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

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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

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

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

Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses.

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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.

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

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.

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.

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

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

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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

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

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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

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

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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.

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...

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.

[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.

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

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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.

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

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.

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...

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

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.

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...

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.

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

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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.

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.

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...

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

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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.

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.

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.

An evolutionary framework for association testing in resequencing studies.

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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.

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.

BFAST: an alignment tool for large scale genome resequencing.

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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.

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.

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

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.

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

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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.

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)

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

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...

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

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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.

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...

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.

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.

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...

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

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.

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.

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

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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.

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.

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.

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

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.

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.

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.

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

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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.

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

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.

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.

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.

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

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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/.

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.

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.

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.

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.

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:...

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

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

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.

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...

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...

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

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

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

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.

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.

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.

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.

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.

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.

Contribution of FKBP5 genetic variation to gemcitabine treatment and survival in pancreatic adenocarcinoma.

Directory of Open Access Journals (Sweden)

Katarzyna A Ellsworth

Full Text Available FKBP51, (FKBP5, is a negative regulator of Akt. Variability in FKBP5 expression level is a major factor contributing to variation in response to chemotherapeutic agents including gemcitabine, a first line treatment for pancreatic cancer. Genetic variation in FKBP5 could influence its function and, ultimately, treatment response of pancreatic cancer.We set out to comprehensively study the role of genetic variation in FKBP5 identified by Next Generation DNA resequencing on response to gemcitabine treatment of pancreatic cancer by utilizing both tumor and germline DNA samples from 43 pancreatic cancer patients, including 19 paired normal-tumor samples. Next, genotype-phenotype association studies were performed with overall survival as well as with FKBP5 gene expression in tumor using the same samples in which resequencing had been performed, followed by functional genomics studies.In-depth resequencing identified 404 FKBP5 single nucleotide polymorphisms (SNPs in normal and tumor DNA. SNPs with the strongest associations with survival or FKBP5 expression were subjected to functional genomic study. Electromobility shift assay showed that the rs73748206 "A(T" SNP altered DNA-protein binding patterns, consistent with significantly increased reporter gene activity, possibly through its increased binding to Glucocorticoid Receptor (GR. The effect of rs73748206 was confirmed on the basis of its association with FKBP5 expression by affecting the binding to GR in lymphoblastoid cell lines derived from the same patients for whom DNA was used for resequencing.This comprehensive FKBP5 resequencing study provides insights into the role of genetic variation in variation of gemcitabine response.

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.

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.

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....

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.

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

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.

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.

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.

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...

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

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.

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

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.

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.

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

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.

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.

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.

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

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.

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.

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.

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...

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.

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.

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

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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.

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

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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.

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

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.

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.)

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

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.

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.

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.

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)

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.

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

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.

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

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

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.

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.

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

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

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.

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)

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.

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.

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....

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...

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.

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.

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.

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

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.

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)

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

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. 

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.

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.

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.

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

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.

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.

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

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.

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.

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

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

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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

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

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

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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.

Mid-depth temperature maximum in an estuarine lake

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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.

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

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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.

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

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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.

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)

Visual Discomfort and Depth-of-Field

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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.

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)

Injection-depth-locking axial motion guided handheld micro-injector using CP-SSOCT.

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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.

Does footprint depth correlate with foot motion and pressure?

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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.

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

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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.

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.

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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.

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.

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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.

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

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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.

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

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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.

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

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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.

Subring Depth, Frobenius Extensions, and Towers

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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.

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

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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

Nanometric depth resolution from multi-focal images in microscopy.

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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.

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

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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.

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

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)

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

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

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.)

Sediment transport and mixing depth on a coral reef sand apron

Science.gov (United States)

Vila-Concejo, Ana; Harris, Daniel L.; Power, Hannah E.; Shannon, Amelia M.; Webster, Jody M.

2014-10-01

This paper investigates the mechanics of sediment transport on a subtidal sand apron located on a coral reef environment. In this environment 100% of the sediment is carbonate bioclasts generated in situ. The sand apron is located on the back reef and only affected by waves during high tides. It is commonly accepted in the literature that sand aprons are features that prograde lagoonwards and that most of the progradation occurs during high-energy events. Measurements of water depths, waves, currents and near bed suspended sediment concentrations (all at 10 Hz) on the sand apron were undertaken over a nine day intensive field campaign over both spring and neap tides; waves and tides were also measured in the lagoon. The topography and bathymetry of the sand apron were measured and mixing depth was obtained on three transects using depth of disturbance rods. We found that sediment transport on sand aprons is not solely restricted to high-energy events but occurs on a daily basis during spring tides. The main factor controlling the sediment transport was the water depth above the bed, with depths of 2-2.3 m allowing waves to promote the most sediment transport. This corresponds to a depth over the reef crest of 1.6-1.9 m. The second most important control was waves; transport was observed when Hs on the apron was 0.1 m or greater. In contrast, current magnitude was not a controlling mechanism for sediment entrainment but did affect sediment transport. The morphology of the sand apron was shown to affect the direction of currents with the currents also expected to influence the morphology of the sand apron. The currents measured during this field campaign were aligned with a shallow channel in the sand apron. Mixing depths were small (< 2.5 cm) yet they were larger than the values predicted by empirical formulae for gentle siliciclastic ocean beaches.

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...

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.

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

Depth profiling: RBS versus energy-dispersive X-ray imaging using scanning transmission electron microscopy

International Nuclear Information System (INIS)

Markwitz, Andreas

2000-01-01

Rutherford backscattering spectrometry (RBS) is known to be one of the techniques ideal for analysis of thin films. Elemental concentrations of matrix components and impurities can be investigated as well as depth profiles of almost each element of the periodic table. Best of all, RBS has both a high sensitivity and a high depth resolution, and is a non-destructive analysis technique that does not require specific sample preparation. Solid-state samples are mounted without preparation inside a high-vacuum analysis chamber. However, depth-related interpretation of elemental depth profiles requires the material density of the specimen and stopping power values to be taken into consideration. In many cases, these parameters can be estimated with sufficient precision. However, the assumed density can be inaccurate for depth scales in the nanometer range. For example, in the case of Ge nanoclusters in 500 nm thick SiO 2 layers, uncertainty is related to the actual position of a very thin Ge nanocluster band. Energy-dispersive X-ray emission (EDX) spectroscopy, using a high-resolution scanning transmission electron microscope (STEM) can assist in removing this uncertainty. By preparing a thin section of the specimen, EDX can be used to identify the position of the Ge nanocluster band very precisely, by correlating the Ge profile with the depth profiles of silicon and oxygen. However, extraction of the concentration profiles from STEM-EDX spectra is in general not straightforward. Therefore, a combination of the two very different analysis techniques is often the best and only successful way to extract high-resolution concentration profiles

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.

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.

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.

Study of the disorder by means of the superconducting penetration depth

International Nuclear Information System (INIS)

Arce, R.D.

1982-11-01

Measurements of the weak magnetic field penetration depth in the amorphous superconducting systems Lasub(1-x) Msub(x), being M = Cu, Al, Ga and Au, and in the Zr 70 Cu 30 system are presented. Measurements of the sample geometrical factors and the flux expulsion between the lowest temperature reached and the critical temperature, allows the determination of zero temperature penetration depth. The measurement of the flux expulsion as a function of temperature is used to determine the temperature dependence of penetration depth, used to evaluate the temperature dependence superconducting gap. The magnetization measurements have been made using an rf-SQUID. The evolution of the penetration depth with annealing is studied in the La 70 Cu 30 and Zr 70 Cu 30 systems. Measurements of the electrical resistivity and the critical temperature are used to verify the Gorkov equations in these materials. The variation of the penetration depth with annealing suggests that a metallurgical phase separation occurs within the submicrometer range. Penetration depth measurement is a tool to detect this type of phase separation in high kappa materials. (M.E.L.) [es

Accurate molecular diagnosis of phenylketonuria and tetrahydrobiopterin-deficient hyperphenylalaninemias using high-throughput targeted sequencing

Science.gov (United States)

Trujillano, Daniel; Perez, Belén; González, Justo; Tornador, Cristian; Navarrete, Rosa; Escaramis, Georgia; Ossowski, Stephan; Armengol, Lluís; Cornejo, Verónica; Desviat, Lourdes R; Ugarte, Magdalena; Estivill, Xavier

2014-01-01

Genetic diagnostics of phenylketonuria (PKU) and tetrahydrobiopterin (BH4) deficient hyperphenylalaninemia (BH4DH) rely on methods that scan for known mutations or on laborious molecular tools that use Sanger sequencing. We have implemented a novel and much more efficient strategy based on high-throughput multiplex-targeted resequencing of four genes (PAH, GCH1, PTS, and QDPR) that, when affected by loss-of-function mutations, cause PKU and BH4DH. We have validated this approach in a cohort of 95 samples with the previously known PAH, GCH1, PTS, and QDPR mutations and one control sample. Pooled barcoded DNA libraries were enriched using a custom NimbleGen SeqCap EZ Choice array and sequenced using a HiSeq2000 sequencer. The combination of several robust bioinformatics tools allowed us to detect all known pathogenic mutations (point mutations, short insertions/deletions, and large genomic rearrangements) in the 95 samples, without detecting spurious calls in these genes in the control sample. We then used the same capture assay in a discovery cohort of 11 uncharacterized HPA patients using a MiSeq sequencer. In addition, we report the precise characterization of the breakpoints of four genomic rearrangements in PAH, including a novel deletion of 899 bp in intron 3. Our study is a proof-of-principle that high-throughput-targeted resequencing is ready to substitute classical molecular methods to perform differential genetic diagnosis of hyperphenylalaninemias, allowing the establishment of specifically tailored treatments a few days after birth. PMID:23942198

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.

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.

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.

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....

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.

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.

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).

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.

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.

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

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.

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.

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

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.

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.)

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

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.

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.

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.

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...

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%.

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.

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.

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.

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.)

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.

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.

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.

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.

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.

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

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.

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

Development of the point-depletion code DEPTH

International Nuclear Information System (INIS)

She, Ding; Wang, Kan; Yu, Ganglin

2013-01-01

Highlights: ► The DEPTH code has been developed for the large-scale depletion system. ► DEPTH uses the data library which is convenient to couple with MC codes. ► TTA and matrix exponential methods are implemented and compared. ► DEPTH is able to calculate integral quantities based on the matrix inverse. ► Code-to-code comparisons prove the accuracy and efficiency of DEPTH. -- Abstract: The burnup analysis is an important aspect in reactor physics, which is generally done by coupling of transport calculations and point-depletion calculations. DEPTH is a newly-developed point-depletion code of handling large burnup depletion systems and detailed depletion chains. For better coupling with Monte Carlo transport codes, DEPTH uses data libraries based on the combination of ORIGEN-2 and ORIGEN-S and allows users to assign problem-dependent libraries for each depletion step. DEPTH implements various algorithms of treating the stiff depletion systems, including the Transmutation trajectory analysis (TTA), the Chebyshev Rational Approximation Method (CRAM), the Quadrature-based Rational Approximation Method (QRAM) and the Laguerre Polynomial Approximation Method (LPAM). Three different modes are supported by DEPTH to execute the decay, constant flux and constant power calculations. In addition to obtaining the instantaneous quantities of the radioactivity, decay heats and reaction rates, DEPTH is able to calculate the integral quantities by a time-integrated solver. Through calculations compared with ORIGEN-2, the validity of DEPTH in point-depletion calculations is proved. The accuracy and efficiency of depletion algorithms are also discussed. In addition, an actual pin-cell burnup case is calculated to illustrate the DEPTH code performance in coupling with the RMC Monte Carlo code

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.

Photothermal radiometric determination of thermal diffusivity depth profiles in a dental resin

International Nuclear Information System (INIS)

MartInez-Torres, P; Alvarado-Gil, J J; Mandelis, A

2010-01-01

The depth of curing due to photopolymerization in a commercial dental resin is studied using photothermal radiometry. The sample consists of a thick layer of resin on which a thin metallic layer is deposited guaranteeing full opacity of the sample. In this case, purely thermal-wave inverse problem techniques without the interference of optical profiles can be used. Thermal profiles are obtained by heating the coating with a modulated laser beam and performing a modulation frequency scan. Before each frequency scan, photopolymerization was induced using a high power blue LED. However due to the fact that dental resins are highly light dispersive materials, the polymerization process depends strongly on the optical absorption coefficient inducing a depth dependent thermal diffusion in the sample. It is shown that using a robust depth profilometric inverse method one can reconstruct the thermal diffusivity profile of the photopolymerized resin.

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.

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.

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.

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.

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)

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.

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

Science.gov (United States)

David, Fabrice P A; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J; Lefebvre, Gregory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

2014-01-01

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch.

The very deep hole concept - Geoscientific appraisal of conditions at great depth

International Nuclear Information System (INIS)

Juhlin, C.; Wallroth, T.; Smellie, J.; Leijon, B.; Eliasson, T.; Ljunggren, C.; Beswick, J.

1998-06-01

One of the alternative systems for disposal of high-level radioactive nuclear waste being studied by SKB is the very deep hole (2000 - 4000 m) concept. As part of SKB's research programme a study has been carried out to increase the level of knowledge on the expected geological conditions in the depth interval 1000-5000 m in older crystalline rock. As a first step, existing data from relevant areas throughout the world have been compiled. The majority of the data come from deep boreholes, mines, and surface geophysical surveys. An attempt has been made to interpret these data in an integrated manner and to develop a conceptual geological model on the conditions in the Baltic Shield down to a depth of 5 km. One of the main features of the suggested model is that the upper 1 km of crust contains significantly more open fractures than the rock below. However, hydraulically conductive fractures and fracture zones may exist at great depth. In areas of low topography active groundwater circulation is primarily limited to the upper 1 km with the water below 1 km having high salinity. The high salinity reflects the near hydraulically stagnant conditions which exist relatively shallow in areas of low topography. In areas with greater topographic relief fresh water penetrates to great depth and near stagnant conditions are first encountered much deeper. The report also covers how the studied parameters which describe the geological conditions vary with depth. A number of recommendations are made on how the presented conceptual model can be tested and improved aside from obtaining data from new boreholes. These recommendations include the following geoscientific surveys and studies: Reflection and refraction seismics for mapping discrete sub-horizontal fracture zones and the upper more fractured part of the crust; Geoelectric methods for mapping the depth to saline water; Detailed hydrogeological measurements in existing deep boreholes; Isotope studies on fracture minerals

The very deep hole concept - Geoscientific appraisal of conditions at great depth

Energy Technology Data Exchange (ETDEWEB)

Juhlin, C. [Christopher Juhlin Consulting (Sweden); Wallroth, T. [Bergab Consulting Geologists (Sweden); Smellie, J.; Leijon, B. [Conterra AB (Sweden); Eliasson, T. [Geological Survey of Sweden (Sweden); Ljunggren, C. [Vattenfall Hydropower AB (Sweden); Beswick, J. [EDECO Petroleum Services Ltd. (United Kingdom)

1998-06-01

One of the alternative systems for disposal of high-level radioactive nuclear waste being studied by SKB is the very deep hole (2000 - 4000 m) concept. As part of SKB`s research programme a study has been carried out to increase the level of knowledge on the expected geological conditions in the depth interval 1000-5000 m in older crystalline rock. As a first step, existing data from relevant areas throughout the world have been compiled. The majority of the data come from deep boreholes, mines, and surface geophysical surveys. An attempt has been made to interpret these data in an integrated manner and to develop a conceptual geological model on the conditions in the Baltic Shield down to a depth of 5 km. One of the main features of the suggested model is that the upper 1 km of crust contains significantly more open fractures than the rock below. However, hydraulically conductive fractures and fracture zones may exist at great depth. In areas of low topography active groundwater circulation is primarily limited to the upper 1 km with the water below 1 km having high salinity. The high salinity reflects the near hydraulically stagnant conditions which exist relatively shallow in areas of low topography. In areas with greater topographic relief fresh water penetrates to great depth and near stagnant conditions are first encountered much deeper. The report also covers how the studied parameters which describe the geological conditions vary with depth. A number of recommendations are made on how the presented conceptual model can be tested and improved aside from obtaining data from new boreholes. These recommendations include the following geoscientific surveys and studies: Reflection and refraction seismics for mapping discrete sub-horizontal fracture zones and the upper more fractured part of the crust; Geoelectric methods for mapping the depth to saline water; Detailed hydrogeological measurements in existing deep boreholes; Isotope studies on fracture minerals

Targeted exonic sequencing of GWAS loci in the high extremes of the plasma lipids distribution

NARCIS (Netherlands)

Patel, Aniruddh P.; Peloso, Gina M.; Pirruccello, James P.; Johansen, Christopher T.; Dubé, Joseph B.; Larach, Daniel B.; Ban, Matthew R.; Dallinge-Thie, Geesje M.; Gupta, Namrata; Boehnke, Michael; Abecasis, Gonçalo R.; Kastelein, John J. P.; Hovingh, G. Kees; Hegele, Robert A.; Rader, Daniel J.; Kathiresan, Sekar

2016-01-01

Genome-wide association studies (GWAS) for plasma lipid levels have mapped numerous genomic loci, with each region often containing many protein-coding genes. Targeted re-sequencing of exons is a strategy to pinpoint causal variants and genes. We performed solution-based hybrid selection of 9008

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

Impact of sequencing depth on the characterization of the microbiome and resistome.

Science.gov (United States)

Zaheer, Rahat; Noyes, Noelle; Ortega Polo, Rodrigo; Cook, Shaun R; Marinier, Eric; Van Domselaar, Gary; Belk, Keith E; Morley, Paul S; McAllister, Tim A

2018-04-12

Developments in high-throughput next generation sequencing (NGS) technology have rapidly advanced the understanding of overall microbial ecology as well as occurrence and diversity of specific genes within diverse environments. In the present study, we compared the ability of varying sequencing depths to generate meaningful information about the taxonomic structure and prevalence of antimicrobial resistance genes (ARGs) in the bovine fecal microbial community. Metagenomic sequencing was conducted on eight composite fecal samples originating from four beef cattle feedlots. Metagenomic DNA was sequenced to various depths, D1, D0.5 and D0.25, with average sample read counts of 117, 59 and 26 million, respectively. A comparative analysis of the relative abundance of reads aligning to different phyla and antimicrobial classes indicated that the relative proportions of read assignments remained fairly constant regardless of depth. However, the number of reads being assigned to ARGs as well as to microbial taxa increased significantly with increasing depth. We found a depth of D0.5 was suitable to describe the microbiome and resistome of cattle fecal samples. This study helps define a balance between cost and required sequencing depth to acquire meaningful results.

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.

Observability-in-depth: An essential complement to the defense-in-depth safety strategy in the nuclear industry

Energy Technology Data Exchange (ETDEWEB)

Favaro, Francesca M.; Saleh, Joseph H. [Georgia Institute of Technology, Atlanta (United States)

2014-12-15

Defense-in-depth is a fundamental safety principle for the design and operation of nuclear power plants. Despite its general appeal, defense-in-depth is not without its drawbacks, which include its potential for concealing the occurrence of hazardous states in a system, and more generally rendering the latter more opaque for its operators and managers, thus resulting in safety blind spots. This in turn translates into a shrinking of the time window available for operators to identify an unfolding hazardous condition or situation and intervene to abate it. To prevent this drawback from materializing, we propose propose in this work a novel safety principle termed 'observability-in-depth'. We characterize it as the set of provisions technical, operational, and organizational designed to enable the monitoring and identification of emerging hazardous conditions and accident pathogens in real-time and over different time-scales. Observability-in-depth also requires the monitoring of conditions of all safety barriers that implement defense-in-depth; and in so doing it supports sense making of identified hazardous conditions, and the understanding of potential accident sequences that might follow (how they can propagate). Observability-in-depth is thus an information-centric principle, and its importance in accident prevention is in the value of the information it provides and actions or safety interventions it spurs. We examine several 'event reports' from the U.S. Nuclear Regulatory Commission database, which illustrate specific instances of violation of the observability-in-depth safety principle and the consequences that followed (e.g., unmonitored releases and loss of containments). We also revisit the Three Mile Island accident in light of the proposed principle, and identify causes and consequences of the lack of observability-in-depth related to this accident sequence. We illustrate both the benefits of adopting the observability-in-depth

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.

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.

Cuff depth and continuous chest auscultation method for determination of tracheal tube insertion depth in nasal intubation: observational study.

Science.gov (United States)

Ouchi, Kentaro; Sugiyama, Kazuna

2016-04-01

Incorrect endobronchial placement of the tracheal tube can lead to serious complications. Hence, it is necessary to determine the accuracy of tracheal tube positioning. Markers are included on tracheal tubes, in the process of their manufacture, as indicators of approximate intubation depth. In addition, continuous chest auscultation has been used for determining the proper position of the tube. We examined insertion depth using the cuff depth and continuous chest auscultation method (CC method), compared with insertion depth determined by the marker method, to assess the accuracy of these methods. After induction of anesthesia, tracheal intubation was performed in each patient. In the CC method, the depth of tube insertion was measured when the cuff had passed through the glottis, and again when breath sounds changed in quality; the depth of tube insertion was determined from these values. In the marker method, the depth of tube insertion was measured and determined when the marker of the tube had reached the glottis, using insertion depth according to the marker as an index. Insertion depth by the marker method was 26.6 ± 1.2 cm and by the CC method was 28.0 ± 1.2 cm (P < 0.0001). The CC method indicated a significantly greater depth than the marker method. This study determined the safe range of tracheal tube placement. Tube positions determined by the CC method were about 1 cm deeper than those determined by the marker. This information is important to prevent accidental one-lung ventilation and accidental extubation. UMIN No. UMIN000011375.

Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas.

Directory of Open Access Journals (Sweden)

Haigang Qi

Full Text Available Single nucleotide polymorphisms (SNPs are widely used in genetics and genomics research. The Pacific oyster (Crassostrea gigas is an economically and ecologically important marine bivalve, and it possesses one of the highest levels of genomic DNA variation among animal species. Pacific oyster SNPs have been extensively investigated; however, the mechanisms by which these SNPs may be used in a high-throughput, transferable, and economical manner remain to be elucidated. Here, we constructed an oyster 190K SNP array using Affymetrix Axiom genotyping technology. We designed 190,420 SNPs on the chip; these SNPs were selected from 54 million SNPs identified through re-sequencing of 472 Pacific oysters collected in China, Japan, Korea, and Canada. Our genotyping results indicated that 133,984 (70.4% SNPs were polymorphic and successfully converted on the chip. The SNPs were distributed evenly throughout the oyster genome, located in 3,595 scaffolds with a length of ~509.4 million; the average interval spacing was 4,210 bp. In addition, 111,158 SNPs were distributed in 21,050 coding genes, with an average of 5.3 SNPs per gene. In comparison with genotypes obtained through re-sequencing, ~69% of the converted SNPs had a concordance rate of >0.971; the mean concordance rate was 0.966. Evaluation based on genotypes of full-sib family individuals revealed that the average genotyping accuracy rate was 0.975. Carrying 133 K polymorphic SNPs, our oyster 190K SNP array is the first commercially available high-density SNP chip for mollusks, with the highest throughput. It represents a valuable tool for oyster genome-wide association studies, fine linkage mapping, and population genetics.

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.

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

The measurement of dose at 70 micrometres' depth using thermoluminescent dosimeters (tlds)

International Nuclear Information System (INIS)

Jones, A.R.

1989-01-01

The measurement of dose with thermoluminescent dosimeters (TLD) at a tissue-equivalent depth of 70 μm can be done in three ways. These are by using: very thin TLDs (made by cementing fine, powdered, TLD particles to a high-temperature plastic film); opaque TLDs whose surface alone is sensitive. (Light emitted at a greater depth has a low probability of emergence and, thus, they behave as if they were thin.); at least three TLDs covered with absorbers of differing thickness. The approaches were studied using examples of dosimeter arrangements of the three types. The characteristics which were measured to form a basis of comparison were: the performance at high and low doses; the effect of changing angle of incidence and beta-ray energy; the effect on performance of repeated irradiation, annealing and reading. It was concluded that the very thin TLDs (powdered) are the best suited to the measurement of doses at 70 μm depth

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.

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.

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.

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...

Determination of the neutralization depth of concrete under the aggressive environment influence

Science.gov (United States)

Morzhukhina, Anastasia; Nikitin, Stanislav; Akimova, Elena

2018-03-01

Aggressive environments have a significant impact on destruction of many reinforced concrete structures, such as high-rise constructions or chemical plants. For example, some high-rise constructions are equipped with a swimming pool, so they are exposed to chloride ions in the air. Penetration of aggressive chemical substances into the body of concrete contributes to acceleration of reinforced concrete structure corrosion that in turn leads to load bearing capacity loss and destruction of the building. The article considers and analyzes the main technologies for calculating penetration depth of various aggressive substances into the body of concrete. The calculation of corrosion depth was made for 50-year service life.

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)

DOC concentrations across a depth-dependent light gradient on a Caribbean coral reef

Directory of Open Access Journals (Sweden)

Benjamin Mueller

2017-06-01

Full Text Available Photosynthates released by benthic primary producers (BPP, such as reef algae and scleractinian corals, fuel the dissolved organic carbon (DOC production on tropical coral reefs. DOC concentrations near BPP have repeatedly been observed to be elevated compared to those in the surrounding water column. As the DOC release of BPP increases with increasing light availability, elevated DOC concentrations near them will, in part, also depend on light availability. Consequently, DOC concentrations are likely to be higher on the shallow, well-lit reef terrace than in deeper sections on the fore reef slope. We measured in situ DOC concentrations and light intensity in close proximity to the reef alga Dictyota sp. and the scleractinian coral Orbicella faveolata along a depth-dependent light gradient from 5 to 20 m depth and compared these to background concentrations in the water column. At 10 m (intermediate light, DOC concentrations near Dictyota sp. were elevated by 15 µmol C L−1 compared to background concentrations in the water column, but not at 5 and 20 m (high and low light, respectively, or near O. faveolata at any of the tested depths. DOC concentrations did not differ between depths and thereby light environments for any of the tested water types. However, water type and depth appear to jointly affect in situ DOC concentrations across the tested depth-dependent light gradient. Corroborative ex situ measurements of excitation pressure on photosystem II suggest that photoinhibition in Dictyota sp. is likely to occur at light intensities that are commonly present on Curaçaoan coral reefs under high light levels at 5 m depth during midday. Photoinhibition may have thereby reduced the DOC release of Dictyota sp. and DOC concentrations in its close proximity. Our results indicate that the occurrence of elevated DOC concentrations did not follow a natural light gradient across depth. Instead, a combination of multiple factors, such as water type

DOC concentrations across a depth-dependent light gradient on a Caribbean coral reef.

Science.gov (United States)

Mueller, Benjamin; Meesters, Erik H; van Duyl, Fleur C

2017-01-01

Photosynthates released by benthic primary producers (BPP), such as reef algae and scleractinian corals, fuel the dissolved organic carbon (DOC) production on tropical coral reefs. DOC concentrations near BPP have repeatedly been observed to be elevated compared to those in the surrounding water column. As the DOC release of BPP increases with increasing light availability, elevated DOC concentrations near them will, in part, also depend on light availability. Consequently, DOC concentrations are likely to be higher on the shallow, well-lit reef terrace than in deeper sections on the fore reef slope. We measured in situ DOC concentrations and light intensity in close proximity to the reef alga Dictyota sp. and the scleractinian coral Orbicella faveolata along a depth-dependent light gradient from 5 to 20 m depth and compared these to background concentrations in the water column. At 10 m (intermediate light), DOC concentrations near Dictyota sp. were elevated by 15 µmol C L -1 compared to background concentrations in the water column, but not at 5 and 20 m (high and low light, respectively), or near O. faveolata at any of the tested depths. DOC concentrations did not differ between depths and thereby light environments for any of the tested water types. However, water type and depth appear to jointly affect in situ DOC concentrations across the tested depth-dependent light gradient. Corroborative ex situ measurements of excitation pressure on photosystem II suggest that photoinhibition in Dictyota sp. is likely to occur at light intensities that are commonly present on Curaçaoan coral reefs under high light levels at 5 m depth during midday. Photoinhibition may have thereby reduced the DOC release of Dictyota sp. and DOC concentrations in its close proximity. Our results indicate that the occurrence of elevated DOC concentrations did not follow a natural light gradient across depth. Instead, a combination of multiple factors, such as water type, light

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

Relation between 1m depth temperature and average geothermal gradient at 75cm depth in geothermal fields

OpenAIRE

江原, 幸雄

2009-01-01

Shallow ground temperatures such as 1m depth temperature have been measured to delineate thermal anomalies of geothermal fields and also to estimate heat discharge rates from geothermal fields. As a result, a close linear relation between 1m depth temperature and average geothermal gradient at 75cm depth has been recognized in many geothermal fields and was used to estimate conductive heat discharge rates. However, such a linear relation may show that the shallow thermal regime in geothermal ...

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

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.)

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.

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

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.

Depth-profiling using X-ray photoelectron spectroscopy

International Nuclear Information System (INIS)

Pijolat, M.; Hollinger, G.

1980-12-01

The possibilities of X-ray photoelectron spectroscopy (or ESCA) for depth-profiling into shallow depths (approximately 10-100 A) have been studied. The method of ion-sputtering removal has first been investigated in order to improve its depth-resolution (approximately 50-150 A). A procedure which eliminates the effects due to the resolution function of the instrumental probe (analysed depth approximately 50 A) has been settled; but it is not yet sufficient, and the sputter - broadening due to the ion-induced damages must be taken into account (broadening function approximately 50 A for approximately 150 A removal). Because of serious difficulties in estimating the broadening function an alternative is to develop non destructive methods, so a new method based on the dependence of the analysed depth with the electron emission angle is presented. The extraction of the concentration profile from angular distribution experiments is achieved, in the framework of a flat-layer model, by minimizing the difference between theoretical and experimental relative intensities. The applicability and limitations of the method are discussed on the basis of computer simulation results. The depth probed is of the order of 3 lambda (lambda being the value of the inelastic mean free path, typically 10-20 A) and the depth-resolution is of the order of lambda/3 [fr

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).

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)

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.

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.

Visual attention and the apprehension of spatial relations: the case of depth.

Science.gov (United States)

Moore, C M; Elsinger, C L; Lleras, A

2001-05-01

Several studies have shown that targets defined on the basis of the spatial relations between objects yield highly inefficient visual search performance (e.g., Logan, 1994; Palmer, 1994), suggesting that the apprehension of spatial relations may require the selective allocation of attention within the scene. In the present study, we tested the hypothesis that depth relations might be different in this regard and might support efficient visual search. This hypothesis was based, in part, on the fact that many perceptual organization processes that are believed to occur early and in parallel, such as figure-ground segregation and perceptual completion, seem to depend on the assignment of depth relations. Despite this, however, using increasingly salient cues to depth (Experiments 2-4) and including a separate test of the sufficiency of the most salient depth cue used (Experiment 5), no evidence was found to indicate that search for a target defined by depth relations is any different than search for a target defined by other types of spatial relations, with regard to efficiency of search. These findings are discussed within the context of the larger literature on early processing of three-dimensional characteristics of visual scenes.

Directional dependence of depth of correlation due to in-plane fluid shear in microscopic particle image velocimetry

International Nuclear Information System (INIS)

Olsen, Michael G

2009-01-01

An analytical model for the microscopic particle image velocimetry (microPIV) correlation signal peak in a purely shearing flow was derived for the case of in-plane shearing (out-of-plane shearing was not considered). This model was then used to derive equations for the measured velocity weighting functions for the two velocity components, and the weighting functions were in turn used to define the depths of correlation associated with the two measured velocity components. The depth of correlation for the velocity component perpendicular to the shear was found to be unaffected by the shear rate. However, the depth of correlation for the velocity component in the direction of the shear was found to be highly dependent on the shear rate, with the depth of correlation increasing as the shear rate increased. Thus, in a flow with shear, there is not a single value for the depth of correlation within an interrogation region. Instead, the depth of correlation exhibits directional dependence, with a different depth of correlation for each of the two measured velocity components. The increase in the depth of correlation due to the shear rate is greater for large numerical aperture objectives than for small numerical aperture objectives. This increase in the depth of correlation in a shearing flow can be quite large, with increases in the depth of correlation exceeding 100% being very possible for high numerical aperture objectives. The effects of out-of-plane shear are beyond the capabilities of this analysis, although the possible consequences of out-of-plane shear are discussed

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.

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.

Excess carrier depths profiles in Cu(In,Ga)(S,Se){sub 2} absorbers from spectral photoluminescence

Energy Technology Data Exchange (ETDEWEB)

Koenne, Nils; Knabe, Sebastian; Bauer, Gottfried H. [Institute of Physics, CvO University Oldenburg (Germany); Witte, Wolfram; Hariskos, Dimitrios [Zentrum fuer Sonnenenergie- und Wasserstoff-Forschung Baden-Wuerttemberg (ZSW), Stuttgart (Germany); Meeder, Alexander [SULFURCELL Solartechnik GmbH, Berlin (Germany)

2011-07-01

The polycrystalline structure of chalcopyrite absorbers, such as Cu(In,Ga)(S,Se){sub 2} and their complex metallurgical composition results in lateral and depth dependent inhomogeneities. The spectral photoluminescence (PL) recorded from front and rear side of these chalcopyrite thin-film systems shows a distinct different behavior in particular of the high energy PL-wing which is strongly governed by absorption/emission approaching unity, as well as by re-absorption of emitted PL-photons and their depth dependent origin, say excess carrier depth profile. We define a contrast parameter for the high energy PL-yield of the fluxes recorded from front side and rear side and we proof the origin of the experimental contrast with numerical simulations of spectral PL-yields via Planck's generalized law for different depth profiles of excess carriers and band gap/absorption coefficients. By comparison of experimental contrast parameters with results from numerical simulations we conclude a set of regimes of realistic combinations of depth profiles for excess carriers and band gaps.

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

Experimental evidence concerning the significant information depth of electron backscatter diffraction (EBSD)

Energy Technology Data Exchange (ETDEWEB)

Wisniewski, Wolfgang, E-mail: wolfgang.w@uni-jena.de [Otto-Schott-Institut, Jena University, Fraunhoferstr. 6, 07743 Jena (Germany); Saager, Stefan [Fraunhofer Institute for Organic Electronics, Electron Beam and Plasma Technology FEP, Winterbergstraße 28, 01277 Dresden (Germany); Böbenroth, Andrea [Fraunhofer Institute for the Microstructure of Materials and Systems IMWS, Walter-Huelse-Straße 1, 06120 Halle (Saale) (Germany); Rüssel, Christian [Otto-Schott-Institut, Jena University, Fraunhoferstr. 6, 07743 Jena (Germany)

2017-02-15

Experiments concerning the information depth of electron backscatter diffraction (EBSD) are performed on samples featuring an amorphous wedge on a crystalline substrate and a crystalline wedge on an amorphous substrate. The effects of the acceleration voltage and exemplary software settings on the ability to measure through an amorphous layer are presented. Changes in the EBSD-signal could be detected through a ≈142 nm thick layer of amorphous Si while orientation measurements could be performed through a ≈116 nm thick layer when using a voltage of 30 kV. The complexity of the information depth significant to a given EBSD-pattern and the multiple parameters influencing it are discussed. It is suggested that a “core information depth” is significant to high quality patterns while a larger “maximum information depth” becomes relevant when the pattern quality decreases or the sample is inhomogeneous within the information volume, i.e. in the form of partially crystalline materials or crystal layers in the nm scale. - Highlights: • Experimental evidence of the significant information depth of EBSD is presented. • Effects of the voltage and exemplary software settings are discussed. • Dependence of the significant information depth on the pattern quality is proposed. • The information depth may reach up to 142 nm in Si when using a voltage of 30 kV. • The information depth depends on the available technology.

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.

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.

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.

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

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

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...

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.

Induction Thermography for Surface Crack Detection and Depth Determination

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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.

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...

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.)

Local bilinear multiple-output quantile/depth regression

Czech Academy of Sciences Publication Activity Database

Hallin, M.; Lu, Z.; Paindaveine, D.; Šiman, Miroslav

2015-01-01

Roč. 21, č. 3 (2015), s. 1435-1466 ISSN 1350-7265 R&D Projects: GA MŠk(CZ) 1M06047 Institutional support: RVO:67985556 Keywords : conditional depth * growth chart * halfspace depth * local bilinear regression * multivariate quantile * quantile regression * regression depth Subject RIV: BA - General Mathematics Impact factor: 1.372, year: 2015 http://library.utia.cas.cz/separaty/2015/SI/siman-0446857.pdf

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

Prediction of Soil Solum Depth Using Topographic Attributes in Some Hilly Land of Koohrang in Central Zagros

Directory of Open Access Journals (Sweden)

A. Mehnatkesh

2016-02-01

profiles were dug and described; and the solum thickness was measured for each profile. DEM data were created by using a 1:2,5000 topographic map. Topographical indices were generated from the DEM using TAS software. Terrain attributes in two categories, primary and secondary (compound attributes; primary attributes are included elevation, slope, aspect, catchment area, dispersal area, plan curvature, profile curvature, tangential curvature, shaded relief. Secondary or compound attributes such as soil water content or the potential for sheet erosion, stream power index, wetness index, and sediment transport index. Correlation coefficients to define relationships between soil depth and terrain attributes, and analysis of variance by Duncan test were done using the SPSS software. The statistical software SPSS was used for developing multiple linear regression models. Terrain attributes were selected as the independent variables and soil depth was employed as dependent variable in the model. Thirty sampling sites were used to validate the developed soil-landscape model. In testing soil-landscape model, we calculated two indices from the observed and predicted values included mean error (ME and root mean square error (RMSE. Results and Discussion: The soil depth in the studied profiles varied from 30 cm to 150 cm with an average of 108.6 cm. Relatively high variability (CV = 76% was obtained for soil depth in the study area. The linear correlation analysis of the 12 topographic attributes and one soil property (soil depth, showed that there was a significant correlation among 36 of the 77 attribute pairs. Soil depth showed high positive significant correlations with catchment area, plan curvature, and wetness index, and showed high negative correlation with sediment transport index, sediment power index and slope. Low positive significant correlations of soil depth were identified with tangential curvature, and profile curvature. Moreover, soil depth was negatively correlated

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.

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

Depth to Curie temperature across the central Red Sea from magnetic data using the de-fractal method

Science.gov (United States)

Salem, Ahmed; Green, Chris; Ravat, Dhananjay; Singh, Kumar Hemant; East, Paul; Fairhead, J. Derek; Mogren, Saad; Biegert, Ed

2014-06-01

The central Red Sea rift is considered to be an embryonic ocean. It is characterised by high heat flow, with more than 90% of the heat flow measurements exceeding the world mean and high values extending to the coasts - providing good prospects for geothermal energy resources. In this study, we aim to map the depth to the Curie isotherm (580 °C) in the central Red Sea based on magnetic data. A modified spectral analysis technique, the “de-fractal spectral depth method” is developed and used to estimate the top and bottom boundaries of the magnetised layer. We use a mathematical relationship between the observed power spectrum due to fractal magnetisation and an equivalent random magnetisation power spectrum. The de-fractal approach removes the effect of fractal magnetisation from the observed power spectrum and estimates the parameters of depth to top and depth to bottom of the magnetised layer using iterative forward modelling of the power spectrum. We applied the de-fractal approach to 12 windows of magnetic data along a profile across the central Red Sea from onshore Sudan to onshore Saudi Arabia. The results indicate variable magnetic bottom depths ranging from 8.4 km in the rift axis to about 18.9 km in the marginal areas. Comparison of these depths with published Moho depths, based on seismic refraction constrained 3D inversion of gravity data, showed that the magnetic bottom in the rift area corresponds closely to the Moho, whereas in the margins it is considerably shallower than the Moho. Forward modelling of heat flow data suggests that depth to the Curie isotherm in the centre of the rift is also close to the Moho depth. Thus Curie isotherm depths estimated from magnetic data may well be imaging the depth to the Curie temperature along the whole profile. Geotherms constrained by the interpreted Curie isotherm depths have subsequently been calculated at three points across the rift - indicating the variation in the likely temperature profile with

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)

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

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.

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.)

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.)

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.

A study on depth-scaling of plastic phantom in electron beam dosimetry

International Nuclear Information System (INIS)

Kojima, T.; Saitoh, H.; Kawachi, T.; Katayose, T.; Myojyoyama, A.

2005-01-01

In recommendations of several standard dosimetry, water is defined as the reference medium, however, the water substitute plastic phantoms are highly discouraged. Nevertheless, in the case of accurate chamber positioning in water is not possible, or no waterproof chamber is available, their use is permitted at beam qualities R 50 2 (E 0 pl obtained from a ratio of electron average penetration depth; z av , half value depth ratio; (R 50 ) w,m from Monte Carlo dose calculation and that from measurements, are compared each other. As a result, there are slight differences in depth-scaling factor between obtained from simulation results and from measurements. These results indicate that c pl has to be studied more detail for the sake of precise electron dosimetry in plastic phantoms. (author)

OBSERVABILITY-IN-DEPTH: AN ESSENTIAL COMPLEMENT TO THE DEFENSE-IN-DEPTH SAFETY STRATEGY IN THE NUCLEAR INDUSTRY1

Directory of Open Access Journals (Sweden)

FRANCESCA M. FAVARÒ

2014-12-01

We examine several “event reports” from the U.S. Nuclear Regulatory Commission database, which illustrate specific instances of violation of the observability-in-depth safety principle and the consequences that followed (e.g., unmonitored releases and loss of containments. We also revisit the Three Mile Island accident in light of the proposed principle, and identify causes and consequences of the lack of observability-in-depth related to this accident sequence. We illustrate both the benefits of adopting the observability-in-depth safety principle and the adverse consequences when this principle is violated or not implemented. This work constitutes a first step in the development of the observability-in-depth safety principle, and we hope this effort invites other researchers and safety professionals to further explore and develop this principle and its implementation.

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)

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.

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)

Reconstruction of original indium distribution in InGaAs quantum wells from experimental SIMS depth profiles

Energy Technology Data Exchange (ETDEWEB)

Kudriavtsev, Yu., E-mail: yuriyk@cinvestav.mx [Departamento Ingeniería Eléctrica – SEES, CINVESTAV-IPN, Av. IPN #2508, D.F., México (Mexico); Asomoza, R. [Departamento Ingeniería Eléctrica – SEES, CINVESTAV-IPN, Av. IPN #2508, D.F., México (Mexico); Gallardo-Hernandez, S.; Ramirez-Lopez, M.; Lopez-Lopez, M. [Departamento de Física, CINVESTAV-IPN, México (Mexico); Nevedomsky, V.; Moiseev, K. [Ioffe Physical Technical Institute, S-Petersburg (Russian Federation)

2014-11-15

Depth profiling analysis of InGaAs/GaAs hetero-structures grown by MBE on GaAs (0 0 1) substrates is reported. A novel two-step procedure for de-convolving experimental SIMS depth distribution is employed and the original In distribution in InGaAs quantum wells (QW) is estimated. The QW thickness calculated from the de-convolved profiles is shown to be in good agreement with the cross-sectional TEM images. The experimental In depth profile is shifted from the original In distribution due to the ion mixing process during depth profiling analysis. It is shown that the de-convolution procedure is suitable for reconstruction of the original QW width and depth by SIMS even for relatively high primary ion energies.

Depth-weighted robust multivariate regression with application to sparse data

KAUST Repository

Dutta, Subhajit; Genton, Marc G.

2017-01-01

A robust method for multivariate regression is developed based on robust estimators of the joint location and scatter matrix of the explanatory and response variables using the notion of data depth. The multivariate regression estimator possesses desirable affine equivariance properties, achieves the best breakdown point of any affine equivariant estimator, and has an influence function which is bounded in both the response as well as the predictor variable. To increase the efficiency of this estimator, a re-weighted estimator based on robust Mahalanobis distances of the residual vectors is proposed. In practice, the method is more stable than existing methods that are constructed using subsamples of the data. The resulting multivariate regression technique is computationally feasible, and turns out to perform better than several popular robust multivariate regression methods when applied to various simulated data as well as a real benchmark data set. When the data dimension is quite high compared to the sample size it is still possible to use meaningful notions of data depth along with the corresponding depth values to construct a robust estimator in a sparse setting.

Depth-weighted robust multivariate regression with application to sparse data

KAUST Repository

Dutta, Subhajit

2017-04-05

A robust method for multivariate regression is developed based on robust estimators of the joint location and scatter matrix of the explanatory and response variables using the notion of data depth. The multivariate regression estimator possesses desirable affine equivariance properties, achieves the best breakdown point of any affine equivariant estimator, and has an influence function which is bounded in both the response as well as the predictor variable. To increase the efficiency of this estimator, a re-weighted estimator based on robust Mahalanobis distances of the residual vectors is proposed. In practice, the method is more stable than existing methods that are constructed using subsamples of the data. The resulting multivariate regression technique is computationally feasible, and turns out to perform better than several popular robust multivariate regression methods when applied to various simulated data as well as a real benchmark data set. When the data dimension is quite high compared to the sample size it is still possible to use meaningful notions of data depth along with the corresponding depth values to construct a robust estimator in a sparse setting.

Controlling Force and Depth in Friction Stir Welding

Science.gov (United States)

Adams, Glynn; Loftus, Zachary; McCormac, Nathan; Venable, Richard

2005-01-01

Feedback control of the penetration force applied to a pin tool in friction stir welding has been found to be a robust and reliable means for controlling the depth of penetration of the tool. This discovery has made it possible to simplify depth control and to weld with greater repeatability, even on workpieces with long weld joints. Prior to this discovery, depths of penetration in friction stir welding were controlled by hard-tooled roller assemblies or by depth actuators controlled by feedback from such external sensors as linear variable-differential transformers or laser-based devices. These means of control are limited: A hard-tooled roller assembly confines a pin tool to a preset depth that cannot be changed easily during the welding process. A measurement by an external sensor is only an indirect indicative of the depth of penetration, and computations to correlate such a measurement with a depth of penetration are vulnerable to error. The present force-feedback approach exploits the proportionality between the depth and the force of penetration Unlike a depth measurement taken by an external sensor, a force measurement can be direct because it can be taken by a sensor coupled directly to the pin tool. The reading can be processed through a modern electronic servo control system to control an actuator to keep the applied penetration force at the desired level. In comparison with the older depth-control methods described above, this method offers greater sensitivity to plasticizing of the workpiece metal and is less sensitive to process noise, resulting in a more consistent process. In an experiment, a tapered panel was friction stir welded while controlling the force of penetration according to this method. The figure is a plot of measurements taken during the experiment, showing that force was controlled with a variation of 200 lb (890 N), resulting in control of the depth of penetration with a variation of 0.004 in. (0.1 mm).

Bulk-fill resin composites: polymerization contraction, depth of cure, and gap formation.

Science.gov (United States)

Benetti, A R; Havndrup-Pedersen, C; Honoré, D; Pedersen, M K; Pallesen, U

2015-01-01

The bulk-filling of deep, wide dental cavities is faster and easier than traditional incremental restoration. However, the extent of cure at the bottom of the restoration should be carefully examined in combination with the polymerization contraction and gap formation that occur during the restorative procedure. The aim of this study, therefore, was to compare the depth of cure, polymerization contraction, and gap formation in bulk-fill resin composites with those of a conventional resin composite. To achieve this, the depth of cure was assessed in accordance with the International Organization for Standardization 4049 standard, and the polymerization contraction was determined using the bonded-disc method. The gap formation was measured at the dentin margin of Class II cavities. Five bulk-fill resin composites were investigated: two high-viscosity (Tetric EvoCeram Bulk Fill, SonicFill) and three low-viscosity (x-tra base, Venus Bulk Fill, SDR) materials. Compared with the conventional resin composite, the high-viscosity bulk-fill materials exhibited only a small increase (but significant for Tetric EvoCeram Bulk Fill) in depth of cure and polymerization contraction, whereas the low-viscosity bulk-fill materials produced a significantly larger depth of cure and polymerization contraction. Although most of the bulk-fill materials exhibited a gap formation similar to that of the conventional resin composite, two of the low-viscosity bulk-fill resin composites, x-tra base and Venus Bulk Fill, produced larger gaps.

Techniques of surface optical breakdown prevention for low-depths femtosecond waveguides writing

International Nuclear Information System (INIS)

Bukharin, M A; Skryabin, N N; Ganin, D V; Khudyakov, D V; Vartapetov, S.K.

2016-01-01

We demonstrated technique of direct femtosecond waveguide writing at record low depth (2-15 μm) under surface of lithium niobate, that play a key role in design of electrooptical modulators with low operating voltage. To prevent optical breakdown of crystal surface we used high numerical aperture objectives for focusing of light and non-thermal regime of inscription in contrast to widespread femtosecond writing technique at depths of tens micrometers or higher. Surface optical breakdown threshold was measured for both x- and z- cut crystals. Inscribed waveguides were examined for intrinsic microstructure. It also reported sharp narrowing of operating pulses energy range with writing depth under the surface of crystal, that should be taken in account when near-surface waveguides design. Novelty of the results consists in reduction of inscription depth under the surface of crystals that broadens applications of direct femtosecond writing technique to full formation of near-surface waveguides and postproduction precise geometry correction of near-surfaces optical integrated circuits produced with proton-exchanged technique. (paper)

Impact of depth and location of the wells on vibrational resonance in a triple-well system

Science.gov (United States)

Chen, Zhijuan; Ning, Lijuan

2018-04-01

The effect of depth and location of a triple-well potential on vibrational resonance is investigated in a quintic oscillator driven by a low-frequency force and a high-frequency force. The values of low-frequency ω and amplitude g of the high-frequency force at which vibrational resonance occurs are derived both numerically and theoretically. It is found that: as ω varies, at most one resonance takes place and the response amplitude at resonance depends on the depth and the location of the potential wells. When g is altered, the depth and location of wells can control the number of resonances, resulting in two, three and four resonances. The system parameters can be adjusted by controlling the depth and position of the wells to achieve optimum vibrational resonance. Furthermore, the changes induced by these two quantities in the tristable system are found to be richer than those induced in bistable systems.

Distribution and depth of bottom-simulating reflectors in the Nankai subduction margin

Science.gov (United States)

Ohde, Akihiro; Otsuka, Hironori; Kioka, Arata; Ashi, Juichiro

2018-04-01

Surface heat flow has been observed to be highly variable in the Nankai subduction margin. This study presents an investigation of local anomalies in surface heat flows on the undulating seafloor in the Nankai subduction margin. We estimate the heat flows from bottom-simulating reflectors (BSRs) marking the lower boundaries of the methane hydrate stability zone and evaluate topographic effects on heat flow via two-dimensional thermal modeling. BSRs have been used to estimate heat flows based on the known stability characteristics of methane hydrates under low-temperature and high-pressure conditions. First, we generate an extensive map of the distribution and subseafloor depths of the BSRs in the Nankai subduction margin. We confirm that BSRs exist at the toe of the accretionary prism and the trough floor of the offshore Tokai region, where BSRs had previously been thought to be absent. Second, we calculate the BSR-derived heat flow and evaluate the associated errors. We conclude that the total uncertainty of the BSR-derived heat flow should be within 25%, considering allowable ranges in the P-wave velocity, which influences the time-to-depth conversion of the BSR position in seismic images, the resultant geothermal gradient, and thermal resistance. Finally, we model a two-dimensional thermal structure by comparing the temperatures at the observed BSR depths with the calculated temperatures at the same depths. The thermal modeling reveals that most local variations in BSR depth over the undulating seafloor can be explained by topographic effects. Those areas that cannot be explained by topographic effects can be mainly attributed to advective fluid flow, regional rapid sedimentation, or erosion. Our spatial distribution of heat flow data provides indispensable basic data for numerical studies of subduction zone modeling to evaluate margin parallel age dependencies of subducting plates.[Figure not available: see fulltext.

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.

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.)

Quantum finite-depth memory channels: Case study

International Nuclear Information System (INIS)

Rybar, Tomas; Ziman, Mario

2009-01-01

We analyze the depth of the memory of quantum memory channels generated by a fixed unitary transformation describing the interaction between the principal system and internal degrees of freedom of the process device. We investigate the simplest case of a qubit memory channel with a two-level memory system. In particular, we explicitly characterize all interactions for which the memory depth is finite. We show that the memory effects are either infinite, or they disappear after at most two uses of the channel. Memory channels of finite depth can be to some extent controlled and manipulated by so-called reset sequences. We show that actions separated by the sequences of inputs of the length of the memory depth are independent and constitute memoryless channels.

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

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....

Effect of pictorial depth cues, binocular disparity cues and motion parallax depth cues on lightness perception in three-dimensional virtual scenes.

Directory of Open Access Journals (Sweden)

Michiteru Kitazaki

2008-09-01

Full Text Available Surface lightness perception is affected by scene interpretation. There is some experimental evidence that perceived lightness under bi-ocular viewing conditions is different from perceived lightness in actual scenes but there are also reports that viewing conditions have little or no effect on perceived color. We investigated how mixes of depth cues affect perception of lightness in three-dimensional rendered scenes containing strong gradients of illumination in depth.Observers viewed a virtual room (4 m width x 5 m height x 17.5 m depth with checkerboard walls and floor. In four conditions, the room was presented with or without binocular disparity (BD depth cues and with or without motion parallax (MP depth cues. In all conditions, observers were asked to adjust the luminance of a comparison surface to match the lightness of test surfaces placed at seven different depths (8.5-17.5 m in the scene. We estimated lightness versus depth profiles in all four depth cue conditions. Even when observers had only pictorial depth cues (no MP, no BD, they partially but significantly discounted the illumination gradient in judging lightness. Adding either MP or BD led to significantly greater discounting and both cues together produced the greatest discounting. The effects of MP and BD were approximately additive. BD had greater influence at near distances than far.These results suggest the surface lightness perception is modulated by three-dimensional perception/interpretation using pictorial, binocular-disparity, and motion-parallax cues additively. We propose a two-stage (2D and 3D processing model for lightness perception.

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

Tritium depth profiling by AMS in carbon samples from fusion experiments

International Nuclear Information System (INIS)

Friedrich, M.; Pilz, W.; Sun, G.; Behrisch, R.; Garcia-Rosales, C.

2001-01-01

Tritium depth profiling measurements by accelerator mass spectrometry have been performed at a facility installed at the Rossendorf 3 MV Tandetron. In order to achieve an uniform erosion at the target surface inside of a commercial Cs ion sputtering source and to avoid edge effects, the samples were mechanically scanned inside of a commercial Cs sputter ion source. The sputtered negative ions were mass analysed by the injection magnet of the Tandetron. The tritium ions are counted after the acceleration with semiconductor detectors. Depth profiles have been measured for carbon samples which had been exposed to the plasma at the first wall of the Garching fusion experiment ASDEX-Upgrade and from the European fusion experiment JET, Culham/UK. A dedicated AMS facility with an air-insulated 100 kV tandem accelerator for depth profiling measurements at samples with high tritium concentration is under construction. First results of test operation are presented. (orig.)

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

Responses of Plant Community Composition to Long-term Changes in Snow Depth at the Great Basin Desert - Sierra Nevada ecotone.

Science.gov (United States)

Loik, M. E.

2015-12-01

Snowfall is the dominant hydrologic input for many high-elevation ecosystems of the western United States. Many climate models envision changes in California's Sierra Nevada snow pack characteristics, which would severely impact the storage and release of water for one of the world's largest economies. Given the importance of snowfall for future carbon cycling in high elevation ecosystems, how will these changes affect seedling recruitment, plant mortality, and community composition? To address this question, experiments utilize snow fences to manipulate snow depth and melt timing at a desert-montane ecotone in eastern California, USA. Long-term April 1 snow pack depth averages 1344 mm (1928-2015) but is highly variable from year to year. Snow fences increased equilibrium drift snow depth by 100%. Long-term changes in snow depth and melt timing are associated with s shift from shurbs to graminoids where snow depth was increased for >50 years. Changes in snow have impacted growth for only three plant species. Moreover, annual growth ring increments of the conifers Pinus jeffreyi and Pi. contorta were not equally sensitive to snow depth. There were over 8000 seedlings of the shrubs Artemisia tridentata and Purshia tridentata found in 6300 m2 in summer 2009, following about 1400 mm of winter snow and spring rain. The frequency of seedlings of A. tridentata and P. tridentata were much lower on increased-depth plots compared to ambient-depth, and reduced-depth plots. Survival of the first year was lowest for A. tridentata. Survival of seedlings from the 2008 cohort was much higher for P. tridentata than A. tridentata during the 2011-2015 drought. Results indicate complex interactions between snow depth and plant community characteristics, and that responses of plants at this ecotone may not respond similarly to increases vs. decreases in snow depth. These changes portend altered carbon uptake in this region under future snowfall scenarios.

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

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.

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.

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.

Assessment of geomechanical properties, maximum depth and excavation damaged zone aspects - Expert report

International Nuclear Information System (INIS)

Amann, F.; Löw, S.; Perras, M.

2015-11-01

This comprehensive report published by the Swiss National Nuclear Safety Inspectorate ENSI discusses the expert report published on the need for the assessment of geomechanical properties and maximum depth of repositories for high, medium and low-activity nuclear wastes. Also, aspects concerning excavation damaged zones (EDZ) are considered. These are all criteria for the selection of sites as part of Phase 2 of the Swiss waste disposal project. Four questions are examined: are NAGRA’s documented basic considerations and calculations on Opalinus Clay comprehensive enough and correct, are the calculations on maximum depth correct, are the proposed storage perimeters correct with respect to depth and will NAGRA be able to take possible excavation damaged zones (EDZ) into account? Literature and references concerning the subject are quoted

Magnetotelluric inversion for depth-to-basement estimation

DEFF Research Database (Denmark)

Cai, Hongzhu; Zhdanov, Michael

2015-01-01

The magnetotelluric (MT) method can be effectively applied for depth-to-basement estimation, because there exists a strong contrast in resistivity between a conductive sedimentary basin and a resistive crystalline basement. Conventional inversions of MT data are usually aimed at determining...... the volumetric distribution of the conductivity within the inversion domain. By the nature of the MT method, the recovered distribution of the subsurface conductivity is typically diffusive, which makes it difficult to select the sediment-basement interface. This paper develops a novel approach to 3D MT...... inversion for the depth-to-basement estimate. The key to this approach is selection of the model parameterization with the depth to basement being the major unknown parameter. In order to estimate the depth to the basement, the inversion algorithm recovers both the thickness and the conductivities...

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

Spatiotemporal Characteristics for the Depth from Luminance Contrast

Directory of Open Access Journals (Sweden)

Kazuya Matsubara

2011-05-01

Full Text Available Images with higher luminance contrast tend to be perceived closer in depth. To investigate a spatiotemporal characteristic of this effect, we evaluated subjective depth of a test stimulus with various spatial and temporal frequencies. For the purpose, the depth of a reference stimulus was matched to that of the test stimulus by changing the binocular disparity. The results showed that the test stimulus was perceived closer with higher luminance contrast for all conditions. Contrast efficiency was obtained from the contrast that provided the subjective depth for each spatiotemporal frequency. The shape of the contrast efficiency function was spatially low-pass and temporally band-pass. This characteristic is different from the one measure for a detection task. This suggests that only subset of contrast signals are used for depth from contrast.

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

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

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.

EDOVE: Energy and Depth Variance-Based Opportunistic Void Avoidance Scheme for Underwater Acoustic Sensor Networks.

Science.gov (United States)

Bouk, Safdar Hussain; Ahmed, Syed Hassan; Park, Kyung-Joon; Eun, Yongsoon

2017-09-26

Underwater Acoustic Sensor Network (UASN) comes with intrinsic constraints because it is deployed in the aquatic environment and uses the acoustic signals to communicate. The examples of those constraints are long propagation delay, very limited bandwidth, high energy cost for transmission, very high signal attenuation, costly deployment and battery replacement, and so forth. Therefore, the routing schemes for UASN must take into account those characteristics to achieve energy fairness, avoid energy holes, and improve the network lifetime. The depth based forwarding schemes in literature use node's depth information to forward data towards the sink. They minimize the data packet duplication by employing the holding time strategy. However, to avoid void holes in the network, they use two hop node proximity information. In this paper, we propose the Energy and Depth variance-based Opportunistic Void avoidance (EDOVE) scheme to gain energy balancing and void avoidance in the network. EDOVE considers not only the depth parameter, but also the normalized residual energy of the one-hop nodes and the normalized depth variance of the second hop neighbors. Hence, it avoids the void regions as well as balances the network energy and increases the network lifetime. The simulation results show that the EDOVE gains more than 15 % packet delivery ratio, propagates 50 % less copies of data packet, consumes less energy, and has more lifetime than the state of the art forwarding schemes.

Surfing depth on a behaviour change website: predictors and effects on behaviour.

Science.gov (United States)

Jacobs, Nele; De Bourdeaudhuij, Ilse; Claes, Neree

2010-03-01

The primary objectives of the present study were to gain insight into website use and to predict the surfing depth on a behaviour change website and its effect on behaviour. Two hundred eight highly educated adults from the intervention condition of a randomised trial received access to a medical intervention, individual coaching (by e-mail, post, telephone or face-to-face) and a behaviour change website. Website use (e.g. surfing depth, page view duration) was registered. Online questionnaires for physical activity and fat intake were filled out at baseline and after 6 months. Hierarchical linear regression was used to predict surfing depth and its effect on behaviour. Seventy-five per cent of the participants visited the website. Fifty-one and fifty-six per cent consulted the physical activity and fat intake feedback, respectively. The median surfing depth was 2. The total duration of interventions by e-mail predicted deeper surfing (beta=0.36; pSurfing depth did not predict changes in fat intake (beta=-0.07; p=0.45) or physical activity (beta=-0.03; p=0.72). Consulting the physical activity feedback led to more physical activity (beta=0.23; p=0.01). The findings from the present study can be used to guide future website development and improve the information architecture of behaviour change websites.

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.

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations.

Science.gov (United States)

Fuentes-Pardo, Angela P; Ruzzante, Daniel E

2017-10-01

Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology. © 2017 John Wiley & Sons Ltd.

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)

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.

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.

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.

Multifunctionality is affected by interactions between green roof plant species, substrate depth, and substrate type.

Science.gov (United States)

Dusza, Yann; Barot, Sébastien; Kraepiel, Yvan; Lata, Jean-Christophe; Abbadie, Luc; Raynaud, Xavier

2017-04-01

Green roofs provide ecosystem services through evapotranspiration and nutrient cycling that depend, among others, on plant species, substrate type, and substrate depth. However, no study has assessed thoroughly how interactions between these factors alter ecosystem functions and multifunctionality of green roofs. We simulated some green roof conditions in a pot experiment. We planted 20 plant species from 10 genera and five families (Asteraceae, Caryophyllaceae, Crassulaceae, Fabaceae, and Poaceae) on two substrate types (natural vs. artificial) and two substrate depths (10 cm vs. 30 cm). As indicators of major ecosystem functions, we measured aboveground and belowground biomasses, foliar nitrogen and carbon content, foliar transpiration, substrate water retention, and dissolved organic carbon and nitrates in leachates. Interactions between substrate type and depth strongly affected ecosystem functions. Biomass production was increased in the artificial substrate and deeper substrates, as was water retention in most cases. In contrast, dissolved organic carbon leaching was higher in the artificial substrates. Except for the Fabaceae species, nitrate leaching was reduced in deep, natural soils. The highest transpiration rates were associated with natural soils. All functions were modulated by plant families or species. Plant effects differed according to the observed function and the type and depth of the substrate. Fabaceae species grown on natural soils had the most noticeable patterns, allowing high biomass production and high water retention but also high nitrate leaching from deep pots. No single combination of factors enhanced simultaneously all studied ecosystem functions, highlighting that soil-plant interactions induce trade-offs between ecosystem functions. Substrate type and depth interactions are major drivers for green roof multifunctionality.

Recent Intermediate Depth Earthquakes in El Salvador, Central Mexico, Cascadia and South-West Japan

Science.gov (United States)

Lemoine, A.; Gardi, A.; Gutscher, M.; Madariaga, R.

2001-12-01

We studied occurence and source parameters of several recent intermediate depth earthquakes. We concentrated on the Mw=7.7 salvadorian earthquake which took place on January 13, 2001. It was a good example of the high seismic risk associated to such kind of events which occur closer to the coast than the interplate thrust events. The Salvadorian earthquake was an intermediate depth downdip extensional event which occured inside the downgoing Cocos plate, next to the downdip flexure where the dip increases sharply before the slab sinks more steeply. This location corresponds closely to the position of the Mw=5.7 1996 and Mw=7.3 1982 downdip extensional events. Several recent intermediate depth earthquakes occured in subduction zones exhibiting a ``flat slab'' geometry with three distinct flexural bends where flexural stress may be enhanced. The Mw=6.7 Geiyo event showed a downdip extensional mechanism with N-S striking nodal planes. This trend was highly oblique to the trench (Nankai Trough), yet consistent with westward steepening at the SW lateral termination of the SW Japan flat slab. The Mw=6.8 Olympia earthquake in the Cascadia subduction zone occured at the downdip termination of the Juan de Fuca slab, where plate dip increases from about 5o to over 30o. The N-S orientation of the focal planes, parallel to the trench indicated downdip extension. The location at the downdip flexure corresponds closely to the estimated positions of the 1949 M7.1 Olympia and 1965 M6.5 Seattle-Tacoma events. Between 1994 and 1999, in Central Mexico, an unusually high intermediate depth seismicity occured where several authors proposed a flat geometry for the Cocos plate. Seven events of magnitude between Mw=5.9 and Mw=7.1 occured. Three of them were downdip compressional and four where down-dip extensional. We can explain these earthquakes by flexural stresses at down-dip and lateral terminations of the supposed flat segment. Even if intermediate depth earthquakes occurence could

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

The penetrating depth analysis of Lunar Penetrating Radar onboard Chang’e-3 rover

Science.gov (United States)

Xing, Shu-Guo; Su, Yan; Feng, Jian-Qing; Dai, Shun; Xiao, Yuan; Ding, Chun-Yu; Li, Chun-Lai

2017-04-01

Lunar Penetrating Radar (LPR) has successfully been used to acquire a large amount of scientific data during its in-situ detection. The analysis of penetrating depth can help to determine whether the target is within the effective detection range and contribute to distinguishing useful echoes from noise. First, this study introduces two traditional methods, both based on a radar transmission equation, to calculate the penetrating depth. The only difference between the two methods is that the first method adopts system calibration parameters given in the calibration report and the second one uses high-voltage-off radar data. However, some prior knowledge and assumptions are needed in the radar equation and the accuracy of assumptions will directly influence the final results. Therefore, a new method termed the Correlation Coefficient Method (CCM) is provided in this study, which is only based on radar data without any a priori assumptions. The CCM can obtain the penetrating depth according to the different correlation between reflected echoes and noise. To be exact, there is a strong correlation in the useful reflected echoes and a random correlation in the noise between adjacent data traces. In addition, this method can acquire a variable penetrating depth along the profile of the rover, but only one single depth value can be obtained from traditional methods. Through a simulation, the CCM has been verified as an effective method to obtain penetration depth. The comparisons and analysis of the calculation results of these three methods are also implemented in this study. Finally, results show that the ultimate penetrating depth of Channel 1 and the estimated penetrating depth of Channel 2 range from 136.9 m to 165.5 m ({\\varepsilon }r=6.6) and from 13.0 m to 17.5 m ({\\varepsilon }r=2.3), respectively.

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

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.

A variant reference data set for the Africanized honeybee, Apis mellifera.

Science.gov (United States)

Kadri, Samir M; Harpur, Brock A; Orsi, Ricardo O; Zayed, Amro

2016-11-08

The Africanized honeybee (AHB) is a population of Apis mellifera found in the Americas. AHBs originated in 1956 in Rio Clara, Brazil where imported African A. m. scutellata escaped and hybridized with local populations of European A. mellifera. Africanized populations can now be found from Northern Argentina to the Southern United States. AHBs-often referred to as 'Killer Bees'- are a major concern to the beekeeping industry as well as a model for the evolutionary genetics of colony defence. We performed high coverage pooled-resequencing of 360 diploid workers from 30 Brazilian AHB colonies using Illumina Hi-Seq (150 bp PE). This yielded a high density SNP data set with an average read depth at each site of 20.25 reads. With 3,606,720 SNPs and 155,336 SNPs within 11,365 genes, this data set is the largest genomic resource available for AHBs and will enable high-resolution studies of the population dynamics, evolution, and genetics of this successful biological invader, in addition to facilitating the development of SNP-based tools for identifying AHBs.

DEPTH-CHARGE static and time-dependent perturbation/sensitivity system for nuclear reactor core analysis. Revision I. [DEPTH-CHARGE code

Energy Technology Data Exchange (ETDEWEB)

White, J.R.

1985-04-01

This report provides the background theory, user input, and sample problems required for the efficient application of the DEPTH-CHARGE system - a code black for both static and time-dependent perturbation theory and data sensitivity analyses. The DEPTH-CHARGE system is of modular construction and has been implemented within the VENTURE-BURNER computational system at Oak Ridge National Laboratory. The DEPTH module (coupled with VENTURE) solves for the three adjoint functions of Depletion Perturbation Theory and calculates the desired time-dependent derivatives of the response with respect to the nuclide concentrations and nuclear data utilized in the reference model. The CHARGE code is a collection of utility routines for general data manipulation and input preparation and considerably extends the usefulness of the system through the automatic generation of adjoint sources, estimated perturbed responses, and relative data sensitivity coefficients. Combined, the DEPTH-CHARGE system provides, for the first time, a complete generalized first-order perturbation/sensitivity theory capability for both static and time-dependent analyses of realistic multidimensional reactor models. This current documentation incorporates minor revisions to the original DEPTH-CHARGE documentation (ORNL/CSD-78) to reflect some new capabilities within the individual codes.

The Correlation between Insertion Depth of Prodisc-C Artificial Disc and Postoperative Kyphotic Deformity: Clinical Importance of Insertion Depth of Artificial Disc.

Science.gov (United States)

Lee, Do-Youl; Kim, Se-Hoon; Suh, Jung-Keun; Cho, Tai-Hyoung; Chung, Yong-Gu

2012-09-01

This study was designed to investigate the correlation between insertion depth of artificial disc and postoperative kyphotic deformity after Prodisc-C total disc replacement surgery, and the range of artificial disc insertion depth which is effective in preventing postoperative whole cervical or segmental kyphotic deformity. A retrospective radiological analysis was performed in 50 patients who had undergone single level total disc replacement surgery. Records were reviewed to obtain demographic data. Preoperative and postoperative radiographs were assessed to determine C2-7 Cobb's angle and segmental angle and to investigate postoperative kyphotic deformity. A formula was introduced to calculate insertion depth of Prodisc-C artificial disc. Statistical analysis was performed to search the correlation between insertion depth of Prodisc-C artificial disc and postoperative kyphotic deformity, and to estimate insertion depth of Prodisc-C artificial disc to prevent postoperative kyphotic deformity. In this study no significant statistical correlation was observed between insertion depth of Prodisc-C artificial disc and postoperative kyphotic deformity regarding C2-7 Cobb's angle. Statistical correlation between insertion depth of Prodisc-C artificial disc and postoperative kyphotic deformity was observed regarding segmental angle (p<0.05). It failed to estimate proper insertion depth of Prodisc-C artificial disc effective in preventing postoperative kyphotic deformity. Postoperative segmental kyphotic deformity is associated with insertion depth of Prodisc-C artificial disc. Anterior located artificial disc leads to lordotic segmental angle and posterior located artificial disc leads to kyphotic segmental angle postoperatively. But C2-7 Cobb's angle is not affected by artificial disc location after the surgery.

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.

Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth.

Science.gov (United States)

Brown, Alastair; Thatje, Sven

2014-05-01

Bathymetric biodiversity patterns of marine benthic invertebrates and demersal fishes have been identified in the extant fauna of the deep continental margins. Depth zonation is widespread and evident through a transition between shelf and slope fauna from the shelf break to 1000 m, and a transition between slope and abyssal fauna from 2000 to 3000 m; these transitions are characterised by high species turnover. A unimodal pattern of diversity with depth peaks between 1000 and 3000 m, despite the relatively low area represented by these depths. Zonation is thought to result from the colonisation of the deep sea by shallow-water organisms following multiple mass extinction events throughout the Phanerozoic. The effects of low temperature and high pressure act across hierarchical levels of biological organisation and appear sufficient to limit the distributions of such shallow-water species. Hydrostatic pressures of bathyal depths have consistently been identified experimentally as the maximum tolerated by shallow-water and upper bathyal benthic invertebrates at in situ temperatures, and adaptation appears required for passage to deeper water in both benthic invertebrates and demersal fishes. Together, this suggests that a hyperbaric and thermal physiological bottleneck at bathyal depths contributes to bathymetric zonation. The peak of the unimodal diversity-depth pattern typically occurs at these depths even though the area represented by these depths is relatively low. Although it is recognised that, over long evolutionary time scales, shallow-water diversity patterns are driven by speciation, little consideration has been given to the potential implications for species distribution patterns with depth. Molecular and morphological evidence indicates that cool bathyal waters are the primary site of adaptive radiation in the deep sea, and we hypothesise that bathymetric variation in speciation rates could drive the unimodal diversity-depth pattern over time. Thermal

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 ...

Inferring river bathymetry via Image-to-Depth Quantile Transformation (IDQT)

Science.gov (United States)

Legleiter, Carl

2016-01-01

Conventional, regression-based methods of inferring depth from passive optical image data undermine the advantages of remote sensing for characterizing river systems. This study introduces and evaluates a more flexible framework, Image-to-Depth Quantile Transformation (IDQT), that involves linking the frequency distribution of pixel values to that of depth. In addition, a new image processing workflow involving deep water correction and Minimum Noise Fraction (MNF) transformation can reduce a hyperspectral data set to a single variable related to depth and thus suitable for input to IDQT. Applied to a gravel bed river, IDQT avoided negative depth estimates along channel margins and underpredictions of pool depth. Depth retrieval accuracy (R25 0.79) and precision (0.27 m) were comparable to an established band ratio-based method, although a small shallow bias (0.04 m) was observed. Several ways of specifying distributions of pixel values and depths were evaluated but had negligible impact on the resulting depth estimates, implying that IDQT was robust to these implementation details. In essence, IDQT uses frequency distributions of pixel values and depths to achieve an aspatial calibration; the image itself provides information on the spatial distribution of depths. The approach thus reduces sensitivity to misalignment between field and image data sets and allows greater flexibility in the timing of field data collection relative to image acquisition, a significant advantage in dynamic channels. IDQT also creates new possibilities for depth retrieval in the absence of field data if a model could be used to predict the distribution of depths within a reach.

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

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)

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)

Three dimensional live-cell STED microscopy at increased depth using a water immersion objective

Science.gov (United States)

Heine, Jörn; Wurm, Christian A.; Keller-Findeisen, Jan; Schönle, Andreas; Harke, Benjamin; Reuss, Matthias; Winter, Franziska R.; Donnert, Gerald

2018-05-01

Modern fluorescence superresolution microscopes are capable of imaging living cells on the nanometer scale. One of those techniques is stimulated emission depletion (STED) which increases the microscope's resolution many times in the lateral and the axial directions. To achieve these high resolutions not only close to the coverslip but also at greater depths, the choice of objective becomes crucial. Oil immersion objectives have frequently been used for STED imaging since their high numerical aperture (NA) leads to high spatial resolutions. But during live-cell imaging, especially at great penetration depths, these objectives have a distinct disadvantage. The refractive index mismatch between the immersion oil and the usually aqueous embedding media of living specimens results in unwanted spherical aberrations. These aberrations distort the point spread functions (PSFs). Notably, during z- and 3D-STED imaging, the resolution increase along the optical axis is majorly hampered if at all possible. To overcome this limitation, we here use a water immersion objective in combination with a spatial light modulator for z-STED measurements of living samples at great depths. This compact design allows for switching between objectives without having to adapt the STED beam path and enables on the fly alterations of the STED PSF to correct for aberrations. Furthermore, we derive the influence of the NA on the axial STED resolution theoretically and experimentally. We show under live-cell imaging conditions that a water immersion objective leads to far superior results than an oil immersion objective at penetration depths of 5-180 μm.

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,...

Effect of insertion depth on helical antenna performance in a muscle-equivalent phantom

Energy Technology Data Exchange (ETDEWEB)

Reeves, J W; Meeson, S; Birch, M J [Department of Clinical Physics, Royal London Hospital, 56-76 Ashfield Street, London, E1 1BB (United Kingdom)

2005-06-21

Barrett's oesophagus is considered to increase the risk of cancer 30 fold. A set of helical microwave antennas was designed to investigate their potential use in the thermal therapy of Barrett's oesophagus. For treatment, a balloon filled with muscle-equivalent material encapsulates the antenna. The effects of insertion depth and coil-spacing on the thermal distribution produced by the antennas (20-35 mm) were characterized. The 35 mm helical antenna, with a coil-spacing of 3.6 mm resulted in uniform heating for an insertion depth of 40 mm. It was observed that the resultant temperature distribution produced, by the antennas, was dependent on the insertion depth within the phantom. For all antennas studied, deeper insertion resulted in two high intensity regions, approximately 1/4 and 3/4 along the antenna length. In contrast, shallow insertion resulted in predominant tip heating with undesirable heating at the phantom entry point. However, by manipulating the coil-spacing of the helix, uniform temperature profiles were achieved for a range of insertion depths.

Re- and Demineralization Characteristics of Enamel Depending on Baseline Mineral Loss and Lesion Depth in situ.

Science.gov (United States)

Wierichs, Richard J; Lausch, Julian; Meyer-Lueckel, Hendrik; Esteves-Oliveira, Marcella

2016-01-01

The aim of this double-blinded, randomized, cross-over in situ study was to evaluate the re- and demineralization characteristics of sound enamel as well as lowly and highly demineralized caries-like enamel lesions after the application of different fluoride compounds. In each of three experimental legs of 4 weeks, 21 participants wore intraoral mandibular appliances containing 4 bovine enamel specimens (2 lowly and 2 highly demineralized). Each specimen included one sound enamel and either one lowly demineralized (7 days, pH 4.95) or one highly demineralized (21 days, pH 4.95) lesion, and was positioned 1 mm below the acrylic under a plastic mesh. The three randomly allocated treatments (application only) included the following dentifrices: (1) 1,100 ppm F as NaF, (2) 1,100 ppm F as SnF2 and (3) 0 ppm F (fluoride-free) as negative control. Differences in integrated mineral loss (x0394;x0394;Z) and lesion depth (x0394;LD) were calculated between values before and after the in situ period using transversal microradiography. Of the 21 participants, 6 did not complete the study and 2 were excluded due to protocol violation. Irrespectively of the treatment, higher baseline mineral loss and lesion depth led to a less pronounced change in mineral loss and lesion depth. Except for x0394;x0394;Z of the dentifrice with 0 ppm F, sound surfaces showed significantly higher x0394;x0394;Z and x0394;LD values compared with lowly and highly demineralized lesions (p test). Re- and demineralization characteristics of enamel depended directly on baseline mineral loss and lesion depth. Treatment groups should therefore be well balanced with respect to baseline mineral loss and lesion depth. © 2016 S. Karger AG, Basel.

An optical fiber expendable seawater temperature/depth profile sensor

Science.gov (United States)

Zhao, Qiang; Chen, Shizhe; Zhang, Keke; Yan, Xingkui; Yang, Xianglong; Bai, Xuejiao; Liu, Shixuan

2017-10-01

Marine expendable temperature/depth profiler (XBT) is a disposable measuring instrument which can obtain temperature/depth profile data quickly in large area waters and mainly used for marine surveys, scientific research, military application. The temperature measuring device is a thermistor in the conventional XBT probe (CXBT)and the depth data is only a calculated value by speed and time depth calculation formula which is not an accurate measurement result. Firstly, an optical fiber expendable temperature/depth sensor based on the FBG-LPG cascaded structure is proposed to solve the problems of the CXBT, namely the use of LPG and FBG were used to detect the water temperature and depth, respectively. Secondly, the fiber end reflective mirror is used to simplify optical cascade structure and optimize the system performance. Finally, the optical path is designed and optimized using the reflective optical fiber end mirror. The experimental results show that the sensitivity of temperature and depth sensing based on FBG-LPG cascade structure is about 0.0030C and 0.1%F.S. respectively, which can meet the requirements of the sea water temperature/depth observation. The reflectivity of reflection mirror is in the range from 48.8% to 72.5%, the resonant peak of FBG and LPG are reasonable and the whole spectrum are suitable for demodulation. Through research on the optical fiber XBT (FXBT), the direct measurement of deep-sea temperature/depth profile data can be obtained simultaneously, quickly and accurately. The FXBT is a new all-optical seawater temperature/depth sensor, which has important academic value and broad application prospect and is expected to replace the CXBT in the future.

Alternate approach for calculating hardness based on residual indentation depth: Comparison with experiments

Science.gov (United States)

Ananthakrishna, G.; K, Srikanth

2018-03-01

It is well known that plastic deformation is a highly nonlinear dissipative irreversible phenomenon of considerable complexity. As a consequence, little progress has been made in modeling some well-known size-dependent properties of plastic deformation, for instance, calculating hardness as a function of indentation depth independently. Here, we devise a method of calculating hardness by calculating the residual indentation depth and then calculate the hardness as the ratio of the load to the residual imprint area. Recognizing the fact that dislocations are the basic defects controlling the plastic component of the indentation depth, we set up a system of coupled nonlinear time evolution equations for the mobile, forest, and geometrically necessary dislocation densities. Within our approach, we consider the geometrically necessary dislocations to be immobile since they contribute to additional hardness. The model includes dislocation multiplication, storage, and recovery mechanisms. The growth of the geometrically necessary dislocation density is controlled by the number of loops that can be activated under the contact area and the mean strain gradient. The equations are then coupled to the load rate equation. Our approach has the ability to adopt experimental parameters such as the indentation rates, the geometrical parameters defining the Berkovich indenter, including the nominal tip radius. The residual indentation depth is obtained by integrating the Orowan expression for the plastic strain rate, which is then used to calculate the hardness. Consistent with the experimental observations, the increasing hardness with decreasing indentation depth in our model arises from limited dislocation sources at small indentation depths and therefore avoids divergence in the limit of small depths reported in the Nix-Gao model. We demonstrate that for a range of parameter values that physically represent different materials, the model predicts the three characteristic

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.

Depth-encoded all-fiber swept source polarization sensitive OCT

Science.gov (United States)

Wang, Zhao; Lee, Hsiang-Chieh; Ahsen, Osman Oguz; Lee, ByungKun; Choi, WooJhon; Potsaid, Benjamin; Liu, Jonathan; Jayaraman, Vijaysekhar; Cable, Alex; Kraus, Martin F.; Liang, Kaicheng; Hornegger, Joachim; Fujimoto, James G.

2014-01-01

Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of conventional OCT and can assess depth-resolved tissue birefringence in addition to intensity. Most existing PS-OCT systems are relatively complex and their clinical translation remains difficult. We present a simple and robust all-fiber PS-OCT system based on swept source technology and polarization depth-encoding. Polarization multiplexing was achieved using a polarization maintaining fiber. Polarization sensitive signals were detected using fiber based polarization beam splitters and polarization controllers were used to remove the polarization ambiguity. A simplified post-processing algorithm was proposed for speckle noise reduction relaxing the demand for phase stability. We demonstrated systems design for both ophthalmic and catheter-based PS-OCT. For ophthalmic imaging, we used an optical clock frequency doubling method to extend the imaging range of a commercially available short cavity light source to improve polarization depth-encoding. For catheter based imaging, we demonstrated 200 kHz PS-OCT imaging using a MEMS-tunable vertical cavity surface emitting laser (VCSEL) and a high speed micromotor imaging catheter. The system was demonstrated in human retina, finger and lip imaging, as well as ex vivo swine esophagus and cardiovascular imaging. The all-fiber PS-OCT is easier to implement and maintain compared to previous PS-OCT systems and can be more easily translated to clinical applications due to its robust design. PMID:25401008

Limit-order book resiliency after effective market orders: spread, depth and intensity

Science.gov (United States)

Xu, Hai-Chuan; Chen, Wei; Xiong, Xiong; Zhang, Wei; Zhou, Wei-Xing; Stanley, H. Eugene

2017-07-01

In order-driven markets, limit-order book (LOB) resiliency is an important microscopic indicator of market quality when the order book is hit by a liquidity shock and plays an essential role in the design of optimal submission strategies of large orders. However, the evolutionary behavior of LOB resilience around liquidity shocks is not well understood empirically. Using order flow data sets of Chinese stocks, we quantify and compare the LOB dynamics characterized by the bid-ask spread, the LOB depth and the order intensity surrounding effective market orders with different aggressiveness. We find that traders are more likely to submit effective market orders when the spreads are relatively low, the same-side depth is high, and the opposite-side depth is low. Such phenomenon is especially significant when the initial spread is 1 tick. Although the resiliency patterns show obvious diversity after different types of market orders, the spread and depth can return to the sample average within 20 best limit updates. The price resiliency behavior is dominant following aggressive market buy orders, while the price continuation behavior is dominant following less-aggressive market sell orders. Moreover, the resiliency stimulus of buy-sell shock is asymmetrical. The intensities of limit sell orders after market buy orders’ shock are always higher than the intensities of limit buy orders after market sell orders’ shock. The resiliency behavior of spread and depth is linked to limit order intensity.

Depth Measurement Based on Infrared Coded Structured Light

Directory of Open Access Journals (Sweden)

Tong Jia

2014-01-01

Full Text Available Depth measurement is a challenging problem in computer vision research. In this study, we first design a new grid pattern and develop a sequence coding and decoding algorithm to process the pattern. Second, we propose a linear fitting algorithm to derive the linear relationship between the object depth and pixel shift. Third, we obtain depth information on an object based on this linear relationship. Moreover, 3D reconstruction is implemented based on Delaunay triangulation algorithm. Finally, we utilize the regularity of the error curves to correct the system errors and improve the measurement accuracy. The experimental results show that the accuracy of depth measurement is related to the step length of moving object.

Multiview Depth-Image Compression Using an Extended H.264 Encoder

NARCIS (Netherlands)

Morvan, Y.; Farin, D.S.; With, de P.H.N.; Blanc-Talon, J.; Philips, W.

2007-01-01

This paper presents a predictive-coding algorithm for the compression of multiple depth-sequences obtained from a multi-camera acquisition setup. The proposed depth-prediction algorithm works by synthesizing a virtual depth-image that matches the depth-image (of the predicted camera). To generate

Auditory sensitivity to spectral modulation phase reversal as a function of modulation depth.

Science.gov (United States)

Buss, Emily; Grose, John

2018-01-01

The present study evaluated auditory sensitivity to spectral modulation by determining the modulation depth required to detect modulation phase reversal. This approach may be preferable to spectral modulation detection with a spectrally flat standard, since listeners appear unable to perform the task based on the detection of temporal modulation. While phase reversal thresholds are often evaluated by holding modulation depth constant and adjusting modulation rate, holding rate constant and adjusting modulation depth supports rate-specific assessment of modulation processing. Stimuli were pink noise samples, filtered into seven octave-wide bands (0.125-8 kHz) and spectrally modulated in dB. Experiment 1 measured performance as a function of modulation depth to determine appropriate units for adaptive threshold estimation. Experiment 2 compared thresholds in dB for modulation detection with a flat standard and modulation phase reversal; results supported the idea that temporal cues were available at high rates for the former but not the latter. Experiment 3 evaluated spectral modulation phase reversal thresholds for modulation that was restricted to either one or two neighboring bands. Flanking bands of unmodulated noise had a larger detrimental effect on one-band than two-band targets. Thresholds for high-rate modulation improved with increasing carrier frequency up to 2 kHz, whereas low-rate modulation appeared more consistent across frequency, particularly in the two-band condition. Experiment 4 measured spectral weights for spectral modulation phase reversal detection and found higher weights for bands in the spectral center of the stimulus than for the lowest (0.125 kHz) or highest (8 kHz) band. Experiment 5 compared performance for highly practiced and relatively naïve listeners, and found weak evidence of a larger practice effect at high than low spectral modulation rates. These results provide preliminary data for a task that may provide a better estimate of

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

The maximum economic depth of groundwater abstraction for irrigation

Science.gov (United States)

Bierkens, M. F.; Van Beek, L. P.; de Graaf, I. E. M.; Gleeson, T. P.

2017-12-01

Over recent decades, groundwater has become increasingly important for agriculture. Irrigation accounts for 40% of the global food production and its importance is expected to grow further in the near future. Already, about 70% of the globally abstracted water is used for irrigation, and nearly half of that is pumped groundwater. In many irrigated areas where groundwater is the primary source of irrigation water, groundwater abstraction is larger than recharge and we see massive groundwater head decline in these areas. An important question then is: to what maximum depth can groundwater be pumped for it to be still economically recoverable? The objective of this study is therefore to create a global map of the maximum depth of economically recoverable groundwater when used for irrigation. The maximum economic depth is the maximum depth at which revenues are still larger than pumping costs or the maximum depth at which initial investments become too large compared to yearly revenues. To this end we set up a simple economic model where costs of well drilling and the energy costs of pumping, which are a function of well depth and static head depth respectively, are compared with the revenues obtained for the irrigated crops. Parameters for the cost sub-model are obtained from several US-based studies and applied to other countries based on GDP/capita as an index of labour costs. The revenue sub-model is based on gross irrigation water demand calculated with a global hydrological and water resources model, areal coverage of crop types from MIRCA2000 and FAO-based statistics on crop yield and market price. We applied our method to irrigated areas in the world overlying productive aquifers. Estimated maximum economic depths range between 50 and 500 m. Most important factors explaining the maximum economic depth are the dominant crop type in the area and whether or not initial investments in well infrastructure are limiting. In subsequent research, our estimates of

Fossil intermediate-depth earthquakes in subducting slabs linked to differential stress release

Science.gov (United States)

Scambelluri, Marco; Pennacchioni, Giorgio; Gilio, Mattia; Bestmann, Michel; Plümper, Oliver; Nestola, Fabrizio

2017-12-01

The cause of intermediate-depth (50-300 km) seismicity in subduction zones is uncertain. It is typically attributed either to rock embrittlement associated with fluid pressurization, or to thermal runaway instabilities. Here we document glassy pseudotachylyte fault rocks—the products of frictional melting during coseismic faulting—in the Lanzo Massif ophiolite in the Italian Western Alps. These pseudotachylytes formed at subduction-zone depths of 60-70 km in poorly hydrated to dry oceanic gabbro and mantle peridotite. This rock suite is a fossil analogue to an oceanic lithospheric mantle that undergoes present-day subduction. The pseudotachylytes locally preserve high-pressure minerals that indicate an intermediate-depth seismic environment. These pseudotachylytes are important because they are hosted in a near-anhydrous lithosphere free of coeval ductile deformation, which excludes an origin by dehydration embrittlement or thermal runaway processes. Instead, our observations indicate that seismicity in cold subducting slabs can be explained by the release of differential stresses accumulated in strong dry metastable rocks.

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.

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.

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)

Electrochemical depth profiling of multilayer metallic structures: An aluminum brazing sheet

International Nuclear Information System (INIS)

Afshar, F. Norouzi; Ambat, R.; Kwakernaak, C.; Wit, J.H.W. de; Mol, J.M.C.; Terryn, H.

2012-01-01

Highlights: ► Localized electrochemical cell and glow discharge optical emission spectrometry were used. ► An electrochemical depth profile of an aluminum brazing sheet was obtained. ► The electrochemical responses were correlated to the microstructural features. - Abstract: Combinatory localized electrochemical cell and glow discharge optical emission spectrometry (GDOES) measurements were performed to obtain a thorough in depth electrochemical characterization of an aluminum brazing sheet. By defining electrochemical criteria i.e. breakdown potential, corrosion potential, cathodic and anodic reactivities, and tracking their changes as a function of depth, the evolution of electrochemical responses through out the material thickness were analyzed and correlated to the corresponding microstructural features. Polarization curves in 1 wt% NaCl solution at pH 2.8 were obtained at different depths from the surface using controlled sputtering in a glow discharge optical emission spectrometer as a sample preparation technique. The anodic and cathodic reactivity of the top surface areas were significantly higher than that of the bulk, thus indicating these areas to be more susceptible to localized attack. Consistent with this, optical microscopy and scanning electron microscope analysis revealed a relatively high density of fine intermetallic and silicon particles at these areas. The corrosion mechanism of the top layers was identified to be intergranular and pitting corrosion, while lower sensitivity to these localized attacks were detected toward the brazing sheet core. The results highlight the successful application of the electrochemical depth profiling approach in prediction of the corrosion behavior of the aluminum brazing sheet and the importance of the electrochemical activity of the outer 10 μm in controlling the corrosion performance of the aluminum brazing sheet.

Depth discrimination in acousto-optic cerebral blood flow measurement simulation

Science.gov (United States)

Tsalach, A.; Schiffer, Z.; Ratner, E.; Breskin, I.; Zeitak, R.; Shechter, R.; Balberg, M.

2016-03-01

Monitoring cerebral blood flow (CBF) is crucial, as inadequate perfusion, even for relatively short periods of time, may lead to brain damage or even death. Thus, significant research efforts are directed at developing reliable monitoring tools that will enable continuous, bed side, simple and cost-effective monitoring of CBF. All existing non invasive bed side monitoring methods, which are mostly NIRS based, such as Laser Doppler or DCS, tend to underestimate CBF in adults, due to the indefinite effect of extra-cerebral tissues on the obtained signal. If those are to find place in day to day clinical practice, the contribution of extra-cerebral tissues must be eliminated and data from the depth (brain) should be extracted and discriminated. Recently, a novel technique, based on ultrasound modulation of light was developed for non-invasive, continuous CBF monitoring (termed ultrasound-tagged light (UTL or UT-NIRS)), and shown to correlate with readings of 133Xe SPECT and laser Doppler. We have assembled a comprehensive computerized simulation, modeling this acousto-optic technique in a highly scattering media. Using the combination of light and ultrasound, we show how depth information may be extracted, thus distinguishing between flow patterns taking place at different depths. Our algorithm, based on the analysis of light modulated by ultrasound, is presented and examined in a computerized simulation. Distinct depth discrimination ability is presented, suggesting that using such method one can effectively nullify the extra-cerebral tissues influence on the obtained signals, and specifically extract cerebral flow data.

Matching and correlation computations in stereoscopic depth perception.

Science.gov (United States)

Doi, Takahiro; Tanabe, Seiji; Fujita, Ichiro

2011-03-02

A fundamental task of the visual system is to infer depth by using binocular disparity. To encode binocular disparity, the visual cortex performs two distinct computations: one detects matched patterns in paired images (matching computation); the other constructs the cross-correlation between the images (correlation computation). How the two computations are used in stereoscopic perception is unclear. We dissociated their contributions in near/far discrimination by varying the magnitude of the disparity across separate sessions. For small disparity (0.03°), subjects performed at chance level to a binocularly opposite-contrast (anti-correlated) random-dot stereogram (RDS) but improved their performance with the proportion of contrast-matched (correlated) dots. For large disparity (0.48°), the direction of perceived depth reversed with an anti-correlated RDS relative to that for a correlated one. Neither reversed nor normal depth was perceived when anti-correlation was applied to half of the dots. We explain the decision process as a weighted average of the two computations, with the relative weight of the correlation computation increasing with the disparity magnitude. We conclude that matching computation dominates fine depth perception, while both computations contribute to coarser depth perception. Thus, stereoscopic depth perception recruits different computations depending on the disparity magnitude.

Estimation of optimal nasotracheal tube depth in adult patients.

Science.gov (United States)

Ji, Sung-Mi

2017-12-01

The aim of this study was to estimate the optimal depth of nasotracheal tube placement. We enrolled 110 patients scheduled to undergo oral and maxillofacial surgery, requiring nasotracheal intubation. After intubation, the depth of tube insertion was measured. The neck circumference and distances from nares to tragus, tragus to angle of the mandible, and angle of the mandible to sternal notch were measured. To estimate optimal tube depth, correlation and regression analyses were performed using clinical and anthropometric parameters. The mean tube depth was 28.9 ± 1.3 cm in men (n = 62), and 26.6 ± 1.5 cm in women (n = 48). Tube depth significantly correlated with height (r = 0.735, P < 0.001). Distances from nares to tragus, tragus to angle of the mandible, and angle of the mandible to sternal notch correlated with depth of the endotracheal tube (r = 0.363, r = 0.362, and r = 0.546, P < 0.05). The tube depth also correlated with the sum of these distances (r = 0.646, P < 0.001). We devised the following formula for estimating tube depth: 19.856 + 0.267 × sum of the three distances (R 2 = 0.432, P < 0.001). The optimal tube depth for nasotracheally intubated adult patients correlated with height and sum of the distances from nares to tragus, tragus to angle of the mandible, and angle of the mandible to sternal notch. The proposed equation would be a useful guide to determine optimal nasotracheal tube placement.

Constraining the CMB optical depth through the dispersion measure of cosmological radio transients

International Nuclear Information System (INIS)

Fialkov, A.; Loeb, A.

2016-01-01

The dispersion measure of extragalactic radio transients can be used to measure the column density of free electrons in the intergalactic medium. The same electrons also scatter the Cosmic Microwave Background (CMB) photons, affecting precision measurements of cosmological parameters. We explore the connection between the dispersion measure of radio transients existing during the Epoch of Reionization (EoR) and the total optical depth for the CMB showing that the existence of such transients would provide a new sensitive probe of the CMB optical depth. As an example, we consider the population of FRBs. Assuming they exist during the EoR, we show that: (i) such sources can probe the reionization history by measuring the optical depth to sub-percent accuracy, and (ii) they can be detected with high significance by an instrument such as the Square Kilometer Array.

Constraining the CMB optical depth through the dispersion measure of cosmological radio transients

Energy Technology Data Exchange (ETDEWEB)

Fialkov, A.; Loeb, A., E-mail: anastasia.fialkov@cfa.harvard.edu, E-mail: aloeb@cfa.harvard.edu [Institute for Teory and Computation, Harvard University, 60 Garden Street, MS-51, Cambridge, MA, 02138 (United States)

2016-05-01

The dispersion measure of extragalactic radio transients can be used to measure the column density of free electrons in the intergalactic medium. The same electrons also scatter the Cosmic Microwave Background (CMB) photons, affecting precision measurements of cosmological parameters. We explore the connection between the dispersion measure of radio transients existing during the Epoch of Reionization (EoR) and the total optical depth for the CMB showing that the existence of such transients would provide a new sensitive probe of the CMB optical depth. As an example, we consider the population of FRBs. Assuming they exist during the EoR, we show that: (i) such sources can probe the reionization history by measuring the optical depth to sub-percent accuracy, and (ii) they can be detected with high significance by an instrument such as the Square Kilometer Array.

Magnitude, precision, and realism of depth perception in stereoscopic vision.

Science.gov (United States)

Hibbard, Paul B; Haines, Alice E; Hornsey, Rebecca L

2017-01-01

Our perception of depth is substantially enhanced by the fact that we have binocular vision. This provides us with more precise and accurate estimates of depth and an improved qualitative appreciation of the three-dimensional (3D) shapes and positions of objects. We assessed the link between these quantitative and qualitative aspects of 3D vision. Specifically, we wished to determine whether the realism of apparent depth from binocular cues is associated with the magnitude or precision of perceived depth and the degree of binocular fusion. We presented participants with stereograms containing randomly positioned circles and measured how the magnitude, realism, and precision of depth perception varied with the size of the disparities presented. We found that as the size of the disparity increased, the magnitude of perceived depth increased, while the precision with which observers could make depth discrimination judgments decreased. Beyond an initial increase, depth realism decreased with increasing disparity magnitude. This decrease occurred well below the disparity limit required to ensure comfortable viewing.

Non-destructive microstructural analysis with depth resolution

Energy Technology Data Exchange (ETDEWEB)

Zolotoyabko, E. E-mail: zloto@tx.technion.ac.il; Quintana, J.P

2003-01-01

A depth-sensitive X-ray diffraction technique has been developed with the aim of studying microstructural modifications in inhomogeneous polycrystalline materials. In that method, diffraction profiles are measured at different X-ray energies varied by small steps. X-rays at higher energies probe deeper layers of material. Depth-resolved structural information is retrieved by comparing energy-dependent diffraction profiles. The method provides non-destructive depth profiling of the preferred orientation, grain size, microstrain fluctuations and residual strains. This technique is applied to the characterization of seashells. Similarly, energy-variable X-ray diffraction can be used for the non-destructive characterization of different laminated structures and composite materials.

Deuterium Depth Profile in Neutron-Irradiated Tungsten Exposed to Plasma

International Nuclear Information System (INIS)

Shimada, Masashi; Cao, G.; Hatano, Y.; Oda, T.; Oya, Y.; Hara, M.; Calderoni, P.

2011-01-01

The effect of radiation damage has been mainly simulated using high-energy ion bombardment. The ions, however, are limited in range to only a few microns into the surface. Hence, some uncertainty remains about the increase of trapping at radiation damage produced by 14 MeV fusion neutrons, which penetrate much farther into the bulk material. With the Japan-US joint research project: Tritium, Irradiations, and Thermofluids for America and Nippon (TITAN), the tungsten samples (99.99 % pure from A.L.M.T., 6mm in diameter, 0.2mm in thickness) were irradiated to high flux neutrons at 50 C and to 0.025 dpa in the High Flux Isotope Reactor (HFIR) at the Oak Ridge National Laboratory (ORNL). Subsequently, the neutron-irradiated tungsten samples were exposed to a high-flux deuterium plasma (ion flux: 1021-1022 m-2s-1, ion fluence: 1025-1026 m-2) in the Tritium Plasma Experiment (TPE) at the Idaho National Laboratory (INL). First results of deuterium retention in neutron-irradiated tungsten exposed in TPE have been reported previously. This paper presents the latest results in our on-going work of deuterium depth profiling in neutron-irradiated tungsten via nuclear reaction analysis. The experimental data is compared with the result from non neutron-irradiated tungsten, and is analyzed with the Tritium Migration Analysis Program (TMAP) to elucidate the hydrogen isotope behavior such as retention and depth distribution in neutron-irradiated and non neutron-irradiated tungsten.

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.

Spatial resolution in depth-controlled surface sensitive x-ray techniques

International Nuclear Information System (INIS)

Yun, W.B.; Viccaro, P.J.

1992-01-01

The spatial resolution along the surface normal and the total depth probed are two important parameters in depth-controlled surface sensitive X-ray techniques employing grazing incidence geometry. The two parameters are analyzed in terms of optical properties (refractive indices) of the media involved and parameters of the incident X-ray beam: beam divergence, X-ray energy, and spectral bandwidth. We derive analytical expressions of the required beam divergence and spectral bandwidth of the incident beam as a function of the two parameters. Sample calculations are made for X-ray energies between 0.1 and 100 keV and for solid Be, Cu, and Au, representing material matrices consisting of low, medium, and high atomic number elements. A brief discussion on obtaining the required beam divergence and spectral bandwidth from present X-ray sources and optics is given

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.

Defence in Depth: Assessment of Comprehensiveness and Further Strengthening of the Concept

Energy Technology Data Exchange (ETDEWEB)

Misak, J., E-mail: Jozef.Misak@ujv.cz

2014-10-15

Full text: Defence in depth concept based on multiple levels of protection of the workers, public and the environment against radiation harm is and should remain an essential strategy for ensuring safety of nuclear power plants. This strategy should be comprehensively implemented through all stages of the plant lifetime, from the siting through construction and operation up to decommissioning. First part of the presentation will introduce a screening method developed by the IAEA as a tool facilitating the assessment of the comprehensiveness of defence in depth and will indicate further possibilities for using and updating the approach by taking into account recent lessons learned. Although it is clear that it is not possible for any industrial facility including nuclear power plants to fully eliminate the risk, further strengthening the defence in depth in particular at level 4 dealing with design extension conditions gives very high confidence in prevention and effective mitigation of severe accidents so that they are either practically eliminated or their consequences are limited in area and time. Second part of the presentation will discuss several issues associated with current efforts for strengthening the defence in depth, including the issues of practical elimination, independence and diversity of safety provisions at different levels of defence. (author)

The Influence of Observer's Voluntary Action on Perception of Kinetic Depth Display

Directory of Open Access Journals (Sweden)

Daishi Nakamura

2011-05-01

Full Text Available A 3D object such as plural points distributed in 3D space appears flat when rear projected onto a translucent screen. Its 3D shape becomes apparent when it is rotated about an axis parallel to the screen (KDE. The relative motion of the points gives depth information but perspective information is not present. So, the relative depth of points can be perceived but not their depth order. It is impossible to tell which is the front and which is the back of the objects. The 3D object is ambiguous with respect to its reflection in the projection plane. As a result the object periodically appears to reverse in depth as well as direction of rotation. This study investigated if observer's manual control for the stimulus change removes ambiguity of KDE. In the experiment, the stimulus change was coincided with the rotation of a crank handle rotated rightward or leftward by the observer. The result showed that manual control considerably removed the ambiguity: the perceived direction of rotation from KDE coincided the manual control at a high rate. Prolonged viewing, however, made reverse the apparent rotation. We measured duration of initial rotation. The manual control extended the mean duration.

Application of Microtremor Array Analysis to Estimate the Bedrock Depth in the Beijing Plain area

Science.gov (United States)

Xu, P.; Ling, S.; Liu, J.; Su, W.

2013-12-01

With the rapid expansion of large cities around the world, urban geological survey provides key information regarding resource development and urban construction. Among the major cities of the world, China's capital city Beijing is among the largest cities possessing complex geological structures. The urban geological survey and study in Beijing involves the following aspects: (1) estimating the thickness of the Cenozoic deposit; (2) mapping the three-dimensional structure of the underlying bedrock, as well as its relations to faults and tectonic settings; and (3) assessing the capacity of the city's geological resources in order to support its urban development and operation safety. The geological study of Beijing in general was also intended to provide basic data regarding the urban development and appraisal of engineering and environment geological conditions, as well as underground space resources. In this work, we utilized the microtremor exploration method to estimate the thickness of the bedrock depth, in order to delineate the geological interfaces and improve the accuracy of the bedrock depth map. The microtremor observation sites were located in the Beijing Plain area. Traditional geophysical or geological survey methods were not effective in these areas due to the heavy traffic and dense buildings in the highly-populated urban area. The microtremor exploration method is a Rayleigh-wave inversion technique which extracts its phase velocity dispersion curve from the vertical component of the microtremor array records using the spatial autocorrelation (SPAC) method, then inverts the shear-wave velocity structure. A triple-circular array was adopted for acquiring microtremor data, with the observation radius in ranging from 40 to 300 m, properly adjusted depending on the geological conditions (depth of the bedrock). The collected microtremor data are used to: (1) estimation of phase velocities of Rayleigh-wave from the vertical components of the microtremor

Depth control of a silicon structure fabricated by 100q keV Ar ion beam lithography

Energy Technology Data Exchange (ETDEWEB)

Kawasegi, Noritaka [Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan)]. E-mail: kawasegi@eng.u-toyama.ac.jp; Morita, Noboru [Department of Mechanical and Intellectual Systems Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan)]. E-mail: nmorita@eng.u-toyama.ac.jp; Yamada, Shigeru [Department of Mechanical and Intellectual Systems Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan)]. E-mail: syamada@eng.u-toyama.ac.jp; Takano, Noboru [Department of Mechanical and Intellectual Systems Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan)]. E-mail: takano@eng.u-toyama.ac.jp; Oyama, Tatsuo [Department of Mechanical and Intellectual Systems Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555 (Japan)]. E-mail: ohyama@eng.u-toyama.ac.jp; Momota, Sadao [Department of Intelligent Mechanical Systems Engineering, Kochi University of Technology, 185 Tosayamada, Kami, Kochi 782-8502 (Japan)]. E-mail: momota.sadao@kochi-tech.ac.jp; Taniguchi, Jun [Department of Applied Electronics, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510 (Japan)]. E-mail: junt@te.noda.tus.ac.jp; Miyamoto, Iwao [Department of Applied Electronics, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510 (Japan)]. E-mail: iwao@te.noda.tus.ac.jp

2007-01-15

Ion beam lithography of a silicon surface using an Ar ion beam with an ion energy in the order of hundreds of keV is demonstrated in this study. A specially designed ion irradiation facility was employed that enabled generation and irradiation with a highly accelerated and highly charged Ar ion beam. An ion-beam-induced amorphous layer on a silicon substrate can be selectively etched in hydrofluoric acid, whereas, a non-irradiated area is scarcely etched and, consequently, a concave structure can be fabricated on the irradiated area. To control the depth of the structure, parameters for dependence of the depth on ion irradiation were investigated. As a result, the depth of irradiated area can be controlled by the ion energy that is adjusted by the acceleration voltage and the ion charge. In addition, the etch resistance of the irradiated area increases with an increase in ion energy due to the crystalline layer formed on the surface. Simulation results reveal that the depth is strongly related to the defect distribution induced by ion irradiation. These results indicate the potential use of this method for novel three-dimensional lithography.

Determination of in-depth contamination in concrete using a non-destructive technique

International Nuclear Information System (INIS)

Boden, S.; Cantrel, E.

2007-01-01

The decommissioning of the BR3 (Belgian Reactor 3) approaches its final phase, in which the building structures are being decontaminated and either denuclearized for possible reuse or demolished. Apart from the presence of naturally occurring radionuclides in building materials, other radionuclides might be present due to activation or contamination. The BR3 bioshield has been exposed to rather high neutron leakage fluxes during the reactor operation and is therefore activated. Building structure contamination usually results from leakages during reactor operation, releases due to maintenance works or even dismantling operations. In case of in-depth contamination in concrete it is important to know the exact in-depth profile before decontamination, in order to minimize the amount of radioactive waste that will be produced during the decontamination process and to optimize both the decontamination process and the final control measurements. Common non-destructive analyses used in decommissioning are usually based on the measurement of beta radiation, using e.g. hand-held plastic scintillators. This kind of measurement technique can not be used to determine in-depth contamination. Therefore, most of the decontamination specialists currently base themselves on the results of the radiological analysis of samples taken by core drilling. The use of such a destructive method implies a number of disadvantages: it is time consuming and therefore costly and the different sample preparation steps can conceivably lead to cross-contamination. Moreover, one only receives results of a limited number of points, while the in-depth contamination is usually very inhomogeneously distributed and the relationship between in-depth contamination and surface contamination and/or dose rate (hotspot detection) is generally rather poor.The objective therefore is to test the use of the ISOCS (In Situ Object Counting System) for the determination of contamination depth

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.

Forecasted Flood Depth Grids Providing Early Situational Awareness to FEMA during the 2017 Atlantic Hurricane Season

Science.gov (United States)

Jones, M.; Longenecker, H. E., III

2017-12-01

The 2017 hurricane season brought the unprecedented landfall of three Category 4 hurricanes (Harvey, Irma and Maria). FEMA is responsible for coordinating the federal response and recovery efforts for large disasters such as these. FEMA depends on timely and accurate depth grids to estimate hazard exposure, model damage assessments, plan flight paths for imagery acquisition, and prioritize response efforts. In order to produce riverine or coastal depth grids based on observed flooding, the methodology requires peak crest water levels at stream gauges, tide gauges, high water marks, and best-available elevation data. Because peak crest data isn't available until the apex of a flooding event and high water marks may take up to several weeks for field teams to collect for a large-scale flooding event, final observed depth grids are not available to FEMA until several days after a flood has begun to subside. Within the last decade NOAA's National Weather Service (NWS) has implemented the Advanced Hydrologic Prediction Service (AHPS), a web-based suite of accurate forecast products that provide hydrograph forecasts at over 3,500 stream gauge locations across the United States. These forecasts have been newly implemented into an automated depth grid script tool, using predicted instead of observed water levels, allowing FEMA access to flood hazard information up to 3 days prior to a flooding event. Water depths are calculated from the AHPS predicted flood stages and are interpolated at 100m spacing along NHD hydrolines within the basin of interest. A water surface elevation raster is generated from these water depths using an Inverse Distance Weighted interpolation. Then, elevation (USGS NED 30m) is subtracted from the water surface elevation raster so that the remaining values represent the depth of predicted flooding above the ground surface. This automated process requires minimal user input and produced forecasted depth grids that were comparable to post

Response of seasonal soil freeze depth to climate change across China

Science.gov (United States)

Peng, Xiaoqing; Zhang, Tingjun; Frauenfeld, Oliver W.; Wang, Kang; Cao, Bin; Zhong, Xinyue; Su, Hang; Mu, Cuicui

2017-05-01

The response of seasonal soil freeze depth to climate change has repercussions for the surface energy and water balance, ecosystems, the carbon cycle, and soil nutrient exchange. Despite its importance, the response of soil freeze depth to climate change is largely unknown. This study employs the Stefan solution and observations from 845 meteorological stations to investigate the response of variations in soil freeze depth to climate change across China. Observations include daily air temperatures, daily soil temperatures at various depths, mean monthly gridded air temperatures, and the normalized difference vegetation index. Results show that soil freeze depth decreased significantly at a rate of -0.18 ± 0.03 cm yr-1, resulting in a net decrease of 8.05 ± 1.5 cm over 1967-2012 across China. On the regional scale, soil freeze depth decreases varied between 0.0 and 0.4 cm yr-1 in most parts of China during 1950-2009. By investigating potential climatic and environmental driving factors of soil freeze depth variability, we find that mean annual air temperature and ground surface temperature, air thawing index, ground surface thawing index, and vegetation growth are all negatively associated with soil freeze depth. Changes in snow depth are not correlated with soil freeze depth. Air and ground surface freezing indices are positively correlated with soil freeze depth. Comparing these potential driving factors of soil freeze depth, we find that freezing index and vegetation growth are more strongly correlated with soil freeze depth, while snow depth is not significant. We conclude that air temperature increases are responsible for the decrease in seasonal freeze depth. These results are important for understanding the soil freeze-thaw dynamics and the impacts of soil freeze depth on ecosystem and hydrological process.

Temporal consistent depth map upscaling for 3DTV

Science.gov (United States)

Schwarz, Sebastian; Sjöström, Mârten; Olsson, Roger

2014-03-01

The ongoing success of three-dimensional (3D) cinema fuels increasing efforts to spread the commercial success of 3D to new markets. The possibilities of a convincing 3D experience at home, such as three-dimensional television (3DTV), has generated a great deal of interest within the research and standardization community. A central issue for 3DTV is the creation and representation of 3D content. Acquiring scene depth information is a fundamental task in computer vision, yet complex and error-prone. Dedicated range sensors, such as the Time­ of-Flight camera (ToF), can simplify the scene depth capture process and overcome shortcomings of traditional solutions, such as active or passive stereo analysis. Admittedly, currently available ToF sensors deliver only a limited spatial resolution. However, sophisticated depth upscaling approaches use texture information to match depth and video resolution. At Electronic Imaging 2012 we proposed an upscaling routine based on error energy minimization, weighted with edge information from an accompanying video source. In this article we develop our algorithm further. By adding temporal consistency constraints to the upscaling process, we reduce disturbing depth jumps and flickering artifacts in the final 3DTV content. Temporal consistency in depth maps enhances the 3D experience, leading to a wider acceptance of 3D media content. More content in better quality can boost the commercial success of 3DTV.

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.

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

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

The use of consumer depth cameras for 3D surface imaging of people with obesity: A feasibility study.

Science.gov (United States)

Wheat, J S; Clarkson, S; Flint, S W; Simpson, C; Broom, D R

2018-05-21

Three dimensional (3D) surface imaging is a viable alternative to traditional body morphology measures, but the feasibility of using this technique with people with obesity has not been fully established. Therefore, the aim of this study was to investigate the validity, repeatability and acceptability of a consumer depth camera 3D surface imaging system in imaging people with obesity. The concurrent validity of the depth camera based system was investigated by comparing measures of mid-trunk volume to a gold-standard. The repeatability and acceptability of the depth camera system was assessed in people with obesity at a clinic. There was evidence of a fixed systematic difference between the depth camera system and the gold standard but excellent correlation between volume estimates (r 2 =0.997), with little evidence of proportional bias. The depth camera system was highly repeatable - low typical error (0.192L), high intraclass correlation coefficient (>0.999) and low technical error of measurement (0.64%). Depth camera based 3D surface imaging was also acceptable to people with obesity. It is feasible (valid, repeatable and acceptable) to use a low cost, flexible 3D surface imaging system to monitor the body size and shape of people with obesity in a clinical setting. Copyright © 2018 Asia Oceania Association for the Study of Obesity. Published by Elsevier Ltd. All rights reserved.

Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing

Directory of Open Access Journals (Sweden)

Kai Zhang

2017-05-01

Full Text Available Foxtail millet (Setaria italica is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding.

Depth-dependent effects of culling-do mesophotic lionfish populations undermine current management?

Science.gov (United States)

Andradi-Brown, Dominic A; Grey, Rachel; Hendrix, Alicia; Hitchner, Drew; Hunt, Christina L; Gress, Erika; Madej, Konrad; Parry, Rachel L; Régnier-McKellar, Catriona; Jones, Owen P; Arteaga, María; Izaguirre, Andrea P; Rogers, Alex D; Exton, Dan A

2017-05-01

Invasive lionfish ( Pterois volitans and P. miles ) have spread widely across the western Atlantic and are recognized as a major threat to native marine biodiversity. Although lionfish inhabit both shallow reefs and mesophotic coral ecosystems (MCEs; reefs from 30 to 150 m depth), the primary management response implemented by many countries has been diver-led culling limited to reefs less than 30 m. However, many reef fish undergo ontogenetic migrations, with the largest and therefore most fecund individuals found at greatest depths. Here, we study lionfish density, body size, maturity and dietary patterns across the depth gradient from the surface down to 85 m on heavily culled reefs around Utila, Honduras. We found lionfish at increased densities, body size and weight on MCEs compared with shallow reefs, with MCEs also containing the greatest proportion of actively spawning females, while shallow reefs contained the greatest proportion of immature lionfish. We then compared lionfish behaviour in response to divers on shallow culled and mesophotic unculled Utilan reefs, and on shallow unculled reefs in Tela Bay, on the Honduran mainland. We found that mesophotic lionfish exhibited high alert distances, consistent with individuals previously exposed to culling despite being below the depth limits of removal. In addition, when examining stomach content, we found that fish were the major component of lionfish diets across the depth gradient. Importantly, our results suggest that despite adjacent shallow culling, MCEs retain substantial lionfish populations that may be disproportionately contributing towards continued lionfish recruitment onto the shallow reefs of Utila, potentially undermining current culling-based management.

Depth-dependent effects of culling—do mesophotic lionfish populations undermine current management?

Science.gov (United States)

Grey, Rachel; Hendrix, Alicia; Hitchner, Drew; Gress, Erika; Madej, Konrad; Parry, Rachel L.; Régnier-McKellar, Catriona; Jones, Owen P.; Arteaga, María; Izaguirre, Andrea P.; Rogers, Alex D.; Exton, Dan A.

2017-01-01

Invasive lionfish (Pterois volitans and P. miles) have spread widely across the western Atlantic and are recognized as a major threat to native marine biodiversity. Although lionfish inhabit both shallow reefs and mesophotic coral ecosystems (MCEs; reefs from 30 to 150 m depth), the primary management response implemented by many countries has been diver-led culling limited to reefs less than 30 m. However, many reef fish undergo ontogenetic migrations, with the largest and therefore most fecund individuals found at greatest depths. Here, we study lionfish density, body size, maturity and dietary patterns across the depth gradient from the surface down to 85 m on heavily culled reefs around Utila, Honduras. We found lionfish at increased densities, body size and weight on MCEs compared with shallow reefs, with MCEs also containing the greatest proportion of actively spawning females, while shallow reefs contained the greatest proportion of immature lionfish. We then compared lionfish behaviour in response to divers on shallow culled and mesophotic unculled Utilan reefs, and on shallow unculled reefs in Tela Bay, on the Honduran mainland. We found that mesophotic lionfish exhibited high alert distances, consistent with individuals previously exposed to culling despite being below the depth limits of removal. In addition, when examining stomach content, we found that fish were the major component of lionfish diets across the depth gradient. Importantly, our results suggest that despite adjacent shallow culling, MCEs retain substantial lionfish populations that may be disproportionately contributing towards continued lionfish recruitment onto the shallow reefs of Utila, potentially undermining current culling-based management. PMID:28573007

3D Auger quantitative depth profiling of individual nanoscaled III–V heterostructures

Energy Technology Data Exchange (ETDEWEB)

Hourani, W. [Univ. Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France); Gorbenko, V. [Univ. Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France); Univ. Grenoble Alpes, LTM, CNRS, F-38000 Grenoble (France); Barnes, J.-P.; Guedj, C. [Univ. Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France); Cipro, R.; Moeyaert, J.; David, S.; Bassani, F.; Baron, T. [Univ. Grenoble Alpes, LTM, CNRS, F-38000 Grenoble (France); Martinez, E., E-mail: eugenie.martinez@cea.fr [Univ. Grenoble Alpes, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38054 Grenoble (France)

2016-11-15

Highlights: • The nanoscale chemical characterization of III–V heterostructures is performed using Auger depth profiling below decananometric spatial resolution. • Reliable indium quantification is achieved on planar structures for thicknesses down to 9 nm. • Quantitative 3D compositional depth profiles are obtained on patterned structures, with sufficient lateral resolution to analyze one single trench. • The Auger intrinsic spatial resolution is estimated around 150–200 nm using a comparison with HAADF-STEM. • Auger and SIMS provide reliable in-depth chemical analysis of such complex 3D heterostructures, in particular regarding indium quantification. - Abstract: The nanoscale chemical characterization of III–V heterostructures is performed using Auger depth profiling below decananometric spatial resolution. This technique is successfully applied to quantify the elemental composition of planar and patterned III–V heterostructures containing InGaAs quantum wells. Reliable indium quantification is achieved on planar structures for thicknesses down to 9 nm. Quantitative 3D compositional depth profiles are obtained on patterned structures, for trench widths down to 200 nm. The elemental distributions obtained in averaged and pointed mode are compared. For this last case, we show that Zalar rotation during sputtering is crucial for a reliable indium quantification. Results are confirmed by comparisons with secondary ion mass spectrometry, photoluminescence spectroscopy, transmission electron microscopy and electron dispersive X-ray spectroscopy. The Auger intrinsic spatial resolution is quantitatively measured using an original methodology based on the comparison with high angle annular dark field scanning transmission electron microscopy measurements at the nanometric scale.

Noninvasive measurement of burn wound depth applying infrared thermal imaging (Conference Presentation)

Science.gov (United States)

Jaspers, Mariëlle E.; Maltha, Ilse M.; Klaessens, John H.; Vet, Henrica C.; Verdaasdonk, Rudolf M.; Zuijlen, Paul P.

2016-02-01

In burn wounds early discrimination between the different depths plays an important role in the treatment strategy. The remaining vasculature in the wound determines its healing potential. Non-invasive measurement tools that can identify the vascularization are therefore considered to be of high diagnostic importance. Thermography is a non-invasive technique that can accurately measure the temperature distribution over a large skin or tissue area, the temperature is a measure of the perfusion of that area. The aim of this study was to investigate the clinimetric properties (i.e. reliability and validity) of thermography for measuring burn wound depth. In a cross-sectional study with 50 burn wounds of 35 patients, the inter-observer reliability and the validity between thermography and Laser Doppler Imaging were studied. With ROC curve analyses the ΔT cut-off point for different burn wound depths were determined. The inter-observer reliability, expressed by an intra-class correlation coefficient of 0.99, was found to be excellent. In terms of validity, a ΔT cut-off point of 0.96°C (sensitivity 71%; specificity 79%) differentiates between a superficial partial-thickness and deep partial-thickness burn. A ΔT cut-off point of -0.80°C (sensitivity 70%; specificity 74%) could differentiate between a deep partial-thickness and a full-thickness burn wound. This study demonstrates that thermography is a reliable method in the assessment of burn wound depths. In addition, thermography was reasonably able to discriminate among different burn wound depths, indicating its potential use as a diagnostic tool in clinical burn practice.

A Simulation-based Randomized Controlled Study of Factors Influencing Chest Compression Depth

Directory of Open Access Journals (Sweden)

Kelsey P. Mayrand

2015-12-01

Full Text Available Introduction: Current resuscitation guidelines emphasize a systems approach with a strong emphasis on quality cardiopulmonary resuscitation (CPR. Despite the American Heart Association (AHA emphasis on quality CPR for over 10 years, resuscitation teams do not consistently meet recommended CPR standards. The objective is to assess the impact on chest compression depth of factors including bed height, step stool utilization, position of the rescuer’s arms and shoulders relative to the point of chest compression, and rescuer characteristics including height, weight, and gender. Methods: Fifty-six eligible subjects, including physician assistant students and first-year emergency medicine residents, were enrolled and randomized to intervention (bed lowered and step stool readily available and control (bed raised and step stool accessible, but concealed groups. We instructed all subjects to complete all interventions on a high-fidelity mannequin per AHA guidelines. Secondary end points included subject arm angle, height, weight group, and gender. Results: Using an intention to treat analysis, the mean compression depths for the intervention and control groups were not significantly different. Subjects positioning their arms at a 90-degree angle relative to the sagittal plane of the mannequin’s chest achieved a mean compression depth significantly greater than those compressing at an angle less than 90 degrees. There was a significant correlation between using a step stool and achieving the correct shoulder position. Subject height, weight group, and gender were all independently associated with compression depth. Conclusion: Rescuer arm position relative to the patient’s chest and step stool utilization during CPR are modifiable factors facilitating improved chest compression depth.

Seed drill depth control system for precision seeding

DEFF Research Database (Denmark)

Kirkegaard Nielsen, Søren; Munkholm, Lars Juhl; Lamandé, Mathieu

2018-01-01

acting on the drill coulters, which generates unwanted vibrations and, consequently, a non-uniform seed placement. Therefore, a proof-of-concept dynamic coulter depth control system for a low-cost seed drill was developed and studied in a field experiment. The performance of the active control system...... depth control system this variability was reduced to±2 mm. The system with the active control system operated more accurately at an operational speed of 12 km h−1 than at 4 km h−1 without the activated control system.......An adequate and uniform seeding depth is crucial for the homogeneous development of a crop, as it affects time of emergence and germination rate. The considerable depth variations observed during seeding operations - even for modern seed drills - are mainly caused by variability in soil resistance...

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...

Probe depth matters in dermal microdialysis sampling of benzoic acid after topical application

DEFF Research Database (Denmark)

Holmgaard, R; Benfeldt, E; Bangsgaard, N

2012-01-01

-2 mm) and deep (>2 mm) positioning of the linear MD probe in the dermis of human abdominal skin, followed by topical application of 4 mg/ml of benzoic acid (BA) in skin chambers overlying the probes. Dialysate was sampled every hour for 12 h and analysed for BA content by high-performance liquid...... chromatography. Probe depth was measured by 20-MHz ultrasound scanning. The area under the time-versus-concentration curve (AUC) describes the drug exposure in the tissue during the experiment and is a relevant parameter to compare for the 3 dermal probe depths investigated. The AUC(0-12) were: superficial...... significantly different from each other (p value paper demonstrates that there is an inverse relationship between the depth of the probe in the dermis and the amount of drug sampled following topical penetration ex vivo. The result is of relevance to the in vivo situation, and it can...

Snow depth manipulation experiments in a dry and a moist tundra

Science.gov (United States)

Kwon, M. J.; Czimczik, C. I.; Jung, J. Y.; Kim, M.; Lee, Y. K.; Nam, S.; Wagner, I.

2017-12-01

As a result of global warming, precipitation in the Arctic is expected to increase by 25-50% by the end of this century, mostly in the form of snow. However, precipitation patterns vary considerable in space and time, and future precipitation patterns are highly uncertain at local and regional scales. The amount of snowfall (or snow depth) influences a number of ecosystem properties in Arctic ecosystems, such as soil temperature over winter and soil moisture in the following growing season. These modifications then affect rates of carbon-related soil processes and photosynthesis, thus CO2 exchange rates between terrestrial ecosystems and the atmosphere. In this study, we investigate the effects of snow depth on the magnitude, sources and temporal dynamics of CO2 fluxes. We installed snow fences in a dry dwarf-shrub (Cambridge Bay, Canada; 69° N, 105° W) and a moist low-shrub (Council, Alaska, USA; 64° N, 165° W) tundra in summer 2017, and established control, and increased and reduced snow depth plots at each snow fence. Summertime CO2 flux rates (net ecosystem exchange, ecosystem respiration, gross primary production) and the fractions of autotrophic and heterotrophic respiration to ecosystem respiration were measured using manual chambers and radiocarbon signatures. Wintertime CO2 flux rates will be measured using soda lime adsorption technique and forced diffusion chambers. Soil temperature and moisture at multiple depths, as well as changes in soil properties and microbial communities will be also observed, to research whether these changes affect CO2 flux rates or patterns. Our study will elucidate how future snow depth and its impact on soil physical and biogeochemical properties influence the magnitude and sources of tundra-atmosphere CO2 exchange in the rapidly warming Arctic.

Calculation of mixed depth for some metal-Si systems

International Nuclear Information System (INIS)

Poker, D.B.

1986-01-01

The linearity of mixing during ion beam mixing of metals on Si has been found to depend critically upon the method by which the mixed depth is determined. For nonstoichiometric, diffuse mixing, several methods of calculating the mixed depth may be used, namely: integrated area, moment, error function, and 10%-90%. For stoichiometric mixing, the determination of the mixed depth is somewhat more straightforward, and several of the same methods may be used. Some of these methods suffer from the exhibition of an initial offset due to the finite detector resolution. An empirical method of removing the offset using a cubic correction is an improvement, but adds a nonlinear perturbation to the power law dependence on dose, approaching 2/3 for small depths. The effect of detector resolution on the measured depth of mixing is given for several methods, using simulated data with a linear increase in depth as a function of dose. The results effect on the exponent of a power law fit to the dose dependence is given. Only the moment method is immune to the resolution effects

Size matters: Perceived depth magnitude varies with stimulus height.

Science.gov (United States)

Tsirlin, Inna; Wilcox, Laurie M; Allison, Robert S

2016-06-01

Both the upper and lower disparity limits for stereopsis vary with the size of the targets. Recently, Tsirlin, Wilcox, and Allison (2012) suggested that perceived depth magnitude from stereopsis might also depend on the vertical extent of a stimulus. To test this hypothesis we compared apparent depth in small discs to depth in long bars with equivalent width and disparity. We used three estimation techniques: a virtual ruler, a touch-sensor (for haptic estimates) and a disparity probe. We found that depth estimates were significantly larger for the bar stimuli than for the disc stimuli for all methods of estimation and different configurations. In a second experiment, we measured perceived depth as a function of the height of the bar and the radius of the disc. Perceived depth increased with increasing bar height and disc radius suggesting that disparity is integrated along the vertical edges. We discuss size-disparity correlation and inter-neural excitatory connections as potential mechanisms that could account for these results. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of Shear Fracture on In-depth Profile Modification of Weak Gels

Institute of Scientific and Technical Information of China (English)

Li Xianjie; Song Xinwang; Yue Xiang'an; Hou Jirui; Fang Lichun; Zhang Huazhen

2007-01-01

Two sand packs were filled with fine glass beads and quartz sand respectively. The characteristics of crosslinked polymer flowing through the sand packs as well as the influence of shear fracture of porous media on the in-depth profile modification of the weak gel generated from the crosslinked polymer were investigated. The results indicated that under the dynamic condition crosslinking reaction happened in both sand packs,and the weak gels in these two cases became small gel particles after water flooding. The differences were:the dynamic gelation time in the quartz sand pack was longer than that in the glass bead pack. Residual resistance factor (FRR) caused by the weak gel in the quartz sand pack was smaller than that in the glass bead pack. The weak gel became gel particles after being scoured by subsequent flood water. A weak gel with uniform apparent viscosity and sealing characteristics was generated in every part of the glass bead pack,which could not only move deeply into the sand pack but also seal the high capacity channels again when it reached the deep part. The weak gel performed in-depth profile modification in the glass bead pack,while in the quartz sand pack,the weak gel was concentrated with 100 cm from the entrance of the sand pack. When propelled by the subsequent flood water,the weak gel could move towards the deep part of the sand pack but then became tiny gel particles and could not effectively seal the high capacity channels there. The in-depth profile modification of the weak gel was very weak in the quartz sand pack. It was the shear fracture of porous media that mainly affected the properties and weakened the in-depth profile modification of the weak gel.

Regrowth of Cirsium arvense from intact roots and root fragments at different soil depths

Directory of Open Access Journals (Sweden)

Thomsen, Mette Goul

2014-02-01

Full Text Available In the present work we measured the shoot rate from intact roots and from root fragments of Cirsium arvense at different digging depths and the number of leaves were used as estimate of minimum regenerative capacity. The experiments were performed on four sites with three or four repetitions of each treatment. On each site plot, the soil was removed down to a given depth within a 1 x 1 m square. All plant parts was excavated from the soil and the soil was either replaced without any root material, or roots of C. arvense was cut into 10 cm long fragments and replaced into the source hole. Shoot number, aboveground biomass and number of leaves were measured. Digging depth and time explained 50% - 60% of the variation in biomass (P<0.001. Replacement of root fragments increased the shoot number in one out of four treatments but did not affect biomass produced compared to production from undisturbed root systems. Number of leaves showed that shoots from all digging depths passed the level of minimum regenerative capacity. We conclude that the intact root system from all depths was able to regenerate within one season and it has a high contribution to the produced biomass compared with root fragments in the upper soil layers.

Evaluating UAV and LiDAR Retrieval of Snow Depth in a Coniferous Forest in Arizona

Science.gov (United States)

Van Leeuwen, W. J. D.; Broxton, P.; Biederman, J. A.

2017-12-01

Remote sensing of snow depth and cover in forested environments is challenging. Trees interfere with the remote sensing of snowpack below the canopy and cause large variations in the spatial distribution of the snowpack itself (e.g. between below canopy environments to shaded gaps to open clearings). The distribution of trees and topographic variation make it challenging to monitor the snowpack with in-situ observations. Airborne LiDAR has improved our ability to monitor snowpack over large areas in montane and forested environments because of its high sampling rate and ability to penetrate the canopy. However, these LiDAR flights can be too expensive and time-consuming to process, making it hard to use them for real-time snow monitoring. In this research, we evaluate Structure from Motion (SfM) as an alternative to Airborne LiDAR to generate high-resolution snow depth data in forested environments. This past winter, we conducted a snow field campaign over Arizona's Mogollon Rim where we acquired aerial LiDAR, multi-angle aerial photography from a UAV, and extensive field observations of snow depth at two sites. LiDAR and SFM derived snow depth maps were generated by comparing "snow-on" and "snow-off" LiDAR and SfM data. The SfM- and LiDAR-generated snow depth maps were similar at a site with fewer trees, though there were more discrepancies at a site with more trees. Both compared reasonably well with the field observations at the sparser forested site, with poorer agreement at the denser forested site. Finally, although the SfM produced point clouds with much higher point densities than the aerial LiDAR, the SfM was not able to produce meaningful snow depth estimates directly underneath trees and had trouble in areas with deep shadows. Based on these findings, we are optimizing our UAV data acquisition strategies for this upcoming field season. We are using these data, along with high-resolution hydrological modeling, to gain a better understanding of how

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

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.

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.

Preliminary results of the aerosol optical depth retrieval in Johor, Malaysia

International Nuclear Information System (INIS)

Lim, H Q; Lau, A M S; Kanniah, K D

2014-01-01

Monitoring of atmospheric aerosols over the urban area is important as tremendous amounts of pollutants are released by industrial activities and heavy traffic flow. Air quality monitoring by satellite observation provides better spatial coverage, however, detailed aerosol properties retrieval remains a challenge. This is due to the limitation of aerosol retrieval algorithm on high reflectance (bright surface) areas. The aim of this study is to retrieve aerosol optical depth over urban areas of Iskandar Malaysia; the main southern development zone in Johor state, using Moderate Resolution Imaging Spectroradiometer (MODIS) 500 m resolution data. One of the important steps is the aerosol optical depth retrieval is to characterise different types of aerosols in the study area. This information will be used to construct a Look Up Table containing the simulated aerosol reflectance and corresponding aerosol optical depth. Thus, in this study we have characterised different aerosol types in the study area using Aerosol Robotic Network (AERONET) data. These data were processed using cluster analysis and the preliminary results show that the area is consisting of coastal urban (65%), polluted urban (27.5%), dust particles (6%) and heavy pollution (1.5%) aerosols

Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats

Directory of Open Access Journals (Sweden)

Guido Bonthond

2018-02-01

Full Text Available Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.

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

Sensor and control for consistent seed drill coulter depth

DEFF Research Database (Denmark)

Kirkegaard Nielsen, Søren; Nørremark, Michael; Green, Ole

2016-01-01

The consistent depth placement of seeds is vital for achieving the optimum yield of agricultural crops. In state-of-the-art seeding machines, the depth of drill coulters will vary with changes in soil resistance. This paper presents the retrofitting of an angle sensor to the pivoting point...... by a sub-millimetre accurate positioning system (iGPS, Nikon Metrology NV, Belgium) mounted on the drill coulter. At a drill coulter depth of 55 mm and controlled by an ordinary fixed spring loaded down force only, the change in soil resistance decreased the mean depth by 23 mm. By dynamically controlling...

Contributions of depth filter components to protein adsorption in bioprocessing.

Science.gov (United States)

Khanal, Ohnmar; Singh, Nripen; Traylor, Steven J; Xu, Xuankuo; Ghose, Sanchayita; Li, Zheng J; Lenhoff, Abraham M

2018-04-16

Depth filtration is widely used in downstream bioprocessing to remove particulate contaminants via depth straining and is therefore applied to harvest clarification and other processing steps. However, depth filtration also removes proteins via adsorption, which can contribute variously to impurity clearance and to reduction in product yield. The adsorption may occur on the different components of the depth filter, that is, filter aid, binder, and cellulose filter. We measured adsorption of several model proteins and therapeutic proteins onto filter aids, cellulose, and commercial depth filters at pH 5-8 and ionic strengths filter component in the adsorption of proteins with different net charges, using confocal microscopy. Our findings show that a complete depth filter's maximum adsorptive capacity for proteins can be estimated by its protein monolayer coverage values, which are of order mg/m 2 , depending on the protein size. Furthermore, the extent of adsorption of different proteins appears to depend on the nature of the resin binder and its extent of coating over the depth filter surface, particularly in masking the cation-exchanger-like capacity of the siliceous filter aids. In addition to guiding improved depth filter selection, the findings can be leveraged in inspiring a more intentional selection of components and design of depth filter construction for particular impurity removal targets. © 2018 Wiley Periodicals, Inc.

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.

Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis.

Science.gov (United States)

Guo, Yan; Dai, Yulin; Yu, Hui; Zhao, Shilin; Samuels, David C; Shyr, Yu

2017-03-01

Analyses of high throughput sequencing data starts with alignment against a reference genome, which is the foundation for all re-sequencing data analyses. Each new release of the human reference genome has been augmented with improved accuracy and completeness. It is presumed that the latest release of human reference genome, GRCh38 will contribute more to high throughput sequencing data analysis by providing more accuracy. But the amount of improvement has not yet been quantified. We conducted a study to compare the genomic analysis results between the GRCh38 reference and its predecessor GRCh37. Through analyses of alignment, single nucleotide polymorphisms, small insertion/deletions, copy number and structural variants, we show that GRCh38 offers overall more accurate analysis of human sequencing data. More importantly, GRCh38 produced fewer false positive structural variants. In conclusion, GRCh38 is an improvement over GRCh37 not only from the genome assembly aspect, but also yields more reliable genomic analysis results. Copyright © 2017. Published by Elsevier Inc.

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.

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.

The Enhancement of 3D Scans Depth Resolution Obtained by Confocal Scanning of Porous Materials

Science.gov (United States)

Martisek, Dalibor; Prochazkova, Jana

2017-12-01

The 3D reconstruction of simple structured materials using a confocal microscope is widely used in many different areas including civil engineering. Nonetheless, scans of porous materials such as concrete or cement paste are highly problematic. The well-known problem of these scans is low depth resolution in comparison to the horizontal and vertical resolution. The degradation of the image depth resolution is caused by systematic errors and especially by different random events. Our method is focused on the elimination of such random events, mainly the additive noise. We use an averaging method based on the Lindeberg-Lévy theorem that improves the final depth resolution to a level comparable with horizontal and vertical resolution. Moreover, using the least square method, we also precisely determine the limit value of a depth resolution. Therefore, we can continuously evaluate the difference between current resolution and the optimal one. This substantially simplifies the scanning process because the operator can easily determine the required number of scans.

The Enhancement of 3D Scans Depth Resolution Obtained by Confocal Scanning of Porous Materials

Directory of Open Access Journals (Sweden)

Martisek Dalibor

2017-12-01

Full Text Available The 3D reconstruction of simple structured materials using a confocal microscope is widely used in many different areas including civil engineering. Nonetheless, scans of porous materials such as concrete or cement paste are highly problematic. The well-known problem of these scans is low depth resolution in comparison to the horizontal and vertical resolution. The degradation of the image depth resolution is caused by systematic errors and especially by different random events. Our method is focused on the elimination of such random events, mainly the additive noise. We use an averaging method based on the Lindeberg-Lévy theorem that improves the final depth resolution to a level comparable with horizontal and vertical resolution. Moreover, using the least square method, we also precisely determine the limit value of a depth resolution. Therefore, we can continuously evaluate the difference between current resolution and the optimal one. This substantially simplifies the scanning process because the operator can easily determine the required number of scans.

Observed damage during Argon gas cluster depth profiles of compound semiconductors

Energy Technology Data Exchange (ETDEWEB)

Barlow, Anders J., E-mail: anders.barlow@ncl.ac.uk; Portoles, Jose F.; Cumpson, Peter J. [National EPSRC XPS Users' Service (NEXUS), School of Mechanical and Systems Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU (United Kingdom)

2014-08-07

Argon Gas Cluster Ion Beam (GCIB) sources have become very popular in XPS and SIMS in recent years, due to the minimal chemical damage they introduce in the depth-profiling of polymer and other organic materials. These GCIB sources are therefore particularly useful for depth-profiling polymer and organic materials, but also (though more slowly) the surfaces of inorganic materials such as semiconductors, due to the lower roughness expected in cluster ion sputtering compared to that introduced by monatomic ions. We have examined experimentally a set of five compound semiconductors, cadmium telluride (CdTe), gallium arsenide (GaAs), gallium phosphide (GaP), indium arsenide (InAs), and zinc selenide (ZnSe) and a high-κ dielectric material, hafnium oxide (HfO), in their response to argon cluster profiling. An experimentally determined HfO etch rate of 0.025 nm/min (3.95 × 10{sup −2} amu/atom in ion) for 6 keV Ar gas clusters is used in the depth scale conversion for the profiles of the semiconductor materials. The assumption has been that, since the damage introduced into polymer materials is low, even though sputter yields are high, then there is little likelihood of damaging inorganic materials at all with cluster ions. This seems true in most cases; however, in this work, we report for the first time that this damage can in fact be very significant in the case of InAs, causing the formation of metallic indium that is readily visible even to the naked eye.

Minimum critical crack depths in pressure vessels guidelines for nondestructive testing

International Nuclear Information System (INIS)

Crossley, M.R.; Townley, C.H.A.

1983-09-01

Estimates of the minimum critical depths which can be expected in high quality vessels designed to certain British and American Code rules are given. A simple means of allowing for fatigue crack growth in service is included. The data which are presented can be used to decide what sensitivity and what reporting levels should be employed during an ultrasonic inspection of a pressure vessel. It is emphasised that the minimum crack depths are those which would be relevant to a vessel in which the material is stressed to its maximum permitted value during operation. Stresses may, in practice, be significantly less than this. Less restrictive inspection standards may be established, if it were considered worthwhile to carry out a detailed stress analysis of the particular vessel under examination. (author)

Data-based depth estimation of an incoming autonomous underwater vehicle.

Science.gov (United States)

Yang, T C; Xu, Wen

2016-10-01

The data-based method for estimating the depth of a moving source is demonstrated experimentally for an incoming autonomous underwater vehicle traveling toward a vertical line array (VLA) of receivers at constant speed/depth. The method assumes no information on the sound-speed and bottom profile. Performing a wavenumber analysis of a narrowband signal for each hydrophone, the energy of the (modal) spectral peaks as a function of the receiver depth is used to estimate the depth of the source, traveling within the depth span of the VLA. This paper reviews the theory, discusses practical implementation issues, and presents the data analysis results.

The Hengill geothermal area, Iceland: Variation of temperature gradients deduced from the maximum depth of seismogenesis

Science.gov (United States)

Foulger, G. R.

1995-04-01

Given a uniform lithology and strain rate and a full seismic data set, the maximum depth of earthquakes may be viewed to a first order as an isotherm. These conditions are approached at the Hengill geothermal area S. Iceland, a dominantly basaltic area. The likely strain rate calculated from thermal and tectonic considerations is 10 -15 s -1, and temperature measurements from four drill sites within the area indicate average, near-surface geothermal gradients of up to 150 °C km -1 throughout the upper 2 km. The temperature at which seismic failure ceases for the strain rates likely at the Hengill geothermal area is determined by analogy with oceanic crust, and is about 650 ± 50 °C. The topographies of the top and bottom of the seismogenic layer were mapped using 617 earthquakes located highly accurately by performing a simultaneous inversion for three-dimensional structure and hypocentral parameters. The thickness of the seismogenic layer is roughly constant and about 3 km. A shallow, aseismic, low-velocity volume within the spreading plate boundary that crosses the area occurs above the top of the seismogenic layer and is interpreted as an isolated body of partial melt. The base of the seismogenic layer has a maximum depth of about 6.5 km beneath the spreading axis and deepens to about 7 km beneath a transform zone in the south of the area. Beneath the high-temperature part of the geothermal area, the maximum depth of earthquakes may be as shallow as 4 km. The geothermal gradient below drilling depths in various parts of the area ranges from 84 ± 9 °Ckm -1 within the low-temperature geothermal area of the transform zone to 138 ± 15 °Ckm -1 below the centre of the high-temperature geothermal area. Shallow maximum depths of earthquakes and therefore high average geothermal gradients tend to correlate with the intensity of the geothermal area and not with the location of the currently active spreading axis.

Numerical Investigation on Effect of Immersed Blade Depth on the Performance of Undershot Water Turbines

Directory of Open Access Journals (Sweden)

Yah Nor Fadilah

2016-01-01

Full Text Available Energy, especially electricity, plays a vital role in global social and economic development. High annual rain rate in Malaysia seems a good potential for electricity generation especially through small hydro powers. Undershot water turbines are one of the hydropower turbines used for many years. However, the effect of blade depth immersed in the flowing water is not fully investigated. Therefore, the purpose of this paper is to study the effect of immersed blade depth for straight blade undershot water turbine in power generation by using Computational Fluid Dynamics (CFD method. ANSYS CFX 15.0 was used to perform three dimensional analysis under steady state, incompressible, and non-isothermal conditions. The water wheel with number of blades of 6 and four different immersed depth was applied for each simulation. There are four different immersed depth was applied to each simulation, which are 20 mm, 40 mm, 60 mm and 80 mm. From the simulation result, it was found that the optimum immersed depth is 40 mm where the torque load and power generated were 0.264 N.m and 1.318 Watt respectively.

In-depth research of domestic nuclear patent information

International Nuclear Information System (INIS)

Mo Dan; Gao Anna; Li Dongbin; Lu Yanjia; Ren Chao

2014-01-01

Based on the domestic patent information, combined with examples, this article makes an in-depth discussion on the domestic nuclear patent information. The author puts forward for the patent information research, the appropriate retrieval of patent documents is the basis,and the correct quantitative statistical analysis of patent documents is the key, and in-depth qualitative analysis of patent documents is the core. It is expected to provide information support and guarantee for the technical innovation and scientific research personnel in the nuclear field through in-depth study of domestic nuclear information. (authors)

Determination of rock depth using artificial intelligence techniques

Institute of Scientific and Technical Information of China (English)

R. Viswanathan; Pijush Samui

2016-01-01

This article adopts three artificial intelligence techniques, Gaussian Process Regression (GPR), Least Square Support Vector Machine (LSSVM) and Extreme Learning Machine (ELM), for prediction of rock depth (d) at any point in Chennai. GPR, ELM and LSSVM have been used as regression techniques. Latitude and longitude are also adopted as inputs of the GPR, ELM and LSSVM models. The performance of the ELM, GPR and LSSVM models has been compared. The developed ELM, GPR and LSSVM models produce spatial variability of rock depth and offer robust models for the prediction of rock depth.

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.

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)

Transformation of soil organic matter in a Japanese larch forest. Radiocarbon and stable carbon isotope compositions versus soil depth

International Nuclear Information System (INIS)

Liu Wei; Moriizumi, Jun; Yamazawa, Hiromi; Iida, Takao

2008-01-01

Soil organic matter at a depth of 0-55 cm, collected from a Japanese larch forest area, was separated into particulate organic matter (size >53 μm), particulate organic matter (size 14 C and δ 13 C values were determined. The Δ 14 C values of particulate matters decreased greatly from 128 per mille to -278 per mille, indicating a relative increase of resistant organic components in particulate matters. That of humic acid matter decreased from 183 per mille to -139 per mille. For these of organic matter fractions at the same depth, the Δ 14 C values of particulate matter (size >53μm) are smallest and those of humic acid matter are the largest. That indicates that a high contribution of young organic matter to the humic acid matter exists and transformation tendency of particulate matter may be from coarse to small in the particulate size. Positive Δ 14 C values appeared at a depth of 10 cm, 25 cm, and 35 cm for the particulate organic matter (size >53μm), particulate organic matter (size 14 C values of the humic acid matter also infects that the bomb carbon has reached the depth of 35 cm. Additionally, the Δ 14 C values of these three kinds of organic matters ranged from 50 per mille to 183 per mille at a depth of 0-7 cm, which were not smaller than that of litter in the forest area, indicating high proportion of modern, plants-derived soil organic matter in this depth ranges. The δ 13 C values increased from -28 per mille to -23 per mille with the increase depth of 0-55 cm. The δ 13 C values of humic acid matter are approximately less than that of particulate matters at the same depth, which may be explained as a high contribution of young organic matter to the humic acid matter. (author)

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

Defence-in-depth and development of safety requirements for advanced nuclear reactors

International Nuclear Information System (INIS)

Carnino, A.; Gasparini, M.

2002-01-01

The paper addresses a general approach for the preparation of the design safety requirements using the IAEA Safety Objectives and the strategy of defence-in-depth. It proposes a general method (top-down approach) to prepare safety requirements for a given kind of reactor using the IAEA requirements for nuclear power plants as a starting point through a critical interpretation and application of the strategy of defence-in-depth. The IAEA has recently developed a general methodology for screening the defence-in-depth of nuclear power plants starting from the fundamental safety objectives as proposed in the IAEA Safety Fundamentals. This methodology may provide a useful tool for the preparation of safety requirements for the design and operation of any kind of reactor. Currently the IAEA is preparing the technical basis for the development of safety requirements for Modular High Temperature Gas Reactors, with the aim of showing the viability of the method. A draft TECDOC has been prepared and circulated among several experts for comments. This paper is largely based on the content of the draft TECDOC. (authors)

Semi-Automatic Image Labelling Using Depth Information

Directory of Open Access Journals (Sweden)

Mostafa Pordel

2015-05-01

Full Text Available Image labeling tools help to extract objects within images to be used as ground truth for learning and testing in object detection processes. The inputs for such tools are usually RGB images. However with new widely available low-cost sensors like Microsoft Kinect it is possible to use depth images in addition to RGB images. Despite many existing powerful tools for image labeling, there is a need for RGB-depth adapted tools. We present a new interactive labeling tool that partially automates image labeling, with two major contributions. First, the method extends the concept of image segmentation from RGB to RGB-depth using Fuzzy C-Means clustering, connected component labeling and superpixels, and generates bounding pixels to extract the desired objects. Second, it minimizes the interaction time needed for object extraction by doing an efficient segmentation in RGB-depth space. Very few clicks are needed for the entire procedure compared to existing, tools. When the desired object is the closest object to the camera, which is often the case in robotics applications, no clicks at all are required to accurately extract the object.

Tensor-guided fitting of subduction slab depths

Science.gov (United States)

Bazargani, Farhad; Hayes, Gavin P.

2013-01-01

Geophysical measurements are often acquired at scattered locations in space. Therefore, interpolating or fitting the sparsely sampled data as a uniform function of space (a procedure commonly known as gridding) is a ubiquitous problem in geophysics. Most gridding methods require a model of spatial correlation for data. This spatial correlation model can often be inferred from some sort of secondary information, which may also be sparsely sampled in space. In this paper, we present a new method to model the geometry of a subducting slab in which we use a data‐fitting approach to address the problem. Earthquakes and active‐source seismic surveys provide estimates of depths of subducting slabs but only at scattered locations. In addition to estimates of depths from earthquake locations, focal mechanisms of subduction zone earthquakes also provide estimates of the strikes of the subducting slab on which they occur. We use these spatially sparse strike samples and the Earth’s curved surface geometry to infer a model for spatial correlation that guides a blended neighbor interpolation of slab depths. We then modify the interpolation method to account for the uncertainties associated with the depth estimates.

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.

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....

ISLSCP II Ecosystem Rooting Depths

Data.gov (United States)