kara, Adna; Mahirogulları, Mahir

    2016-03-01

    Some of the most important causes of shoulder pain are inflammation and degenerative changes in the rotator cuff (RC). Magnetic resonance imaging (MRI) is a noninvasive and safe imaging modality. MRI can be used for the evaluation of cuff tendinopathy. In this study, we evaluated the relationship between glenoid cavity depth and cuff tendinopathy and we investigated glenoid cavity depth on the pathogenesis of cuff tendinopathy. We retrospectively evaluated 215 patients who underwent MRI. Of these, 60 patients showed cuff tendinopathy (group A) and 54 patients showed no pathology (group B). Glenoid cavity depth was calculated in the coronal and transverse planes. The mean axial depth was 1.7 ± 0.9 and the mean coronal depth 3.8 ± 0.9, for group A. The mean axial depth was 3.5 ± 0.7 and the mean coronal depth 1.5 ± 0.8, for group B. There were significant differences in the axial and coronal depths between the two groups. High coronal and low axial depth of the glenoid cavity can be used to diagnose RC tendinitis.

  2. Depth and degree of melting of komatiites

    Science.gov (United States)

    Herzberg, Claude

    1992-04-01

    High pressure melting experiments have permitted new constraints to be placed on the depth and degree of partial melting of komatiites. Komatiites from Gorgona Island were formed by relatively low degrees of pseudoinvariant melting involving L + Ol + Opx + Cpx + Gt on the solidus at 40 kbar, about 130 km depth. Munro-type komatiites were separated from a harzburgite residue (L + Ol + Opx) at pressures that were poorly constrained, but were probably around 50 kbar, about 165 km depth; the degree of partial melting was less than 40 percent. Secular variations in the geochemistry of komatiites could have formed in response to a reduction in the temperature and pressure of melting with time. The 3.5 Ga Barberton komatiites and the 2.7 Ga Munro-type komatiities could have formed in plumes that were hotter than the present-day mantle by 500 deg and 300 deg, respectively. When excess temperatures are this size, melting is deeper and volcanism changes from basaltic to momatiitic. The komatiities from Gorgona Island, which are Mesozoic in age, may be representative of komatiities that are predicted to occur in oceanic plateaus of Cretaceous age throughout the Pacific (Storey et al., 1991).

  3. GNF Defense in Depth Update

    Energy Technology Data Exchange (ETDEWEB)

    Lingenfelter, Andrew A.; Schneider, Robert J.; Cantonwine, Paul E.; Moore, Brian; Rea, John; Crawford, Douglas C. [Global Nuclear Fuel, P.O. Box 780 M/C H25, Wilmington, NC 28402 (United States)

    2009-06-15

    Global Nuclear Fuel (GNF) has designed, fabricated, and placed into operation more than 9 million fuel rods in approximately 135 thousand assemblies. Customer satisfaction has always compelled GNF to reduce fuel rod failures (defined here as fuel rods that breach or leak in service), However, increasing success with and subsequent expectations for economic performance of nuclear reactor plants have raised broader Industry emphasis on fuel reliability. In 2005, GNF established its Defense-in-Depth (DID) Program for the purpose of focusing attention on the many aspects of fuel design, fabrication, performance, and utilization that affect fuel reliability as well as on the key methods that govern the utilization of GNF fuel. The Program is structured to address each of the identified in-service, fuel failure mechanisms. This paper provides a summary of GNF fuel performance, following previous updates. This paper will discuss recent GNF fuel reliability and channel performance, GNF2 introduction status, and methods. GNF's more recent fuel experience includes approximately 3.8 million GE11/13 (9x9) and GE12/14 (10x10) fuel rods, well over half of which are the GE12/14 design. (Those figures also include roughly 25,000 recently-introduced GNF2 fuel rods.) Reliability, expressed as annual, observed fuel failure rates (i.e., number of rods failed each year divided by the number of opportunities, or fuel rods in service), has improved for each year since 2005. The GNF fuel failure rate for years leading up to 2007 and 2008 has been on the order of 5 to 7 ppm (excluding the corrosion events of 2001-2003), and as of this writing (January 2009) the current in-service failure has decreased to around 1.5 ppm. Failures in GE14 fuel rod failures have been primarily due to debris-fretting (> 60%), with other failures being duty-related or yet undetermined. The only failure observed in GNF2 to date was a single, early-life debris failure in a bundle not equipped with GNF

  4. Secondary neutral mass spectrometry depth profile analysis of silicides

    International Nuclear Information System (INIS)

    Beckmann, P.; Kopnarski, M.; Oechsner, H.

    1985-01-01

    The Direct Bombardment Mode (DBM) of Secondary Neutral Mass Spectrometry (SNMS) has been applied for depth profile analysis of two different multilayer systems containing metal silicides. Due to the extremely high depth resolution obtained with low energy SNMS structural details down to only a few atomic distances are detected. Stoichiometric information on internal oxides and implanted material is supplied by the high quantificability of SNMS. (Author)

  5. Cognitive psychology and depth psychology backgrounds

    International Nuclear Information System (INIS)

    Fritzsche, A.F.

    1986-01-01

    The sixth chapter gives an insight into the risk perception process which is highly determined by emotions, and, thus, deals with the psychological backgrounds of both the conscious cognitive and the subconscious intuitive realms of the human psyche. The chapter deals with the formation of opinion and the origination of an attitude towards an issue; cognitive-psychological patterns of thinking from the field of risk perception; the question of man's rationality; pertinent aspects of group behaviour; depth psychological backgrounds of the fear of technology; the collective subconscious; nuclear energy as a preferred object of projection for various psychological problems of modern man. (HSCH) [de

  6. 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.

  7. 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.

  8. Distribution in depth of quasars

    International Nuclear Information System (INIS)

    Schmidt, M.; Green, R.F.

    1980-01-01

    The authors discuss the distribution in depth of different kinds of quasars: quasi-stellar radio sources with steep radio spectrum, those with flat radio spectrum, and optically selected quasars. All exhibit an increase of space density with distance to a different degree. The optically selected quasars, in particular, show a steep increase of surface density with magnitude. The steepness of the increase is inconsistent with a uniform distribution of quasars in the local hypothesis. In the cosmological hypothesis the co-moving space density of optically selected quasars increases by a factor of 100,000 to a redshift of 2, and by factors of 1000 and 10 for steep-spectrum and flat-spectrum radio quasars, respectively. (Auth.)

  9. Simplicial band depth for multivariate functional data

    KAUST Repository

    López-Pintado, Sara

    2014-03-05

    We propose notions of simplicial band depth for multivariate functional data that extend the univariate functional band depth. The proposed simplicial band depths provide simple and natural criteria to measure the centrality of a trajectory within a sample of curves. Based on these depths, a sample of multivariate curves can be ordered from the center outward and order statistics can be defined. Properties of the proposed depths, such as invariance and consistency, can be established. A simulation study shows the robustness of this new definition of depth and the advantages of using a multivariate depth versus the marginal depths for detecting outliers. Real data examples from growth curves and signature data are used to illustrate the performance and usefulness of the proposed depths. © 2014 Springer-Verlag Berlin Heidelberg.

  10. Sedimentary basins reconnaissance using the magnetic Tilt-Depth method

    Science.gov (United States)

    Salem, A.; Williams, S.; Samson, E.; Fairhead, D.; Ravat, D.; Blakely, R.J.

    2010-01-01

    We compute the depth to the top of magnetic basement using the Tilt-Depth method from the best available magnetic anomaly grids covering the continental USA and Australia. For the USA, the Tilt-Depth estimates were compared with sediment thicknesses based on drilling data and show a correlation of 0.86 between the datasets. If random data were used then the correlation value goes to virtually zero. There is little to no lateral offset of the depth of basinal features although there is a tendency for the Tilt-Depth results to be slightly shallower than the drill depths. We also applied the Tilt-Depth method to a local-scale, relatively high-resolution aeromagnetic survey over the Olympic Peninsula of Washington State. The Tilt-Depth method successfully identified a variety of important tectonic elements known from geological mapping. Of particular interest, the Tilt-Depth method illuminated deep (3km) contacts within the non-magnetic sedimentary core of the Olympic Mountains, where magnetic anomalies are subdued and low in amplitude. For Australia, the Tilt-Depth estimates also give a good correlation with known areas of shallow basement and sedimentary basins. Our estimates of basement depth are not restricted to regional analysis but work equally well at the micro scale (basin scale) with depth estimates agreeing well with drill hole and seismic data. We focus on the eastern Officer Basin as an example of basin scale studies and find a good level of agreement between previously-derived basin models. However, our study potentially reveals depocentres not previously mapped due to the sparse distribution of well data. This example thus shows the potential additional advantage of the method in geological interpretation. The success of this study suggests that the Tilt-Depth method is useful in estimating the depth to crystalline basement when appropriate quality aeromagnetic anomaly data are used (i.e. line spacing on the order of or less than the expected depth to

  11. Fish depth distributions in the Lower Mississippi River

    Science.gov (United States)

    Killgore, K. J.; Miranda, Leandro E.

    2014-01-01

    A substantial body of literature exists about depth distribution of fish in oceans, lakes and reservoirs, but less is known about fish depth distribution in large rivers. Most of the emphasis on fish distributions in rivers has focused on longitudinal and latitudinal spatial distributions. Knowledge on depth distribution is necessary to understand species and community habitat needs. Considering this void, our goal was to identify patterns in fish benthic distribution along depth gradients in the Lower Mississippi River. Fish were collected over 14 years in depths down to 27 m. Fish exhibited non-random depth distributions that varied seasonally and according to species. Species richness was highest in shallow water, with about 50% of the 62 species detected no longer collected in water deeper than 8 m and about 75% no longer collected in water deeper than 12 m. Although richness was highest in shallow water, most species were not restricted to shallow water. Rather, most species used a wide range of depths. A weak depth zonation occurred, not as strong as that reported for deep oceans and lakes. Larger fish tended to occur in deeper water during the high-water period of an annual cycle, but no correlation was evident during the low-water period. The advent of landscape ecology has guided river research to search for spatial patterns along the length of the river and associated floodplains. Our results suggest that fish assemblages in large rivers are also structured vertically. 

  12. Development and Applications of Time of Flight Neutron Depth Profiling

    International Nuclear Information System (INIS)

    Cady, Bingham; Unlu, Kenan

    2005-01-01

    The depth profiles of intentional or intrinsic constituents of a sample provide valuable information for the characterization of materials. For example, the subtle differences in spatial distribution and composition of many chemical species in the near surface region and across interfacial boundaries can significantly alter the electronic and optical properties of materials. A number of analytical techniques for depth profiling have been developed during the last two decades. neutron Depth Profiling (NDP) is one of the leading analytical techniques. The NDP is a nondestructive near surface technique that utilizes thermal/cold neutron beam to measure the concentration of specific light elements versus their depth in materials. The depth is obtained from the energy loss of protons, alphas or recoil atoms in substrate materials. Since the charged particle energy determination using surface barrier detector is used for NDP, the depth resolution is highly dependent on the detectors an d detection instruments. The depth resolutions of a few tens of nm are achieved with available NDP facilities in the world. However, the performance of NDP needs to be improved in order to obtain a few A depth resolutions

  13. Attenuation properties and percentage depth dose of tannin-based Rhizophora spp. particleboard phantoms using computed tomography (CT) and treatment planning system (TPS) at high energy x-ray beams

    Energy Technology Data Exchange (ETDEWEB)

    Yusof, M. F. Mohd, E-mail: mfahmi@usm.my [School of Physics, Universiti Sains Malaysia, 11800 Penang (Malaysia); School of Health Sciences, Universiti Sains Malaysia, 16150 Kota Bharu, Kelantan (Malaysia); Abdullah, R. [School of Health Sciences, Universiti Sains Malaysia, 16150 Kota Bharu, Kelantan (Malaysia); Tajuddin, A. A. [School of Physics, Universiti Sains Malaysia, 11800 Penang (Malaysia); Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Penang (Malaysia); Hashim, R. [School of Industrial Technologies, Universiti Sains Malaysia, 11800 Penang (Malaysia); Bauk, S. [Physics Section, School of Distance Education, Universiti Sains Malaysia, 11800 Penang (Malaysia)

    2016-01-22

    A set of tannin-based Rhizophora spp. particleboard phantoms with dimension of 30 cm x 30 cm was fabricated at target density of 1.0 g/cm{sup 3}. The mass attenuation coefficient of the phantom was measured using {sup 60}Co gamma source. The phantoms were scanned using Computed Tomography (CT) scanner and the percentage depth dose (PDD) of the phantom was calculated using treatment planning system (TPS) at 6 MV and 10 MV x-ray and compared to that in solid water phantoms. The result showed that the mass attenuation coefficient of tannin-based Rhizohora spp. phantoms was near to the value of water with χ{sup 2} value of 1.2. The measured PDD also showed good agreement with solid water phantom at both 6 MV and 10 MV x-ray with percentage deviation below 8% at depth beyond the maximum dose, Z{sub max}.

  14. Depth-resolved ballistic imaging in a low-depth-of-field optical Kerr gated imaging system

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Yipeng; Tan, Wenjiang, E-mail: tanwenjiang@mail.xjtu.edu.cn; Si, Jinhai; Ren, YuHu; Xu, Shichao; Hou, Xun [Key Laboratory for Physical Electronics and Devices of the Ministry of Education and Shaanxi Key Lab of Information Photonic Technique, School of Electronics and Information Engineering, Xi' an Jiaotong University, Xianning-xilu 28, Xi' an 710049 (China); Tong, Junyi [Departments of Applied Physics, Xi' an University of Technology, Xi' an 710048 (China)

    2016-09-07

    We demonstrate depth-resolved imaging in a ballistic imaging system, in which a heterodyned femtosecond optical Kerr gate is introduced to extract useful imaging photons for detecting an object hidden in turbid media and a compound lens is proposed to ensure both the depth-resolved imaging capability and the long working distance. Two objects of about 15-μm widths hidden in a polystyrene-sphere suspension have been successfully imaged with approximately 600-μm depth resolution. Modulation-transfer-function curves with the object in and away from the object plane have also been measured to confirm the depth-resolved imaging capability of the low-depth-of-field (low-DOF) ballistic imaging system. This imaging approach shows potential for application in research of the internal structure of highly scattering fuel spray.

  15. 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...

  16. Updating default depths in the ISC bulletin

    Science.gov (United States)

    Bolton, Maiclaire K.; Storchak, Dmitry A.; Harris, James

    2006-09-01

    The International Seismological Centre (ISC) publishes the definitive global bulletin of earthquake locations. In the ISC bulletin, we aim to obtain a free depth, but often this is not possible. Subsequently, the first option is to obtain a depth derived from depth phases. If depth phases are not available, we then use the reported depth from a reputable local agency. Finally, as a last resort, we set a default depth. In the past, common depths of 10, 33, or multiples of 50 km have been assigned. Assigning a more meaningful default depth, specific to a seismic region will increase the consistency of earthquake locations within the ISC bulletin and allow the ISC to publish better positions and magnitude estimates. It will also improve the association of reported secondary arrivals to corresponding seismic events. We aim to produce a global set of default depths, based on a typical depth for each area, from well-constrained events in the ISC bulletin or where depth could be constrained using a consistent set of depth phase arrivals provided by a number of different reporters. In certain areas, we must resort to using other assumptions. For these cases, we use a global crustal model (Crust2.0) to set default depths to half the thickness of the crust.

  17. Measurements of seasonal frost depth by frost tube in Japan

    Science.gov (United States)

    Harada, K.; Yoshikawa, K.; Iwahana, G.; Stanilovskaya, J. V.; Sawada, Y.; Sone, T.

    2017-12-01

    Since 2011 winter season, frost depths have been measured as an outreach program in Hokkaido, northern part of Japan, where seasonal ground freezing occurs in winter. Frost depths were measured in elementary, junior high and high schools in order to emphasis their interest for earth sciences. At schools, using simple frost tube, measurements were conducted directly once a week by students or teacher during ground freezing under no snow-removal condition. A lecture was made in class and a frost tube was set at schoolyard, as the same tube and protocol as UAF's Permafrost Outreach Program, using clear tube with blue-colored water. In 2011 winter season, we started measurements at three schools, and the number of school extended to 32 in 2016 season, 26 elementary schools, 5 junior high schools and one high school. We visited schools in summer time or just before frost season to talk about the method of measurement, and measurements by students started just after ground freezing. After the end of frozen period, we visited schools again to explain results of each school or another schools in Japan, Alaska, Canada or Russia. The measured frost depths in Hokkaido ranged widely, from only a few centimeter to more than 50 cm. However, some schools had no frost depth due to heavy snow. We confirmed that the frost depth strongly depends on air temperature and snow depth. The lecture was made to student why the frost depth ranged widely, and the effect of snow was explained by using the example of igloo. In order to validate the effect of snow and to compare frost depths, we tried to measure frost depths under snow-removal and no snow-removal conditions at the same elementary school. At the end of December, depths had no significant difference between these conditions, and the difference went to 14 cm after one month, with about 30 cm of snow depth. After these measurements and lectures, students noticed snow has a role as insulator and affects the frost depth.

  18. Depth-dependent positron annihilation in different polymers

    Energy Technology Data Exchange (ETDEWEB)

    Yang, J.; Zhang, P.; Cheng, G.D.; Li, D.X.; Wu, H.B.; Li, Z.X.; Cao, X.Z. [Key Laboratory of Nuclear Analysis Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, No. 19 Yuquan Lu, Beijing 100049 (China); Jia, Q.J. [Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, No. 19 Yuquan Lu, Beijing 100049 (China); Yu, R.S. [Key Laboratory of Nuclear Analysis Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, No. 19 Yuquan Lu, Beijing 100049 (China); Wang, B.Y., E-mail: wangboy@ihep.ac.cn [Key Laboratory of Nuclear Analysis Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, No. 19 Yuquan Lu, Beijing 100049 (China)

    2013-09-01

    Depth-dependent positron annihilation Doppler broadening measurements were conducted for polymers with different chemical compositions. Variations of the S parameter with respect to incident positron energy were observed. For pure hydrocarbons PP, HDPE and oxygen-containing polymer PC, S parameter rises with increasing positron implantation depth. While for PI and fluoropolymers like PTFE, ETFE and PVF, S parameter decreases with higher positron energy. For chlorine-containing polymer PVDC, S parameter remains nearly constant at all incident positron energies. It is suggested that these three variation trends are resulted from a competitive effect between the depth-dependent positronium formation and the influence of highly electronegative atoms on positron annihilation characteristics.

  19. EOP TDRs (Temperature-Depth-Recordings) Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Temperature-depth-recorders (TDRs) were attached to commercial longline and research Cobb trawl gear to obtain absolute depth and temperature measurement during...

  20. Simplicial band depth for multivariate functional data

    KAUST Repository

    Ló pez-Pintado, Sara; Sun, Ying; Lin, Juan K.; Genton, Marc G.

    2014-01-01

    sample of curves. Based on these depths, a sample of multivariate curves can be ordered from the center outward and order statistics can be defined. Properties of the proposed depths, such as invariance and consistency, can be established. A simulation

  1. Visual Discomfort and Depth-of-Field

    Directory of Open Access Journals (Sweden)

    Louise O'Hare

    2013-05-01

    Full Text Available Visual discomfort has been reported for certain visual stimuli and under particular viewing conditions, such as stereoscopic viewing. In stereoscopic viewing, visual discomfort can be caused by a conflict between accommodation and convergence cues that may specify different distances in depth. Earlier research has shown that depth-of-field, which is the distance range in depth in the scene that is perceived to be sharp, influences both the perception of egocentric distance to the focal plane, and the distance range in depth between objects in the scene. Because depth-of-field may also be in conflict with convergence and the accommodative state of the eyes, we raised the question of whether depth-of-field affects discomfort when viewing stereoscopic photographs. The first experiment assessed whether discomfort increases when depth-of-field is in conflict with coherent accommodation–convergence cues to distance in depth. The second experiment assessed whether depth-of-field influences discomfort from a pre-existing accommodation–convergence conflict. Results showed no effect of depth-of-field on visual discomfort. These results suggest therefore that depth-of-field can be used as a cue to depth without inducing discomfort in the viewer, even when cue conflicts are large.

  2. Investigation on a procedure for optimal axial depth of cut accuracy in micromilling

    DEFF Research Database (Denmark)

    Bissacco, Giuliano; Hansen, Hans Nørgaard; De Chiffre, Leonardo

    2005-01-01

    On the basis of a previously developed procedure for control of axial depth of cut in high accuracy micromilling operations, this paper presents an investigation on the estimation of the uncertainty of the set axial depth of cut.......On the basis of a previously developed procedure for control of axial depth of cut in high accuracy micromilling operations, this paper presents an investigation on the estimation of the uncertainty of the set axial depth of cut....

  3. Extreme depth-of-field intraocular lenses

    Science.gov (United States)

    Baker, Kenneth M.

    1996-05-01

    A new technology brings the full aperture single vision pseudophakic eye's effective hyperfocal distance within the half-meter range. A modulated index IOL containing a subsurface zeroth order coherent microlenticular mosaic defined by an index gradient adds a normalizing function to the vergences or parallactic angles of incoming light rays subtended from field object points and redirects them, in the case of near-field images, to that of far-field images. Along with a scalar reduction of the IOL's linear focal range, this results in an extreme depth of field with a narrow depth of focus and avoids the focal split-up, halo, and inherent reduction in contrast of multifocal IOLs. A high microlenticular spatial frequency, which, while still retaining an anisotropic medium, results in a nearly total zeroth order propagation throughout the visible spectrum. The curved lens surfaces still provide most of the refractive power of the IOL, and the unique holographic fabrication technology is especially suitable not only for IOLs but also for contact lenses, artificial corneas, and miniature lens elements for cameras and other optical devices.

  4. Junction depth measurement using carrier illumination

    International Nuclear Information System (INIS)

    Borden, Peter

    2001-01-01

    Carrier Illumination [trade mark] (CI) is a new method recently developed to meet the need for a non-destructive, high throughput junction depth measurement on patterned wafers. A laser beam creates a quasi-static excess carrier profile in the semiconductor underlying the activated junction. The excess carrier profile is fairly constant below the junction, and drops rapidly in the junction, creating a steep index of refraction gradient at the junction edge. Interference with light reflected from this index gradient provides a signal that is analyzed to determine the junction depth. The paper summarizes evaluation of performance in full NMOS and PMOS process flows, on both bare and patterned wafers. The aims have been to validate (1) performance in the presence of underlying layers typically found at the source/drain (S/D) process steps and (2) measurement on patterned wafers. Correlation of CI measurements to SIMS and transistor drive current are shown. The data were obtained from NMOS structures using As S/D and LDD implants. Correlations to SRP, SIMS and sheet resistance are shown for PMOS structures using B 11 LDD implants. Gage capability measurements are also presented

  5. Effective depth of spermatogonia in man

    International Nuclear Information System (INIS)

    Casey, R.; Jewett, M.A.S.; Facey, R.A.

    1982-01-01

    Dosimetry for sperm cells irradiated by high-energy betas requires precise knowledge of the effective depth of the spermatogonia, and hence the thickness of overlying tissues (scrotum plus tunics)), because beta dose rate changes very rapidly with depth. Measurements were made on 25 volunteers and surgical patients by mechanical caliper during surgery (2), by ultrasound (14), or by both (9), all at 20 deg C air temperature. The tunica albuginea (TA) measured 0.1 mm. The surgical results (TA excluded) were 2.0 mm, σ = 0.3 mm (n = 11). The ultrasound results (TA included) were 2.2 mm,σ = 0.6 mm (n = 23). There was no correlation of scrotal thickness with age (24-83 years) and only a very weak correlation (r = 0.3) with body mass. There was no decrease in scrotal thickness (at 20 deg C) with further warming but there was an increase (to 3.3 mm from 2.3 mm) with chilling before measurement. Ultrasound is shown to be valid for such measurements. (author)

  6. Aerosol Optical Depth Over India

    Science.gov (United States)

    David, Liji Mary; Ravishankara, A. R.; Kodros, John K.; Venkataraman, Chandra; Sadavarte, Pankaj; Pierce, Jeffrey R.; Chaliyakunnel, Sreelekha; Millet, Dylan B.

    2018-04-01

    Tropospheric aerosol optical depth (AOD) over India was simulated by Goddard Earth Observing System (GEOS)-Chem, a global 3-D chemical-transport model, using SMOG (Speciated Multi-pOllutant Generator from Indian Institute of Technology Bombay) and GEOS-Chem (GC) (current inventories used in the GEOS-Chem model) inventories for 2012. The simulated AODs were 80% (SMOG) and 60% (GC) of those measured by the satellites (Moderate Resolution Imaging Spectroradiometer and Multi-angle Imaging SpectroRadiometer). There is no strong seasonal variation in AOD over India. The peak AOD values are observed/simulated during summer. The simulated AOD using SMOG inventory has particulate black and organic carbon AOD higher by a factor 5 and 3, respectively, compared to GC inventory. The model underpredicted coarse-mode AOD but agreed for fine-mode AOD with Aerosol Robotic Network data. It captured dust only over Western India, which is a desert, and not elsewhere, probably due to inaccurate dust transport and/or noninclusion of other dust sources. The calculated AOD, after dust correction, showed the general features in its observed spatial variation. Highest AOD values were observed over the Indo-Gangetic Plain followed by Central and Southern India with lowest values in Northern India. Transport of aerosols from Indo-Gangetic Plain and Central India into Eastern India, where emissions are low, is significant. The major contributors to total AOD over India are inorganic aerosol (41-64%), organic carbon (14-26%), and dust (7-32%). AOD over most regions of India is a factor of 5 or higher than over the United States.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Is visual short-term memory depthful?

    Science.gov (United States)

    Reeves, Adam; Lei, Quan

    2014-03-01

    Does visual short-term memory (VSTM) depend on depth, as it might be if information was stored in more than one depth layer? Depth is critical in natural viewing and might be expected to affect retention, but whether this is so is currently unknown. Cued partial reports of letter arrays (Sperling, 1960) were measured up to 700 ms after display termination. Adding stereoscopic depth hardly affected VSTM capacity or decay inferred from total errors. The pattern of transposition errors (letters reported from an uncued row) was almost independent of depth and cue delay. We conclude that VSTM is effectively two-dimensional. Copyright © 2014 Elsevier Ltd. All rights reserved.

  13. 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.

  14. An efficient parallel algorithm: Poststack and prestack Kirchhoff 3D depth migration using flexi-depth iterations

    Science.gov (United States)

    Rastogi, Richa; Srivastava, Abhishek; Khonde, Kiran; Sirasala, Kirannmayi M.; Londhe, Ashutosh; Chavhan, Hitesh

    2015-07-01

    This paper presents an efficient parallel 3D Kirchhoff depth migration algorithm suitable for current class of multicore architecture. The fundamental Kirchhoff depth migration algorithm exhibits inherent parallelism however, when it comes to 3D data migration, as the data size increases the resource requirement of the algorithm also increases. This challenges its practical implementation even on current generation high performance computing systems. Therefore a smart parallelization approach is essential to handle 3D data for migration. The most compute intensive part of Kirchhoff depth migration algorithm is the calculation of traveltime tables due to its resource requirements such as memory/storage and I/O. In the current research work, we target this area and develop a competent parallel algorithm for post and prestack 3D Kirchhoff depth migration, using hybrid MPI+OpenMP programming techniques. We introduce a concept of flexi-depth iterations while depth migrating data in parallel imaging space, using optimized traveltime table computations. This concept provides flexibility to the algorithm by migrating data in a number of depth iterations, which depends upon the available node memory and the size of data to be migrated during runtime. Furthermore, it minimizes the requirements of storage, I/O and inter-node communication, thus making it advantageous over the conventional parallelization approaches. The developed parallel algorithm is demonstrated and analysed on Yuva II, a PARAM series of supercomputers. Optimization, performance and scalability experiment results along with the migration outcome show the effectiveness of the parallel algorithm.

  15. Slab tears and intermediate-depth seismicity

    Science.gov (United States)

    Meighan, Hallie E.; ten Brink, Uri S.; Pulliam, Jay

    2013-01-01

    Active tectonic regions where plate boundaries transition from subduction to strike slip can take several forms, such as triple junctions, acute, and obtuse corners. Well-documented slab tears that are associated with high rates of intermediate-depth seismicity are considered here: Gibraltar arc, the southern and northern ends of the Lesser Antilles arc, and the northern end of Tonga trench. Seismicity at each of these locations occurs, at times, in the form of swarms or clusters, and various authors have proposed that each marks an active locus of tear propagation. The swarms and clusters start at the top of the slab below the asthenospheric wedge and extend 30–60 km vertically downward within the slab. We propose that these swarms and clusters are generated by fluid-related embrittlement of mantle rocks. Focal mechanisms of these swarms generally fit the shear motion that is thought to be associated with the tearing process.

  16. Next Generation Nuclear Plant Defense-in-Depth Approach

    International Nuclear Information System (INIS)

    Wallace, Edward G.; Fleming, Karl N.; Burns, Edward M.

    2009-01-01

    The purpose of this paper is to (1) document the definition of defense-in-depth and the pproach that will be used to assure that its principles are satisfied for the NGNP project and (2) identify the specific questions proposed for preapplication discussions with the NRC. Defense-in-depth is a safety philosophy in which multiple lines of defense and conservative design and evaluation methods are applied to assure the safety of the public. The philosophy is also intended to deliver a design that is tolerant to uncertainties in knowledge of plant behavior, component reliability or operator performance that might compromise safety. This paper includes a review of the regulatory foundation for defense-in-depth, a definition of defense-in-depth that is appropriate for advanced reactor designs based on High Temperature Gas-cooled Reactor (HTGR) technology, and an explanation of how this safety philosophy is achieved in the NGNP.

  17. Subring Depth, Frobenius Extensions, and Towers

    Directory of Open Access Journals (Sweden)

    Lars Kadison

    2012-01-01

    Full Text Available The minimum depth d(B,A of a subring B⊆A introduced in the work of Boltje, Danz and Külshammer (2011 is studied and compared with the tower depth of a Frobenius extension. We show that d(B,A < ∞ if A is a finite-dimensional algebra and Be has finite representation type. Some conditions in terms of depth and QF property are given that ensure that the modular function of a Hopf algebra restricts to the modular function of a Hopf subalgebra. If A⊇B is a QF extension, minimum left and right even subring depths are shown to coincide. If A⊇B is a Frobenius extension with surjective Frobenius, homomorphism, its subring depth is shown to coincide with its tower depth. Formulas for the ring, module, Frobenius and Temperley-Lieb structures are noted for the tower over a Frobenius extension in its realization as tensor powers. A depth 3 QF extension is embedded in a depth 2 QF extension; in turn certain depth n extensions embed in depth 3 extensions if they are Frobenius extensions or other special ring extensions with ring structures on their relative Hochschild bar resolution groups.

  18. Junction depth dependence of breakdown in silicon detector diodes

    International Nuclear Information System (INIS)

    Beck, G.A.; Carter, A.A.; Carter, J.R.; Greenwood, N.M.; Lucas, A.D.; Munday, D.J.; Pritchard, T.W.; Robinson, D.; Wilburn, C.D.; Wyllie, K.

    1996-01-01

    The high voltage capability of detector diodes fabricated in the planar process is limited by the high field generated at the edge of the junction.We have fabricated diodes with increased junction depth with respect to our standard process and find a significantly higher breakdown voltage,in reasonable agreement with previous studies of junction breakdown. (orig.)

  19. Assessment of defence in depth for nuclear power plants

    International Nuclear Information System (INIS)

    2005-01-01

    Defence in depth is a comprehensive approach to safety that has been developed by nuclear power experts to ensure with high confidence that the public and the environment are protected from any hazards posed by the use of nuclear power for the generation of electricity. The concepts of defence in depth and safety culture have served the nuclear power industry well as a basic philosophy for the safe design and operation of nuclear power plants. Properly applied, defence in depth ensures that no single human error or equipment failure at one level of defence, nor even a combination of failures at more than one level of defence, propagates to jeopardize defence in depth at the subsequent level or leads to harm to the public or the environment. The importance of the concept of defence in depth is underlined in IAEA Safety Standards, in particular in the requirements set forth in the Safety Standards: Safety of Nuclear Power Plants: Design (NS-R-1) and Safety Assessment and Verification for Nuclear Power Plants (NS-G-1.2). A specific report, Defence in Depth in Nuclear Safety (INSAG-10), describes the objectives, strategy, implementation and future development in the area of defence in depth in nuclear and radiation safety. In the report Basic Safety Principles for Nuclear Power Plants (INSAG-12), defence in depth is recognized as one of the fundamental safety principles that underlie the safety of nuclear power plants. In consonance with those high level publications, this Safety Report provides more specific technical information on the implementation of this concept in the siting, design, construction and operation of nuclear power plants. It describes a method for comprehensive and balanced review of the provisions required for implementing defence in depth in existing plants. This publication is intended to provide guidance primarily for the self-assessment by plant operators of the comprehensiveness and quality of defence in depth provisions. It can be used

  20. Mapping the Flavor Contributing Traits on "Fengwei Melon" (Cucumis melo L. Chromosomes Using Parent Resequencing and Super Bulked-Segregant Analysis.

    Directory of Open Access Journals (Sweden)

    Hong Zhang

    Full Text Available We used a next-generation high-throughput sequencing platform to resequence the Xinguowei and Shouxing melon cultivars, the parents of Fengwei melon. We found 84% of the reads (under a coverage rate of "13×" placed on the reference genome DHL92. There were 2,550,000 single-nucleotide polymorphisms and 140,000 structural variations in the two genomes. We also identified 1,290 polymorphic genes between Xinguowei and Shouxing. We combined specific length amplified fragment sequencing (SLAF-seq and bulked-segregant analysis (super-BSA to analyze the two parents and the F2 extreme phenotypes. This combined method yielded 12,438,270 reads, 46,087 SLAF tags, and 4,480 polymorphic markers (average depth of 161.81×. There were six sweet trait-related regions containing 13 differential SLAF markers, and 23 sour trait-related regions containing 48 differential SLAF markers. We further fine-mapped the sweet trait to the genomic regions on chromosomes 6, 10, 11, and 12. Correspondingly, we mapped the sour trait-related genomic regions to chromosomes 2, 3, 4, 5, 9, and 12. Finally, we positioned nine of the 61 differential markers in the sweet and sour trait candidate regions on the parental genome. These markers corresponded to one sweet and eight sour trait-related genes. Our study provides a basis for marker-assisted breeding of desirable sweet and sour traits in Fengwei melons.

  1. Coding of Depth Images for 3DTV

    DEFF Research Database (Denmark)

    Zamarin, Marco; Forchhammer, Søren

    In this short paper a brief overview of the topic of coding and compression of depth images for multi-view image and video coding is provided. Depth images represent a convenient way to describe distances in the 3D scene, useful for 3D video processing purposes. Standard approaches...... for the compression of depth images are described and compared against some recent specialized algorithms able to achieve higher compression performances. Future research directions close the paper....

  2. Variation of curve number with storm depth

    Science.gov (United States)

    Banasik, K.; Hejduk, L.

    2012-04-01

    The NRCS Curve Number (known also as SCS-CN) method is well known as a tool in predicting flood runoff depth from small ungauged catchment. The traditional way of determination the CNs, based on soil characteristics, land use and hydrological conditions, seemed to have tendency to overpredict the floods in some cases. Over 30 year rainfall-runoff data, collected in two small (A=23.4 & 82.4 km2), lowland, agricultural catchments in Center of Poland (Banasik & Woodward 2010), were used to determine runoff Curve Number and to check a tendency of changing. The observed CN declines with increasing storm size, which according recent views of Hawkins (1993) could be classified as a standard response of watershed. The analysis concluded, that using CN value according to the procedure described in USDA-SCS Handbook one receives representative value for estimating storm runoff from high rainfall depths in the analyzes catchments. This has been confirmed by applying "asymptotic approach" for estimating the watershed curve number from the rainfall-runoff data. Furthermore, the analysis indicated that CN, estimated from mean retention parameter S of recorded events with rainfall depth higher than initial abstraction, is also approaching the theoretical CN. The observed CN, ranging from 59.8 to 97.1 and from 52.3 to 95.5, in the smaller and the larger catchment respectively, declines with increasing storm size, which has been classified as a standard response of watershed. The investigation demonstrated also changeability of the CN during a year, with much lower values during the vegetation season. Banasik K. & D.E. Woodward (2010). "Empirical determination of curve number for a small agricultural watrshed in Poland". 2nd Joint Federal Interagency Conference, Las Vegas, NV, June 27 - July 1, 2010 (http://acwi.gov/sos/pubs/2ndJFIC/Contents/10E_Banasik_ 28_02_10. pdf). Hawkins R. H. (1993). "Asymptotic determination of curve numbers from data". Journal of Irrigation and Drainage

  3. Depth Perception In Remote Stereoscopic Viewing Systems

    Science.gov (United States)

    Diner, Daniel B.; Von Sydow, Marika

    1989-01-01

    Report describes theoretical and experimental studies of perception of depth by human operators through stereoscopic video systems. Purpose of such studies to optimize dual-camera configurations used to view workspaces of remote manipulators at distances of 1 to 3 m from cameras. According to analysis, static stereoscopic depth distortion decreased, without decreasing stereoscopitc depth resolution, by increasing camera-to-object and intercamera distances and camera focal length. Further predicts dynamic stereoscopic depth distortion reduced by rotating cameras around center of circle passing through point of convergence of viewing axes and first nodal points of two camera lenses.

  4. Directional Joint Bilateral Filter for Depth Images

    Directory of Open Access Journals (Sweden)

    Anh Vu Le

    2014-06-01

    Full Text Available Depth maps taken by the low cost Kinect sensor are often noisy and incomplete. Thus, post-processing for obtaining reliable depth maps is necessary for advanced image and video applications such as object recognition and multi-view rendering. In this paper, we propose adaptive directional filters that fill the holes and suppress the noise in depth maps. Specifically, novel filters whose window shapes are adaptively adjusted based on the edge direction of the color image are presented. Experimental results show that our method yields higher quality filtered depth maps than other existing methods, especially at the edge boundaries.

  5. ACCURACY ANALYSIS OF KINECT DEPTH DATA

    Directory of Open Access Journals (Sweden)

    K. Khoshelham

    2012-09-01

    Full Text Available This paper presents an investigation of the geometric quality of depth data obtained by the Kinect sensor. Based on the mathematical model of depth measurement by the sensor a theoretical error analysis is presented, which provides an insight into the factors influencing the accuracy of the data. Experimental results show that the random error of depth measurement increases with increasing distance to the sensor, and ranges from a few millimetres up to about 4 cm at the maximum range of the sensor. The accuracy of the data is also found to be influenced by the low resolution of the depth measurements.

  6. The coefficient of friction of chrysotile gouge at seismogenic depths

    Science.gov (United States)

    Moore, Diane E.; Lockner, D.A.; Tanaka, H.; Iwata, K.

    2004-01-01

    We report new strength data for the serpentine mineral chrysotile at effective normal stresses, ??sn between 40 and 200 MPa in the temperature range 25??-280??C. Overall, the coefficient of friction, ?? (= shear stress/effective normal stress) of water-saturated chrysotile gouge increases both with increasing temperature and ??sn, but the rates vary and the temperature-related increases begin at ???100??C. As a result, a frictional strength minimum (?? = 0.1) occurs at low ??sn at about 100??C. Maximum strength (?? = 0.55) results from a combination of high normal stress and high temperature. The low-strength region is characterized by velocity strengthening and the high-strength region by velocity-weakening behavior. Thoroughly dried chrysotile has ?? = 0.7 and is velocity-weakening. The frictional properties of chrysolite can be explained in its tendency to adsorb large amounts of water that acts as a lubricant during shear. The water is progressively driven off the fiber surfaces with increasing temperature and pressure, causing chrysotile to approach its dry strength. Depth profiles for a chrysotile-lined fault constructed from these data would pass through a strength minimum at ???3 km depth, where sliding should be stable. Below that depth, strength increases rapidly as does the tendency for unstable (seismic) slip. Such a trend would not have been predicted from the room-temperature data. These results therefore illustrate the potential hazards of extrapolating room-temperature friction data to predict fault zone behavior at depth. This depth profile for chrysotile is consistent with the pattern of slip on the Hayward fault, which creeps aseismically at shallow depths but which may be locked below 5 km depth. ?? 2004 by V. H. Winston and Son, Inc. All rights reserved.

  7. Resilience to Changing Snow Depth in a Shrubland Ecosystem.

    Science.gov (United States)

    Loik, M. E.

    2008-12-01

    Snowfall is the dominant hydrologic input for high elevations and latitudes of the arid- and semi-arid western United States. Sierra Nevada snowpack provides numerous important services for California, but is vulnerable to anthropogenic forcing of the coupled ocean-atmosphere system. GCM and RCM scenarios envision reduced snowpack and earlier melt under a warmer climate, but how will these changes affect soil and plant water relations and ecosystem processes? And, how resilient will this ecosystem be to short- and long-term forcing of snow depth and melt timing? To address these questions, our experiments utilize large- scale, long-term roadside snow fences to manipulate snow depth and melt timing in eastern California, USA. Interannual snow depth averages 1344 mm with a CV of 48% (April 1, 1928-2008). Snow fences altered snow melt timing by up to 18 days in high-snowfall years, and affected short-term soil moisture pulses less in low- than medium- or high-snowfall years. Sublimation in this arid location accounted for about 2 mol m- 2 of water loss from the snowpack in 2005. Plant water potential increased after the ENSO winter of 2005 and stayed relatively constant for the following three years, even after the low snowfall of winter 2007. Over the long-term, changes in snow depth and melt timing have impacted cover or biomass of Achnatherum thurberianum, Elymus elemoides, and Purshia tridentata. Growth of adult conifers (Pinus jeffreyi and Pi. contorta) was not equally sensitive to snow depth. Thus, complex interactions between snow depth, soil water inputs, physiological processes, and population patterns help drive the resilience of this ecosystem to changes in snow depth and melt timing.

  8. An Exploration of the Needling Depth in Acupuncture: The Safe Needling Depth and the Needling Depth of Clinical Efficacy

    Directory of Open Access Journals (Sweden)

    Jaung-Geng Lin

    2013-01-01

    Full Text Available Objective. To explore the existing scientific information regarding safe needling depth of acupuncture points and the needling depth of clinical efficacy. Methods. We searched the PubMed, EMBASE, Cochrane, Allied and Complementary Medicine (AMED, The National Center for Complementary and Alternative Medicine (NCCAM, and China National Knowledge Infrastructure (CNKI databases to identify relevant monographs and related references from 1991 to 2013. Chinese journals and theses/dissertations were hand searched. Results. 47 studies were recruited and divided into 6 groups by measuring tools, that is, MRI, in vivo evaluation, CT, ultrasound, dissected specimen of cadavers, and another group with clinical efficacy. Each research was analyzed for study design, definition of safe depth, and factors that would affect the measured depths. Depths of clinical efficacy were discussed from the perspective of de-qi and other clinical observations. Conclusions. Great inconsistency in depth of each point measured from different subject groups and tools exists. The definition of safe depth should be established through standardization. There is also lack of researches to compare the clinical efficacy. A well-designed clinical trial selecting proper measuring tools to decide the actual and advisable needling depth for each point, to avoid adverse effects or complications and promote optimal clinical efficacy, is a top priority.

  9. Mid-depth temperature maximum in an estuarine lake

    Science.gov (United States)

    Stepanenko, V. M.; Repina, I. A.; Artamonov, A. Yu; Gorin, S. L.; Lykossov, V. N.; Kulyamin, D. V.

    2018-03-01

    The mid-depth temperature maximum (TeM) was measured in an estuarine Bol’shoi Vilyui Lake (Kamchatka peninsula, Russia) in summer 2015. We applied 1D k-ɛ model LAKE to the case, and found it successfully simulating the phenomenon. We argue that the main prerequisite for mid-depth TeM development is a salinity increase below the freshwater mixed layer, sharp enough in order to increase the temperature with depth not to cause convective mixing and double diffusion there. Given that this condition is satisfied, the TeM magnitude is controlled by physical factors which we identified as: radiation absorption below the mixed layer, mixed-layer temperature dynamics, vertical heat conduction and water-sediments heat exchange. In addition to these, we formulate the mechanism of temperature maximum ‘pumping’, resulting from the phase shift between diurnal cycles of mixed-layer depth and temperature maximum magnitude. Based on the LAKE model results we quantify the contribution of the above listed mechanisms and find their individual significance highly sensitive to water turbidity. Relying on physical mechanisms identified we define environmental conditions favouring the summertime TeM development in salinity-stratified lakes as: small-mixed layer depth (roughly, ~wind and cloudless weather. We exemplify the effect of mixed-layer depth on TeM by a set of selected lakes.

  10. Does footprint depth correlate with foot motion and pressure?

    Science.gov (United States)

    Bates, K T; Savage, R; Pataky, T C; Morse, S A; Webster, E; Falkingham, P L; Ren, L; Qian, Z; Collins, D; Bennett, M R; McClymont, J; Crompton, R H

    2013-06-06

    Footprints are the most direct source of evidence about locomotor biomechanics in extinct vertebrates. One of the principal suppositions underpinning biomechanical inferences is that footprint geometry correlates with dynamic foot pressure, which, in turn, is linked with overall limb motion of the trackmaker. In this study, we perform the first quantitative test of this long-standing assumption, using topological statistical analysis of plantar pressures and experimental and computer-simulated footprints. In computer-simulated footprints, the relative distribution of depth differed from the distribution of both peak and pressure impulse in all simulations. Analysis of footprint samples with common loading inputs and similar depths reveals that only shallow footprints lack significant topological differences between depth and pressure distributions. Topological comparison of plantar pressures and experimental beach footprints demonstrates that geometry is highly dependent on overall print depth; deeper footprints are characterized by greater relative forefoot, and particularly toe, depth than shallow footprints. The highlighted difference between 'shallow' and 'deep' footprints clearly emphasizes the need to understand variation in foot mechanics across different degrees of substrate compliance. Overall, our results indicate that extreme caution is required when applying the 'depth equals pressure' paradigm to hominin footprints, and by extension, those of other extant and extinct tetrapods.

  11. Hydrologic Regulation of Plant Rooting Depth and Vice Versa

    Science.gov (United States)

    Fan, Y.; Miguez-Macho, G.

    2017-12-01

    How deep plant roots go and why may hold the answer to several questions regarding the co-evolution of terrestrial life and its environment. In this talk we explore how plant rooting depth responds to the hydrologic plumbing system in the soil/regolith/bedrocks, and vice versa. Through analyzing 2200 root observations of >1000 species along biotic (life form, genus) and abiotic (precipitation, soil, drainage) gradients, we found strong sensitivities of rooting depth to local soil water profiles determined by precipitation infiltration depth from the top (reflecting climate and soil), and groundwater table depth from below (reflecting topography-driven land drainage). In well-drained uplands, rooting depth follows infiltration depth; in waterlogged lowlands, roots stay shallow avoiding oxygen stress below the water table; in between, high productivity and drought can send roots many meters down to groundwater capillary fringe. We explore the global significance of this framework using an inverse model, and the implications to the coevolution of deep roots and the CZ in the Early-Mid Devonian when plants colonized the upland environments.

  12. Metrology aspects of SIMS depth profiling for advanced ULSI processes

    International Nuclear Information System (INIS)

    Budrevich, Andre; Hunter, Jerry

    1998-01-01

    As the semiconductor industry roadmap passes through the 0.1 μm technology node, the junction depth of the transistor source/drain extension will be required to be less than 20 nm and the well doping will be near 1.0 μm in depth. The development of advanced ULSI processing techniques requires the evolution of new metrology tools to ensure process capability. High sensitivity (ppb) coupled with excellent depth resolution (1 nm) makes SIMS the technique of choice for measuring the in-depth chemical distribution of these dopants with high precision and accuracy. This paper will discuss the issues, which impact the accuracy and precision of SIMS measurements of ion implants (both shallow and deep). First this paper will discuss common uses of the SIMS technique in the technology development and manufacturing of advanced ULSI processes. In the second part of this paper the ability of SIMS to make high precision measurements of ion implant depth profiles will be studied

  13. Depth of origin of atoms sputtered from crystalline targets

    International Nuclear Information System (INIS)

    Shapiro, M.H.; Trovato, E.; Tombrello, T.A.

    2001-01-01

    Recently, V.I. Shulga and W. Eckstein (Nucl. Instr. and Meth. B 145 (1998) 492) investigated the depth of origin of atoms sputtered from random elemental targets using the Monte Carlo code TRIM.SP and the lattice code OKSANA. They found that the mean depth of origin is proportional to N -0.86 , where N is the atomic density; and that the most probable escape depth is ∼λ 0 /2, where λ 0 is the mean atomic distance. Since earlier molecular dynamics simulations with small crystalline elemental targets typically produced a most probable escape depth of zero (i.e., most sputtered atoms came from the topmost layer of the target), we have carried out new molecular dynamics simulations of sputtered atom escape depths with much larger crystalline targets. Our new results, which include the bcc targets Cs, Rb and W, as well as the fcc targets Cu and Au predict that the majority of sputtered atoms come from the first atomic layer for the bcc(1 0 0), bcc(1 1 1), fcc(1 0 0) and fcc(1 1 1) targets studied. For the high-atomic density targets Cu, Au and W, the mean depth of origin of sputtered atoms typically is less than 0.25λ 0 . For the low-atomic density targets Cs and Rb, the mean depth of origin of sputtered atoms is considerably larger, and depends strongly on the crystal orientation. We show that the discrepancy between the single-crystal and amorphous target depth of origin values can be resolved by applying a simple correction to the single-crystal results

  14. Depth of source from long period P-waves

    International Nuclear Information System (INIS)

    Roy, Falguni

    1986-01-01

    Short period (SP) seismograms are much better than long period (LP) seismograms to get the time resolution needed for the focal depth estimation. However, complex scattering effects due to crustal inhomogeneities and also the multi-pathing of signals usually complicate the short period records. On the other hand the seismograms from long period signals demonstrate clear coherent body waves. Therefore, for intermediate depths (15-60 km) prediction error filtering of LP signals will be useful for identifying the depth phases. Such a study has been carried out in the first part of this report. In a group of 7 events, the p p phases have been extracted from LP signals and the depths so estimated compared well with the published data. For explosions at shallow depths (depth p phases will tend to cancel each other in LP seismograms. As the source depth increases, the cancellation becomes less effective. This feature can be used for the identification of an event as well as for getting an estimate of the source depth. This phenomenon can be successfully exploited for identifying multiple explosions, because at teleseismic distances (Δ > 30 o ) no LP (around 20s period) P waves will be seen in the seismogram due to such events whereas relatively strong SP signals and LP Rayleigh waves will be observed. This phenomenon has been studied for 16 events. For three of these events having m b as high as 6.1 and presumed to be underground explosions, one could not see any P wave on remaining 13 events (which were classified as earthquakes), it was possible to set a threshold value of m b above which an earthquake should produce LP P-wave signals at a given distance. (author)

  15. Focal depth measurement of scanning helium ion microscope

    International Nuclear Information System (INIS)

    Guo, Hongxuan; Itoh, Hiroshi; Wang, Chunmei; Zhang, Han; Fujita, Daisuke

    2014-01-01

    When facing the challenges of critical dimension measurement of complicated nanostructures, such as of the three dimension integrated circuit, characterization of the focal depth of microscopes is important. In this Letter, we developed a method for characterizing the focal depth of a scanning helium ion microscope (HIM) by using an atomic force microscope tip characterizer (ATC). The ATC was tilted in a sample chamber at an angle to the scanning plan. Secondary electron images (SEIs) were obtained at different positions of the ATC. The edge resolution of the SEIs shows the nominal diameters of the helium ion beam at different focal levels. With this method, the nominal shapes of the helium ion beams were obtained with different apertures. Our results show that a small aperture is necessary to get a high spatial resolution and high depth of field images with HIM. This work provides a method for characterizing and improving the performance of HIM.

  16. A new method for depth profiling

    International Nuclear Information System (INIS)

    Chittleborough, C.W.; Chaudhri, M.A.; Rouse, J.L.

    1978-01-01

    A simple method for obtaining depth profiles of concentrations has been developed for charged particle induced nuclear reactions which produce γ-rays or neutrons. This method is particularly suitable for non-resonant reactions but is also applicable to resonant reactions and can examine the concentration of the sought nuclide throughout the entire activation depth of the incoming particles in the matrix

  17. Depth of origin of magma in eruptions.

    Science.gov (United States)

    Becerril, Laura; Galindo, Ines; Gudmundsson, Agust; Morales, Jose Maria

    2013-09-26

    Many volcanic hazard factors--such as the likelihood and duration of an eruption, the eruption style, and the probability of its triggering large landslides or caldera collapses--relate to the depth of the magma source. Yet, the magma source depths are commonly poorly known, even in frequently erupting volcanoes such as Hekla in Iceland and Etna in Italy. Here we show how the length-thickness ratios of feeder dykes can be used to estimate the depth to the source magma chamber. Using this method, accurately measured volcanic fissures/feeder-dykes in El Hierro (Canary Islands) indicate a source depth of 11-15 km, which coincides with the main cloud of earthquake foci surrounding the magma chamber associated with the 2011-2012 eruption of El Hierro. The method can be used on widely available GPS and InSAR data to calculate the depths to the source magma chambers of active volcanoes worldwide.

  18. Integration time for the perception of depth from motion parallax.

    Science.gov (United States)

    Nawrot, Mark; Stroyan, Keith

    2012-04-15

    The perception of depth from relative motion is believed to be a slow process that "builds-up" over a period of observation. However, in the case of motion parallax, the potential accuracy of the depth estimate suffers as the observer translates during the viewing period. Our recent quantitative model for the perception of depth from motion parallax proposes that relative object depth (d) can be determined from retinal image motion (dθ/dt), pursuit eye movement (dα/dt), and fixation distance (f) by the formula: d/f≈dθ/dα. Given the model's dynamics, it is important to know the integration time required by the visual system to recover dα and dθ, and then estimate d. Knowing the minimum integration time reveals the incumbent error in this process. A depth-phase discrimination task was used to determine the time necessary to perceive depth-sign from motion parallax. Observers remained stationary and viewed a briefly translating random-dot motion parallax stimulus. Stimulus duration varied between trials. Fixation on the translating stimulus was monitored and enforced with an eye-tracker. The study found that relative depth discrimination can be performed with presentations as brief as 16.6 ms, with only two stimulus frames providing both retinal image motion and the stimulus window motion for pursuit (mean range=16.6-33.2 ms). This was found for conditions in which, prior to stimulus presentation, the eye was engaged in ongoing pursuit or the eye was stationary. A large high-contrast masking stimulus disrupted depth-discrimination for stimulus presentations less than 70-75 ms in both pursuit and stationary conditions. This interval might be linked to ocular-following response eye-movement latencies. We conclude that neural mechanisms serving depth from motion parallax generate a depth estimate much more quickly than previously believed. We propose that additional sluggishness might be due to the visual system's attempt to determine the maximum dθ/dα ratio

  19. Scene depth estimation using a moving camera

    International Nuclear Information System (INIS)

    Sune, Jean-Luc

    1995-01-01

    This thesis presents a solution of the depth-from-motion problem. The movement of the monocular observer is known. We have focused our research on a direct method which avoid the optical flow estimation required by classical approaches. The direct application of this method is not exploitable. We need to define a validity domain to extract the set of image points where it is possible to get a correct depth value. Also, we use a multi-scale approach to improve the derivatives estimation. The depth estimation for a given scale is obtained by the minimisation of an energy function established in the context of statistic regularization. A fusion operator, merging the various spatial and temporal scales, has been used to estimate the final depth map. A correction-prediction schema is used to integrate the temporal information from an image sequence. The predicted depth map is considered as an additional observation and integrated in the fusion process. At each time, an error depth map is associated to the estimated depth map. (author) [fr

  20. Hydrologic controls on equilibrium soil depths

    Science.gov (United States)

    Nicótina, L.; Tarboton, D. G.; Tesfa, T. K.; Rinaldo, A.

    2011-04-01

    This paper deals with modeling the mutual feedbacks between runoff production and geomorphological processes and attributes that lead to patterns of equilibrium soil depth. Our primary goal is an attempt to describe spatial patterns of soil depth resulting from long-term interactions between hydrologic forcings and soil production, erosion, and sediment transport processes under the framework of landscape dynamic equilibrium. Another goal is to set the premises for exploiting the role of soil depths in shaping the hydrologic response of a catchment. The relevance of the study stems from the massive improvement in hydrologic predictions for ungauged basins that would be achieved by using directly soil depths derived from geomorphic features remotely measured and objectively manipulated. Hydrological processes are here described by explicitly accounting for local soil depths and detailed catchment topography. Geomorphological processes are described by means of well-studied geomorphic transport laws. The modeling approach is applied to the semiarid Dry Creek Experimental Watershed, located near Boise, Idaho. Modeled soil depths are compared with field data obtained from an extensive survey of the catchment. Our results show the ability of the model to describe properly the mean soil depth and the broad features of the distribution of measured data. However, local comparisons show significant scatter whose origins are discussed.

  1. The Antiproton Depth-Dose Curve in Water

    DEFF Research Database (Denmark)

    Bassler, Niels; Holzscheiter, Michael; Jäkel, Oliver

    2008-01-01

    We have measured the depth-dose curve of 126 MeV antiprotons in a water phantom using ionization chambers. Since the antiproton beam provided by CERN has a pulsed structure and possibly carries a high-LET component from the antiproton annihilation, it is necessary to correct the acquired charge...

  2. Human action recognition with depth cameras

    CERN Document Server

    Wang, Jiang; Wu, Ying

    2014-01-01

    Action recognition technology has many real-world applications in human-computer interaction, surveillance, video retrieval, retirement home monitoring, and robotics. The commoditization of depth sensors has also opened up further applications that were not feasible before. This text focuses on feature representation and machine learning algorithms for action recognition from depth sensors. After presenting a comprehensive overview of the state of the art, the authors then provide in-depth descriptions of their recently developed feature representations and machine learning techniques, includi

  3. Defence in Depth and Ageing Management

    Energy Technology Data Exchange (ETDEWEB)

    Fabbri, S.; Vega, G.; Diluch, A.; Versaci, R., E-mail: versaci@cnea.gov.ar [Comisión Nacional de Energía Atómica, Buenos Aires (Argentina)

    2014-10-15

    Accident prevention is the first safety priority of both designers and operators. It is achieved through the use of reliable structures, components, systems and procedures in a plant operated by personnel who are committed to a strong safety culture. For future nuclear power plants, consideration of multiple failures and severe accidents will be achieved in a more systematic and complete way from the design stage. Defence in depth (DID) consists of a hierarchical deployment of different levels of equipment and procedures in order to maintain the effectiveness of physical barriers placed between radioactive materials and workers, the public or the environment, in normal operation, anticipated operational occurrences and, for some barriers, in accidents at the plant. The primary way of preventing accidents is to achieve a high quality in design, construction and operation of the plant, and thereby to ensure that deviations from normal operation are infrequent. The best way to meet these premises of effectiveness of the barriers and the Systems, Structures and Components (SSCs) is to develop an ageing management programme to prevent potential failures and accidents. In this work we will refer to the ageing management programme for Atucha I and Atucha II power plants and to the Atucha I spent fuel storage. (author)

  4. On modeling of beryllium molten depths in simulated plasma disruptions

    International Nuclear Information System (INIS)

    Tsotridis, G.; Rother, H.

    1996-01-01

    Plasma-facing components in tokamak-type fusion reactors are subjected to intense heat loads during plasma disruptions. The influence of high heat fluxes on the depth of heat-affected zones of pure beryllium metal and beryllium containing very low levels of surface active impurities is studied by using a two-dimensional transient computer model that solves the equations of motion and energy. Results are presented for a range of energy densities and disruption times. Under certain conditions, impurities, through their effect on surface tension, create convective flows and hence influence the flow intensities and the resulting depths of the beryllium molten layers during plasma disruptions. The calculated depths of the molten layers are also compared with other mathematical models that are based on the assumption that heat is transported through the material by conduction only. 32 refs., 6 figs., 1 tab

  5. Depth distribution of martensite in xenon implanted stainless steels

    International Nuclear Information System (INIS)

    Johansen, A.; Johnson, E.; Sarholt-Kristensen, L.; Steenstrup, S.; Hayashi, N.; Sakamoto, I.

    1989-01-01

    The amount of stress-induced martensite and its distribution in depth in xenon implanted austenitic stainless steel poly- and single crystals have been measured by Rutherford backscattering and channeling analysis, depth selective conversion electron Moessbauer spectroscopy, cross-sectional transmission electron microscopy and x-ray diffraction analysis. In low nickel 17/7, 304 and 316 commercial stainless steels and in 17:13 single crystals the martensitic transformation starts at the surface and develops towards greater depth with increasing xenon fluence. The implanted layer is nearly completely transformed, and the interface between martensite and austenite is rather sharp and well defined. In high nickel 310 commercial stainless steel and 15:19 and 20:19 single crystals, on the other hand, only insignificant amounts of martensite are observed. (orig.)

  6. Estimating floodwater depths from flood inundation maps and topography

    Science.gov (United States)

    Cohen, Sagy; Brakenridge, G. Robert; Kettner, Albert; Bates, Bradford; Nelson, Jonathan M.; McDonald, Richard R.; Huang, Yu-Fen; Munasinghe, Dinuke; Zhang, Jiaqi

    2018-01-01

    Information on flood inundation extent is important for understanding societal exposure, water storage volumes, flood wave attenuation, future flood hazard, and other variables. A number of organizations now provide flood inundation maps based on satellite remote sensing. These data products can efficiently and accurately provide the areal extent of a flood event, but do not provide floodwater depth, an important attribute for first responders and damage assessment. Here we present a new methodology and a GIS-based tool, the Floodwater Depth Estimation Tool (FwDET), for estimating floodwater depth based solely on an inundation map and a digital elevation model (DEM). We compare the FwDET results against water depth maps derived from hydraulic simulation of two flood events, a large-scale event for which we use medium resolution input layer (10 m) and a small-scale event for which we use a high-resolution (LiDAR; 1 m) input. Further testing is performed for two inundation maps with a number of challenging features that include a narrow valley, a large reservoir, and an urban setting. The results show FwDET can accurately calculate floodwater depth for diverse flooding scenarios but also leads to considerable bias in locations where the inundation extent does not align well with the DEM. In these locations, manual adjustment or higher spatial resolution input is required.

  7. Monocular depth effects on perceptual fading.

    Science.gov (United States)

    Hsu, Li-Chuan; Kramer, Peter; Yeh, Su-Ling

    2010-08-06

    After prolonged viewing, a static target among moving non-targets is perceived to repeatedly disappear and reappear. An uncrossed stereoscopic disparity of the target facilitates this Motion-Induced Blindness (MIB). Here we test whether monocular depth cues can affect MIB too, and whether they can also affect perceptual fading in static displays. Experiment 1 reveals an effect of interposition: more MIB when the target appears partially covered by, than when it appears to cover, its surroundings. Experiment 2 shows that the effect is indeed due to interposition and not to the target's contours. Experiment 3 induces depth with the watercolor illusion and replicates Experiment 1. Experiments 4 and 5 replicate Experiments 1 and 3 without the use of motion. Since almost any stimulus contains a monocular depth cue, we conclude that perceived depth affects perceptual fading in almost any stimulus, whether dynamic or static. Copyright 2010 Elsevier Ltd. All rights reserved.

  8. Depth to Bedrock: Isopach of Unconsolidated Materials

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — This vector dataset gives the approximate depth to bedrock (in feet) from Iowa's current land surface. This 50 foot isopach data was derived from the Digital...

  9. Sputtering as a means of depth profiling

    International Nuclear Information System (INIS)

    Whitton, J.L.

    1978-01-01

    Probably the most common technique for determination of depth profiles by sputtering is that of secondary ion mass spectrometry. Many problems occur in the important step of converting the time (of sputtering) scale to a depth scale and these problems arise before the secondary ions are ejected. An attempt is made to present a comprehensive list of the effects that should be taken into consideration in the use of sputtering as a means of depth profiling. The various parameters liable to affect the depth profile measurements are listed in four sections: beam conditions; target conditions; experimental environment; and beam-target interactions. The effects are discussed and where interplay occurs, cross-reference is made and examples are provided where possible. (B.R.H.)

  10. Rand Corporation Mean Monthly Global Snow Depth

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — All available monthly snow depth climatologies were integrated by the Rand Corporation, in the early 1980s, into one global (excluding Africa and South America)...

  11. The Beryllium 7 Depth Distribution Study

    International Nuclear Information System (INIS)

    Jalal Sharib; Zainudin Othman; Dainee Nor Fardzila Ahmad Tugi

    2014-01-01

    The aim of this paper is to study the evolution of 7Be depth distribution in a soil profile. The soil samples have been collected by using plastic core in bare area in Bangi, Malaysia. Each of the soil core samples has been sectioned into 2 mm increments to a depth of 4 cm and the samples are subsequently oven dried at 45°C and gently disaggregated. The sample is passed through a < 2 mm sieve and packed into plastic pot for 7Be analysis using gamma spectrometry with a 24 hour count time. From the findings, show the 7Be depth penetration from this study decreases exponentially with depth and is confined within the top few centimeters and similar with other works been reported. The further discussion for this findings will be presented in full paper. (author)

  12. Capturing Motion and Depth Before Cinematography.

    Science.gov (United States)

    Wade, Nicholas J

    2016-01-01

    Visual representations of biological states have traditionally faced two problems: they lacked motion and depth. Attempts were made to supply these wants over many centuries, but the major advances were made in the early-nineteenth century. Motion was synthesized by sequences of slightly different images presented in rapid succession and depth was added by presenting slightly different images to each eye. Apparent motion and depth were combined some years later, but they tended to be applied separately. The major figures in this early period were Wheatstone, Plateau, Horner, Duboscq, Claudet, and Purkinje. Others later in the century, like Marey and Muybridge, were stimulated to extend the uses to which apparent motion and photography could be applied to examining body movements. These developments occurred before the birth of cinematography, and significant insights were derived from attempts to combine motion and depth.

  13. Wavefield Extrapolation in Pseudo-depth Domain

    KAUST Repository

    Ma, Xuxin

    2011-12-11

    Wave-equation based seismic migration and inversion tools are widely used by the energy industry to explore hydrocarbon and mineral resources. By design, most of these techniques simulate wave propagation in a space domain with the vertical axis being depth measured from the surface. Vertical depth is popular because it is a straightforward mapping of the subsurface space. It is, however, not computationally cost-effective because the wavelength changes with local elastic wave velocity, which in general increases with depth in the Earth. As a result, the sampling per wavelength also increases with depth. To avoid spatial aliasing in deep fast media, the seismic wave is oversampled in shallow slow media and therefore increase the total computation cost. This issue is effectively tackled by using the vertical time axis instead of vertical depth. This is because in a vertical time representation, the "wavelength" is essentially time period for vertical rays. This thesis extends the vertical time axis to the pseudo-depth axis, which features distance unit while preserving the properties of the vertical time representation. To explore the potentials of doing wave-equation based imaging in the pseudo-depth domain, a Partial Differential Equation (PDE) is derived to describe acoustic wave in this new domain. This new PDE is inherently anisotropic because the use of a constant vertical velocity to convert between depth and vertical time. Such anisotropy results in lower reflection coefficients compared with conventional space domain modeling results. This feature is helpful to suppress the low wavenumber artifacts in reverse-time migration images, which are caused by the widely used cross-correlation imaging condition. This thesis illustrates modeling acoustic waves in both conventional space domain and pseudo-depth domain. The numerical tool used to model acoustic waves is built based on the lowrank approximation of Fourier integral operators. To investigate the potential

  14. Naturalistic depth perception and binocular vision

    OpenAIRE

    Maiello, G.

    2017-01-01

    Humans continuously move both their eyes to redirect their foveae to objects at new depths. To correctly execute these complex combinations of saccades, vergence eye movements and accommodation changes, the visual system makes use of multiple sources of depth information, including binocular disparity and defocus. Furthermore, during development, both fine-tuning of oculomotor control as well as correct eye growth are likely driven by complex interactions between eye movements, accommodation,...

  15. Generators for finite depth subfactor planar algebras

    Indian Academy of Sciences (India)

    The main result of Kodiyalam and Tupurani [3] shows that a subfactor planar algebra of finite depth is singly generated with a finite presentation. If P is a subfactor planar algebra of depth k, it is shown there that a single 2k-box generates P. It is natural to ask what the smallest s is such that a single s-box generates P. While ...

  16. FINANCIAL DEPTH AND FINANCIAL ACCESS IN INDONESIA

    OpenAIRE

    Sigit Setiawan

    2015-01-01

    This study is intended to analyze the current levels of financial depth and financial access in Indonesia and to analyze the factors affecting them. The analysis method used was a combination of descriptive quantitative, benchmarking, and literature reviews. The conclusion is that the financial depth in Indonesia has not shown a satisfactory level since it was the lowest, or the second lowest ranked country among the sampled countries. Meanwhile, the financial access in Indonesia is relativel...

  17. A brain electrophysiological correlate of depth perception

    International Nuclear Information System (INIS)

    Akay, Ahmet; Celebi, Gurbuz

    2009-01-01

    To investigate brain electrical activity accompanying depth perception using random-dot stereograms. Additional experiments were conducted to ascertain the specificity of this potential to depth perception. In the present study, we performed 3 different and independent experiments on 34 subjects to establish the relationship between depth perception and its cortical electrophysiological correlate. Visual evoked potentials in response to visual stimulation by random-dot stereograms were recorded. To achieve this goal, a data acquisition and analysis system, different from common visual evoked potential recording systems, consisting of 2 personal computers, was used. One of the computers was used to generate the visual stimulus patterns and the other to record and digitally average the potentials evoked by the stimuli. This study was carried out at the Department of Biophysics of Ege University Medical School, Izmir, Turkey, from April to December, 2006. A negative potential component, which is thought to arise in association with depth perception, was recorded from the occipital region from 30 of the 34 subjects. Typically, it had a mean latency of 211.46 ms and 6.40 micron V amplitude. The negative potential is related to depth perception, as this component is present in the responses to stimulus, which carries disparity information but is absent when the stimulus is switched to no disparity information. Additional experiments also showed that the specificity of this component to depth perception becomes evident beyond doubt. (author)

  18. Total Variation Depth for Functional Data

    KAUST Repository

    Huang, Huang

    2016-11-15

    There has been extensive work on data depth-based methods for robust multivariate data analysis. Recent developments have moved to infinite-dimensional objects such as functional data. In this work, we propose a new notion of depth, the total variation depth, for functional data. As a measure of depth, its properties are studied theoretically, and the associated outlier detection performance is investigated through simulations. Compared to magnitude outliers, shape outliers are often masked among the rest of samples and harder to identify. We show that the proposed total variation depth has many desirable features and is well suited for outlier detection. In particular, we propose to decompose the total variation depth into two components that are associated with shape and magnitude outlyingness, respectively. This decomposition allows us to develop an effective procedure for outlier detection and useful visualization tools, while naturally accounting for the correlation in functional data. Finally, the proposed methodology is demonstrated using real datasets of curves, images, and video frames.

  19. Buoyancy of gas-filled bladders at great depth

    Science.gov (United States)

    Priede, Imants G.

    2018-02-01

    At high hydrostatic pressures exceeding 20 MPa or 200 bar, equivalent to depths exceeding ca.2000 m, the behaviour of gases deviates significantly from the predictions of standard equations such as Boyle's Law, the Ideal Gas Law and Van der Waals equation. The predictions of these equations are compared with experimental data for nitrogen, oxygen and air at 0 °C and 15 °C, at pressures up to 1100 bar (110 MPa) equivalent to full ocean depth of ca. 11000 m. Owing to reduced compressibility of gases at high pressures, gas-filled bladders at full ocean depth have a density of 847 kg m-3 for Oxygen, 622 kg m-3 for Nitrogen and 660 kg m-3 for air providing potentially useful buoyancy comparable with that available from man-made materials. This helps explain why some of the deepest-living fishes at ca. 7000 m depth (700 bar or 70 MPa) have gas-filled swim bladders. A table is provided of the density and buoyancy of oxygen, nitrogen and air at 0 °C and 15 °C from 100 to 1100 bar.

  20. Depth resolution and preferential sputtering in depth profiling of sharp interfaces

    International Nuclear Information System (INIS)

    Hofmann, S.; Han, Y.S.; Wang, J.Y.

    2017-01-01

    Highlights: • Interfacial depth resolution from MRI model depends on sputtering rate differences. • Depth resolution critically depends on the dominance of roughness or atomic mixing. • True (depth scale) and apparent (time scale) depth resolutions are different. • Average sputtering rate approximately yields true from apparent depth resolution. • Profiles by SIMS and XPS are different but similar to surface concentrations. - Abstract: The influence of preferential sputtering on depth resolution of sputter depth profiles is studied for different sputtering rates of the two components at an A/B interface. Surface concentration and intensity depth profiles on both the sputtering time scale (as measured) and the depth scale are obtained by calculations with an extended Mixing-Roughness-Information depth (MRI)-model. The results show a clear difference for the two extreme cases (a) preponderant roughness and (b) preponderant atomic mixing. In case (a), the interface width on the time scale (Δt(16–84%)) increases with preferential sputtering if the faster sputtering component is on top of the slower sputtering component, but the true resolution on the depth scale (Δz(16–84%)) stays constant. In case (b), the interface width on the time scale stays constant but the true resolution on the depth scale varies with preferential sputtering. For similar order of magnitude of the atomic mixing and the roughness parameters, a transition state between the two extremes is obtained. While the normalized intensity profile of SIMS represents that of the surface concentration, an additional broadening effect is encountered in XPS or AES by the influence of the mean electron escape depth which may even cause an additional matrix effect at the interface.

  1. Depth resolution and preferential sputtering in depth profiling of sharp interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Hofmann, S. [Max Planck Institute for Intelligent Systems (formerly MPI for Metals Research), Heisenbergstrasse 3, D-70569 Stuttgart (Germany); Han, Y.S. [Department of Physics, Shantou University, 243 Daxue Road, Shantou, 515063 Guangdong (China); Wang, J.Y., E-mail: wangjy@stu.edu.cn [Department of Physics, Shantou University, 243 Daxue Road, Shantou, 515063 Guangdong (China)

    2017-07-15

    Highlights: • Interfacial depth resolution from MRI model depends on sputtering rate differences. • Depth resolution critically depends on the dominance of roughness or atomic mixing. • True (depth scale) and apparent (time scale) depth resolutions are different. • Average sputtering rate approximately yields true from apparent depth resolution. • Profiles by SIMS and XPS are different but similar to surface concentrations. - Abstract: The influence of preferential sputtering on depth resolution of sputter depth profiles is studied for different sputtering rates of the two components at an A/B interface. Surface concentration and intensity depth profiles on both the sputtering time scale (as measured) and the depth scale are obtained by calculations with an extended Mixing-Roughness-Information depth (MRI)-model. The results show a clear difference for the two extreme cases (a) preponderant roughness and (b) preponderant atomic mixing. In case (a), the interface width on the time scale (Δt(16–84%)) increases with preferential sputtering if the faster sputtering component is on top of the slower sputtering component, but the true resolution on the depth scale (Δz(16–84%)) stays constant. In case (b), the interface width on the time scale stays constant but the true resolution on the depth scale varies with preferential sputtering. For similar order of magnitude of the atomic mixing and the roughness parameters, a transition state between the two extremes is obtained. While the normalized intensity profile of SIMS represents that of the surface concentration, an additional broadening effect is encountered in XPS or AES by the influence of the mean electron escape depth which may even cause an additional matrix effect at the interface.

  2. Black silicon method X: a review on high speed and selective plasma etching of silicon with profile control: an in-depth comparison between Bosch and cryostat DRIE processes as a roadmap to next generation equipment

    International Nuclear Information System (INIS)

    Jansen, H V; De Boer, M J; Unnikrishnan, S; Louwerse, M C; Elwenspoek, M C

    2009-01-01

    An intensive study has been performed to understand and tune deep reactive ion etch (DRIE) processes for optimum results with respect to the silicon etch rate, etch profile and mask etch selectivity (in order of priority) using state-of-the-art dual power source DRIE equipment. The research compares pulsed-mode DRIE processes (e.g. Bosch technique) and mixed-mode DRIE processes (e.g. cryostat technique). In both techniques, an inhibitor is added to fluorine-based plasma to achieve directional etching, which is formed out of an oxide-forming (O 2 ) or a fluorocarbon (FC) gas (C 4 F 8 or CHF 3 ). The inhibitor can be introduced together with the etch gas, which is named a mixed-mode DRIE process, or the inhibitor can be added in a time-multiplexed manner, which will be termed a pulsed-mode DRIE process. Next, the most convenient mode of operation found in this study is highlighted including some remarks to ensure proper etching (i.e. step synchronization in pulsed-mode operation and heat control of the wafer). First of all, for the fabrication of directional profiles, pulsed-mode DRIE is far easier to handle, is more robust with respect to the pattern layout and has the potential of achieving much higher mask etch selectivity, whereas in a mixed-mode the etch rate is higher and sidewall scalloping is prohibited. It is found that both pulsed-mode CHF 3 and C 4 F 8 are perfectly suited to perform high speed directional etching, although they have the drawback of leaving the FC residue at the sidewalls of etched structures. They show an identical result when the flow of CHF 3 is roughly 30 times the flow of C 4 F 8 , and the amount of gas needed for a comparable result decreases rapidly while lowering the temperature from room down to cryogenic (and increasing the etch rate). Moreover, lowering the temperature lowers the mask erosion rate substantially (and so the mask selectivity improves). The pulsed-mode O 2 is FC-free but shows only tolerable anisotropic results at

  3. TOPICAL REVIEW: Black silicon method X: a review on high speed and selective plasma etching of silicon with profile control: an in-depth comparison between Bosch and cryostat DRIE processes as a roadmap to next generation equipment

    Science.gov (United States)

    Jansen, H V; de Boer, M J; Unnikrishnan, S; Louwerse, M C; Elwenspoek, M C

    2009-03-01

    An intensive study has been performed to understand and tune deep reactive ion etch (DRIE) processes for optimum results with respect to the silicon etch rate, etch profile and mask etch selectivity (in order of priority) using state-of-the-art dual power source DRIE equipment. The research compares pulsed-mode DRIE processes (e.g. Bosch technique) and mixed-mode DRIE processes (e.g. cryostat technique). In both techniques, an inhibitor is added to fluorine-based plasma to achieve directional etching, which is formed out of an oxide-forming (O2) or a fluorocarbon (FC) gas (C4F8 or CHF3). The inhibitor can be introduced together with the etch gas, which is named a mixed-mode DRIE process, or the inhibitor can be added in a time-multiplexed manner, which will be termed a pulsed-mode DRIE process. Next, the most convenient mode of operation found in this study is highlighted including some remarks to ensure proper etching (i.e. step synchronization in pulsed-mode operation and heat control of the wafer). First of all, for the fabrication of directional profiles, pulsed-mode DRIE is far easier to handle, is more robust with respect to the pattern layout and has the potential of achieving much higher mask etch selectivity, whereas in a mixed-mode the etch rate is higher and sidewall scalloping is prohibited. It is found that both pulsed-mode CHF3 and C4F8 are perfectly suited to perform high speed directional etching, although they have the drawback of leaving the FC residue at the sidewalls of etched structures. They show an identical result when the flow of CHF3 is roughly 30 times the flow of C4F8, and the amount of gas needed for a comparable result decreases rapidly while lowering the temperature from room down to cryogenic (and increasing the etch rate). Moreover, lowering the temperature lowers the mask erosion rate substantially (and so the mask selectivity improves). The pulsed-mode O2 is FC-free but shows only tolerable anisotropic results at -120 °C. The

  4. TRENDS IN ESTIMATED MIXING DEPTH DAILY MAXIMUMS

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, R; Amy DuPont, A; Robert Kurzeja, R; Matt Parker, M

    2007-11-12

    Mixing depth is an important quantity in the determination of air pollution concentrations. Fireweather forecasts depend strongly on estimates of the mixing depth as a means of determining the altitude and dilution (ventilation rates) of smoke plumes. The Savannah River United States Forest Service (USFS) routinely conducts prescribed fires at the Savannah River Site (SRS), a heavily wooded Department of Energy (DOE) facility located in southwest South Carolina. For many years, the Savannah River National Laboratory (SRNL) has provided forecasts of weather conditions in support of the fire program, including an estimated mixing depth using potential temperature and turbulence change with height at a given location. This paper examines trends in the average estimated mixing depth daily maximum at the SRS over an extended period of time (4.75 years) derived from numerical atmospheric simulations using two versions of the Regional Atmospheric Modeling System (RAMS). This allows for differences to be seen between the model versions, as well as trends on a multi-year time frame. In addition, comparisons of predicted mixing depth for individual days in which special balloon soundings were released are also discussed.

  5. The ocean depths: Elf's target for 1997

    International Nuclear Information System (INIS)

    Anon.

    1995-01-01

    Elf has long since been aware of the potential of sedimentary basins in the ocean depths. For this reason, the group has been preparing to descend to these depths for many years. Today, it is setting itself the target of being ready to optimise as from 1997 a discovery made in the depth between 400 and 1500 m of water in Africa. In the Gulf of Guinea, most of the neighbouring countries have opened up their deep sea offshore areas, in order to try to renew their reserves on the verge of the third millennium. Indeed a great similarity can be seen between the West African and the Brazilian ocean depths. In the African offshore areas, Elf has acquired or renewed eight blocks, four of which are in Nigeria, one in the Congo, one in Gabon and two in Angola. The group is also interested in the ocean depths which are now accessible in the North Sea, whether in the Norwegian (Voring and More) of British (Western Shetlands) areas. (author). 1 fig

  6. Prototype development or multi-cavity ion chamber for depth dose measurement

    International Nuclear Information System (INIS)

    Nayak, M.K.; Sahu, T.K.; Haridas, G.; Bandyopadhyay, Tapas; Tripathi, R.M.; Nandedkar, R.V.

    2016-01-01

    In high energy electron accelerators, when the electrons interact with vacuum chamber or surrounding structural material, Bremsstrahlung x-rays are produced. It is having a broad spectrum extending up to the electron energies. Dose measured as a function of depth due to electromagnetic cascade will give rise to depth dose curve. To measure the online depth dose profile in an absorber medium, when high energy electron or Bremsstrahlung is incident, a prototype Multi-Cavity Ion Chamber (MCIC) detector is developed. The paper describes the design and development of the MCIC for measurement of depth dose profile

  7. Hydrologic controls on the development of equilibrium soil depths

    Science.gov (United States)

    Nicotina, L.; Tarboton, D. G.; Tesfa, T. K.; Rinaldo, A.

    2010-12-01

    The object of the present work was the study of the coevolution of runoff production and geomorphological processes and its effects on the formation of equilibrium soil depth by focusing on their mutual feedbacks. The primary goal of this work is to describe spatial patterns of soil depth resulting, under the hypothesis of dynamic equilibrium, from long-term interactions between hydrologic forcings and soil production, erosion and sediment transport processes. These processes dominate the formation of actual soil depth patterns that represent the boundary condition for water redistribution, thus this paper also proposes and attempt to set the premises for decoding their individual role and mutual interactions in shaping the hydrologic response of a catchment. The relevance of the study stems from the massive improvement in hydrologic predictions for ungauged basins that would be achieved by using directly soil depths derived from geomorphic features remotely measured and objectively manipulated. Moreover the setup of a coupled hydrologic-geomorphologic approach represents a first step into the study of such interactions and in particular of the effects of soil moisture in determining soil production functions. Hydrological processes are here described by explicitly accounting for local soil depths and detailed catchment topography from high resolution digital terrain models (DTM). Geomorphological processes are described by means of well-studied geomorphic transport laws. Soil depth is assumed, in the exponential soil production function, as a proxy for all the mechanisms that induce mechanical disruption of bedrock and it’s conversion into soil. This formulation, although empirical, has been widely used in the literature and is currently accepted. The modeling approach is applied to the semi-arid Dry Creek Experimental Watershed, located near Boise, Idaho, USA. Modeled soil depths are compared with field data obtained from an extensive survey of the catchment

  8. Depth sensitivity of Lexan polycarbonate detector

    CERN Document Server

    Awad, E M

    1999-01-01

    The dependence of the registration sensitivity of Lexan polycarbonate with depth inside the detector was studied. Samples of Lexan from General Electric were irradiated to two long range ions. These were Ni and Au ions with a projectile energy of 0.3 and 1 GeV/n. Two independent techniques, the track-diameter technique (TDT) and the track profile technique (TPT), were used. The registration sensitivity was measured at depths of 7, 10, 15, 18, 20, 28, 35 and 40 mu m inside the detector. The results of the two techniques show that the detector sensitivity decreases gradually with the depth inside the detector. It reaches 20 % less compared to sensitivity at the surface after 40 mu m have been removed.

  9. Wavefield extrapolation in pseudo-depth domain

    KAUST Repository

    Ma, Xuxin; Alkhalifah, Tariq Ali

    2012-01-01

    Extrapolating seismic waves in Cartesian coordinate is prone to uneven spatial sampling, because the seismic wavelength tends to grow with depth, as velocity increase. We transform the vertical depth axis to a pseudo one using a velocity weighted mapping, which can effectively mitigate this wavelength variation. We derive acoustic wave equations in this new domain based on the direct transformation of the Laplacian derivatives, which admits solutions that are more accurate and stable than those derived from the kinematic transformation. The anisotropic versions of these equations allow us to isolate the vertical velocity influence and reduce its impact on modeling and imaging. The major benefit of extrapolating wavefields in pseudo-depth space is its near uniform wavelength as opposed to the normally dramatic change of wavelength with the conventional approach. Time wavefield extrapolation on a complex velocity shows some of the features of this approach.

  10. Depth sectioning using electron energy loss spectroscopy

    International Nuclear Information System (INIS)

    D'Alfonso, A J; Findlay, S D; Allen, L J; Cosgriff, E C; Kirkland, A I; Nellist, P D; Oxley, M P

    2008-01-01

    The continued development of electron probe aberration correctors for scanning transmission electron microscopy has enabled finer electron probes, allowing atomic resolution column-by-column electron energy loss spectroscopy. Finer electron probes have also led to a decrease in the probe depth of focus, facilitating optical slicing or depth sectioning of samples. The inclusion of post specimen aberration corrected image forming lenses allows for scanning confocal electron microscopy with further improved depth resolution and selectivity. We show that in both scanning transmission electron microscopy and scanning confocal electron microscopy geometries, by performing a three dimensional raster scan through a specimen and detecting electrons scattered with a characteristic energy loss, it will be possible to determine the location of isolated impurities embedded within the bulk.

  11. Depth resolved investigations of boron implanted silicon

    Science.gov (United States)

    Sztucki, M.; Metzger, T. H.; Milita, S.; Berberich, F.; Schell, N.; Rouvière, J. L.; Patel, J.

    2003-01-01

    We have studied the depth distribution and structure of defects in boron implanted silicon (0 0 1). Silicon wafers were implanted with a boron dose of 6×10 15 ions/cm -2 at 32 keV and went through different annealing treatments. Using diffuse X-ray scattering at grazing incidence and exit angles we are able to distinguish between different kinds of defects (point defect clusters and extrinsic stacking faults on {1 1 1} planes) and to determine their depth distribution as a function of the thermal budget. Cross-section transmission electron microscopy was used to gain complementary information. In addition we have determined the strain distribution caused by the boron implantation as a function of depth from rocking curve measurements.

  12. Photodegradation of wood and depth profile analysis

    International Nuclear Information System (INIS)

    Kataoka, Y.

    2008-01-01

    Photochemical degradation is a key process of the weathering that occurs when wood is exposed outdoors. It is also a major cause of the discoloration of wood in indoor applications. The effects of sunlight on the chemical composition of wood are superficial in nature, but estimates of the depth at which photodegradation occurs in wood vary greatly from 80 microm to as much as 2540 mic rom. Better understanding of the photodegradation of wood through depth profile analysis is desirable because it would allow the development of more effective photo-protective treatments that target the surface layers of wood most susceptible to photodegradation. This paper briefly describes fundamental aspects of photodegradation of wood and reviews progress made in the field of depth profile study on the photodegradation of wood. (author)

  13. Shallow surface depth profiling with atomic resolution

    International Nuclear Information System (INIS)

    Xi, J.; Dastoor, P.C.; King, B.V.; O'Connor, D.J.

    1999-01-01

    It is possible to derive atomic layer-by-layer composition depth profiles from popular electron spectroscopic techniques, such as X-ray photoelectron spectroscopy (XPS) or Auger electron spectroscopy (AES). When ion sputtering assisted AES or XPS is used, the changes that occur during the establishment of the steady state in the sputtering process make these techniques increasingly inaccurate for depths less than 3nm. Therefore non-destructive techniques of angle-resolved XPS (ARXPS) or AES (ARAES) have to be used in this case. In this paper several data processing algorithms have been used to extract the atomic resolved depth profiles of a shallow surface (down to 1nm) from ARXPS and ARAES data

  14. Factors controlling contrail cirrus optical depth

    Directory of Open Access Journals (Sweden)

    B. Kärcher

    2009-08-01

    Full Text Available Aircraft contrails develop into contrail cirrus by depositional growth and sedimentation of ice particles and horizontal spreading due to wind shear. Factors controlling this development include temperature, ice supersaturation, thickness of ice-supersaturated layers, and vertical gradients in the horizontal wind field. An analytical microphysical cloud model is presented and validated that captures these processes. Many individual contrail cirrus are simulated that develop differently owing to the variability in the controlling factors, resulting in large samples of cloud properties that are statistically analyzed. Contrail cirrus development is studied over the first four hours past formation, similar to the ages of line-shaped contrails that were tracked in satellite imagery on regional scales. On these time scales, contrail cirrus optical depth and microphysical variables exhibit a marked variability, expressed in terms of broad and skewed probability distribution functions. Simulated mean optical depths at a wavelength of 0.55 μm range from 0.05-0.5 and a substantial fraction 20-50% of contrail cirrus stay subvisible (optical depth <0.02, depending on meteorological conditions.

    A detailed analysis based on an observational case study over the continental USA suggests that previous satellite measurements of line-shaped persistent contrails have missed about 89%, 50%, and 11% of contrails with optical depths 0-0.05, 0.05-0.1, and 0.1-0.2, respectively, amounting to 65% of contrail coverage of all optical depths. When comparing observations with simulations and when estimating the contrail cirrus climate impact, not only mean values but also the variability in optical depth and microphysical properties need to be considered.

  15. Efficient Depth Enhancement Using a Combination of Color and Depth Information.

    Science.gov (United States)

    Lee, Kyungjae; Ban, Yuseok; Lee, Sangyoun

    2017-07-01

    Studies on depth images containing three-dimensional information have been performed for many practical applications. However, the depth images acquired from depth sensors have inherent problems, such as missing values and noisy boundaries. These problems significantly affect the performance of applications that use a depth image as their input. This paper describes a depth enhancement algorithm based on a combination of color and depth information. To fill depth holes and recover object shapes, asynchronous cellular automata with neighborhood distance maps are used. Image segmentation and a weighted linear combination of spatial filtering algorithms are applied to extract object regions and fill disocclusion in the object regions. Experimental results on both real-world and public datasets show that the proposed method enhances the quality of the depth image with low computational complexity, outperforming conventional methods on a number of metrics. Furthermore, to verify the performance of the proposed method, we present stereoscopic images generated by the enhanced depth image to illustrate the improvement in quality.

  16. Depth resolution of secondary ion mass spectrometry

    International Nuclear Information System (INIS)

    Pustovit, A.N.

    2004-01-01

    The effect of the solid body discreteness in the direction of the normal to the sample surface on the depth resolution of the secondary ion mass spectrometry method is analyzed. It is shown that for this case the dependence of the width at the semi-height of the delta profiles of the studied elements depth distribution on the energy and angle of incidence of the initial ions should have the form of the stepwise function. This is experimentally proved by the silicon-germanium delta-layers in the silicon samples [ru

  17. FINANCIAL DEPTH AND FINANCIAL ACCESS IN INDONESIA

    OpenAIRE

    Sigit Setiawan

    2015-01-01

    This study is intended to analyse the current levels of financial depth and financial access in Indonesia and to analyse the factors affecting them. The analysis method used was a combination of descriptive quantitative, benchmarking, and literature reviews. The conclusion is that the financial depth in Indonesia has not shown a satisfactory level since it was the lowest, or the second lowest ranked country among the sampled countries. Meanwhile, the financial access in Indonesia is relativel...

  18. Financial Depth and Financial Access in Indonesia

    OpenAIRE

    Setiawan, Sigit

    2015-01-01

    This study is intended to analyse the current levels of financial depth and financial access in Indonesia and to analyse the factors affecting them. The analysis method used was a combination of descriptive quantitative, benchmarking, and literature reviews. The conclusion is that the financial depth in Indonesia has not shown a satisfactory level since it was the lowest, or the second lowest ranked country among the sampled countries. Meanwhile, the financial access in Indonesia is relativel...

  19. Defence in depth in nuclear safety

    International Nuclear Information System (INIS)

    Jayakumar, J.S.

    2016-01-01

    Nuclear energy is clean and can prevent global warming and hence it has a lot of importance in the current world. In order for the safe and reliable operation of the NPP, a defence in depth concept has been practised, so that even one level of protection fails the subsequent one will contain the hazardous situation. Various levels, both from consideration of the physical barriers and implementation are described in this paper. Three major accidents happened in nuclear reactors are analysed from the defence in depth concept and shortcomings are discussed. (author)

  20. Final disposal of high-level nuclear waste in very deep boreholes. An evaluation based on recent research of bedrock conditions at great depths; Slutfoervaring av hoegaktivt kaernavfall i djupa borrhaal. En utvaerdering baserad paa senare aars forskning om berggrunden paa stora djup

    Energy Technology Data Exchange (ETDEWEB)

    Aahaell, Karl-Inge [Karlstad Univ. (Sweden)

    2007-01-15

    This report evaluates the feasibility of very deep borehole disposal of high-level nuclear waste, e.g., spent nuclear fuel, in the light of recent technological developments and research on the characteristics of bedrock at extreme depths. The evaluation finds that new knowledge in the field of hydrogeology and technical advances in drilling technology have advanced the possibility of using very deep boreholes (3-5 km) for disposal of the Swedish nuclear waste. Decisive factors are (1) that the repository can be located in stable bedrock at a level where the groundwater is isolated from the biosphere, and (2) that the waste can be deposited and the boreholes permanently sealed without causing long-term disturbances in the density-stratification of the groundwater that surrounds the repository. Very deep borehole disposal might offer important advantage compared to the relatively more shallow KBS approach that is presently planned to be used by the Swedish nuclear industry in Sweden, in that it has the potential of being more robust. The reason for this is that very deep borehole disposal appears to permit emplacement of the waste at depths where the entire repository zone would be surrounded by stable, density-stratified groundwater having no contact with the surface, whereas a KBS-3 repository would be surrounded by upwardly mobile groundwater. This hydro-geological difference is a major safety factor, which is particularly apparent in all scenarios that envisage leakage of radioactive substances. Another advantage of a repository at a depth of 3 to 5 km is that it is less vulnerable to impacts from expected events (e.g., changes in groundwater conditions during future ice ages) as well as undesired events (e.g. such as terrorist actions, technical malfunction and major local earthquakes). Decisive for the feasibility of a repository based on the very deep borehole concept is, however, the ability to emplace the waste without failures. In order to achieve this

  1. Nanometric depth resolution from multi-focal images in microscopy.

    Science.gov (United States)

    Dalgarno, Heather I C; Dalgarno, Paul A; Dada, Adetunmise C; Towers, Catherine E; Gibson, Gavin J; Parton, Richard M; Davis, Ilan; Warburton, Richard J; Greenaway, Alan H

    2011-07-06

    We describe a method for tracking the position of small features in three dimensions from images recorded on a standard microscope with an inexpensive attachment between the microscope and the camera. The depth-measurement accuracy of this method is tested experimentally on a wide-field, inverted microscope and is shown to give approximately 8 nm depth resolution, over a specimen depth of approximately 6 µm, when using a 12-bit charge-coupled device (CCD) camera and very bright but unresolved particles. To assess low-flux limitations a theoretical model is used to derive an analytical expression for the minimum variance bound. The approximations used in the analytical treatment are tested using numerical simulations. It is concluded that approximately 14 nm depth resolution is achievable with flux levels available when tracking fluorescent sources in three dimensions in live-cell biology and that the method is suitable for three-dimensional photo-activated localization microscopy resolution. Sub-nanometre resolution could be achieved with photon-counting techniques at high flux levels.

  2. NW Pacific mid-depth ventilation changes during the Holocene

    Science.gov (United States)

    Rella, S.; Uchida, M.

    2010-12-01

    During the last 50 years the oxygen content of North Pacific Intermediate Water primarily originating in the Okhotsk Sea has declined suggesting decreased mid-depth water circulation, likely leading to changes in biological productivity in the NW Pacific realm and a decrease in CO2 drawdown. It is therefore of high interest to elucidate the climate-oceanic interconnections of the present interglacial period (Holocene) in the NW Pacific, in order to predict possible future climate and surface productivity changes associated with a decrease in mid-depth ventilation in this ecologically sensitive region. However, such efforts have been hampered so far by the lack of appropriate sediment cores with fast sedimentation rates during the Holocene. Core CK05-04 that was recovered in 2005 from off Shimokita peninsula, Japan, at ~1000 m depth shows sedimentation rates of ~80 cm/kyr during the Holocene and therefore presents an ideal opportunity to reconstruct for the first time the Holocene ventilation history of the NW Pacific Ocean. We employ Accelerator Mass Spectroscopy (NIES-TERRA, Tsukuba) radiocarbon analysis of co-existing benthic and planktonic foraminifera to conclude on the ventilation age of the mid-depth water using benthic-planktonic radiocarbon age differences. At the conference we would like to present the results.

  3. Incoherently combining logarithmic aspheric lenses for extended depth of field.

    Science.gov (United States)

    Chu, Kaiqin; George, Nicholas; Chi, Wanli

    2009-10-01

    We describe a method for combining concentric logarithmic aspheric lenses in order to obtain an extended depth of field. Substantial improvement in extending the depth of field is obtained by carefully controlling the optical path difference among the concentric lenses so that their outputs combine incoherently. The system is analyzed through diffraction theory and the point spread function is shown to be highly invariant over a long range of object distances. After testing the image performance on a three-dimensional scene, we found that the incoherently combined logarithmic aspheres can provide a high-quality image over an axial distance corresponding to a defocus of +/- 14(lambda/4). Studies of the images of two-point objects are presented to illustrate the resolution of these lenses.

  4. Age-depth modelling with radiocarbon

    International Nuclear Information System (INIS)

    Howarth, J.D.

    2017-01-01

    Chronology is a critical component of any study into the Quaternary because the information about climate and environmental change preserved in sedimentary deposits can only be placed in a useful context when it is associated with a robust chronological framework. This overview will introduce you to the key concepts in age depth modelling.

  5. Soil depth influence on Amazonian ecophysiology

    Science.gov (United States)

    Fagerstrom, I.; Baker, I. T.; Gallup, S.; Denning, A. S.

    2017-12-01

    Models of land-atmosphere interaction are important for simulating present day weather and critical for predictions of future climate. Land-atmosphere interaction models have become increasingly complex in the last 30 years, leading to the need for further studies examining their intricacies and improvement. This research focuses on the effect of variable soil depth on Amazonian Gross Primary Production (GPP), respiration, and their combination into overall carbon flux. We evaluate a control, which has a universal soil depth of 10 meters, with two experiments of variable soil depths. To conduct this study we ran the 3 models for the period 2000-2012, evaluating similarities and differences between them. We focus on the Amazon rain forest, and compare differences in components of carbon flux. Not surprisingly, we find that the main differences between the models arises in regions where the soil depth is dissimilar between models. However, we did not observe significant differences in GPP between known drought, wet, and average years; interannual variability in carbon dynamics was less than anticipated. We also anticipated that differences between models would be most significant during the dry season, but found discrepancies that persisted through the entire annual cycle.

  6. Effects of tailwater depth on spillway aeration

    African Journals Online (AJOL)

    2011-04-15

    Apr 15, 2011 ... Hydraulic structures such as spillways or weirs with their water-air controlling mechanisms are not only important for their structural properties but also for their effects on downstream ecology. Tailwater depth is an important factor affecting dissolved oxygen transfer and aeration rates of spillways. In this ...

  7. Visual discomfort and depth-of-field

    NARCIS (Netherlands)

    O'Hare, L.; Zhang, T.; Nefs, H.T.; Hibbard, P.B.

    2013-01-01

    Visual discomfort has been reported for certain visual stimuli and under particular viewing conditions, such as stereoscopic viewing. In stereoscopic viewing, visual discomfort can be caused by a conflict between accommodation and convergence cues that may specify different distances in depth.

  8. Sampling depth confounds soil acidification outcomes

    Science.gov (United States)

    In the northern Great Plains (NGP) of North America, surface sampling depths of 0-15 or 0-20 cm are suggested for testing soil characteristics such as pH. However, acidification is often most pronounced near the soil surface. Thus, sampling deeper can potentially dilute (increase) pH measurements an...

  9. Depth dependent stress revealed by aftershocks

    Science.gov (United States)

    Narteau, C.; Shebalin, P.

    2017-12-01

    Aftershocks occur in response to perturbations of the state of stress induced either by earthquakes or human activities. Along major strike-slip fault segments of the San Andreas fault system, the time-delay before the onset of the power-law aftershock decay rate (the c-value) varies by three orders of magnitude in the first twenty kilometers below the surface. Despite the influence of the lithostatic stress, there is no continuous change in c-value with respect to depth. Instead, two decay phases are separated by an abrupt increase at an intermediate depth range of 2 to 5 km. This transitional regime is the only one observed in fluid-injection-induced seismic areas. This provides strong evidence for the role of fluid and a porosity reduction mechanism at depth of few kilometers in active fault zones. Aftershock statistics can then be used to predict the evolution the differential shear stress with depth until the brittle-ductile transition is reached.

  10. Verifying optimal depth settings for LFAS

    NARCIS (Netherlands)

    Lam, F.P.A.; Beerens, S.P.; Ainslie, M.A.

    2006-01-01

    Naval operations in coastal waters are challenging the modelling support in several disciplines. An important instrument for undersea defence in the littoral is the LFAS sonar. To adapt to the local acoustic environment, LFAS sonars can adjust their operation depth to increase the coverage of the

  11. The case for transparent depth display

    NARCIS (Netherlands)

    Kooi, F.L.

    2003-01-01

    Purpose: The continuing developments in display technology have resulted in the ability to present increasing amounts of data on computer displays. One of the coming break-throughs is generally believed to be the introduction of '3-D displays': displays with a true sense of depth. Though these types

  12. Estimating the Rut Depth by UAV Photogrammetry

    Directory of Open Access Journals (Sweden)

    Paavo Nevalainen

    2017-12-01

    Full Text Available The rut formation during forest operations is an undesirable phenomenon. A methodology is being proposed to measure the rut depth distribution of a logging site by photogrammetric point clouds produced by unmanned aerial vehicles (UAV. The methodology includes five processing steps that aim at reducing the noise from the surrounding trees and undergrowth for identifying the trails. A canopy height model is produced to focus the point cloud on the open pathway around the forest machine trail. A triangularized ground model is formed by a point cloud filtering method. The ground model is vectorized using the histogram of directed curvatures (HOC method to produce an overall ground visualization. Finally, a manual selection of the trails leads to an automated rut depth profile analysis. The bivariate correlation (Pearson’s r between rut depths measured manually and by UAV photogrammetry is r = 0.67 . The two-class accuracy a of detecting the rut depth exceeding 20 cm is a = 0.65 . There is potential for enabling automated large-scale evaluation of the forestry areas by using autonomous drones and the process described.

  13. Safety in depth for nuclear waste disposal

    Energy Technology Data Exchange (ETDEWEB)

    Ringwood, T [Australian National Univ., Canberra. Research School of Earth Sciences

    1980-11-27

    A nuclear waste disposal strategy is described in which the radionuclides are immobilised in widely-dispersed drill holes in an extremely stable and leach resistant titanate ceramic form (SYNROC) at depths of 1500 to 4000 metres. The advantages of this method over that of burying such wastes in large centralised mined repositories at 500 to 700 metres in suitable geological strata are examined.

  14. Glow discharge depth analysis of metallic elements in steels

    International Nuclear Information System (INIS)

    Berneron, R.

    The glow discharge lamp designed by Grimm gives new possibilities in the optical spectrometry. The plasma produced is a cool emissive source and its advantages are the following: low spectral background, no reabsorption, linear calibration, very stable emission, very high yield. The sputtering produced by ionic bombardment of the sample enables the depth repartition of several elements to be made in the same run [fr

  15. Subjective method of refractometry and depth of focus

    Science.gov (United States)

    Sergienko, Nikolai M.; Gromova, Anastasia; Sergienko, Nikolai

    2012-01-01

    Purpose To study the impact of the depth of focus on subjective refraction and distribution of myopic and hyperopic refractions. Methods A total of 450 eyes of 305 subjects in the age range of 23–34 years were recruited for the study. A distribution of refractions was examined using a traditional method of the subjective refractometry on the basis of point-like posterior focus notion. Correction of the results was made on the assumption that the emmetropic eye retains high visual acuity when applying convex lenses with values which are fewer or equal to the depth of focus values. The following values of the depth of focus were used: ±0.55 D, ±0.35 D and ±0.2 D for visual acuity 1.0, 1.5 and 2.0, respectively. Results Application of the traditional method of refractometry produced the following occurrence of refractions: hypermetropia 59.3%, myopia 22% and emmetropia 18.7%. After correction of the initial results of values of the depth of focus the distribution of refractions was as follows: hypermetropia 12.7%, myopia 22% and emmetropia 65.3%. Conclusion The traditional method of subjective refractometry with application of trial lenses was developed on the basis of data of large optical aberrations and significant depth of focus which values should be taken into account during interpretation of results of subjective refractometry. Our data regarding to prevalence of emmetropic refraction falls in line with basic science provisions in respect of the physiology of the eye.

  16. Electroacoustic Process Study of Plasma Sparker Under Different Water Depth

    KAUST Repository

    Huang, Yifan

    2015-01-05

    The plasma sparker has been applied in oceanic high-resolution seismic exploration for decades. Normally it is towed on the water surface. This is suitable for shallow water, but if the water depth is great, the resolution will decrease dramatically, especially in the horizontal direction. This paper proposes the concept of a deep-towed plasma sparker and presents an experimental study of plasma sparker performance in terms of electric parameters, bubble behavior, and acoustic characteristics. The results show that hydrostatic pressure at a source depth ranging from 1 to 2000 m has a negligible influence on the electric parameters but a strong influence on bubble behavior, wherein both the maximum bubble radius and oscillation period are decreased. The collapse pulse vanishes when the source depth reaches 1000 m or deeper, and no bubble oscillation can be distinguished. The source level (evaluated by the expansion pulse) is also decreased as the source depth increases; moreover, the greater the discharge energy, the smaller the source level loss. The discharge energy per electrode should be greater than 20 J for the deep-towed plasma sparker, which can make the source level loss induced by hydrostatic pressure smaller than the transmission loss. The fast Fourier transform (FFT) results show that the dominant energy is around 20 kHz, which is mainly induced by the expansion pulse and its oscillation. According to the simulation results, the fundamental frequency of the acoustic waveform increases with source depth in accord with a log linear trend, and also reaches tens of kilohertz in deep water. So, before the development of deep-towed plasma sparker, a new technical solution will need to be developed to solve this problem. © 1976-2012 IEEE.

  17. Compression force-depth relationship during out-of-hospital cardiopulmonary resuscitation.

    Science.gov (United States)

    Tomlinson, A E; Nysaether, J; Kramer-Johansen, J; Steen, P A; Dorph, E

    2007-03-01

    Recent clinical studies reporting the high frequency of inadequate chest compression depth (compression depth in certain patients. Using a specially designed monitor/defibrillator equipped with a sternal pad fitted with an accelerometer and a pressure sensor, compression force and depth was measured during CPR in 91 adult out-of-hospital cardiac arrest patients. There was a strong non-linear relationship between the force of compression and depth achieved. Mean applied force for all patients was 30.3+/-8.2 kg and mean absolute compression depth 42+/-8 mm. For 87 of 91 patients 38 mm compression depth was obtained with less than 50 kg. Stiffer chests were compressed more forcefully than softer chests (pcompressed more deeply than stiffer chests (p=0.001). The force needed to reach 38 mm compression depth (F38) and mean compression force were higher for males than for females: 29.8+/-14.5 kg versus 22.5+/-10.2 kg (pcompression depth with age, but a significant 1.5 kg mean decrease in applied force for each 10 years increase in age (pcompressions performed. Average residual force during decompression was 1.7+/-1.0 kg, corresponding to an average residual depth of 3+/-2 mm. In most out-of-hospital cardiac arrest victims adequate chest compression depth can be achieved by a force<50 kg, indicating that an average sized and fit rescuer should be able to perform effective CPR in most adult patients.

  18. Using elastic peak electron spectroscopy for enhanced depth resolution in sputter profiling

    International Nuclear Information System (INIS)

    Hofmann, S.; Kesler, V.

    2002-01-01

    Elastic peak electron spectroscopy (EPES) is an alternative to AES in sputter depth profiling of thin film structures. In contrast to AES, EPES depth profiling is not influenced by chemical effects. The high count rate ensures a good signal to noise ratio, that is lower measurement times and/or higher precision. In addition, because of the elastically scattered electrons travel twice through the sample, the effective escape depth is reduced, an important factor for the depth resolution function. Thus, the depth resolution is increased. EPES depth profiling was successfully applied to a Ge/Si multilayer structure. For an elastic peak energy of 1.0 keV the information depth is considerably lower (0.8 nm) as compared to the Ge (LMM, 1147 eV) peak (1.6 nm) used in AES depth profiling, resulting in a respectively improved depth resolution for EPES profiling under otherwise similar profiling conditions. EPES depth profiling is successfully applied to measure small diffusion lengths at Ge/Si interfaces of the order of 1 nm. (Authors)

  19. Knee Kinetics during Squats of Varying Loads and Depths in Recreationally Trained Females.

    Science.gov (United States)

    Flores, Victoria; Becker, James; Burkhardt, Eric; Cotter, Joshua

    2018-03-06

    The back squat exercise is typically practiced with varying squat depths and barbell loads. However, depth has been inconsistently defined, resulting in unclear safety precautions when squatting with loads. Additionally, females exhibit anatomical and kinematic differences to males which may predispose them to knee joint injuries. The purpose of this study was to characterize peak knee extensor moments (pKEMs) at three commonly practiced squat depths of above parallel, parallel, and full depth, and with three loads of 0% (unloaded), 50%, and 85% depth-specific one repetition maximum (1RM) in recreationally active females. Nineteen females (age, 25.1 ± 5.8 years; body mass, 62.5 ± 10.2 kg; height, 1.6 ± 0.10 m; mean ± SD) performed squats of randomized depth and load. Inverse dynamics were used to obtain pKEMs from three-dimensional knee kinematics. Depth and load had significant interaction effects on pKEMs (p = 0.014). Significantly greater pKEMs were observed at full depth compared to parallel depth with 50% 1RM load (p = 0.001, d = 0.615), and 85% 1RM load (p = 0.010, d = 0.714). Greater pKEMs were also observed at full depth compared to above parallel depth with 50% 1RM load (p = 0.003, d = 0.504). Results indicate effect of load on female pKEMs do not follow a progressively increasing pattern with either increasing depth or load. Therefore, when high knee loading is a concern, individuals are must carefully consider both the depth of squat being performed and the relative load they are using.

  20. Depth of Cervical Intraepithelial Neoplasia Grade 3 in Peruvian Women: Implications for Therapeutic Depth of Necrosis.

    Science.gov (United States)

    Taxa, Luis; Jeronimo, Jose; Alonzo, Todd A; Gage, Julia; Castle, Philip E; Cremer, Miriam L; Felix, Juan C

    2018-01-01

    To determine the involvement of cervical intraepithelial neoplasia grade 3 (CIN3) in a population of women in a lower-resource setting. One hundred twelve consecutive cone excision specimens with histological diagnosis of CIN3 were retrieved from the National Institute of Neoplastic Diseases in Lima Peru. Two pathologists independently evaluated each specimen microscopically and confirmed 107 cases that could be measured by optical micrometry. Depth and breadth of the lesions were measured microscopically. The mean maximal depth of cervical involvement by CIN3 was 2 ± 0.13 mm; depth was less than 3.5 mm in 89.7% of cases and less than 5 mm in 93.5%. Mean breadth of CIN3 was 7.3 ± 4.4 mm; breadth was less than 15.9 mm in 95% of cases and less than 20.5 mm in 99.7%. The correlation coefficient between breadth and depth of CIN3 was 0.61. No significant correlation was found between age and depth. Depth of CIN3 involvement in a developing country is significantly deeper than that reported in the United States. Treatment selection for women with CIN3 and risk of treatment failure may vary between developing and developed countries because of the difference in the depth of lesions. Countries with underscreened populations need to consider the increased disease severity in devising treatment strategies.

  1. Investigation of the shallow depth explosions

    International Nuclear Information System (INIS)

    Kamegai, M.

    1976-01-01

    An investigation of the nuclear explosions at shallow depth is made. A combination of an explosion code and an effects code proves to be an excellent tool for this study. A numerical simulation of ''Johnie Boy'' shows that the energy coupling to the air takes place in two stages; first by a rising mound, and then by a vented source. The thermal effects are examined for a 1 kt source at three depths of burial. The ''mushroom effect'' leaves a hot radiative plasma in the upper level and cold materials in the lower region of the debris. The temperature and the energy density of the debris can give an upper limit on the thermal output

  2. MR determination of neonatal spinal canal depth.

    Science.gov (United States)

    Arthurs, Owen; Thayyil, Sudhin; Wade, Angie; Chong, W K Kling; Sebire, Neil J; Taylor, Andrew M

    2012-08-01

    Lumbar punctures (LPs) are frequently performed in neonates and often result in traumatic haemorrhagic taps. Knowledge of the distance from the skin to the middle of the spinal canal (mid-spinal canal depth - MSCD) may reduce the incidence of traumatic taps, but there is little data in extremely premature or low birth weight neonates. Here, we determined the spinal canal depth at post-mortem in perinatal deaths using magnetic resonance imaging (MRI). Spinal canal depth was measured in 78 post-mortem foetuses and perinatal cases (mean gestation 26 weeks; mean weight 1.04kg) at the L3/L4 inter-vertebral space at post-mortem MRI. Both anterior (ASCD) and posterior (PSCD) spinal canal depth were measured; MSCD was calculated and modelled against weight and gestational age. ASCD and PSCD (mm) correlated significantly with weight and gestational age (all r>0.8). A simple linear model MSCD (mm)=3×Weight (kg)+5 was the best fit, identifying an SCD value within the correct range for 87.2% (68/78) (95% CI (78.0, 92.9%)) cases. Gestational age did not add significantly to the predictive value of the model. There is a significant correlation between MSCD and body weight at post-mortem MRI in foetuses and perinatal deaths. If this association holds in preterm neonates, use of the formula MSCD (mm)=3×Weight (kg)+5 could result in fewer traumatic LPs in this population. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  3. MR determination of neonatal spinal canal depth

    Energy Technology Data Exchange (ETDEWEB)

    Arthurs, Owen, E-mail: owenarthurs@uk2.net [Centre for Cardiovascular MR, Great Ormond Street Hospital for Children, London WC1N 3JH (United Kingdom); Thayyil, Sudhin, E-mail: s.thayyil@ucl.ac.uk [Academic Neonatology, Institute for Women' s Health, London WC1E 6AU (United Kingdom); Wade, Angie, E-mail: a.wade@ucl.ac.uk [Centre for Paediatric Epidemiology and Biostatistics, UCL Institute of Child Health, London (United Kingdom); Chong, W.K., E-mail: Kling.Chong@gosh.nhs.uk [Paediatric Neuroradiology, Great Ormond Street Hospital for Children, London (United Kingdom); Sebire, Neil J., E-mail: Neil.Sebire@gosh.nhs.uk [Histopathology, Great Ormond Street Hospital for Children, London WC1E 6AU (United Kingdom); Taylor, Andrew M., E-mail: a.taylor76@ucl.ac.uk [Centre for Cardiovascular MR, Cardiorespiratory Unit, Great Ormond Street Hospital for Children and UCL Institute of Cardiovascular Science, London WC1E 6AU (United Kingdom)

    2012-08-15

    Objectives: Lumbar punctures (LPs) are frequently performed in neonates and often result in traumatic haemorrhagic taps. Knowledge of the distance from the skin to the middle of the spinal canal (mid-spinal canal depth - MSCD) may reduce the incidence of traumatic taps, but there is little data in extremely premature or low birth weight neonates. Here, we determined the spinal canal depth at post-mortem in perinatal deaths using magnetic resonance imaging (MRI). Patients and methods: Spinal canal depth was measured in 78 post-mortem foetuses and perinatal cases (mean gestation 26 weeks; mean weight 1.04 kg) at the L3/L4 inter-vertebral space at post-mortem MRI. Both anterior (ASCD) and posterior (PSCD) spinal canal depth were measured; MSCD was calculated and modelled against weight and gestational age. Results: ASCD and PSCD (mm) correlated significantly with weight and gestational age (all r > 0.8). A simple linear model MSCD (mm) = 3 Multiplication-Sign Weight (kg) + 5 was the best fit, identifying an SCD value within the correct range for 87.2% (68/78) (95% CI (78.0, 92.9%)) cases. Gestational age did not add significantly to the predictive value of the model. Conclusion: There is a significant correlation between MSCD and body weight at post-mortem MRI in foetuses and perinatal deaths. If this association holds in preterm neonates, use of the formula MSCD (mm) = 3 Multiplication-Sign Weight (kg) + 5 could result in fewer traumatic LPs in this population.

  4. Mobile Variable Depth Sampling System Design Study

    International Nuclear Information System (INIS)

    BOGER, R.M.

    2000-01-01

    A design study is presented for a mobile, variable depth sampling system (MVDSS) that will support the treatment and immobilization of Hanford LAW and HLW. The sampler can be deployed in a 4-inch tank riser and has a design that is based on requirements identified in the Level 2 Specification (latest revision). The waste feed sequence for the MVDSS is based on Phase 1, Case 3S6 waste feed sequence. Technical information is also presented that supports the design study

  5. Mobile Variable Depth Sampling System Design Study

    Energy Technology Data Exchange (ETDEWEB)

    BOGER, R.M.

    2000-08-25

    A design study is presented for a mobile, variable depth sampling system (MVDSS) that will support the treatment and immobilization of Hanford LAW and HLW. The sampler can be deployed in a 4-inch tank riser and has a design that is based on requirements identified in the Level 2 Specification (latest revision). The waste feed sequence for the MVDSS is based on Phase 1, Case 3S6 waste feed sequence. Technical information is also presented that supports the design study.

  6. Hydrogen depth profiling using elastic recoil detection

    International Nuclear Information System (INIS)

    Doyle, B.L.; Peercy, P.S.

    1979-01-01

    The elastic recoil detection (ERD) analysis technique for H profiling in the near surface regions of solids is described. ERD is shown to have the capability of detecting H and its isotopes down to concentrations of approx. 0.01 at. % with a depth resolution of a few hundred angstroms. Is is demonstrated that 2.4-MeV He ions can be used successfully to profile 1 H and 2 D using this technique. 12 figures

  7. Coding In-depth Semistructured Interviews

    DEFF Research Database (Denmark)

    Campbell, John L.; Quincy, Charles; Osserman, Jordan

    2013-01-01

    Many social science studies are based on coded in-depth semistructured interview transcripts. But researchers rarely report or discuss coding reliability in this work. Nor is there much literature on the subject for this type of data. This article presents a procedure for developing coding schemes...... useful for situations where a single knowledgeable coder will code all the transcripts once the coding scheme has been established. This approach can also be used with other types of qualitative data and in other circumstances....

  8. [Measurement of the depth of anaesthesia].

    Science.gov (United States)

    Schmidt, G N; Müller, J; Bischoff, P

    2008-01-01

    One of the most important mandates of the anaesthesiologist is to control the depth of anaesthesia. An unsolved problem is that a straight definition of the depth of anaesthesia does not exist. Concerning this it is rational to separate hypnosis from analgesia, from muscle relaxation and from block of cardiovascular reactions. Clinical surrogate parameters such as blood pressure and heart rate are not well-suited for a valid statement about the depth of hypnosis. To answer this question the brain has become the focus of interest as the target of anaesthesia. It is possible to visualize the brain's electrical activity from anelectroencephalogram (EEG). The validity of the spontaneous EEG as an anesthetic depth monitor is limited by the multiphasic activity, especially when anaesthesia is induced (excitation) and in deep anaesthesia (burst suppression). Recently, various commercial monitoring systems have been introduced to solve this problem. These monitoring systems use different interpretations of the EEG or auditory-evoked potentials (AEP). These derived and calculated variables have no pure physiological basis. For that reason a profound knowledge of the algorithms and a validation of the monitoring systems is an indispensable prerequisite prior to their routine clinical use. For the currently available monitoring systems various studies have been reported. At this time it is important to know that the actual available monitors can only value the sedation and not the other components of anaesthesia. For example, they cannot predict if a patient will react to a painful stimulus or not. In the future it would be desirable to develop parameters which allow an estimate of the other components of anaesthesia in addition to the presently available monitoring systems to estimate sedation and muscle relaxation. These could be sensoric-evoked potentials to estimate analgesia and AEPs for the detection of awareness.

  9. Tritium depth profiling in carbon samples from fusion experiments

    International Nuclear Information System (INIS)

    Friedrich, M.; Pilz, W.; Sun, G.; Behrisch, R.; Garcia-Rosales, C.; Bekris, N.; Penzhorn, R.-D.

    2000-01-01

    Tritium depth profiling by accelerator mass spectrometry has been performed at the Rossendorf 3 MV Tandetron. Tritium particles are counted after the accelerator using a semiconductor detector, while deuterium and other light elements are simultaneously measured with the Faraday cup between the injection magnet and the accelerator. Depth profiles have been measured in carbon samples cut from the first wall tiles of the Garching fusion experiment ASDEX-Upgrade and of the European fusion experiment JET, Culham/UK. Tritium contents in the JET samples were up to six orders higher than in samples from ASDEX-Upgrade. Tritium beam currents from samples with high tritium content were measured partly in the Faraday cup before the accelerator. A dedicated tritium AMS facility with an air-insulated 100 kV tandem accelerator is under construction

  10. Ion induced optical emission for surface and depth profile analysis

    International Nuclear Information System (INIS)

    White, C.W.

    1977-01-01

    Low-energy ion bombardment of solid surfaces results in the emission of infrared, visible, and ultraviolet radiation produced by inelastic ion-solid collision processes. The emitted optical radiation provides important insight into low-energy particle-solid interactions and provides the basis for an analysis technique which can be used for surface and depth profile analysis with high sensitivity. The different kinds of collision induced optical radiation emitted as a result of low-energy particle-solid collisions are reviewed. Line radiation arising from excited states of sputtered atoms or molecules is shown to provide the basis for surface and depth profile analysis. The spectral characteristics of this type of radiation are discussed and applications of the ion induced optical emission technique are presented. These applications include measurements of ion implant profiles, detection sensitivities for submonolayer quantities of impurities on elemental surfaces, and the detection of elemental impurities on complex organic substrates

  11. Impeller Submergence Depth for Stirred Tanks

    Directory of Open Access Journals (Sweden)

    Thiyam T. Devi

    2011-11-01

    Full Text Available Impeller submergence governs the performance of mixing tanks employed in oxygen transfer operation. Present work experimentally investigates the effect of impeller submergence depths on oxygen transfer and corresponding power consumption. It has been found that at higher range of impeller submergence, mixing tanks consume less power and gives higher values of oxygen transfer coefficient. Optimal range of submergence depth is 0.7 to 0.9 times the impeller diameter. Copyright ©2011 BCREC UNDIP. All rights reserved.(Received: 4th March 2011; Revised: 12nd July 2011; Accepted: 14th July 2011[How to Cite: T.T. Devi, A.P. Sinha, M. Thakre, and B. Kumar. (2011. Impeller Submergence Depth for Stirred Tanks. Bulletin of Chemical Reaction Engineering & Catalysis, 6 (2: 123-128. doi:10.9767/bcrec.6.2.826.123-128][How to Link / DOI: http://dx.doi.org/10.9767/bcrec.6.2.826.123-128 || or local: http://ejournal.undip.ac.id/index.php/bcrec/article/view/826] | View in 

  12. Low-Depth Quantum Simulation of Materials

    Directory of Open Access Journals (Sweden)

    Ryan Babbush

    2018-03-01

    Full Text Available Quantum simulation of the electronic structure problem is one of the most researched applications of quantum computing. The majority of quantum algorithms for this problem encode the wavefunction using N Gaussian orbitals, leading to Hamiltonians with O(N^{4} second-quantized terms. We avoid this overhead and extend methods to condensed phase materials by utilizing a dual form of the plane wave basis which diagonalizes the potential operator, leading to a Hamiltonian representation with O(N^{2} second-quantized terms. Using this representation, we can implement single Trotter steps of the Hamiltonians with linear gate depth on a planar lattice. Properties of the basis allow us to deploy Trotter- and Taylor-series-based simulations with respective circuit depths of O(N^{7/2} and O[over ˜](N^{8/3} for fixed charge densities. Variational algorithms also require significantly fewer measurements in this basis, ameliorating a primary challenge of that approach. While our approach applies to the simulation of arbitrary electronic structure problems, the basis sets explored in this work will be most practical for treating periodic systems, such as crystalline materials, in the near term. We conclude with a proposal to simulate the uniform electron gas (jellium using a low-depth variational ansatz realizable on near-term quantum devices. From these results, we identify simulations of low-density jellium as a promising first setting to explore quantum supremacy in electronic structure.

  13. Bit-depth scalable video coding with new inter-layer prediction

    Directory of Open Access Journals (Sweden)

    Chiang Jui-Chiu

    2011-01-01

    Full Text Available Abstract The rapid advances in the capture and display of high-dynamic range (HDR image/video content make it imperative to develop efficient compression techniques to deal with the huge amounts of HDR data. Since HDR device is not yet popular for the moment, the compatibility problems should be considered when rendering HDR content on conventional display devices. To this end, in this study, we propose three H.264/AVC-based bit-depth scalable video-coding schemes, called the LH scheme (low bit-depth to high bit-depth, the HL scheme (high bit-depth to low bit-depth, and the combined LH-HL scheme, respectively. The schemes efficiently exploit the high correlation between the high and the low bit-depth layers on the macroblock (MB level. Experimental results demonstrate that the HL scheme outperforms the other two schemes in some scenarios. Moreover, it achieves up to 7 dB improvement over the simulcast approach when the high and low bit-depth representations are 12 bits and 8 bits, respectively.

  14. Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

    Science.gov (United States)

    Patil, Gunvant; Vuong, Tri D; Kale, Sandip; Valliyodan, Babu; Deshmukh, Rupesh; Zhu, Chengsong; Wu, Xiaolei; Bai, Yonghe; Yungbluth, Dennis; Lu, Fang; Kumpatla, Siva; Grover Shannon, J; Varshney, Rajeev K; Nguyen, Henry T

    2018-04-04

    The cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil and high sucrose. In this study, an inter-specific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3x depth. Based on 91,342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high-resolution bin map was developed (4,070 bins). In addition to bin mapping, QTL analysis for protein, oil and sucrose was performed using 3,343 polymorphic SNPs (3K-SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared and a significant concordance was observed between bin and 3K-SNP markers. Importantly, the bin map derived from next generation sequencing technology enhanced mapping resolution (from 1325 Kb to 50 Kb). A total of 5, 9 and 4 QTLs were identified for protein, oil and sucrose content, respectively and some of the QTLs coincided with soybean domestication related genomic loci. The major QTL for protein and oil was mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL was identified on Chr. 8 (qSuc_08) and harbors putative genes involved in sugar transport. In addition, genome-wide association (GWAS) using 91,342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL based haplotype using whole genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  15. Depth profiling of extended defects in silicon by Rutherford backscattering measurements

    International Nuclear Information System (INIS)

    Gruska, B.; Goetz, G.

    1981-01-01

    Depth profiling of dislocations and stacking faults is carried out by analyzing axial and planar channeling data from As + -and P + -implanted silicon samples annealed at high temperatures. The analyzing procedure is based on the simple two-beam model. The results show that depth profiling of dislocations using planar channeling data is connected with a broadening of the real distributions. A degradation of the defect concentration and a deformation of the profile result for very high defect concentrations (> 5 x 10 5 cm/cm 2 ). All these effects can be neglected by analyzing axial channeling data. Depth profiling of stacking faults is restricted to the determination of the depth distribution of displaced atomic rows or planes. For both the procedures, axial as well as planar channeling measurements, the same depth profiles of displaced atomic rows are obtained. (author)

  16. Monitoring waterbird abundance in wetlands: The importance of controlling results for variation in water depth

    Science.gov (United States)

    Bolduc, F.; Afton, A.D.

    2008-01-01

    Wetland use by waterbirds is highly dependent on water depth, and depth requirements generally vary among species. Furthermore, water depth within wetlands often varies greatly over time due to unpredictable hydrological events, making comparisons of waterbird abundance among wetlands difficult as effects of habitat variables and water depth are confounded. Species-specific relationships between bird abundance and water depth necessarily are non-linear; thus, we developed a methodology to correct waterbird abundance for variation in water depth, based on the non-parametric regression of these two variables. Accordingly, we used the difference between observed and predicted abundances from non-parametric regression (analogous to parametric residuals) as an estimate of bird abundance at equivalent water depths. We scaled this difference to levels of observed and predicted abundances using the formula: ((observed - predicted abundance)/(observed + predicted abundance)) ?? 100. This estimate also corresponds to the observed:predicted abundance ratio, which allows easy interpretation of results. We illustrated this methodology using two hypothetical species that differed in water depth and wetland preferences. Comparisons of wetlands, using both observed and relative corrected abundances, indicated that relative corrected abundance adequately separates the effect of water depth from the effect of wetlands. ?? 2008 Elsevier B.V.

  17. Improving Focal Depth Estimates: Studies of Depth Phase Detection at Regional Distances

    Science.gov (United States)

    Stroujkova, A.; Reiter, D. T.; Shumway, R. H.

    2006-12-01

    The accurate estimation of the depth of small, regionally recorded events continues to be an important and difficult explosion monitoring research problem. Depth phases (free surface reflections) are the primary tool that seismologists use to constrain the depth of a seismic event. When depth phases from an event are detected, an accurate source depth is easily found by using the delay times of the depth phases relative to the P wave and a velocity profile near the source. Cepstral techniques, including cepstral F-statistics, represent a class of methods designed for the depth-phase detection and identification; however, they offer only a moderate level of success at epicentral distances less than 15°. This is due to complexities in the Pn coda, which can lead to numerous false detections in addition to the true phase detection. Therefore, cepstral methods cannot be used independently to reliably identify depth phases. Other evidence, such as apparent velocities, amplitudes and frequency content, must be used to confirm whether the phase is truly a depth phase. In this study we used a variety of array methods to estimate apparent phase velocities and arrival azimuths, including beam-forming, semblance analysis, MUltiple SIgnal Classification (MUSIC) (e.g., Schmidt, 1979), and cross-correlation (e.g., Cansi, 1995; Tibuleac and Herrin, 1997). To facilitate the processing and comparison of results, we developed a MATLAB-based processing tool, which allows application of all of these techniques (i.e., augmented cepstral processing) in a single environment. The main objective of this research was to combine the results of three focal-depth estimation techniques and their associated standard errors into a statistically valid unified depth estimate. The three techniques include: 1. Direct focal depth estimate from the depth-phase arrival times picked via augmented cepstral processing. 2. Hypocenter location from direct and surface-reflected arrivals observed on sparse

  18. Multi-depth valved microfluidics for biofilm segmentation

    International Nuclear Information System (INIS)

    Meyer, M T; Bentley, W E; Ghodssi, R; Subramanian, S; Kim, Y W; Ben-Yoav, H; Gnerlich, M; Gerasopoulos, K

    2015-01-01

    Bacterial biofilms present a societal challenge, as they occur in the majority of infections but are highly resistant to both immune mechanisms and traditional antibiotics. In the pursuit of better understanding biofilm biology for developing new treatments, there is a need for streamlined, controlled platforms for biofilm growth and evaluation. We leverage advantages of microfluidics to develop a system in which biofilms are formed and sectioned, allowing parallel assays on multiple sections of one biofilm. A microfluidic testbed with multiple depth profiles was developed to accommodate biofilm growth and sectioning by hydraulically actuated valves. In realization of the platform, a novel fabrication technique was developed for creating multi-depth microfluidic molds using sequentially patterned photoresist separated and passivated by conformal coatings using atomic layer deposition. Biofilm thickness variation within three separately tested devices was less than 13% of the average thickness in each device, while variation between devices was 23% of the average thickness. In a demonstration of parallel experiments performed on one biofilm within one device, integrated valves were used to trisect the uniform biofilms with one section maintained as a control, and two sections exposed to different concentrations of sodium dodecyl sulfate. The technology presented here for multi-depth microchannel fabrication can be used to create a host of microfluidic devices with diverse architectures. While this work focuses on one application of such a device in biofilm sectioning for parallel experimentation, the tailored architectures enabled by the fabrication technology can be used to create devices that provide new biological information. (paper)

  19. Efficient Deterministic Finite Automata Minimization Based on Backward Depth Information.

    Science.gov (United States)

    Liu, Desheng; Huang, Zhiping; Zhang, Yimeng; Guo, Xiaojun; Su, Shaojing

    2016-01-01

    Obtaining a minimal automaton is a fundamental issue in the theory and practical implementation of deterministic finite automatons (DFAs). A minimization algorithm is presented in this paper that consists of two main phases. In the first phase, the backward depth information is built, and the state set of the DFA is partitioned into many blocks. In the second phase, the state set is refined using a hash table. The minimization algorithm has a lower time complexity O(n) than a naive comparison of transitions O(n2). Few states need to be refined by the hash table, because most states have been partitioned by the backward depth information in the coarse partition. This method achieves greater generality than previous methods because building the backward depth information is independent of the topological complexity of the DFA. The proposed algorithm can be applied not only to the minimization of acyclic automata or simple cyclic automata, but also to automata with high topological complexity. Overall, the proposal has three advantages: lower time complexity, greater generality, and scalability. A comparison to Hopcroft's algorithm demonstrates experimentally that the algorithm runs faster than traditional algorithms.

  20. Multi-depth valved microfluidics for biofilm segmentation

    Science.gov (United States)

    Meyer, M. T.; Subramanian, S.; Kim, Y. W.; Ben-Yoav, H.; Gnerlich, M.; Gerasopoulos, K.; Bentley, W. E.; Ghodssi, R.

    2015-09-01

    Bacterial biofilms present a societal challenge, as they occur in the majority of infections but are highly resistant to both immune mechanisms and traditional antibiotics. In the pursuit of better understanding biofilm biology for developing new treatments, there is a need for streamlined, controlled platforms for biofilm growth and evaluation. We leverage advantages of microfluidics to develop a system in which biofilms are formed and sectioned, allowing parallel assays on multiple sections of one biofilm. A microfluidic testbed with multiple depth profiles was developed to accommodate biofilm growth and sectioning by hydraulically actuated valves. In realization of the platform, a novel fabrication technique was developed for creating multi-depth microfluidic molds using sequentially patterned photoresist separated and passivated by conformal coatings using atomic layer deposition. Biofilm thickness variation within three separately tested devices was less than 13% of the average thickness in each device, while variation between devices was 23% of the average thickness. In a demonstration of parallel experiments performed on one biofilm within one device, integrated valves were used to trisect the uniform biofilms with one section maintained as a control, and two sections exposed to different concentrations of sodium dodecyl sulfate. The technology presented here for multi-depth microchannel fabrication can be used to create a host of microfluidic devices with diverse architectures. While this work focuses on one application of such a device in biofilm sectioning for parallel experimentation, the tailored architectures enabled by the fabrication technology can be used to create devices that provide new biological information.

  1. Location-dependent depth and undermining formation of pressure ulcers.

    Science.gov (United States)

    Takahashi, Yoshiko; Isogai, Zenzo; Mizokami, Fumihiro; Furuta, Katsunori; Nemoto, Tetsuya; Kanoh, Hiroyuki; Yoneda, Masahiko

    2013-08-01

    We examined the location-specific properties of pressure ulcers, focusing on depth and undermining formation, which are often unfavorable factors for ulcer healing. We conducted a retrospective observational study of 2 independent databases on pressure ulcers. Databases from a 200-bed hospital (database A) and a 300-bed hospital (database B) were collected during different time periods. Relationships between ulcer location, ulcer depth, and undermining formation were analyzed. All pressure ulcers were accurately diagnosed and classified according to their locations. A total of 282 pressure ulcers in 189 patients from database A and 232 pressure ulcers in 154 patients from database B were analyzed. It was found that pressure ulcers primarily developed over the sacrum. Ratio of stages III and IV pressure ulcers was high in pressure ulcers of the foot, ankle, and crus on the lower leg. Among the deep pressure ulcers, undermining formation was frequently observed on the greater trochanter, ilium, and sacrum. In contrast, pressure ulcers of the foot, ankle, and crus did not exhibit undermining formation. Our results revealed marked differences in pressure ulcer properties depending on their location. Factors affecting depth and undermining of pressure ulcers appear to be related to anatomical and physical properties of the bone and subcutaneous tissue. Copyright © 2013 Tissue Viability Society. Published by Elsevier Ltd. All rights reserved.

  2. Induction Thermography for Surface Crack Detection and Depth Determination

    Directory of Open Access Journals (Sweden)

    Beate Oswald-Tranta

    2018-02-01

    Full Text Available In the last few years, induction thermography has been established as a non-destructive testing method for localizing surface cracks in metals. The sample to be inspected is heated with a short induced electrical current pulse, and the infrared camera records—during and after the heating pulse—the temperature distribution at the surface. Transforming the temporal temperature development for each pixel to phase information makes not only highly reliable detection of the cracks possible but also allows an estimation of its depth. Finite element simulations were carried out to investigate how the phase contrast depends on parameters such as excitation frequency, pulse duration, material parameters, crack depth, and inclination angle of the crack. From these results, generalized functions for the dependency of the phase difference on all these parameters were derived. These functions can be used as an excellent guideline as to how measurement parameters should be optimized for a given material to be able to detect cracks and estimate their depth. Several experiments on different samples were also carried out, and the results compared with the simulations showed very good agreement.

  3. Kinect Fusion improvement using depth camera calibration

    Science.gov (United States)

    Pagliari, D.; Menna, F.; Roncella, R.; Remondino, F.; Pinto, L.

    2014-06-01

    Scene's 3D modelling, gesture recognition and motion tracking are fields in rapid and continuous development which have caused growing demand on interactivity in video-game and e-entertainment market. Starting from the idea of creating a sensor that allows users to play without having to hold any remote controller, the Microsoft Kinect device was created. The Kinect has always attract researchers in different fields, from robotics to Computer Vision (CV) and biomedical engineering as well as third-party communities that have released several Software Development Kit (SDK) versions for Kinect in order to use it not only as a game device but as measurement system. Microsoft Kinect Fusion control libraries (firstly released in March 2013) allow using the device as a 3D scanning and produce meshed polygonal of a static scene just moving the Kinect around. A drawback of this sensor is the geometric quality of the delivered data and the low repeatability. For this reason the authors carried out some investigation in order to evaluate the accuracy and repeatability of the depth measured delivered by the Kinect. The paper will present a throughout calibration analysis of the Kinect imaging sensor, with the aim of establishing the accuracy and precision of the delivered information: a straightforward calibration of the depth sensor in presented and then the 3D data are correct accordingly. Integrating the depth correction algorithm and correcting the IR camera interior and exterior orientation parameters, the Fusion Libraries are corrected and a new reconstruction software is created to produce more accurate models.

  4. Kinect Fusion improvement using depth camera calibration

    Directory of Open Access Journals (Sweden)

    D. Pagliari

    2014-06-01

    Full Text Available Scene's 3D modelling, gesture recognition and motion tracking are fields in rapid and continuous development which have caused growing demand on interactivity in video-game and e-entertainment market. Starting from the idea of creating a sensor that allows users to play without having to hold any remote controller, the Microsoft Kinect device was created. The Kinect has always attract researchers in different fields, from robotics to Computer Vision (CV and biomedical engineering as well as third-party communities that have released several Software Development Kit (SDK versions for Kinect in order to use it not only as a game device but as measurement system. Microsoft Kinect Fusion control libraries (firstly released in March 2013 allow using the device as a 3D scanning and produce meshed polygonal of a static scene just moving the Kinect around. A drawback of this sensor is the geometric quality of the delivered data and the low repeatability. For this reason the authors carried out some investigation in order to evaluate the accuracy and repeatability of the depth measured delivered by the Kinect. The paper will present a throughout calibration analysis of the Kinect imaging sensor, with the aim of establishing the accuracy and precision of the delivered information: a straightforward calibration of the depth sensor in presented and then the 3D data are correct accordingly. Integrating the depth correction algorithm and correcting the IR camera interior and exterior orientation parameters, the Fusion Libraries are corrected and a new reconstruction software is created to produce more accurate models.

  5. Directional spread parameter at intermediate water depth

    Digital Repository Service at National Institute of Oceanography (India)

    SanilKumar, V.; Deo, M.C.; Anand, N.M.; AshokKumar, K.

    ’ involves only the significant wave height, zero crossing wave period and water depth, the spreading function based on ‘s 3 ’ can be used for practical appli- cation. In the model based on ‘s 3 ’ the mean wave direction is an input and this has...-linearity parameter can be recommended for practical use as it provides an averaged distribution. Acknowledgements The authors would like to thank the Department of Science and Technology, New Delhi, for funding the project titled “Directional wave modelling...

  6. Element depth profiles of porous silicon

    International Nuclear Information System (INIS)

    Kobzev, A.P.; Nikonov, O.A.; Kulik, M.; Zuk, J.; Krzyzanowska, H.; Ochalski, T.J.

    1997-01-01

    Element depth profiles of porous silicon were measured on the Van-de-Graaff accelerator in the energy range of 4 He + ions from 2 to 3.2 MeV. Application of complementary RBS, ERD and 16 O(α,α) 16 O nuclear reaction methods permits us to obtain: 1) the exact silicon, oxygen and hydrogen distribution in the samples, 2) the distribution of partial pore concentrations. The oxygen concentration in porous silicon reaches 30%, which allows one to assume the presence of silicon oxide in the pores and to explain the spectrum shift of luminescence into the blue area

  7. EPA Region 1 - Valley Depth in Meters

    Science.gov (United States)

    Raster of the Depth in meters of EPA-delimited Valleys in Region 1.Valleys (areas that are lower than their neighbors) were extracted from a Digital Elevation Model (USGS, 30m) by finding the local average elevation, subtracting the actual elevation from the average, and selecting areas where the actual elevation was below the average. The landscape was sampled at seven scales (circles of 1, 2, 4, 7, 11, 16, and 22 km radius) to take into account the diversity of valley shapes and sizes. Areas selected in at least four scales were designated as valleys.

  8. A holistic water depth simulation model for small ponds

    Science.gov (United States)

    Ali, Shakir; Ghosh, Narayan C.; Mishra, P. K.; Singh, R. K.

    2015-10-01

    Estimation of time varying water depth and time to empty of a pond is prerequisite for comprehensive and coordinated planning of water resource for its effective utilization. A holistic water depth simulation (HWDS) and time to empty (TE) model for small, shallow ephemeral ponds have been derived by employing the generalized model based on the Green-Ampt equation in the basic water balance equation. The HWDS model includes time varying rainfall, runoff, surface water evaporation, outflow and advancement of wetting front length as external inputs. The TE model includes two external inputs; surface water evaporation and advancement of wetting front length. Both the models also consider saturated hydraulic conductivity and fillable porosity of the pond's bed material as their parameters. The solution of the HWDS model involved numerical iteration in successive time intervals. The HWDS model has successfully evaluated with 3 years of field data from two small ponds located within a watershed in a semi-arid region in western India. The HWDS model simulated time varying water depth in the ponds with high accuracy as shown by correlation coefficient (R2 ⩾ 0.9765), index of agreement (d ⩾ 0.9878), root mean square errors (RMSE ⩽ 0.20 m) and percent bias (PB ⩽ 6.23%) for the pooled data sets of the measured and simulated water depth. The statistical F and t-tests also confirmed the reliability of the HWDS model at probability level, p ⩽ 0.0001. The response of the TE model showed its ability to estimate the time to empty the ponds. An additional field calibration and validation of the HWDS and TE models with observed field data in varied hydro-climatic conditions could be conducted to increase the applicability and credibility of the models.

  9. Depth of origin and angular spectrum of sputtered atoms

    International Nuclear Information System (INIS)

    Vicanek, M.; Jimenez Rodriguez, J.J.; Sigmund, P.

    1989-01-01

    A theoretical analysis is presented of the depth of origin of atoms sputtered from a random target. The physical model aims at high energy sputtering under linear cascade conditions and assumes a dilute source of recoil atoms. The initial distribution of the recoils is assumed isotropic, and their energy distribution is E -2 like without an upper or lower cutoff. The scattering medium is either infinite or bounded by a plane surface. Atoms scatter according to the m=0 power cross section. Electronic stopping is ignored. The sputtered flux, differential in depth of origin, ejection energy and ejection angle has been evaluated by Monte Carlo simulation and by five distinct methods of solution of the linear Boltzmann equation reaching from continuous slowing down neglecting angular scattering to the P 3 approximation and a Gram-Charlier expansion going over spatial moments. The continuous slowing down approximation used in previous work leads to results that are identical to those found from a scheme that only ignores angular scattering but allows for energy loss straggling. Moreover, these predictions match more closely with the Monte Carlo results than any of the approximate analytical schemes that take account of angular scattering. The results confirm the common assertion that the depth of origin of sputtered atoms is determined mainly by the stopping of low energy recoil atoms. The effect of angular scattering turns out to be astonishingly small. The distributions in depth of origin, energy, and angle do not depend significantly on whether the scattering medium is a halfspace or an infinite medium with a reference plane. The angular spectrum comes out only very slightly over cosine from the model as it stands, in agreement with previous experience, but comments are made on essential features that are not incorporated in the physical model but might influence the angular spectrum. (orig./WL)

  10. Limited Genetic Connectivity between Gorgonian Morphotypes along a Depth Gradient.

    Directory of Open Access Journals (Sweden)

    Federica Costantini

    Full Text Available Gorgonian species show a high morphological variability in relation to the environment in which they live. In coastal areas, parameters such as temperature, light, currents, and food availability vary significantly with depth, potentially affecting morphology of the colonies and the structure of the populations, as well as their connectivity patterns. In tropical seas, the existence of connectivity between shallow and deep populations supported the hypothesis that the deep coral reefs could potentially act as (reproductive refugia fostering re-colonization of shallow areas after mortality events. Moreover, this hypothesis is not so clear accepted in temperate seas. Eunicella singularis is one of the most common gorgonian species in Northwestern Mediterranean Sea, playing an important role as ecosystem engineer by providing biomass and complexity to the coralligenous habitats. It has a wide bathymetric distribution ranging from about 10 m to 100 m. Two depth-related morphotypes have been identified, differing in colony morphology, sclerite size and shape, and occurrence of symbiotic algae, but not in mitochondrial DNA haplotypes. In the present study the genetic structure of E. singularis populations along a horizontal and bathymetric gradient was assessed using microsatellites and ITS1 sequences. Restricted gene flow was found at 30-40 m depth between the two Eunicella morphotypes. Conversely, no genetic structuring has been found among shallow water populations within a spatial scale of ten kilometers. The break in gene flow between shallow and deep populations contributes to explain the morphological variability observed at different depths. Moreover, the limited vertical connectivity hinted that the refugia hypothesis does not apply to E. singularis. Re-colonization of shallow water populations, occasionally affected by mass mortality events, should then be mainly fueled by larvae from other shallow water populations.

  11. Depth perception from moving cast shadow in macaque monkey.

    Science.gov (United States)

    Mizutani, Saneyuki; Usui, Nobuo; Yokota, Takanori; Mizusawa, Hidehiro; Taira, Masato; Katsuyama, Narumi

    2015-07-15

    In the present study, we investigate whether the macaque monkey can perceive motion in depth using a moving cast shadow. To accomplish this, we conducted two experiments. In the first experiment, an adult Japanese monkey was trained in a motion discrimination task in depth by binocular disparity. A square was presented on the display so that it appeared with a binocular disparity of 0.12 degrees (initial position), and moved toward (approaching) or away from (receding) the monkey for 1s. The monkey was trained to discriminate the approaching and receding motion of the square by GO/delayed GO-type responses. The monkey showed a significantly high accuracy rate in the task, and the performance was maintained when the position, color, and shape of the moving object were changed. In the next experiment, the change in the disparity was gradually decreased in the motion discrimination task. The results showed that the performance of the monkey declined as the distance of the approaching and receding motion of the square decreased from the initial position. However, when a moving cast shadow was added to the stimulus, the monkey responded to the motion in depth induced by the cast shadow in the same way as by binocular disparity; the reward was delivered randomly or given in all trials to prevent the learning of the 2D motion of the shadow in the frontal plane. These results suggest that the macaque monkey can perceive motion in depth using a moving cast shadow as well as using binocular disparity. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Time-of-flight depth image enhancement using variable integration time

    Science.gov (United States)

    Kim, Sun Kwon; Choi, Ouk; Kang, Byongmin; Kim, James Dokyoon; Kim, Chang-Yeong

    2013-03-01

    Time-of-Flight (ToF) cameras are used for a variety of applications because it delivers depth information at a high frame rate. These cameras, however, suffer from challenging problems such as noise and motion artifacts. To increase signal-to-noise ratio (SNR), the camera should calculate a distance based on a large amount of infra-red light, which needs to be integrated over a long time. On the other hand, the integration time should be short enough to suppress motion artifacts. We propose a ToF depth imaging method to combine advantages of short and long integration times exploiting an imaging fusion scheme proposed for color imaging. To calibrate depth differences due to the change of integration times, a depth transfer function is estimated by analyzing the joint histogram of depths in the two images of different integration times. The depth images are then transformed into wavelet domains and fused into a depth image with suppressed noise and low motion artifacts. To evaluate the proposed method, we captured a moving bar of a metronome with different integration times. The experiment shows the proposed method could effectively remove the motion artifacts while preserving high SNR comparable to the depth images acquired during long integration time.

  13. Compact synchrotron radiation depth lithography facility

    Science.gov (United States)

    Knüppel, O.; Kadereit, D.; Neff, B.; Hormes, J.

    1992-01-01

    X-ray depth lithography allows the fabrication of plastic microstructures with heights of up to 1 mm but with the smallest possible lateral dimensions of about 1 μm. A resist is irradiated with ``white'' synchrotron radiation through a mask that is partially covered with x-ray absorbing microstructures. The plastic microstructure is then obtained by a subsequent chemical development of the irradiated resist. In order to irradiate a reasonably large resist area, the mask and the resist have to be ``scanned'' across the vertically thin beam of the synchrotron radiation. A flexible, nonexpensive and compact scanner apparatus has been built for x-ray depth lithography at the beamline BN1 at ELSA (the 3.5 GeV Electron Stretcher and Accelerator at the Physikalisches Institut of Bonn University). Measurements with an electronic water level showed that the apparatus limits the scanner-induced structure precision to not more than 0.02 μm. The whole apparatus is installed in a vacuum chamber thus allowing lithography under different process gases and pressures.

  14. Optimal depth-based regional frequency analysis

    Directory of Open Access Journals (Sweden)

    H. Wazneh

    2013-06-01

    Full Text Available Classical methods of regional frequency analysis (RFA of hydrological variables face two drawbacks: (1 the restriction to a particular region which can lead to a loss of some information and (2 the definition of a region that generates a border effect. To reduce the impact of these drawbacks on regional modeling performance, an iterative method was proposed recently, based on the statistical notion of the depth function and a weight function φ. This depth-based RFA (DBRFA approach was shown to be superior to traditional approaches in terms of flexibility, generality and performance. The main difficulty of the DBRFA approach is the optimal choice of the weight function ϕ (e.g., φ minimizing estimation errors. In order to avoid a subjective choice and naïve selection procedures of φ, the aim of the present paper is to propose an algorithm-based procedure to optimize the DBRFA and automate the choice of ϕ according to objective performance criteria. This procedure is applied to estimate flood quantiles in three different regions in North America. One of the findings from the application is that the optimal weight function depends on the considered region and can also quantify the region's homogeneity. By comparing the DBRFA to the canonical correlation analysis (CCA method, results show that the DBRFA approach leads to better performances both in terms of relative bias and mean square error.

  15. Optimal depth-based regional frequency analysis

    Science.gov (United States)

    Wazneh, H.; Chebana, F.; Ouarda, T. B. M. J.

    2013-06-01

    Classical methods of regional frequency analysis (RFA) of hydrological variables face two drawbacks: (1) the restriction to a particular region which can lead to a loss of some information and (2) the definition of a region that generates a border effect. To reduce the impact of these drawbacks on regional modeling performance, an iterative method was proposed recently, based on the statistical notion of the depth function and a weight function φ. This depth-based RFA (DBRFA) approach was shown to be superior to traditional approaches in terms of flexibility, generality and performance. The main difficulty of the DBRFA approach is the optimal choice of the weight function ϕ (e.g., φ minimizing estimation errors). In order to avoid a subjective choice and naïve selection procedures of φ, the aim of the present paper is to propose an algorithm-based procedure to optimize the DBRFA and automate the choice of ϕ according to objective performance criteria. This procedure is applied to estimate flood quantiles in three different regions in North America. One of the findings from the application is that the optimal weight function depends on the considered region and can also quantify the region's homogeneity. By comparing the DBRFA to the canonical correlation analysis (CCA) method, results show that the DBRFA approach leads to better performances both in terms of relative bias and mean square error.

  16. Cigarette Mouth Insertion Depths Among Chinese Smokers

    Directory of Open Access Journals (Sweden)

    Hu Q

    2014-12-01

    Full Text Available Vent blocking - where filter ventilation holes are intentionally or unintentionally, partly or completely covered by smokers’ lips during smoking - is an aspect of smoking behavior which can alter mainstream smoke yields. This study was designed to determine if, and to what extent ventilation holes were blocked by smokers’ lips in two cohorts of Chinese smokers. In this study, two groups of samples were collected. One group (1742 butts was collected randomly from public places in six chosen cities. Another (1037 butts was obtained by collecting the butts from identified smokers in Kunming. In this paper, the mouth insertion depth among Chinese smokers was studied for the first time by a staining method employing ninhydrin in ethanol. The results indicate that Chinese smokers exhibit a mouth insertion depth ranging from 1 to 17 mm with an average value of 7.5 AA± 2 mm. In this study, 95% of the ventilated filters examined showed that the vent zone was neither completely nor partially covered by smokers’ lips.

  17. Defence-in-depth and new reactors

    International Nuclear Information System (INIS)

    Bonaca, M.

    2002-01-01

    Defense-in-Depth (DID) is the structured approach to nuclear reactor safety that is at the basis of the safety features of the current generation of operating plants. This approach developed as a means of compensating for uncertainties in equipment and human performance, and it has evolved since the 1950's from its early use as a reactor safety guiding principle to its current broad, systematic application as an overall safety philosophy incorporating lessons learned from the current generation of operating reactors. The NRC white paper on risk-informed and performance based regulation defines DID as ''...an element of the NRC's Safety Philosophy that employs successive compensatory measures to prevent accidents or mitigate damage if a malfunction, accident, or naturally caused event occurs at a nuclear facility. This philosophy ensures that safety will not be wholly dependent on any single element...The net effect of incorporating defense-in-depth...is that the facility...tends to be more tolerant of failures and external challenges''. In practical terms, DID results from the implementation of multiple measures to prevent and mitigate accidents, to contain their consequences, and to establish an acceptable balance between prevention and mitigation. Its pervasive application in reactor safety design and regulation is translated into many precepts and technical requirements of the current body of regulation. (author)

  18. Z-depth integration: a new technique for manipulating z-depth properties in composited scenes

    Science.gov (United States)

    Steckel, Kayla; Whittinghill, David

    2014-02-01

    This paper presents a new technique in the production pipeline of asset creation for virtual environments called Z-Depth Integration (ZeDI). ZeDI is intended to reduce the time required to place elements at the appropriate z-depth within a scene. Though ZeDI is intended for use primarily in two-dimensional scene composition, depth-dependent "flat" animated objects are often critical elements of augmented and virtual reality applications (AR/VR). ZeDI is derived from "deep image compositing", a capacity implemented within the OpenEXR file format. In order to trick the human eye into perceiving overlapping scene elements as being in front of or behind one another, the developer must manually manipulate which pixels of an element are visible in relation to other objects embedded within the environment's image sequence. ZeDI improves on this process by providing a means for interacting with procedurally extracted z-depth data from a virtual environment scene. By streamlining the process of defining objects' depth characteristics, it is expected that the time and energy required for developers to create compelling AR/VR scenes will be reduced. In the proof of concept presented in this manuscript, ZeDI is implemented for pre-rendered virtual scene construction via an AfterEffects software plug-in.

  19. Single-nucleotide polymorphism discovery in Leptographium longiclavatum, a mountain pine beetle-associated symbiotic fungus, using whole-genome resequencing.

    Science.gov (United States)

    Ojeda, Dario I; Dhillon, Braham; Tsui, Clement K M; Hamelin, Richard C

    2014-03-01

    Single-nucleotide polymorphisms (SNPs) are rapidly becoming the standard markers in population genomics studies; however, their use in nonmodel organisms is limited due to the lack of cost-effective approaches to uncover genome-wide variation, and the large number of individuals needed in the screening process to reduce ascertainment bias. To discover SNPs for population genomics studies in the fungal symbionts of the mountain pine beetle (MPB), we developed a road map to discover SNPs and to produce a genotyping platform. We undertook a whole-genome sequencing approach of Leptographium longiclavatum in combination with available genomics resources of another MPB symbiont, Grosmannia clavigera. We sequenced 71 individuals pooled into four groups using the Illumina sequencing technology. We generated between 27 and 30 million reads of 75 bp that resulted in a total of 1, 181 contigs longer than 2 kb and an assembled genome size of 28.9 Mb (N50 = 48 kb, average depth = 125x). A total of 9052 proteins were annotated, and between 9531 and 17,266 SNPs were identified in the four pools. A subset of 206 genes (containing 574 SNPs, 11% false positives) was used to develop a genotyping platform for this species. Using this roadmap, we developed a genotyping assay with a total of 147 SNPs located in 121 genes using the Illumina(®) Sequenom iPLEX Gold. Our preliminary genotyping (success rate = 85%) of 304 individuals from 36 populations supports the utility of this approach for population genomics studies in other MPB fungal symbionts and other fungal nonmodel species. © 2013 John Wiley & Sons Ltd.

  20. Estimation of penetration depth of fission products in cladding Hull

    International Nuclear Information System (INIS)

    Kim, Hee Moon; Jung, Yang Hong; Yoo, Byong Ok; Choo, Yong Sun; Hong, Kwon Pyo

    2005-01-01

    A disposal and a reprocessing for spent fuel rod with high burnup need de-cladding procedure. Pellet in this rod has been separated from a cladding hull to reduce a radioactivity of hull by chemical and mechanical methods. But fission products and actinides(U,Pu) still remain inside of cladding hull by chemical bonding and fission spike, which is called as 'contamination'. More specific removal of this contamination would have been considered. In this study, the sorts of fission products and penetration depth in hull were observed by EPMA test. To analyze this behavior, SRIM 2000 code was also used as energies of fission products and an oxide thickness of hull

  1. Subjective method of refractometry and depth of focus

    OpenAIRE

    Sergienko, Nikolai M.; Gromova, Anastasia; Sergienko, Nikolai

    2012-01-01

    Purpose: To study the impact of the depth of focus on subjective refraction and distribution of myopic and hyperopic refractions. Methods: A total of 450 eyes of 305 subjects in the age range of 23–34 years were recruited for the study. A distribution of refractions was examined using a traditional method of the subjective refractometry on the basis of point-like posterior focus notion. Correction of the results was made on the assumption that the emmetropic eye retains high visual acuity ...

  2. Monitoring microearthquakes with the San Andreas fault observatory at depth

    Science.gov (United States)

    Oye, V.; Ellsworth, W.L.

    2007-01-01

    In 2005, the San Andreas Fault Observatory at Depth (SAFOD) was drilled through the San Andreas Fault zone at a depth of about 3.1 km. The borehole has subsequently been instrumented with high-frequency geophones in order to better constrain locations and source processes of nearby microearthquakes that will be targeted in the upcoming phase of SAFOD. The microseismic monitoring software MIMO, developed by NORSAR, has been installed at SAFOD to provide near-real time locations and magnitude estimates using the high sampling rate (4000 Hz) waveform data. To improve the detection and location accuracy, we incorporate data from the nearby, shallow borehole (???250 m) seismometers of the High Resolution Seismic Network (HRSN). The event association algorithm of the MIMO software incorporates HRSN detections provided by the USGS real time earthworm software. The concept of the new event association is based on the generalized beam forming, primarily used in array seismology. The method requires the pre-computation of theoretical travel times in a 3D grid of potential microearthquake locations to the seismometers of the current station network. By minimizing the differences between theoretical and observed detection times an event is associated and the location accuracy is significantly improved.

  3. Detecting overpressure using the Eaton and Equivalent Depth methods in Offshore Nova Scotia, Canada

    Science.gov (United States)

    Ernanda; Primasty, A. Q. T.; Akbar, K. A.

    2018-03-01

    Overpressure is an abnormal high subsurface pressure of any fluids which exceeds the hydrostatic pressure of column of water or formation brine. In Offshore Nova Scotia Canada, the values and depth of overpressure zone are determined using the eaton and equivalent depth method, based on well data and the normal compaction trend analysis. Since equivalent depth method is using effective vertical stress principle and Eaton method considers physical property ratio (velocity). In this research, pressure evaluation only applicable on Penobscot L-30 well. An abnormal pressure is detected at depth 11804 feet as possibly overpressure zone, based on pressure gradient curve and calculation between the Eaton method (7241.3 psi) and Equivalent Depth method (6619.4 psi). Shales within Abenaki formation especially Baccaro Member is estimated as possible overpressure zone due to hydrocarbon generation mechanism.

  4. Improving depth resolutions in positron beam spectroscopy by concurrent ion-beam sputtering

    Science.gov (United States)

    John, Marco; Dalla, Ayham; Ibrahim, Alaa M.; Anwand, Wolfgang; Wagner, Andreas; Böttger, Roman; Krause-Rehberg, Reinhard

    2018-05-01

    The depth resolution of mono-energetic positron annihilation spectroscopy using a positron beam is shown to improve by concurrently removing the sample surface layer during positron beam spectroscopy. During ion-beam sputtering with argon ions, Doppler-broadening spectroscopy is performed with energies ranging from 3 keV to 5 keV allowing for high-resolution defect studies just below the sputtered surface. With this technique, significantly improved depth resolutions could be obtained even at larger depths when compared to standard positron beam experiments which suffer from extended positron implantation profiles at higher positron energies. Our results show that it is possible to investigate layered structures with a thickness of about 4 microns with significantly improved depth resolution. We demonstrated that a purposely generated ion-beam induced defect profile in a silicon sample could be resolved employing the new technique. A depth resolution of less than 100 nm could be reached.

  5. Differential leaching of 137Cs from sediment core depth fractions of Bombay harbour bay

    International Nuclear Information System (INIS)

    Hemalatha, P.; Desai, M.V.M.

    1998-01-01

    Bombay harbour bay receives 137 Cs from the effluents of research reactors, fuel reprocessing plant and isotope laboratories. 137 Cs is strongly taken up by suspended particulates and sediments and is trapped in the layer lattices of the clay minerals. As the siltation rate is high in the bay, 137 Cs gets distributed vertically along the depth of sediment. NaCl solution has been proved to desorb 137 Cs from clay minerals effectively. NaCl solution of ionic strength 1.6 was used to desorb 137 Cs from depth fractions of a sediment core to obtain a possible gradient of leaching with the depth. A definite rate of leaching was observed for the 137 Cs in the core sediment depth fractions. About 13% to 56% of 137 Cs was leached. As the depth increases removal rate of cesium decreases. This is expected to bring out a relation between age of 137 Cs and rate of its leaching. (author)

  6. Depths of Magma Chambers in the Icelandic Crust

    Science.gov (United States)

    Kelley, D. F.; Kapostasy, D. D.; Barton, M.

    2004-05-01

    There is considerable interest in the structure and thermal state of the crust in Iceland, which lies across the Mid Atlantic Ridge. However, interpretations of seismic and gravity data yield conflicting views of the nature of the lower crust. Some interpretations prefer a model in which the lower crust (15-25 km) is relatively cool and solid, whereas other interpretations, based largely on gravity data, prefer a model in which the lower crust is relatively warm and possibly partially molten. Knowledge of the depth of magma chambers is critical to constrain the geothermal gradient in Icelandic crust and to resolve discrepancies in interpretation of geophysical data. Analyses of aphyric lavas and of glasses in Icelandic lavas erupted from 11 volcanic centers have been compiled. The compositions are picritic and basaltic with SiO2 - 47 to 50 wt%, MgO - 6 to 15wt%, FeO - 8 to 14wt%, to, Na2O - 1.3 to 3.3 wt%, and K2O - 0.03-46 wt%. The pressures of equilibration of these liquids with ol, high-Ca pyx and plag were estimated qualitatively from projections into the pseudoternary system Ol-Di-Silica using methods described by Walker and coworkers and Grove and coworkers. The results (ca. 0.5 GPa) indicate crystallization in magma chambers located at about 16 km depth. Equilibration pressures were also calculated using the method described by Yang and coworkers and by a modified version of this method. Calculated pressures (0.45±0.15 GPa) indicate magma chambers located at 15±4 km depth. Equilibration pressures for Rekjanes Ridge glasses determined using the same techniques are 0.2±0.1 GPa, corresponding to depths of 7.6±3 km. The results indicate the presence of magma chambers in the deep Icelandic crust and that the latter is relatively warm. Shallower chambers (3-7 km) have been identified from seismic studies suggesting a complex magma plumbing system. The results also confirm that magma chambers beneath Iceland are located at greater depths than those beneath the

  7. Campbell penetration depth in Fe-based superconductors

    International Nuclear Information System (INIS)

    Prommapan, Plegchart

    2011-01-01

    A 'true' critical current density, j c , as opposite to commonly measured relaxed persistent (Bean) current, j B , was extracted from the Campbell penetration depth, λ c (T,H) measured in single crystals of LiFeAs, and optimally electron-doped Ba(Fe 0.954 Ni 0.046 ) 2 As 2 (FeNi122). In LiFeAs, the effective pinning potential is nonparabolic, which follows from the magnetic field - dependent Labusch parameter α. At the equilibrium (upon field - cooling), α(H) is non-monotonic, but it is monotonic at a finite gradient of the vortex density. This behavior leads to a faster magnetic relaxation at the lower fields and provides a natural dynamic explanation for the fishtail (second peak) effect. We also find the evidence for strong pinning at the lower fields.The inferred field dependence of the pinning potential is consistent with the evolution from strong pinning, through collective pinning, and eventually to a disordered vortex lattice. The value of j c (2 K) ≅ 1.22 x 10 6 A/cm 2 provide an upper estimate of the current carrying capability of LiFeAs. Overall, vortex behavior of almost isotropic, fully-gapped LiFeAs is very similar to highly anisotropic d-wave cuprate superconductors, the similarity that requires further studies in order to understand unconventional superconductivity in cuprates and pnictides. In addition to LiFeAs, we also report the magnetic penetration depth in BaFe 2 As 2 based superconductors including irradiation of FeNi122. In unirradiated FeNi122, the maximum critical current value is, j c (2K) ≅ 3.3 x 10 6 A/cm 2 . The magnetic-dependent feature was observed near the transition temperature in FeTe 0.53 Se 0.47 and irradiated FeNi122. Because of this feature, further studies are required in order to properly calibrate the Campbell penetration depth. Finally, we detected the crossing between the magnetic penetration depth and London penetration depth in optimally hold-doped Ba 0.6 K 0.4 Fe 2 As 2 (BaK122) and isovalent doped BaFe 2 (As 0

  8. Initial results of tests of depth markers as a surface diagnostic for fusion devices

    Directory of Open Access Journals (Sweden)

    L.A. Kesler

    2017-08-01

    Full Text Available The Accelerator-Based In Situ Materials Surveillance (AIMS diagnostic was developed to perform in situ ion beam analysis (IBA on Alcator C-Mod in August 2012 to study divertor surfaces between shots. These results were limited to studying low-Z surface properties, because the Coulomb barrier precludes nuclear reactions between high-Z elements and the ∼1 MeV AIMS deuteron beam. In order to measure the high-Z erosion, a technique using deuteron-induced gamma emission and a low-Z depth marker is being developed. To determine the depth of the marker while eliminating some uncertainty due to beam and detector parameters, the energy dependence of the ratio of two gamma yields produced from the same depth marker will be used to determine the ion beam energy loss in the surface, and thus the thickness of the high-Z surface. This paper presents the results of initial trials of using an implanted depth marker layer with a deuteron beam and the method of ratios. First tests of a lithium depth marker proved unsuccessful due to the production of conflicting gamma peaks, among other issues. However, successful trials with a boron depth marker show that it is possible to measure the depth of the marker layer with the method of gamma yield ratios.

  9. Mutation detection in cholestatic patients using microarray resequencing of ATP8B1 and ABCB11 [v2; ref status: indexed, http://f1000r.es/yv

    Directory of Open Access Journals (Sweden)

    Kirsten E McKay

    2013-03-01

    Full Text Available Background: Neonatal cholestasis is a common presentation of childhood liver diseases and can be a feature of various conditions including disorders of bile acid biogenesis and transport, various inborn errors of metabolism and perinatal infections. Some inherited metabolic diseases can be easily screened using biochemical assays, however many can only be accurately diagnosed by DNA sequencing. Fluorescent capillary Sanger sequencing (FS is the gold standard method used by clinical laboratories for genetic diagnosis of many inherited conditions; however, it does have limitations. Recently microarray resequencing (MR has been introduced into research and clinical practice as an alternative method for genetic diagnosis of heterogeneous conditions. In this report we compared the accuracy of mutation detection for MR with FS in a group of patients with ‘low-normal’ gamma glutamyl transpeptidase (gGT cholestasis without known molecular diagnoses. Methods: 29 patient DNA samples were tested for mutations in the ATP8B1 and ABCB11 genes using both FS and MR. Other known causes of “low gGT cholestasis” such as ARC syndrome and bile acid biosynthesis disorders were excluded. Results: Mutations were identified in 13/29 samples. In 3/29 samples FS and MR gave discordant results: MR had a false positive rate of 3.4% and a false negative rate of 7%. Conclusions: The major advantage of MR over FS is that multiple genes can be screened in one experiment, allowing rapid and cost-effective diagnoses.  However, we have demonstrated that MR technology is limited in sensitivity. We therefore recommend that MR be used as an initial evaluation, with FS deployed when genetic and clinical or histopathological findings are discordant.

  10. Enhanced depth and mass resolution with HIRBS

    International Nuclear Information System (INIS)

    Yang, Q.; O'Connor, D.J.

    1992-01-01

    The extension of Rutherford backscattering spectrometry (RBS) to heavier mass projectiles (HIRBS) has been limited, as these projectiles cause much more radiation damage in the detectors and curtail their lifetime. Despite this limitation interest in the use of heavier projectiles continues as there are several significant benefits which can accrue from their use. To properly understand the interaction of heavy ions with solids a systematic study of the energy loss and straggling of MeV heavy ions has been conducted and an empirical expression for these terms has been obtained. This expression has allowed the development of a realistic computer simulation which accurately predicts the energy spectra for a wide range of energies, projectiles and targets. In parallel with that study, measurements of the depth resolution of Si/Ge multilayer films using 4-6 MeV C projectiles have been used to verify the simulation. (orig.)

  11. ABDURRAHMAN WAHID, DEPTH ISLAM, AND RELIGIOUS PLURALISM

    Directory of Open Access Journals (Sweden)

    Media Zainul Bahri

    2016-04-01

    Full Text Available This essay elucidates the idea of religious pluralism of Abdurrahman Wahid (1940-2009, a very important figure in the tradition of Indonesian Islam. Wahis’s ideas  of religious pluralism is based on what the so-called “Depth Islam” (DI. DI is different from the usual theological dogmas that only contains concepts and structures. DI  is  not a literal and superficial forms of religion. It is an understanding  that goes beyond the literal texts to look for the principles and spirit of religion in appreciating humanity, diversity and peace.  DI may have arisen because of the long process of religious internalization within Wahid experiences, but it is also a hybrid form, i.e., it is a result of the process of encountering or learning Wahid’s traditions inter-mingling with cultures of the wider world. 

  12. Density distributions and depth in flocks

    Science.gov (United States)

    Lewis, J. M.; Turner, M. S.

    2017-12-01

    Recent experimental evidence suggests that interactions in flocks of birds do not involve a characteristic length scale. Bird flocks have also been revealed to have an inhomogeneous density distribution, with the density of birds near the border greater than near the centre. We introduce a strictly metric-free model for collective behaviour that incorporates a distributed motional bias, providing control of the density distribution. A simple version of this model is then able to provide a good fit to published data for the density variation across flocks of Starlings. We find that it is necessary for individuals on the edge of the flock to have an inward motional bias but that birds in the interior of the flock instead must have an outward bias. We discuss the ability of individuals to determine their depth within a flock and show how this might be achieved by relatively simple analysis of their visual environment.

  13. Spectral entropy in monitoring anesthetic depth.

    Science.gov (United States)

    Escontrela Rodríguez, B; Gago Martínez, A; Merino Julián, I; Martínez Ruiz, A

    2016-10-01

    Monitoring the brain response to hypnotics in general anesthesia, with the nociceptive and hemodynamic stimulus interaction, has been a subject of intense investigation for many years. Nowadays, monitors of depth of anesthesia are based in processed electroencephalogram by different algorithms, some of them unknown, to obtain a simplified numeric parameter approximate to brain activity state in each moment. In this review we evaluate if spectral entropy suitably reflects the brain electric behavior in response to hypnotics and the different intensity nociceptive stimulus effect during a surgical procedure. Copyright © 2015 Sociedad Española de Anestesiología, Reanimación y Terapéutica del Dolor. Publicado por Elsevier España, S.L.U. All rights reserved.

  14. Real-time lossless compression of depth streams

    KAUST Repository

    Schneider, Jens

    2017-08-17

    Various examples are provided for lossless compression of data streams. In one example, a Z-lossless (ZLS) compression method includes generating compacted depth information by condensing information of a depth image and a compressed binary representation of the depth image using histogram compaction and decorrelating the compacted depth information to produce bitplane slicing of residuals by spatial prediction. In another example, an apparatus includes imaging circuitry that can capture one or more depth images and processing circuitry that can generate compacted depth information by condensing information of a captured depth image and a compressed binary representation of the captured depth image using histogram compaction; decorrelate the compacted depth information to produce bitplane slicing of residuals by spatial prediction; and generate an output stream based upon the bitplane slicing.

  15. Depth profile measurement with lenslet images of the plenoptic camera

    Science.gov (United States)

    Yang, Peng; Wang, Zhaomin; Zhang, Wei; Zhao, Hongying; Qu, Weijuan; Zhao, Haimeng; Asundi, Anand; Yan, Lei

    2018-03-01

    An approach for carrying out depth profile measurement of an object with the plenoptic camera is proposed. A single plenoptic image consists of multiple lenslet images. To begin with, these images are processed directly with a refocusing technique to obtain the depth map, which does not need to align and decode the plenoptic image. Then, a linear depth calibration is applied based on the optical structure of the plenoptic camera for depth profile reconstruction. One significant improvement of the proposed method concerns the resolution of the depth map. Unlike the traditional method, our resolution is not limited by the number of microlenses inside the camera, and the depth map can be globally optimized. We validated the method with experiments on depth map reconstruction, depth calibration, and depth profile measurement, with the results indicating that the proposed approach is both efficient and accurate.

  16. Real-time lossless compression of depth streams

    KAUST Repository

    Schneider, Jens

    2017-01-01

    Various examples are provided for lossless compression of data streams. In one example, a Z-lossless (ZLS) compression method includes generating compacted depth information by condensing information of a depth image and a compressed binary representation of the depth image using histogram compaction and decorrelating the compacted depth information to produce bitplane slicing of residuals by spatial prediction. In another example, an apparatus includes imaging circuitry that can capture one or more depth images and processing circuitry that can generate compacted depth information by condensing information of a captured depth image and a compressed binary representation of the captured depth image using histogram compaction; decorrelate the compacted depth information to produce bitplane slicing of residuals by spatial prediction; and generate an output stream based upon the bitplane slicing.

  17. SIMS depth profile analysis of environmental microparticles

    International Nuclear Information System (INIS)

    Konarski, P.

    2000-01-01

    Environmental and technological research demands chemical characterization of aerosol particles so minute in size, that conventional methods for bulk analyses are simply not applicable. In this work novel application of secondary ion mass spectrometry (SIMS) for characterization of microparticles suspended in atmosphere of the working environment of glass plant Thomson Polkolor, Piaseczno and steelworks Huta Sendzimira, Cracow is presented. The new technique based on sample rotation in depth profile analysis of sub-micrometer particulate material was performed on SAJW-02 analyser equipped with Balzers 16 mm quadrupole spectrometer and sample rotation manipulator using 5 keV Ar + and O 2 + ion beams. The results were compared with the standard method used on ims-3f Cameca analyser 12 keV O 2 + ion beam. Grain size distributions of aerosol microparticles were estimated using eight-stage cascade impactor with particle size range of 0.2 μm to 15 μm. Elemental concentration and crystalline structure of the collected dust particles were performed using spark source mass spectrometry and X-ray diffraction methods. SIMS depth profile analysis shows that sub-micrometer particles do not have uniform morphology, The core-shell structure has been observed for particles collected in both factories. Presented models show that the steelworks particles consists mainly of iron and manganese cores. At the shells of these microparticles :lead, chlorine and fluorine are found. The cores of glass plant submicrometer particles consists mainly of lead-zirconium glass covered by a shell containing carbon and copper. Sample rotation technique applied SIMS appears to be an effective tool for environmental microparticle morphology studies. (author)

  18. The Effect of Finite Thickness Extent on Estimating Depth to Basement from Aeromagnetic Data

    Science.gov (United States)

    Blakely, R. J.; Salem, A.; Green, C. M.; Fairhead, D.; Ravat, D.

    2014-12-01

    Depth to basement estimation methods using various components of the spectral content of magnetic anomalies are in common use by geophysicists. Examples of these are the Tilt-Depth and SPI methods. These methods use simple models having the base of the magnetic body at infinity. Recent publications have shown that this 'infinite depth' assumption causes underestimation of the depth to the top of sources, especially in areas where the bottom of the magnetic layer is shallow, as would occur in high heat-flow regions. This error has been demonstrated in both model studies and using real data with seismic or well control. To overcome the limitation of infinite depth this contribution presents the mathematics for a finite depth contact body in the Tilt depth and SPI methods and applies it to the central Red Sea where the Curie isotherm and Moho are shallow. The difference in the depth estimation between the infinite and finite contacts is such a case is significant and can exceed 200%.

  19. Decision trees with minimum average depth for sorting eight elements

    KAUST Repository

    AbouEisha, Hassan M.

    2015-11-19

    We prove that the minimum average depth of a decision tree for sorting 8 pairwise different elements is equal to 620160/8!. We show also that each decision tree for sorting 8 elements, which has minimum average depth (the number of such trees is approximately equal to 8.548×10^326365), has also minimum depth. Both problems were considered by Knuth (1998). To obtain these results, we use tools based on extensions of dynamic programming which allow us to make sequential optimization of decision trees relative to depth and average depth, and to count the number of decision trees with minimum average depth.

  20. Automated sulcal depth measurement on cortical surface reflecting geometrical properties of sulci.

    Directory of Open Access Journals (Sweden)

    Hyuk Jin Yun

    Full Text Available Sulcal depth that is one of the quantitative measures of cerebral cortex has been widely used as an important marker for brain morphological studies. Several studies have employed Euclidean (EUD or geodesic (GED algorithms to measure sulcal depth, which have limitations that ignore sulcal geometry in highly convoluted regions and result in under or overestimated depth. In this study, we proposed an automated measurement for sulcal depth on cortical surface reflecting geometrical properties of sulci, which named the adaptive distance transform (ADT. We first defined the volume region of cerebrospinal fluid between the 3D convex hull and the cortical surface, and constructed local coordinates for that restricted region. Dijkstra's algorithm was then used to compute the shortest paths from the convex hull to the vertices of the cortical surface based on the local coordinates, which may be the most proper approach for defining sulcal depth. We applied our algorithm to both a clinical dataset including patients with mild Alzheimer's disease (AD and 25 normal controls and a simulated dataset whose shape was similar to a single sulcus. The mean sulcal depth in the mild AD group was significantly lower than controls (p = 0.007, normal [mean±SD]: 7.29±0.23 mm, AD: 7.11±0.29 and the area under the receiver operating characteristic curve was relatively high, showing the value of 0.818. Results from clinical dataset that were consistent with former studies using EUD or GED demonstrated that ADT was sensitive to cortical atrophy. The robustness against inter-individual variability of ADT was highlighted through simulation dataset. ADT showed a low and constant normalized difference between the depth of the simulated data and the calculated depth, whereas EUD and GED had high and variable differences. We suggest that ADT is more robust than EUD or GED and might be a useful alternative algorithm for measuring sulcal depth.

  1. Nitrogen Isotopes and Chemocline Depth in Stratified Basins

    Science.gov (United States)

    Fulton, J. M.; Arthur, M. A.

    2006-12-01

    Black shale samples commonly have bulk δ15N values below 0‰, previously interpreted as the result of bacterial nitrogen fixation. In this study we examine the effect of chemocline depth on the δ15N values of water column particulate matter and sediments of two meromictic basins. In particular, we produced δ15N profiles of bulk Black Sea sediments, bulk sediments from Fayetteville Green Lake (FGL), and nutrients and particulates from FGL. We also analyzed pigments from FGL samples to trace the occurrences of deep-dwelling bacteria. Our results suggest that a shallow chemocline leads to relatively 15N-depleted sediments in the absence of nitrogen fixation, probably due to increased availability of ammonium for growth near the chemocline. FGL is meromictic with a shallow chemocline at 20 meters. Ammonium released in the monimolimnion and sediments supports productivity of cyanobacteria and purple (PSB) and green sulfur bacteria near and below the chemocline. The PSB at 20m generate 15N-depleted biomass (δ15N = -3‰), compared with 0 to 3‰ for deep water ammonium. High concentrations of Bchl a extracted from particulate matter at deeper depths, where high sulfide concentrations inhibit PSB growth, suggest that sinking particulate matter contains PSB biomass, transmitting the 15N-depleted signal to the sediments. The Black Sea chemocline depth has varied over the past 7500 years. Published biomarker and pyrite framboid size data suggest that a shallow chemocline persisted through much of the past 7500 years, except for three intervals when the chemocline was deeper than 205 meters. We have measured bulk δ15N on six cores spanning depths from 205 to 2088 meters. Each of the deep chemocline intervals coincides with basin-wide sedimentary δ15N values between 2 and 4‰, compared with values near or below 0‰ for periods characterized by a shallower chemocline. The most 15N-depleted values probably result from a much shallower chemocline than that at present

  2. Simultaneous Mutation Detection in 90 Retinal Disease Genes in Multiple Patients Using a Custom-designed 300-kb Retinal Resequencing Chip

    NARCIS (Netherlands)

    Booij, Judith C.; Bakker, Arne 1; Kulumbetova, Jamilia; Moutaoukil, Youssef; Smeets, Bert; Verheij, Joke; Kroes, Hester Y.; Klaver, Caroline C. W.; van Schooneveld, Mary; Bergen, Arthur A. B.; Florijn, Ralph J.

    Purpose: To develop a high-throughput, cost-effective diagnostic strategy for the identification of known and new mutations in 90 retinal disease genes. Design: Evidence-based study. Participants: Sixty patients with a variety of retinal disorders, including Leber's congenital amaurosis, ocular

  3. Hybridisation-based resequencing of 17 X-linked intellectual disability genes in 135 patients reveals novel mutations in ATRX, SLC6A8 and PQBP1

    NARCIS (Netherlands)

    Jensen, L.R.; Chen, W.; Moser, B.; Lipkowitz, B.; Schroeder, C.; Musante, L.; Tzschach, A.; Kalscheuer, V.M.M.; Meloni, I.; Raynaud, M.; Esch, H. van; Chelly, J.; Brouwer, A.P. de; Hackett, A.; Haar, S. van der; Henn, W.; Gecz, J.; Riess, O.; Bonin, M.; Reinhardt, R.; Ropers, H.H.; Kuss, A.W.

    2011-01-01

    X-linked intellectual disability (XLID), also known as X-linked mental retardation, is a highly genetically heterogeneous condition for which mutations in >90 different genes have been identified. In this study, we used a custom-made sequencing array based on the Affymetrix 50k platform for mutation

  4. Influence of the impurities on the depth of penetration with carbon steel weldings

    Directory of Open Access Journals (Sweden)

    O. Savytsky

    2014-04-01

    Full Text Available In this paper the results of the research about the influence of the impurities on the depth of penetration with carbon steels weldings of different chemical composition are presented. These data suggest that presence of those impurities, such as sulphure and oxygen, in the steel, increases the depth of penetration to 1,3 - 1,5 times compared to welding refined steels. Applying activating fluxes for welding high tensile steels, provides an increase in the depth of penetration of 2 - 3 times.

  5. Generation of synthetic Kinect depth images based on empirical noise model

    DEFF Research Database (Denmark)

    Iversen, Thorbjørn Mosekjær; Kraft, Dirk

    2017-01-01

    The development, training and evaluation of computer vision algorithms rely on the availability of a large number of images. The acquisition of these images can be time-consuming if they are recorded using real sensors. An alternative is to rely on synthetic images which can be rapidly generated....... This Letter describes a novel method for the simulation of Kinect v1 depth images. The method is based on an existing empirical noise model from the literature. The authors show that their relatively simple method is able to provide depth images which have a high similarity with real depth images....

  6. Shaded-Mask Filtering for Extended Depth-of-Field Microscopy

    OpenAIRE

    Escobar García, Isabel María; Saavedra Tortosa, Genaro; Martínez Corral, Manuel; Calatayud, Arnau; Doblas Expósito, Ana Isabel

    2013-01-01

    This paper proposes a new spatial filtering approach for increasing the depth-of-field (DOF) of imaging systems, which is very useful for obtaining sharp images for a wide range of axial positions of the object. Many different techniques have been reported to increase the depth of field. However the main advantage in our method is its simplicity, since we propose the use of purely absorbing beam-shaping elements, which allows a high focal depth with a minimum modification of the optical archi...

  7. Muon background studies for shallow depth Double - Chooz near detector

    Energy Technology Data Exchange (ETDEWEB)

    Gómez, H. [Laboratoire Astroparticule et Cosmologie (APC) - Université Paris 7. Paris (France)

    2015-08-17

    Muon events are one of the main concerns regarding background in neutrino experiments. The placement of experimental set-ups in deep underground facilities reduce considerably their impact on the research of the expected signals. But in the cases where the detector is installed on surface or at shallow depth, muon flux remains high, being necessary their precise identification for further rejection. Total flux, mean energy or angular distributions are some of the parameters that can help to characterize the muons. Empirically, the muon rate can be measured in an experiment by a number of methods. Nevertheless, the capability to determine the muons angular distribution strongly depends on the detector features, while the measurement of the muon energy is quite difficult. Also considering that on-site measurements can not be extrapolated to other sites due to the difference on the overburden and its profile, it is necessary to find an adequate solution to perform the muon characterization. The method described in this work to obtain the main features of the muons reaching the experimental set-up, is based on the muon transport simulation by the MUSIC software, combined with a dedicated sampling algorithm for shallow depth installations based on a modified Gaisser parametrization. This method provides all the required information about the muons for any shallow depth installation if the corresponding overburden profile is implemented. In this work, the method has been applied for the recently commissioned Double - Chooz near detector, which will allow the cross-check between the simulation and the experimental data, as it has been done for the far detector.

  8. Phosphorus conditions at various depths in some mineral soils

    Directory of Open Access Journals (Sweden)

    Armi Kaila

    1963-05-01

    Full Text Available The fractionation method of CHANG and JACKSON (2 was used for the analysing of the distribution of inorganic phosphorus in the topsoil and subsoil of twelve virgin and twelve cultivated soils from various parts of the country; two virgin soils and twenty cultivated soils were studied down to the depths of 60 cm or 70 cm, one even to 2 m. In the more intensively podsolized virgin soils the surface layers, particularly the A2-horizon, are very poor in all the forms of inorganic phosphorus while the enrichment layer will contain fairly high amounts of iron and aluminium bound phosphorus. The application of fertilizers and the other cultivation managements tend to accumulate aluminium and iron bound phosphorus in the plough layer. In some soils the minimum content of calcium bound phosphorus occurs in the layer below the plough layer, but an increase with the depth seems to be typical to it in all the non-Litorina soils, while the first two fractions usually decrease with the depth. In the Litorina soils the iron bound phosphorus is dominant in all the layers studied, but the content of reductant soluble phosphorus is low in these soils, and their content of calcium bound phosphorus is higher than the content of phosphorus bound by aluminium. The predominance of calcium phosphate in the subsoil and the rather low content of reductant soluble and occluded fractions indicate that the chemical weathering in most of our soils is not yet at an advanced stage. The test values determined were in accordance with the results of the fractionation and the estimation of ammonium oxalate soluble aluminium and iron.

  9. Dynamic topography and the Cenozoic carbonate compensation depth

    Science.gov (United States)

    Campbell, S. M.; Moucha, R.; Raymo, M. E.; Derry, L. A.

    2015-12-01

    The carbonate compensation depth (CCD), the ocean depth at which the calcium carbonate accumulation rate goes to zero, can provide valuable insight into climatic and weathering conditions over the Cenozoic. The paleoposition of the CCD can be inferred from sediment core data. As the carbonate accumulation rate decreases linearly with depth between the lysocline and CCD, the CCD can be calculated using a linear regression on multiple sediment cores with known carbonate accumulation rates and paleodepths. It is therefore vital to have well-constrained estimates of paleodepths. Paleodepths are typically calculated using models of thermal subsidence and sediment loading and compaction. However, viscous convection-related stresses in the mantle can warp the ocean floor by hundreds of meters over broad regions and can also vary significantly over millions of years. This contribution to paleobathymetry, termed dynamic topography, can be calculated by modeling mantle flow backwards in time. Herein, we demonstrate the effect dynamic topography has on the inference of the late Cenozoic CCD with an example from the equatorial Pacific, considering sites from IODP Expeditions 320/321. The equatorial Pacific, given its large size and high productivity, is closely tied to the global carbon cycle. Accordingly, long-term changes in the equatorial Pacific CCD can be considered to reflect global changes in weathering fluxes and the carbon cycle, in addition to more regional changes in productivity and thermohaline circulation. We find that, when the dynamic topography contribution to bathymetry is accounted for, the equatorial Pacific CCD is calculated to be appreciably shallower at 30 Ma than previous estimates would suggest, implying a greater deepening of the Pacific CCD over the late Cenozoic.

  10. Muon background studies for shallow depth Double - Chooz near detector

    International Nuclear Information System (INIS)

    Gómez, H.

    2015-01-01

    Muon events are one of the main concerns regarding background in neutrino experiments. The placement of experimental set-ups in deep underground facilities reduce considerably their impact on the research of the expected signals. But in the cases where the detector is installed on surface or at shallow depth, muon flux remains high, being necessary their precise identification for further rejection. Total flux, mean energy or angular distributions are some of the parameters that can help to characterize the muons. Empirically, the muon rate can be measured in an experiment by a number of methods. Nevertheless, the capability to determine the muons angular distribution strongly depends on the detector features, while the measurement of the muon energy is quite difficult. Also considering that on-site measurements can not be extrapolated to other sites due to the difference on the overburden and its profile, it is necessary to find an adequate solution to perform the muon characterization. The method described in this work to obtain the main features of the muons reaching the experimental set-up, is based on the muon transport simulation by the MUSIC software, combined with a dedicated sampling algorithm for shallow depth installations based on a modified Gaisser parametrization. This method provides all the required information about the muons for any shallow depth installation if the corresponding overburden profile is implemented. In this work, the method has been applied for the recently commissioned Double - Chooz near detector, which will allow the cross-check between the simulation and the experimental data, as it has been done for the far detector

  11. In-depth analysis of bicycle hydraulic disc brakes

    Science.gov (United States)

    Maier, Oliver; Györfi, Benedikt; Wrede, Jürgen; Arnold, Timo; Moia, Alessandro

    2017-10-01

    Hydraulic Disc Brakes (HDBs) represent the most recent and innovative bicycle braking system. Especially Electric Bicycles (EBs), which are becoming more and more popular, are equipped with this powerful, unaffected by environmental influences, and low-wear type of brakes. As a consequence of the high braking performance, typical bicycle braking errors lead to more serious accidents. This is the starting point for the development of a Braking Dynamics Assistance system (BDA) to prevent front wheel lockup and nose-over (falling over the handlebars). One of the essential prerequisites for the system design is a better understanding of bicycle HDBs' characteristics. A physical simulation model and a test bench have been built for this purpose. The results of the virtual and real experiments conducted show a high correlation and allow valuable insights into HDBs on bicycles, which have not been studied scientifically in any depth so far.

  12. Role of depth and location of minima of a double-well potential on vibrational resonance

    International Nuclear Information System (INIS)

    Rajasekar, S; Jeyakumari, S; Chinnathambi, V; Sanjuan, M A F

    2010-01-01

    We report our investigation into the role of depth and location of minima of a double-well potential on vibrational resonance in both underdamped and overdamped Duffing oscillators. The systems are driven by both low- and high-frequency periodic forces. We obtain theoretical expressions for the amplitude g of the high-frequency force at which resonances occur. The depth and location of the minima of the potential wells have a distinct effect on vibrational resonance in the underdamped and overdamped cases. In the underdamped system at least one resonance and at most two resonances occur and the number of resonances can be altered by varying the depth and location of the minima of the potential wells. We show that in the overdamped system there is always one and only one resonance, and the value of g at which resonance occurs is independent of the depth of the wells, but varies linearly with the locations of the minima of the wells.

  13. Chemometric characterization of soil depth profiles

    International Nuclear Information System (INIS)

    Krieg, M.; Einax, J.

    1994-01-01

    The application of multivariate-statistical methods to the description of the metal distribution in soil depth profiles is shown. By means of cluster analysis, it is possible to get a first overview of the main differences in the metal status of the soil horizons. In case of anthropogenic soil pollution or geogenic enrichment, cluster analysis was able to detect the extent of the polluted soil layer or the different geological layers. The results of cluster analysis can be confirmed by means of multidimensional variance and discriminant analysis. Methods of discriminant analysis can also be used as a tool to determine the optimum number of variables which has to be measured for the classification of unknown soil samples into different pollution levels. Factor analysis yields an identification of not directly observable relationships between the variables. With additional knowledge about the orographic situation of the area and the probable sources of emission the factor loadings give information on the immission structure at the sampling location. (orig.)

  14. Multichannel optical mapping: investigation of depth information

    Science.gov (United States)

    Sase, Ichiro; Eda, Hideo; Seiyama, Akitoshi; Tanabe, Hiroki C.; Takatsuki, Akira; Yanagida, Toshio

    2001-06-01

    Near infrared (NIR) light has become a powerful tool for non-invasive imaging of human brain activity. Many systems have been developed to capture the changes in regional brain blood flow and hemoglobin oxygenation, which occur in the human cortex in response to neural activity. We have developed a multi-channel reflectance imaging system, which can be used as a `mapping device' and also as a `multi-channel spectrophotometer'. In the present study, we visualized changes in the hemodynamics of the human occipital region in multiple ways. (1) Stimulating left and right primary visual cortex independently by showing sector shaped checkerboards sequentially over the contralateral visual field, resulted in corresponding changes in the hemodynamics observed by `mapping' measurement. (2) Simultaneous measurement of functional-MRI and NIR (changes in total hemoglobin) during visual stimulation showed good spatial and temporal correlation with each other. (3) Placing multiple channels densely over the occipital region demonstrated spatial patterns more precisely, and depth information was also acquired by placing each pair of illumination and detection fibers at various distances. These results indicate that optical method can provide data for 3D analysis of human brain functions.

  15. The variable-depth mobile gammadensitometer (GMPV)

    International Nuclear Information System (INIS)

    Gourdon, J.L.; Davy, M.; Bisson, D.

    1991-01-01

    The continuous control of the density of wearing courses has been common practice in France for nearly twenty years. The instrument used for this purpose, called PSM (Petit Sabot Mobile; the Small Mobile Shoe), consists of a diffusion nucleo-densitometer carried on a mini-tractor. The unit has had to be completely replaced since this equipment is no longer on the market. The new instrument, known as the GMPV, has the following advantages. The depth of measurement is adjustable, so that thin wearing courses can be controlled. The accuracy and reproducibility of measurements are in the neighbourhood of 1% and 0.5% respectively, for a duration of 100 seconds. Handling is easier, thanks to infra-red remote steering of the measuring carriage from the driver's seat, and to a compatible micro-PC making it possible to gather, display, edit and store 200 kilometres of density values per hour. The GMPV is designed for intensive use in strict accordance with safety standards. It is due to be put into normal service in 1991 [fr

  16. Hyperspectral aerosol optical depths from TCAP flights

    Energy Technology Data Exchange (ETDEWEB)

    Shinozuka, Yohei [NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States); Bay Area Environmental REsearch Institute; Johnson, Roy R [NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States); Flynn, Connor J [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Russell, Philip B [NASA Ames Research Center (ARC), Moffett Field, Mountain View, CA (United States); Schmid, Beat [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-06-01

    4STAR (Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research), a hyperspectral airborne sunphotometer, acquired aerosol optical depths (AOD) at 1 Hz during all July 2012 flights of the Two Column Aerosol Project (TCAP). Root-mean-square differences from AERONET ground-based observations were 0.01 at wavelengths between 500-1020 nm, 0.02 at 380 and 1640 nm and 0.03 at 440 nm in four clear-sky fly-over events, and similar in ground side-by-side comparisons. Changes in the above-aircraft AOD across 3- km-deep spirals were typically consistent with integrals of coincident in situ (on DOE Gulfstream 1 with 4STAR) and lidar (on NASA B200) extinction measurements within 0.01, 0.03, 0.01, 0.02, 0.02, 0.02 at 355, 450, 532, 550, 700, 1064 nm, respectively, despite atmospheric variations and combined measurement uncertainties. Finer vertical differentials of the 4STAR measurements matched the in situ ambient extinction profile within 14% for one homogeneous column. For the AOD observed between 350-1660 nm, excluding strong

  17. Depth Perception in Cave and Panorama

    DEFF Research Database (Denmark)

    Mullins, Michael; Strojan, Tadeja Zupancic

    2004-01-01

    This study compares aspects of spatial perception in a physical environment and its virtual representations in a CAVE and Panorama, derived from recent research. To measure accuracy of spatial perception, participants in an experiment were asked to look at identical objects in the three environme......, learning and training in virtual environments; in architectural education; and participatory design processes, in which the dialogue between real and imagined space may take place in virtual . reality environments...... environments and then locate them and identify their shape on scaled drawings.  Results are presented together with statistical analysis. In a discussion of the results, the paper addresses the two hypothetical assertions ? that depth perception in physical reality and its virtual representations in CAVE......This study compares aspects of spatial perception in a physical environment and its virtual representations in a CAVE and Panorama, derived from recent research. To measure accuracy of spatial perception, participants in an experiment were asked to look at identical objects in the three...

  18. Evaluating methods for controlling depth perception in stereoscopic cinematography

    Science.gov (United States)

    Sun, Geng; Holliman, Nick

    2009-02-01

    Existing stereoscopic imaging algorithms can create static stereoscopic images with perceived depth control function to ensure a compelling 3D viewing experience without visual discomfort. However, current algorithms do not normally support standard Cinematic Storytelling techniques. These techniques, such as object movement, camera motion, and zooming, can result in dynamic scene depth change within and between a series of frames (shots) in stereoscopic cinematography. In this study, we empirically evaluate the following three types of stereoscopic imaging approaches that aim to address this problem. (1) Real-Eye Configuration: set camera separation equal to the nominal human eye interpupillary distance. The perceived depth on the display is identical to the scene depth without any distortion. (2) Mapping Algorithm: map the scene depth to a predefined range on the display to avoid excessive perceived depth. A new method that dynamically adjusts the depth mapping from scene space to display space is presented in addition to an existing fixed depth mapping method. (3) Depth of Field Simulation: apply Depth of Field (DOF) blur effect to stereoscopic images. Only objects that are inside the DOF are viewed in full sharpness. Objects that are far away from the focus plane are blurred. We performed a human-based trial using the ITU-R BT.500-11 Recommendation to compare the depth quality of stereoscopic video sequences generated by the above-mentioned imaging methods. Our results indicate that viewers' practical 3D viewing volumes are different for individual stereoscopic displays and viewers can cope with much larger perceived depth range in viewing stereoscopic cinematography in comparison to static stereoscopic images. Our new dynamic depth mapping method does have an advantage over the fixed depth mapping method in controlling stereo depth perception. The DOF blur effect does not provide the expected improvement for perceived depth quality control in 3D cinematography

  19. Rooting depth and root depth distribution of Trifolium repens × T. uniflorum interspecific hybrids.

    Science.gov (United States)

    Nichols, S N; Hofmann, R W; Williams, W M; van Koten, C

    2016-05-20

    Traits related to root depth distribution were examined in Trifolium repens × T. uniflorum backcross 1 (BC 1 ) hybrids to determine whether root characteristics of white clover could be improved by interspecific hybridization. Two white clover cultivars, two T. uniflorum accessions and two BC 1 populations were grown in 1 -m deep tubes of sand culture. Maximum rooting depth and root mass distribution were measured at four harvests over time, and root distribution data were fitted with a regression model to provide measures of root system shape. Morphological traits were measured at two depths at harvest 3. Root system shape of the hybrids was more similar to T. uniflorum than to white clover. The hybrids and T. uniflorum had a higher rate of decrease in root mass with depth than white clover, which would result in higher proportions of root mass in the upper profile. Percentage total root mass at 100-200 mm depth was higher for T. uniflorum than white clover, and for Crusader BC 1 than 'Crusader'. Roots of the hybrids and T. uniflorum also penetrated deeper than those of white clover. T. uniflorum had thicker roots at 50-100 mm deep than the other entries, and more of its fine root mass at 400-500 mm. The hybrids and white clover had more of their fine root mass higher in the profile. Consequently, T. uniflorum had a higher root length density at 400-500 mm than most entries, and a smaller decrease in root length density with depth. These results demonstrate that rooting characteristics of white clover can be altered by hybridization with T. uniflorum, potentially improving water and nutrient acquisition and drought resistance. Root traits of T. uniflorum are likely to be adaptations to soil moisture and fertility in its natural environment. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. Effects of Sowing Media and Sowing Depth on Germination and ...

    African Journals Online (AJOL)

    This study examines the effect of sowing media and sowing depth on the germination and growth of Lecanodiscus cupanoides (Planch.Ex Benth). The germination of L. cupanoides seed was significantly affected by sowing depth and sowing medium at p=0.05. The result of various sowing media and sowing depth showed ...

  1. Computations Of Critical Depth In Rivers With Flood Plains | Okoli ...

    African Journals Online (AJOL)

    Critical flows may occur at more than one depth in rivers with flood plains. The possibility of multiple critical depths affects the water-surface profile calculations. Presently available algorithms determine only one of the critical depths which may lead to large errors. It is the purpose of this paper to present an analytical ...

  2. The effects of multiview depth video compression on multiview rendering

    NARCIS (Netherlands)

    Merkle, P.; Morvan, Y.; Smolic, A.; Farin, D.S.; Mueller, K.; With, de P.H.N.; Wiegang, T.

    2009-01-01

    This article investigates the interaction between different techniques for depth compression and view synthesis rendering with multiview video plus scene depth data. Two different approaches for depth coding are compared, namely H.264/MVC, using temporal and inter-view reference images for efficient

  3. The effect of depth compression on multiview rendering quality

    NARCIS (Netherlands)

    Merkle, P.; Morvan, Y.; Smolic, A.; Farin, D.S.; Mueller, K..; With, de P.H.N.; Wiegand, T.

    2010-01-01

    This paper presents a comparative study on different techniques for depth-image compression and its implications on the quality of multiview video plus depth virtual view rendering. A novel coding algorithm for depth images that concentrates on their special characteristics, namely smooth regions

  4. A depth-dependent formula for shallow water propagation

    NARCIS (Netherlands)

    Sertlek, H.O.; Ainslie, M.A.

    2014-01-01

    In shallow water propagation, the sound field depends on the proximity of the receiver to the sea surface, the seabed, the source depth, and the complementary source depth. While normal mode theory can predict this depth dependence, it can be computationally intensive. In this work, an analytical

  5. Comprehensive analysis of Curie-point depths and lithospheric effective elastic thickness at Arctic Region

    Science.gov (United States)

    Lu, Y.; Li, C. F.

    2017-12-01

    Arctic Ocean remains at the forefront of geological exploration. Here we investigate its deep geological structures and geodynamics on the basis of gravity, magnetic and bathymetric data. We estimate Curie-point depth and lithospheric effective elastic thickness to understand deep geothermal structures and Arctic lithospheric evolution. A fractal exponent of 3.0 for the 3D magnetization model is used in the Curie-point depth inversion. The result shows that Curie-point depths are between 5 and 50 km. Curie depths are mostly small near the active mid-ocean ridges, corresponding well to high heat flow and active shallow volcanism. Large curie depths are distributed mainly at continental marginal seas around the Arctic Ocean. We present a map of effective elastic thickness (Te) of the lithosphere using a multitaper coherence technique, and Te are between 5 and 110 km. Te primarily depends on geothermal gradient and composition, as well as structures in the lithosphere. We find that Te and Curie-point depths are often correlated. Large Te are distributed mainly at continental region and small Te are distributed at oceanic region. The Alpha-Mendeleyev Ridge (AMR) and The Svalbard Archipelago (SA) are symmetrical with the mid-ocean ridge. AMR and SA were formed before an early stage of Eurasian basin spreading, and they are considered as conjugate large igneous provinces, which show small Te and Curie-point depths. Novaya Zemlya region has large Curie-point depths and small Te. We consider that fault and fracture near the Novaya Zemlya orogenic belt cause small Te. A series of transform faults connect Arctic mid-ocean ridge with North Atlantic mid-ocean ridge. We can see large Te near transform faults, but small Curie-point depths. We consider that although temperature near transform faults is high, but mechanically the lithosphere near transform faults are strengthened.

  6. Calculating depths to shallow magnetic sources using aeromagnetic data from the Tucson Basin

    Science.gov (United States)

    Casto, Daniel W.

    2001-01-01

    Using gridded high-resolution aeromagnetic data, the performance of several automated 3-D depth-to-source methods was evaluated over shallow control sources based on how close their depth estimates came to the actual depths to the tops of the sources. For all three control sources, only the simple analytic signal method, the local wavenumber method applied to the vertical integral of the magnetic field, and the horizontal gradient method applied to the pseudo-gravity field provided median depth estimates that were close (-11% to +14% error) to the actual depths. Careful attention to data processing was required in order to calculate a sufficient number of depth estimates and to reduce the occurrence of false depth estimates. For example, to eliminate sampling bias, high-frequency noise and interference from deeper sources, it was necessary to filter the data before calculating derivative grids and subsequent depth estimates. To obtain smooth spatial derivative grids using finite differences, the data had to be gridded at intervals less than one percent of the anomaly wavelength. Before finding peak values in the derived signal grids, it was necessary to remove calculation noise by applying a low-pass filter in the grid-line directions and to re-grid at an interval that enabled the search window to encompass only the peaks of interest. Using the methods that worked best over the control sources, depth estimates over geologic sites of interest suggested the possible occurrence of volcanics nearly 170 meters beneath a city landfill. Also, a throw of around 2 kilometers was determined for a detachment fault that has a displacement of roughly 6 kilometers.

  7. Nuclear method for determination of nitrogen depth distributions in single seeds. [/sup 14/N tracer technique

    Energy Technology Data Exchange (ETDEWEB)

    Sundqvist, B; Gonczi, L; Koersner, I; Bergman, R; Lindh, U

    1974-01-01

    (d,p) reactions in /sup 14/N were used for probing single kernels of seed for nitrogen content and nitrogen depth distributions. Comparison with the Kjeldahl method was made on individual peas and beans. The results were found to be strongly correlated. The technique to obtain depth distributions of nitrogen was also used on high- and low-lysine varieties of barley for which large differences in nitrogen distributions were found.

  8. Hand and goods judgment algorithm based on depth information

    Science.gov (United States)

    Li, Mingzhu; Zhang, Jinsong; Yan, Dan; Wang, Qin; Zhang, Ruiqi; Han, Jing

    2016-03-01

    A tablet computer with a depth camera and a color camera is loaded on a traditional shopping cart. The inside information of the shopping cart is obtained by two cameras. In the shopping cart monitoring field, it is very important for us to determine whether the customer with goods in or out of the shopping cart. This paper establishes a basic framework for judging empty hand, it includes the hand extraction process based on the depth information, process of skin color model building based on WPCA (Weighted Principal Component Analysis), an algorithm for judging handheld products based on motion and skin color information, statistical process. Through this framework, the first step can ensure the integrity of the hand information, and effectively avoids the influence of sleeve and other debris, the second step can accurately extract skin color and eliminate the similar color interference, light has little effect on its results, it has the advantages of fast computation speed and high efficiency, and the third step has the advantage of greatly reducing the noise interference and improving the accuracy.

  9. Depth estimation of complex geometry scenes from light fields

    Science.gov (United States)

    Si, Lipeng; Wang, Qing

    2018-01-01

    The surface camera (SCam) of light fields gathers angular sample rays passing through a 3D point. The consistency of SCams is evaluated to estimate the depth map of scene. But the consistency is affected by several limitations such as occlusions or non-Lambertian surfaces. To solve those limitations, the SCam is partitioned into two segments that one of them could satisfy the consistency constraint. The segmentation pattern of SCam is highly related to the texture of spatial patch, so we enforce a mask matching to describe the shape correlation between segments of SCam and spatial patch. To further address the ambiguity in textureless region, a global method with pixel-wise plane label is presented. Plane label inference at each pixel can recover not only depth value but also local geometry structure, that is suitable for light fields with sub-pixel disparities and continuous view variation. Our method is evaluated on public light field datasets and outperforms the state-of-the-art.

  10. Three-dimensional seismic depth migration

    Science.gov (United States)

    Zhou, Hongbo

    1998-12-01

    One-pass 3-D modeling and migration for poststack seismic data may be implemented by replacing the traditional 45sp° one-way wave equation (a third-order partial differential equation) with a pair of second and first order partial differential equations. Except for an extra correction term, the resulting second order equation has a form similar to Claerbout's 15sp° one-way wave equation, which is known to have a nearly circular horizontal impulse response. In this approach, there is no need to compensate for splitting errors. Numerical tests on synthetic data show that this algorithm has the desirable attributes of being second-order in accuracy and economical to solve. A modification of the Crank-Nicholson implementation maintains stability. Absorbing boundary conditions play an important role in one-way wave extrapolations by reducing reflections at grid edges. Clayton and Engquist's 2-D absorbing boundary conditions for one-way wave extrapolation by depth-stepping in the frequency domain are extended to 3-D using paraxial approximations of the scalar wave equation. Internal consistency is retained by incorporating the interior extrapolation equation with the absorbing boundary conditions. Numerical schemes are designed to make the proposed absorbing boundary conditions both mathematically correct and efficient with negligible extra cost. Synthetic examples illustrate the effectiveness of the algorithm for extrapolation with the 3-D 45sp° one-way wave equation. Frequency-space domain Butterworth and Chebyshev dip filters are implemented. By regrouping the product terms in the filter transfer function into summations, a cascaded (serial) Butterworth dip filter can be made parallel. A parallel Chebyshev dip filter can be similarly obtained, and has the same form as the Butterworth filter; but has different coeffcients. One of the advantages of the Chebyshev filter is that it has a sharper transition zone than that of Butterworth filter of the same order. Both

  11. Exploring Regolith Depth and Cycling on Mars

    Science.gov (United States)

    Fassett, C.; Needham, D. H.; Watters, W. A.; Hundal, C.

    2017-12-01

    Regolith or loose sediment is ubiquitous on the surface of Mars, but our understanding of how this fragmental layer forms and evolves with time is limited. In particular, how regolith thickness varies spatially on Mars is not well known. A common perspective is to start from the canonical model for lunar regolith, which is not unreasonable, given that both Mars and the Moon are heavily cratered surfaces. However, this lunar-like paradigm is not supported by observations of Mars from recent missions. On Mars, bedrock exposures are more common and bedrock is generally closer to the surface than on the Moon, and the processes modifying the regolith differ substantially on the two bodies. Moreover, boulders on the Moon have much shorter lifetimes than on Mars, so boulders are much less common on the lunar surface. The sediment transport processes infilling craters differs dramatically on these two bodies as well. On Mars, fine-grained sediment is efficiently transported (advectively) by wind and trapped in craters rapidly after they form. Lateral transport of lunar regolith is comparatively inefficient and dominated by slow impact-driven (diffusive) transport of regolith. The goal of this contribution is to discuss observational constraints on Mars' regolith depth, and to place observations into a model for Mars landform evolution and regolith cycle. Our operating hypothesis is that the inter-crater surface on Mars is comparatively starved of fine-grained sediment (compared to the Moon), because transport and trapping of fines in craters out-competes physical weathering. Moreover, thick sedimentary bodies on Mars often get (weakly) cemented and lithified due to interactions with fluids, even in the most recent, Amazonian epoch. This is consistent with what is observed at the MER and MSL landing sites and what is known from the SNC meteorites.

  12. Real-time depth monitoring and control of laser machining through scanning beam delivery system

    International Nuclear Information System (INIS)

    Ji, Yang; Grindal, Alexander W; Fraser, James M; Webster, Paul J L

    2015-01-01

    Scanning optics enable many laser applications in manufacturing because their low inertia allows rapid movement of the process beam across the sample. We describe our method of inline coherent imaging for real-time (up to 230 kHz) micron-scale (7–8 µm axial resolution) tracking and control of laser machining depth through a scanning galvo-telecentric beam delivery system. For 1 cm trench etching in stainless steel, we collect high speed intrapulse and interpulse morphology which is useful for further understanding underlying mechanisms or comparison with numerical models. We also collect overall sweep-to-sweep depth penetration which can be used for feedback depth control. For trench etching in silicon, we show the relationship of etch rate with average power and scan speed by computer processing of depth information without destructive sample post-processing. We also achieve three-dimensional infrared continuous wave (modulated) laser machining of a 3.96 × 3.96 × 0.5 mm 3 (length × width × maximum depth) pattern on steel with depth feedback. To the best of our knowledge, this is the first successful demonstration of direct real-time depth monitoring and control of laser machining with scanning optics. (paper)

  13. Palaeoecological studies as a source of peat depth data: A discussion and data compilation for Scotland

    Directory of Open Access Journals (Sweden)

    J. Ratcliffe

    2016-06-01

    Full Text Available The regional/national carbon (C stock of peatlands is often poorly characterised, even for comparatively well-studied areas. A key obstacle to better estimates of landscape C stock is the scarcity of data on peat depth, leading to simplistic assumptions. New measurements of peat depth become unrealistically resource-intensive when considering large areas. Therefore, it is imperative to maximise the use of pre-existing datasets. Here we propose that one potentially valuable and currently unexploited source of peat depth data is palaeoecological studies. We discuss the value of these data and present an initial compilation for Scotland (United Kingdom which consists of records from 437 sites and yields an average depth of 282 cm per site. This figure is likely to be an over-estimate of true average peat depth and is greater than figures used in current estimates of peatland C stock. Depth data from palaeoecological studies have the advantages of wide distribution, high quality, and often the inclusion of valuable supporting information; but also the disadvantage of spatial bias due to the differing motivations of the original researchers. When combined with other data sources, each with its own advantages and limitations, we believe that palaeoecological datasets can make an important contribution to better-constrained estimates of peat depth which, in turn, will lead to better estimates of peatland landscape carbon stock.

  14. Action recognition in depth video from RGB perspective: A knowledge transfer manner

    Science.gov (United States)

    Chen, Jun; Xiao, Yang; Cao, Zhiguo; Fang, Zhiwen

    2018-03-01

    Different video modal for human action recognition has becoming a highly promising trend in the video analysis. In this paper, we propose a method for human action recognition from RGB video to Depth video using domain adaptation, where we use learned feature from RGB videos to do action recognition for depth videos. More specifically, we make three steps for solving this problem in this paper. First, different from image, video is more complex as it has both spatial and temporal information, in order to better encode this information, dynamic image method is used to represent each RGB or Depth video to one image, based on this, most methods for extracting feature in image can be used in video. Secondly, as video can be represented as image, so standard CNN model can be used for training and testing for videos, beside, CNN model can be also used for feature extracting as its powerful feature expressing ability. Thirdly, as RGB videos and Depth videos are belong to two different domains, in order to make two different feature domains has more similarity, domain adaptation is firstly used for solving this problem between RGB and Depth video, based on this, the learned feature from RGB video model can be directly used for Depth video classification. We evaluate the proposed method on one complex RGB-D action dataset (NTU RGB-D), and our method can have more than 2% accuracy improvement using domain adaptation from RGB to Depth action recognition.

  15. Hybridisation-based resequencing of 17 X-linked intellectual disability genes in 135 patients reveals novel mutations in ATRX, SLC6A8 and PQBP1

    Science.gov (United States)

    Jensen, Lars R; Chen, Wei; Moser, Bettina; Lipkowitz, Bettina; Schroeder, Christopher; Musante, Luciana; Tzschach, Andreas; Kalscheuer, Vera M; Meloni, Ilaria; Raynaud, Martine; van Esch, Hilde; Chelly, Jamel; de Brouwer, Arjan P M; Hackett, Anna; van der Haar, Sigrun; Henn, Wolfram; Gecz, Jozef; Riess, Olaf; Bonin, Michael; Reinhardt, Richard; Ropers, Hans-Hilger; Kuss, Andreas W

    2011-01-01

    X-linked intellectual disability (XLID), also known as X-linked mental retardation, is a highly genetically heterogeneous condition for which mutations in >90 different genes have been identified. In this study, we used a custom-made sequencing array based on the Affymetrix 50k platform for mutation screening in 17 known XLID genes in patients from 135 families and found eight single-nucleotide changes that were absent in controls. For four mutations affecting ATRX (p.1761M>T), PQBP1 (p.155R>X) and SLC6A8 (p.390P>L and p.477S>L), we provide evidence for a functional involvement of these changes in the aetiology of intellectual disability. PMID:21267006

  16. Rooting depths of plants relative to biological and environmental factors

    International Nuclear Information System (INIS)

    Foxx, T.S.; Tierney, G.D.; Williams, J.M.

    1984-11-01

    In 1981 to 1982 an extensive bibliographic study was completed to document rooting depths of native plants in the United States. The data base presently contains 1034 citations with approximately 12,000 data elements. In this paper the data were analyzed for rooting depths as related to life form, soil type, geographical region, root type, family, root depth to shoot height ratios, and root depth to root lateral ratios. Average rooting depth and rooting frequencies were determined and related to present low-level waste site maintenance

  17. Seed drill instrumentation for spatial coulter depth measurements

    DEFF Research Database (Denmark)

    Kirkegaard Nielsen, Søren; Munkholm, Lars Juhl; Lamandé, Mathieu

    2017-01-01

    coulter depth varied up to ±5 mm between the blocks. In addition, significant depth variations between the individual coulters were found. The mean depths varied between −14.2 and −25.9 mm for the eleven coulters. The mean shallowest coulter depth (−14.2 mm) was measured for the coulter running...... in the wheel track of the tractor. The power spectral densities (distribution) of the coulter depth oscillation frequencies showed that the majority of oscillations occurred below 0.5 Hz without any natural vibration frequency. The study concluded that the instrumentation concept was functional for on...

  18. Measurements of Epidural Space Depth Using Preexisting CT Scans Correlate with Loss of Resistance Depth during Thoracic Epidural Catheter Placement

    Directory of Open Access Journals (Sweden)

    Nathaniel H. Greene

    2015-01-01

    Full Text Available Background. Thoracic epidural catheters provide the best quality postoperative pain relief for major abdominal and thoracic surgical procedures, but placement is one of the most challenging procedures in the repertoire of an anesthesiologist. Most patients presenting for a procedure that would benefit from a thoracic epidural catheter have already had high resolution imaging that may be useful to assist placement of a catheter. Methods. This retrospective study used data from 168 patients to examine the association and predictive power of epidural-skin distance (ESD on computed tomography (CT to determine loss of resistance depth acquired during epidural placement. Additionally, the ability of anesthesiologists to measure this distance was compared to a radiologist, who specializes in spine imaging. Results. There was a strong association between CT measurement and loss of resistance depth (P35 changed this relationship (P=0.007. The ability of anesthesiologists to make CT measurements was similar to a gold standard radiologist (all individual ICCs>0.9. Conclusions. Overall, this study supports the examination of a recent CT scan to aid in the placement of a thoracic epidural catheter. Making use of these scans may lead to faster epidural placements, fewer accidental dural punctures, and better epidural blockade.

  19. A boundary element model for diffraction of water waves on varying water depth

    Energy Technology Data Exchange (ETDEWEB)

    Poulin, Sanne

    1997-12-31

    In this thesis a boundary element model for calculating diffraction of water waves on varying water depth is presented. The varying water depth is approximated with a perturbed constant depth in the mild-slope wave equation. By doing this, the domain integral which is a result of the varying depth is no longer a function of the unknown wave potential but only a function of position and the constant depth wave potential. The number of unknowns is the resulting system of equations is thus reduced significantly. The integration procedures in the model are tested very thoroughly and it is found that a combination of analytical integration in the singular region and standard numerical integration outside works very well. The gradient of the wave potential is evaluated successfully using a hypersingular integral equation. Deviations from the analytical solution are only found on the boundary or very close to, but these deviations have no significant influence on the accuracy of the solution. The domain integral is evaluated using the dual reciprocity method. The results are compared with a direct integration of the integral, and the accuracy is quite satisfactory. The problem with irregular frequencies is taken care of by the CBIEM (or CHIEF-method) together with a singular value decomposition technique. This method is simple to implement and works very well. The model is verified using Homma`s island as a test case. The test cases are limited to shallow water since the analytical solution is only valid in this region. Several depth ratios are examined, and it is found that the accuracy of the model increases with increasing wave period and decreasing depth ratio. Short waves, e.g. wind generated waves, can allow depth variations up to approximately 2 before the error exceeds 10%, while long waves can allow larger depth ratios. It is concluded that the perturbation idea is highly usable. A study of (partially) absorbing boundary conditions is also conducted. (EG)

  20. Inelastic analysis of finite length and depth cracked tubes

    International Nuclear Information System (INIS)

    Reich, M.; Prachuktam, S.; Gardner, D.

    1977-01-01

    Steam generator tube failure can at times result in reactor safety problems and subsequent premature reactor shutdowns. Typical PWR steam generator units contain thousands of long straight tubes with U-bend sections. These tubes are primarily made from alloy 600 and their sizes vary between 3 / 4 '' and 7 / 8 '' (1.905 cm and 2.223 cm) in diameter with nominal thicknesses of 0.043'' to 0.053'' (0.109 cm to 0.135 cm). Since alloy 600 (and the previously used 304-SS tubes) are ductile, high toughness materials LEFM (linear elastic fracture mechanics) criteria do not apply. This paper concerns itself with the prediction of the failure pressures for typical PWR steam generator tubes with longitudinal finite length and finite depth cracks. Only local plastic overload failure is considered

  1. Depth profiling using C60+ SIMS-Deposition and topography development during bombardment of silicon

    International Nuclear Information System (INIS)

    Gillen, Greg; Batteas, James; Michaels, Chris A.; Chi, Peter; Small, John; Windsor, Eric; Fahey, Albert; Verkouteren, Jennifer; Kim, K.J.

    2006-01-01

    A C 60 + primary ion source has been coupled to an ion microscope secondary ion mass spectrometry (SIMS) instrument to examine sputtering of silicon with an emphasis on possible application of C 60 + depth profiling for high depth resolution SIMS analysis of silicon semiconductor materials. Unexpectedly, C 60 + SIMS depth profiling of silicon was found to be complicated by the deposition of an amorphous carbon layer which buries the silicon substrate. Sputtering of the silicon was observed only at the highest accessible beam energies (14.5 keV impact) or by using oxygen backfilling. C 60 + SIMS depth profiling of As delta-doped test samples at 14.5 keV demonstrated a substantial (factor of 5) degradation in depth resolution compared to Cs + SIMS depth profiling. This degradation is thought to result from the formation of an unusual platelet-like grain structure on the SIMS crater bottoms. Other unusual topographical features were also observed on silicon substrates after high primary ion dose C 60 + bombardment

  2. Depth perception: the need to report ocean biogeochemical rates as functions of temperature, not depth.

    Science.gov (United States)

    Brewer, Peter G; Peltzer, Edward T

    2017-09-13

    For over 50 years, ocean scientists have oddly represented ocean oxygen consumption rates as a function of depth but not temperature in most biogeochemical models. This unique tradition or tactic inhibits useful discussion of climate change impacts, where specific and fundamental temperature-dependent terms are required. Tracer-based determinations of oxygen consumption rates in the deep sea are nearly universally reported as a function of depth in spite of their well-known microbial basis. In recent work, we have shown that a carefully determined profile of oxygen consumption rates in the Sargasso Sea can be well represented by a classical Arrhenius function with an activation energy of 86.5 kJ mol -1 , leading to a Q 10 of 3.63. This indicates that for 2°C warming, we will have a 29% increase in ocean oxygen consumption rates, and for 3°C warming, a 47% increase, potentially leading to large-scale ocean hypoxia should a sufficient amount of organic matter be available to microbes. Here, we show that the same principles apply to a worldwide collation of tracer-based oxygen consumption rate data and that some 95% of ocean oxygen consumption is driven by temperature, not depth, and thus will have a strong climate dependence. The Arrhenius/Eyring equations are no simple panacea and they require a non-equilibrium steady state to exist. Where transient events are in progress, this stricture is not obeyed and we show one such possible example.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'. © 2017 The Author(s).

  3. Depth perception: the need to report ocean biogeochemical rates as functions of temperature, not depth

    Science.gov (United States)

    Brewer, Peter G.; Peltzer, Edward T.

    2017-08-01

    For over 50 years, ocean scientists have oddly represented ocean oxygen consumption rates as a function of depth but not temperature in most biogeochemical models. This unique tradition or tactic inhibits useful discussion of climate change impacts, where specific and fundamental temperature-dependent terms are required. Tracer-based determinations of oxygen consumption rates in the deep sea are nearly universally reported as a function of depth in spite of their well-known microbial basis. In recent work, we have shown that a carefully determined profile of oxygen consumption rates in the Sargasso Sea can be well represented by a classical Arrhenius function with an activation energy of 86.5 kJ mol-1, leading to a Q10 of 3.63. This indicates that for 2°C warming, we will have a 29% increase in ocean oxygen consumption rates, and for 3°C warming, a 47% increase, potentially leading to large-scale ocean hypoxia should a sufficient amount of organic matter be available to microbes. Here, we show that the same principles apply to a worldwide collation of tracer-based oxygen consumption rate data and that some 95% of ocean oxygen consumption is driven by temperature, not depth, and thus will have a strong climate dependence. The Arrhenius/Eyring equations are no simple panacea and they require a non-equilibrium steady state to exist. Where transient events are in progress, this stricture is not obeyed and we show one such possible example. This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'.

  4. Optimum water depth ranges of dominant submersed macrophytes in a natural freshwater lake.

    Science.gov (United States)

    Ye, Bibi; Chu, Zhaosheng; Wu, Aiping; Hou, Zeying; Wang, Shengrui

    2018-01-01

    Macrophytes show a zonal distribution along the lake littoral zone because of their specific preferred water depths while the optimum growth water depths of dominant submersed macrophytes in natural lakes are not well known. We studied the seasonal biomass and frequency patterns of dominant and companion submersed macrophytes along the water depth gradient in Lake Erhai in 2013. The results showed that the species richness and community biomass showed hump-back shaped patterns along the water depth gradient both in polydominant and monodominant communities. Biomass percentage of Potamogenton maackianus showed a hump-back pattern while biomass percentages of Ceratophyllum demersum and Vallisneria natans appeared U-shaped patterns across the water depth gradient in polydominant communities whereas biomass percentage of V. natans increased with the water depth in monodominant communities. Dominant species demonstrated a broader distribution range of water depth than companion species. Frequency and biomass of companion species declined drastically with the water depth whereas those of dominant species showed non-linear patterns across the water depth gradient. Namely, along the water depth gradient, biomass of P. maackianus and V. natans showed hump-back patterns and biomasses of C. demersum displayed a U-shaped pattern in the polydominant communities but biomass of V. natans demonstrated a hump-back pattern in the monodominant communities; frequency of P. maackianus showed a hump-back pattern and C. demersum and V. natans maintained high frequencies in the two types of communities. We can speculate that in Lake Erhai the optimum growth water depths of P. maackianus and C. demersum in the polydominant communities are 2.5-4.5 m and 1-2 m or 5-6 m, respectively and that of V. natans is 3-5 m in the polydominant communities and 2.5-5 m in the monodominant communities. This is the first report that the optimum water depth ranges in the horizontal direction of three

  5. Sub-keV secondary ion mass spectrometry depth profiling: comparison of sample rotation and oxygen flooding

    International Nuclear Information System (INIS)

    Liu, R.; Wee, A.T.S.

    2004-01-01

    Following the increasingly stringent requirements in the characterization of sub-micron IC devices, an understanding of the various factors affecting ultra shallow depth profiling in secondary ion mass spectrometry (SIMS) has become crucial. Achieving high depth resolution (of the order of 1 nm) is critical in the semiconductor industry today, and various methods have been developed to optimize depth resolution. In this paper, we will discuss ultra shallow SIMS depth profiling using B and Ge delta-doped Si samples using low energy 0.5 keV O 2 + primary beams. The relationship between depth resolution of the delta layers and surface topography measured by atomic force microscopy (AFM) is studied. The effect of oxygen flooding and sample rotation, used to suppress surface roughening is also investigated. Oxygen flooding was found to effectively suppress roughening and gives the best depth resolution for B, but sample rotation gives the best resolution for Ge. Possible mechanisms for this are discussed

  6. Into the depths of deep eutectic solvents

    NARCIS (Netherlands)

    Rodriguez, N.; Alves da Rocha, M.A.; Kroon, M.C.

    2015-01-01

    Ionic liquids (ILs) have been successfully tested in a wide range of applications; however, their high price and complicated synthesis make them infeasible for large scale implementation. A decade ago, a new generation of solvents so called deep eutectic solvents (DESs) was reported for the first

  7. Injection-depth-locking axial motion guided handheld micro-injector using CP-SSOCT.

    Science.gov (United States)

    Cheon, Gyeong Woo; Huang, Yong; Kwag, Hye Rin; Kim, Ki-Young; Taylor, Russell H; Gehlbach, Peter L; Kang, Jin U

    2014-01-01

    This paper presents a handheld micro-injector system using common-path swept source optical coherence tomography (CP-SSOCT) as a distal sensor with highly accurate injection-depth-locking. To achieve real-time, highly precise, and intuitive freehand control, the system used graphics processing unit (GPU) to process the oversampled OCT signal with high throughput and a smart customized motion monitoring control algorithm. A performance evaluation was conducted with 60-insertions and fluorescein dye injection tests to show how accurately the system can guide the needle and lock to the target depth. The evaluation tests show our system can guide the injection needle into the desired depth with 4.12 um average deviation error while injecting 50 nl of fluorescein dye.

  8. Depth-based Multi-View 3D Video Coding

    DEFF Research Database (Denmark)

    Zamarin, Marco

    techniques are used to extract dense motion information and generate improved candidate side information. Multiple candidates are merged employing multi-hypothesis strategies. Promising rate-distortion performance improvements compared with state-of-the-art Wyner-Ziv decoders are reported, both when texture......-view video. Depth maps are typically used to synthesize the desired output views, and the performance of view synthesis algorithms strongly depends on the accuracy of depth information. In this thesis, novel algorithms for efficient depth map compression in MVD scenarios are proposed, with particular focus...... on edge-preserving solutions. In a proposed scheme, texture-depth correlation is exploited to predict surface shapes in the depth signal. In this way depth coding performance can be improved in terms of both compression gain and edge-preservation. Another solution proposes a new intra coding mode targeted...

  9. Occlusion edge blur: A cue to relative visual depth

    OpenAIRE

    Marshall, J.A.; Burbeck, C.A.; Ariely, D.; Rolland, J.P.; Martin, K.E.

    1996-01-01

    We studied whether the blur/sharpness of an occlusion boundary between a sharply focused surface and a blurred surface is used as a relative depth cue. Observers judged