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Sample records for high-quality sequence reads

  1. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  2. Get your high-quality low-cost genome sequence

    NARCIS (Netherlands)

    Faino, L.; Thomma, B.P.H.J.

    2014-01-01

    The study of whole-genome sequences has become essential for almost all branches of biological research. Next-generation sequencing (NGS) has revolutionized the scalability, speed, and resolution of sequencing and brought genomic science within reach of academic laboratories that study non-model

  3. A filtering method to generate high quality short reads using illumina paired-end technology.

    Science.gov (United States)

    Eren, A Murat; Vineis, Joseph H; Morrison, Hilary G; Sogin, Mitchell L

    2013-01-01

    Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack of consensus between very similar sequences in metagenomic studies can and often does represent natural variation of biological significance. The common use of machine-assigned quality scores on next generation platforms does not necessarily correlate with accuracy. Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone reads in marker gene analyses and their contribution to spurious OTUs following clustering analysis using QIIME. Our approach can also reduce error in shotgun sequencing data generated from libraries with small, tightly constrained insert sizes. The open-source implementation of this algorithm in Python programming language with user instructions can be obtained from https://github.com/meren/illumina-utils.

  4. A filtering method to generate high quality short reads using illumina paired-end technology.

    Directory of Open Access Journals (Sweden)

    A Murat Eren

    Full Text Available Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack of consensus between very similar sequences in metagenomic studies can and often does represent natural variation of biological significance. The common use of machine-assigned quality scores on next generation platforms does not necessarily correlate with accuracy. Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone reads in marker gene analyses and their contribution to spurious OTUs following clustering analysis using QIIME. Our approach can also reduce error in shotgun sequencing data generated from libraries with small, tightly constrained insert sizes. The open-source implementation of this algorithm in Python programming language with user instructions can be obtained from https://github.com/meren/illumina-utils.

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

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    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.

  6. Exome sequencing generates high quality data in non-target regions

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    Guo Yan

    2012-05-01

    Full Text Available Abstract Background Exome sequencing using next-generation sequencing technologies is a cost efficient approach to selectively sequencing coding regions of human genome for detection of disease variants. A significant amount of DNA fragments from the capture process fall outside target regions, and sequence data for positions outside target regions have been mostly ignored after alignment. Result We performed whole exome sequencing on 22 subjects using Agilent SureSelect capture reagent and 6 subjects using Illumina TrueSeq capture reagent. We also downloaded sequencing data for 6 subjects from the 1000 Genomes Project Pilot 3 study. Using these data, we examined the quality of SNPs detected outside target regions by computing consistency rate with genotypes obtained from SNP chips or the Hapmap database, transition-transversion (Ti/Tv ratio, and percentage of SNPs inside dbSNP. For all three platforms, we obtained high-quality SNPs outside target regions, and some far from target regions. In our Agilent SureSelect data, we obtained 84,049 high-quality SNPs outside target regions compared to 65,231 SNPs inside target regions (a 129% increase. For our Illumina TrueSeq data, we obtained 222,171 high-quality SNPs outside target regions compared to 95,818 SNPs inside target regions (a 232% increase. For the data from the 1000 Genomes Project, we obtained 7,139 high-quality SNPs outside target regions compared to 1,548 SNPs inside target regions (a 461% increase. Conclusions These results demonstrate that a significant amount of high quality genotypes outside target regions can be obtained from exome sequencing data. These data should not be ignored in genetic epidemiology studies.

  7. Long-read sequencing data analysis for yeasts.

    Science.gov (United States)

    Yue, Jia-Xing; Liti, Gianni

    2018-06-01

    Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here, we present a modular computational framework named long-read sequencing data analysis for yeasts (LRSDAY), the first one-stop solution that streamlines this process. Starting from the raw sequencing reads, LRSDAY can produce chromosome-level genome assembly and comprehensive genome annotation in a highly automated manner with minimal manual intervention, which is not possible using any alternative tool available to date. The annotated genomic features include centromeres, protein-coding genes, tRNAs, transposable elements (TEs), and telomere-associated elements. Although tailored for S. cerevisiae, we designed LRSDAY to be highly modular and customizable, making it adaptable to virtually any eukaryotic organism. When applying LRSDAY to an S. cerevisiae strain, it takes ∼41 h to generate a complete and well-annotated genome from ∼100× Pacific Biosciences (PacBio) running the basic workflow with four threads. Basic experience working within the Linux command-line environment is recommended for carrying out the analysis using LRSDAY.

  8. Targeted assembly of short sequence reads.

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    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  9. Flexible taxonomic assignment of ambiguous sequencing reads

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    Jansson Jesper

    2011-01-01

    Full Text Available Abstract Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results.

  10. The need for high-quality whole-genome sequence databases in microbial forensics.

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    Sjödin, Andreas; Broman, Tina; Melefors, Öjar; Andersson, Gunnar; Rasmusson, Birgitta; Knutsson, Rickard; Forsman, Mats

    2013-09-01

    Microbial forensics is an important part of a strengthened capability to respond to biocrime and bioterrorism incidents to aid in the complex task of distinguishing between natural outbreaks and deliberate acts. The goal of a microbial forensic investigation is to identify and criminally prosecute those responsible for a biological attack, and it involves a detailed analysis of the weapon--that is, the pathogen. The recent development of next-generation sequencing (NGS) technologies has greatly increased the resolution that can be achieved in microbial forensic analyses. It is now possible to identify, quickly and in an unbiased manner, previously undetectable genome differences between closely related isolates. This development is particularly relevant for the most deadly bacterial diseases that are caused by bacterial lineages with extremely low levels of genetic diversity. Whole-genome analysis of pathogens is envisaged to be increasingly essential for this purpose. In a microbial forensic context, whole-genome sequence analysis is the ultimate method for strain comparisons as it is informative during identification, characterization, and attribution--all 3 major stages of the investigation--and at all levels of microbial strain identity resolution (ie, it resolves the full spectrum from family to isolate). Given these capabilities, one bottleneck in microbial forensics investigations is the availability of high-quality reference databases of bacterial whole-genome sequences. To be of high quality, databases need to be curated and accurate in terms of sequences, metadata, and genetic diversity coverage. The development of whole-genome sequence databases will be instrumental in successfully tracing pathogens in the future.

  11. Comparative Genomics in Switchgrass Using 61,585 High-Quality Expressed Sequence Tags

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    Christian M. Tobias

    2008-11-01

    Full Text Available The development of genomic resources for switchgrass ( L., a perennial NAD-malic enzyme type C grass, is required to enable molecular breeding and biotechnological approaches for improving its value as a forage and bioenergy crop. Expressed sequence tag (EST sequencing is one method that can quickly sample gene inventories and produce data suitable for marker development or analysis of tissue-specific patterns of expression. Toward this goal, three cDNA libraries from callus, crown, and seedling tissues of ‘Kanlow’ switchgrass were end-sequenced to generate a total of 61,585 high-quality ESTs from 36,565 separate clones. Seventy-three percent of the assembled consensus sequences could be aligned with the sorghum [ (L. Moench] genome at a -value of <1 × 10, indicating a high degree of similarity. Sixty-five percent of the ESTs matched with gene ontology molecular terms, and 3.3% of the sequences were matched with genes that play potential roles in cell-wall biogenesis. The representation in the three libraries of gene families known to be associated with C photosynthesis, cellulose and β-glucan synthesis, phenylpropanoid biosynthesis, and peroxidase activity indicated likely roles for individual family members. Pairwise comparisons of synonymous codon substitutions were used to assess genome sequence diversity and indicated an overall similarity between the two genome copies present in the tetraploid. Identification of EST–simple sequence repeat markers and amplification on two individual parents of a mapping population yielded an average of 2.18 amplicons per individual, and 35% of the markers produced fragment length polymorphisms.

  12. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

    Science.gov (United States)

    Chin, Chen-Shan; Alexander, David H; Marks, Patrick; Klammer, Aaron A; Drake, James; Heiner, Cheryl; Clum, Alicia; Copeland, Alex; Huddleston, John; Eichler, Evan E; Turner, Stephen W; Korlach, Jonas

    2013-06-01

    We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.

  13. Accurate Local-Ancestry Inference in Exome-Sequenced Admixed Individuals via Off-Target Sequence Reads

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    Hu, Youna; Willer, Cristen; Zhan, Xiaowei; Kang, Hyun Min; Abecasis, Gonçalo R.

    2013-01-01

    Estimates of the ancestry of specific chromosomal regions in admixed individuals are useful for studies of human evolutionary history and for genetic association studies. Previously, this ancestry inference relied on high-quality genotypes from genome-wide association study (GWAS) arrays. These high-quality genotypes are not always available when samples are exome sequenced, and exome sequencing is the strategy of choice for many ongoing genetic studies. Here we show that off-target reads generated during exome-sequencing experiments can be combined with on-target reads to accurately estimate the ancestry of each chromosomal segment in an admixed individual. To reconstruct local ancestry, our method SEQMIX models aligned bases directly instead of relying on hard genotype calls. We evaluate the accuracy of our method through simulations and analysis of samples sequenced by the 1000 Genomes Project and the NHLBI Grand Opportunity Exome Sequencing Project. In African Americans, we show that local-ancestry estimates derived by our method are very similar to those derived with Illumina’s Omni 2.5M genotyping array and much improved in relation to estimates that use only exome genotypes and ignore off-target sequencing reads. Software implementing this method, SEQMIX, can be applied to analysis of human population history or used for genetic association studies in admixed individuals. PMID:24210252

  14. Short read sequence typing (SRST: multi-locus sequence types from short reads

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    Inouye Michael

    2012-07-01

    Full Text Available Abstract Background Multi-locus sequence typing (MLST has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven to divide the population and is simple, robust and facilitates comparison of results between laboratories and over time. Over the last decade, researchers and population health specialists have invested substantial effort in building up public MLST databases for nearly 100 different bacterial species, and these databases contain a wealth of important information linked to MLST sequence types such as time and place of isolation, host or niche, serotype and even clinical or drug resistance profiles. Recent advances in sequencing technology mean it is increasingly feasible to perform bacterial population analysis at the whole genome level. This offers massive gains in resolving power and genetic profiling compared to MLST, and will eventually replace MLST for bacterial typing and population analysis. However given the wealth of data currently available in MLST databases, it is crucial to maintain backwards compatibility with MLST schemes so that new genome analyses can be understood in their proper historical context. Results We present a software tool, SRST, for quick and accurate retrieval of sequence types from short read sets, using inputs easily downloaded from public databases. SRST uses read mapping and an allele assignment score incorporating sequence coverage and variability, to determine the most likely allele at each MLST locus. Analysis of over 3,500 loci in more than 500 publicly accessible Illumina read sets showed SRST to be highly accurate at allele assignment. SRST output is compatible with common analysis tools such as eBURST, Clonal Frame or PhyloViz, allowing easy comparison between novel genome data and MLST data. Alignment, fastq and pileup files can also be generated for novel alleles. Conclusions SRST is a novel

  15. JVM: Java Visual Mapping tool for next generation sequencing read.

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    Yang, Ye; Liu, Juan

    2015-01-01

    We developed a program JVM (Java Visual Mapping) for mapping next generation sequencing read to reference sequence. The program is implemented in Java and is designed to deal with millions of short read generated by sequence alignment using the Illumina sequencing technology. It employs seed index strategy and octal encoding operations for sequence alignments. JVM is useful for DNA-Seq, RNA-Seq when dealing with single-end resequencing. JVM is a desktop application, which supports reads capacity from 1 MB to 10 GB.

  16. High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01.

    Science.gov (United States)

    Hu, XinJun; Li, Ang; Lv, LongXian; Yuan, Chunhui; Guo, Lihua; Jiang, Xiawei; Jiang, Haiyin; Qian, GuiRong; Zheng, BeiWen; Guo, Jing; Li, LanJuan

    2014-06-15

    Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales, class Bacilli and phylum Firmicutes. The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolate from a hospital in China. Here we describe the features of S. cohnii subsp. cohnii strain hu-01, together with the genome sequence and its annotation. This is the first genome sequence of the species Staphylococcus cohnii.

  17. High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01

    OpenAIRE

    Hu, XinJun; Li, Ang; Lv, LongXian; Yuan, Chunhui; Guo, Lihua; Jiang, Xiawei; Jiang, Haiyin; Qian, GuiRong; Zheng, BeiWen; Guo, Jing; Li, LanJuan

    2014-01-01

    Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales , class Bacilli and phylum Firmicutes . The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolate from a hospital in China. Here we describe the features of S. cohnii subsp. cohnii strain hu-01, together with the genome sequence and its annotation. This is the first genom...

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

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    Zdepski Anna

    2011-05-01

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

  19. High quality maize centromere 10 sequence reveals evidence of frequent recombination events

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    Thomas Kai Wolfgruber

    2016-03-01

    Full Text Available The ancestral centromeres of maize contain long stretches of the tandemly arranged CentC repeat. The abundance of tandem DNA repeats and centromeric retrotransposons (CR have presented a significant challenge to completely assembling centromeres using traditional sequencing methods. Here we report a nearly complete assembly of the 1.85 Mb maize centromere 10 from inbred B73 using PacBio technology and BACs from the reference genome project. The error rates estimated from overlapping BAC sequences are 7 x 10-6 and 5 x 10-5 for mismatches and indels, respectively. The number of gaps in the region covered by the reassembly was reduced from 140 in the reference genome to three. Three expressed genes are located between 92 and 477 kb of the inferred ancestral CentC cluster, which lies within the region of highest centromeric repeat density. The improved assembly increased the count of full-length centromeric retrotransposons from 5 to 55 and revealed a 22.7 kb segmental duplication that occurred approximately 121,000 years ago. Our analysis provides evidence of frequent recombination events in the form of partial retrotransposons, deletions within retrotransposons, chimeric retrotransposons, segmental duplications including higher order CentC repeats, a deleted CentC monomer, centromere-proximal inversions, and insertion of mitochondrial sequences. Double-strand DNA break (DSB repair is the most plausible mechanism for these events and may be the major driver of centromere repeat evolution and diversity. This repair appears to be mediated by microhomology, suggesting that tandem repeats may have evolved to facilitate the repair of frequent DSBs in centromeres.

  20. Identifying structural variants using linked-read sequencing data.

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    Elyanow, Rebecca; Wu, Hsin-Ta; Raphael, Benjamin J

    2017-11-03

    Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (~5-10) DNA molecules ~50Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants. We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in a individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification - including two recent methods that also analyze linked-reads - on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes. Software is available at compbio.cs.brown.edu/software. braphael@princeton.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  1. High-Quality Exome Sequencing of Whole-Genome Amplified Neonatal Dried Blood Spot DNA

    DEFF Research Database (Denmark)

    Poulsen, Jesper Buchhave; Lescai, Francesco; Grove, Jakob

    2016-01-01

    Stored neonatal dried blood spot (DBS) samples from neonatal screening programmes are a valuable diagnostic and research resource. Combined with information from national health registries they can be used in population-based studies of genetic diseases. DNA extracted from neonatal DBSs can...... be amplified to obtain micrograms of an otherwise limited resource, referred to as whole-genome amplified DNA (wgaDNA). Here we investigate the robustness of exome sequencing of wgaDNA of neonatal DBS samples. We conducted three pilot studies of seven, eight and seven subjects, respectively. For each subject...... we analysed a neonatal DBS sample and corresponding adult whole-blood (WB) reference sample. Different DNA sample types were prepared for each of the subjects. Pilot 1: wgaDNA of 2x3.2mm neonatal DBSs (DBS_2x3.2) and raw DNA extract of the WB reference sample (WB_ref). Pilot 2: DBS_2x3.2, WB...

  2. High-quality genome sequence and description of Bacillus ndiopicus strain FF3T sp. nov.

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    C.I. Lo

    2015-11-01

    Full Text Available Strain FF3T was isolated from the skin-flora of a 39-year-old healthy Senegalese man. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry did not allow any identification. This strain exhibited a 16S rRNA sequence similarity of 96.8% with Bacillus massiliensis, the phylogenetically closest species with standing nomenclature. Using a polyphasic study made of phenotypic and genomic analyses, strain FF3T was Gram-positive, aeroanaerobic and rod shaped and exhibited a genome of 4 068 720 bp with a G+C content of 37.03% that coded 3982 protein-coding and 67 RNA genes (including four rRNA operons. On the basis of these data, we propose the creation of Bacillus ndiopicus sp. nov.

  3. High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond.

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    Gong, Xianzhe; Skrivergaard, Stig; Korsgaard, Benjamin Smed; Schreiber, Lars; Marshall, Ian P G; Finster, Kai; Schramm, Andreas

    2017-01-01

    Strain S3-2 T , isolated from sediment of a frozen freshwater pond, shares 99% 16S rRNA gene sequence identity with strains of the genus Janthinobacterium . Strain S3-2 T is a facultative anaerobe that lacks the ability to produce violacein but shows antibiotic resistance, psychrotolerance, incomplete denitrification, and fermentation. The draft genome of strain S3-2 T has a size of ~5.8 Mbp and contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties of the strain, the low in silico DNA-DNA hybridization (DDH) values with related genomes (<35%), and the low whole genome-based average nucleotide identity (ANI) (<86%) with other strains within the genus Janthinobacterium, we propose that strain S3-2 T is the type strain (= DSM 102223 = LMG 29653) of a new species within this genus. We propose the name Janthinobacterium psychrotolerans sp. nov. to emphasize the capability of the strain to grow at low temperatures.

  4. Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples.

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    Peck, Michelle A; Sturk-Andreaggi, Kimberly; Thomas, Jacqueline T; Oliver, Robert S; Barritt-Ross, Suzanne; Marshall, Charla

    2018-05-01

    Generating mitochondrial genome (mitogenome) data from reference samples in a rapid and efficient manner is critical to harnessing the greater power of discrimination of the entire mitochondrial DNA (mtDNA) marker. The method of long-range target enrichment, Nextera XT library preparation, and Illumina sequencing on the MiSeq is a well-established technique for generating mitogenome data from high-quality samples. To this end, a validation was conducted for this mitogenome method processing up to 24 samples simultaneously along with analysis in the CLC Genomics Workbench and utilizing the AQME (AFDIL-QIAGEN mtDNA Expert) tool to generate forensic profiles. This validation followed the Federal Bureau of Investigation's Quality Assurance Standards (QAS) for forensic DNA testing laboratories and the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines. The evaluation of control DNA, non-probative samples, blank controls, mixtures, and nonhuman samples demonstrated the validity of this method. Specifically, the sensitivity was established at ≥25 pg of nuclear DNA input for accurate mitogenome profile generation. Unreproducible low-level variants were observed in samples with low amplicon yields. Further, variant quality was shown to be a useful metric for identifying sequencing error and crosstalk. Success of this method was demonstrated with a variety of reference sample substrates and extract types. These studies further demonstrate the advantages of using NGS techniques by highlighting the quantitative nature of heteroplasmy detection. The results presented herein from more than 175 samples processed in ten sequencing runs, show this mitogenome sequencing method and analysis strategy to be valid for the generation of reference data. Copyright © 2018 Elsevier B.V. All rights reserved.

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

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    Russo Luis MS

    2011-05-01

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

  6. A Probabilistic Genome-Wide Gene Reading Frame Sequence Model

    DEFF Research Database (Denmark)

    Have, Christian Theil; Mørk, Søren

    We introduce a new type of probabilistic sequence model, that model the sequential composition of reading frames of genes in a genome. Our approach extends gene finders with a model of the sequential composition of genes at the genome-level -- effectively producing a sequential genome annotation...... as output. The model can be used to obtain the most probable genome annotation based on a combination of i: a gene finder score of each gene candidate and ii: the sequence of the reading frames of gene candidates through a genome. The model --- as well as a higher order variant --- is developed and tested...... and are evaluated by the effect on prediction performance. Since bacterial gene finding to a large extent is a solved problem it forms an ideal proving ground for evaluating the explicit modeling of larger scale gene sequence composition of genomes. We conclude that the sequential composition of gene reading frames...

  7. Haematobia irritans dataset of raw sequence reads from Illumina and Pac Bio sequencing of genomic DNA

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    The genome of the horn fly, Haematobia irritans, was sequenced using Illumina- and Pac Bio-based protocols. Following quality filtering, the raw reads have been deposited at NCBI under the BioProject and BioSample accession numbers PRJNA30967 and SAMN07830356, respectively. The Illumina reads are un...

  8. High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot.

    Science.gov (United States)

    Aberg, Karolina A; Xie, Lin Y; Nerella, Srilaxmi; Copeland, William E; Costello, E Jane; van den Oord, Edwin J C G

    2013-05-01

    The potential importance of DNA methylation in the etiology of complex diseases has led to interest in the development of methylome-wide association studies (MWAS) aimed at interrogating all methylation sites in the human genome. When using blood as biomaterial for a MWAS the DNA is typically extracted directly from fresh or frozen whole blood that was collected via venous puncture. However, DNA extracted from dry blood spots may also be an alternative starting material. In the present study, we apply a methyl-CpG binding domain (MBD) protein enrichment-based technique in combination with next generation sequencing (MBD-seq) to assess the methylation status of the ~27 million CpGs in the human autosomal reference genome. We investigate eight methylomes using DNA from blood spots. This data are compared with 1,500 methylomes previously assayed with the same MBD-seq approach using DNA from whole blood. When investigating the sequence quality and the enrichment profile across biological features, we find that DNA extracted from blood spots gives comparable results with DNA extracted from whole blood. Only if the amount of starting material is ≤ 0.5µg DNA we observe a slight decrease in the assay performance. In conclusion, we show that high quality methylome-wide investigations using MBD-seq can be conducted in DNA extracted from archived dry blood spots without sacrificing quality and without bias in enrichment profile as long as the amount of starting material is sufficient. In general, the amount of DNA extracted from a single blood spot is sufficient for methylome-wide investigations with the MBD-seq approach.

  9. Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.

    Directory of Open Access Journals (Sweden)

    Takeru Nakazato

    Full Text Available High-throughput sequencing technology, also called next-generation sequencing (NGS, has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA. As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called "Gendoo". We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called "DBCLS SRA" (http://sra.dbcls.jp/. This service will improve accessibility to high-quality data from SRA.

  10. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.

    Directory of Open Access Journals (Sweden)

    Christopher A Miller

    2011-01-01

    Full Text Available Copy number alterations are important contributors to many genetic diseases, including cancer. We present the readDepth package for R, which can detect these aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. In addition to achieving higher accuracy than existing packages, our tool runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets. In contrast to other published methods, readDepth does not require the sequencing of a reference sample, and uses a robust statistical model that accounts for overdispersed data. It includes a method for effectively increasing the resolution obtained from low-coverage experiments by utilizing breakpoint information from paired end sequencing to do positional refinement. We also demonstrate a method for inferring copy number using reads generated by whole-genome bisulfite sequencing, thus enabling integrative study of epigenomic and copy number alterations. Finally, we apply this tool to two genomes, showing that it performs well on genomes sequenced to both low and high coverage. The readDepth package runs on Linux and MacOSX, is released under the Apache 2.0 license, and is available at http://code.google.com/p/readdepth/.

  11. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  12. A teaching-learning sequence about weather map reading

    Science.gov (United States)

    Mandrikas, Achilleas; Stavrou, Dimitrios; Skordoulis, Constantine

    2017-07-01

    In this paper a teaching-learning sequence (TLS) introducing pre-service elementary teachers (PET) to weather map reading, with emphasis on wind assignment, is presented. The TLS includes activities about recognition of wind symbols, assignment of wind direction and wind speed on a weather map and identification of wind characteristics in a weather forecast. Sixty PET capabilities and difficulties in understanding weather maps were investigated, using inquiry-based learning activities. The results show that most PET became more capable of reading weather maps and assigning wind direction and speed on them. Our results also show that PET could be guided to understand meteorology concepts useful in everyday life and in teaching their future students.

  13. Real-Time Acquisition of High Quality Face Sequences from an Active Pan-Tilt-Zoom Camera

    DEFF Research Database (Denmark)

    Haque, Mohammad A.; Nasrollahi, Kamal; Moeslund, Thomas B.

    2013-01-01

    -based real-time high-quality face image acquisition system, which utilizes pan-tilt-zoom parameters of a camera to focus on a human face in a scene and employs a face quality assessment method to log the best quality faces from the captured frames. The system consists of four modules: face detection, camera...... control, face tracking, and face quality assessment before logging. Experimental results show that the proposed system can effectively log the high quality faces from the active camera in real-time (an average of 61.74ms was spent per frame) with an accuracy of 85.27% compared to human annotated data.......Traditional still camera-based facial image acquisition systems in surveillance applications produce low quality face images. This is mainly due to the distance between the camera and subjects of interest. Furthermore, people in such videos usually move around, change their head poses, and facial...

  14. A sensitive short read homology search tool for paired-end read sequencing data.

    Science.gov (United States)

    Techa-Angkoon, Prapaporn; Sun, Yanni; Lei, Jikai

    2017-10-16

    Homology search is still a significant step in functional analysis for genomic data. Profile Hidden Markov Model-based homology search has been widely used in protein domain analysis in many different species. In particular, with the fast accumulation of transcriptomic data of non-model species and metagenomic data, profile homology search is widely adopted in integrated pipelines for functional analysis. While the state-of-the-art tool HMMER has achieved high sensitivity and accuracy in domain annotation, the sensitivity of HMMER on short reads declines rapidly. The low sensitivity on short read homology search can lead to inaccurate domain composition and abundance computation. Our experimental results showed that half of the reads were missed by HMMER for a RNA-Seq dataset. Thus, there is a need for better methods to improve the homology search performance for short reads. We introduce a profile homology search tool named Short-Pair that is designed for short paired-end reads. By using an approximate Bayesian approach employing distribution of fragment lengths and alignment scores, Short-Pair can retrieve the missing end and determine true domains. In particular, Short-Pair increases the accuracy in aligning short reads that are part of remote homologs. We applied Short-Pair to a RNA-Seq dataset and a metagenomic dataset and quantified its sensitivity and accuracy on homology search. The experimental results show that Short-Pair can achieve better overall performance than the state-of-the-art methodology of profile homology search. Short-Pair is best used for next-generation sequencing (NGS) data that lack reference genomes. It provides a complementary paired-end read homology search tool to HMMER. The source code is freely available at https://sourceforge.net/projects/short-pair/ .

  15. High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.

    Science.gov (United States)

    Huang, Jing; Qiao, Zi Xu; Tang, Jing Wei; Wang, Gejiao

    2015-01-01

    Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32(T) together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32(T) possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.

  16. SRComp: short read sequence compression using burstsort and Elias omega coding.

    Directory of Open Access Journals (Sweden)

    Jeremy John Selva

    Full Text Available Next-generation sequencing (NGS technologies permit the rapid production of vast amounts of data at low cost. Economical data storage and transmission hence becomes an increasingly important challenge for NGS experiments. In this paper, we introduce a new non-reference based read sequence compression tool called SRComp. It works by first employing a fast string-sorting algorithm called burstsort to sort read sequences in lexicographical order and then Elias omega-based integer coding to encode the sorted read sequences. SRComp has been benchmarked on four large NGS datasets, where experimental results show that it can run 5-35 times faster than current state-of-the-art read sequence compression tools such as BEETL and SCALCE, while retaining comparable compression efficiency for large collections of short read sequences. SRComp is a read sequence compression tool that is particularly valuable in certain applications where compression time is of major concern.

  17. Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life

    DEFF Research Database (Denmark)

    Karst, Soeren M; Dueholm, Morten S; McIlroy, Simon J

    2016-01-01

    Ribosomal RNA (rRNA) genes are the consensus marker for determination of microbial diversity on the planet, invaluable in studies of evolution and, for the past decade, high-throughput sequencing of variable regions of ribosomal RNA genes has become the backbone of most microbial ecology studies...... (SSU) rRNA genes and synthetic long read sequencing by molecular tagging, to generate primer-free, full-length SSU rRNA gene sequences from all domains of life, with a median raw error rate of 0.17%. We generated thousands of full-length SSU rRNA sequences from five well-studied ecosystems (soil, human...... gut, fresh water, anaerobic digestion, and activated sludge) and obtained sequences covering all domains of life and the majority of all described phyla. Interestingly, 30% of all bacterial operational taxonomic units were novel, compared to the SILVA database (less than 97% similarity...

  18. ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data.

    Science.gov (United States)

    Luo, Guan-Zheng; Yang, Wei; Ma, Ying-Ke; Wang, Xiu-Jie

    2014-02-01

    Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets. ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.

  19. Long-read sequencing and de novo assembly of a Chinese genome

    Science.gov (United States)

    Short-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arr...

  20. NanoPack: visualizing and processing long read sequencing data.

    Science.gov (United States)

    De Coster, Wouter; D'Hert, Svenn; Schultz, Darrin T; Cruts, Marc; Van Broeckhoven, Christine

    2018-03-14

    Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools. wouter.decoster@molgen.vib-ua.be. Supplementary tables and figures are available at Bioinformatics online.

  1. The complete genome sequence of Escherichia coli EC958: a high quality reference sequence for the globally disseminated multidrug resistant E. coli O25b:H4-ST131 clone.

    Directory of Open Access Journals (Sweden)

    Brian M Forde

    Full Text Available Escherichia coli ST131 is now recognised as a leading contributor to urinary tract and bloodstream infections in both community and clinical settings. Here we present the complete, annotated genome of E. coli EC958, which was isolated from the urine of a patient presenting with a urinary tract infection in the Northwest region of England and represents the most well characterised ST131 strain. Sequencing was carried out using the Pacific Biosciences platform, which provided sufficient depth and read-length to produce a complete genome without the need for other technologies. The discovery of spurious contigs within the assembly that correspond to site-specific inversions in the tail fibre regions of prophages demonstrates the potential for this technology to reveal dynamic evolutionary mechanisms. E. coli EC958 belongs to the major subgroup of ST131 strains that produce the CTX-M-15 extended spectrum β-lactamase, are fluoroquinolone resistant and encode the fimH30 type 1 fimbrial adhesin. This subgroup includes the Indian strain NA114 and the North American strain JJ1886. A comparison of the genomes of EC958, JJ1886 and NA114 revealed that differences in the arrangement of genomic islands, prophages and other repetitive elements in the NA114 genome are not biologically relevant and are due to misassembly. The availability of a high quality uropathogenic E. coli ST131 genome provides a reference for understanding this multidrug resistant pathogen and will facilitate novel functional, comparative and clinical studies of the E. coli ST131 clonal lineage.

  2. Types and sequences of self-regulated reading of low-achieving adolescents in relation to reading task achievement

    NARCIS (Netherlands)

    de Milliano, Ilona; van Gelderen, Amos; Sleegers, P.J.C.

    2016-01-01

    This study examines the relationship between types and sequences of self-regulated reading activities in task-oriented reading with quality of task achievement of 51 low-achieving adolescents (Grade 8). The study used think aloud combined with video observations to analyse the students' approach of

  3. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain.

    Science.gov (United States)

    Osman, Wan Adnawani Meor; van Berkum, Peter; León-Barrios, Milagros; Velázquez, Encarna; Elia, Patrick; Tian, Rui; Ardley, Julie; Gollagher, Margaret; Seshadri, Rekha; Reddy, T B K; Ivanova, Natalia; Woyke, Tanja; Pati, Amrita; Markowitz, Victor; Baeshen, Mohamed N; Baeshen, Naseebh Nabeeh; Kyrpides, Nikos; Reeve, Wayne

    2017-01-01

    10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata . This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T , 10.1601/nm.1334 A 321 T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T , based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata -nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic

  4. PCR-Free Enrichment of Mitochondrial DNA from Human Blood and Cell Lines for High Quality Next-Generation DNA Sequencing.

    Directory of Open Access Journals (Sweden)

    Meetha P Gould

    Full Text Available Recent advances in sequencing technology allow for accurate detection of mitochondrial sequence variants, even those in low abundance at heteroplasmic sites. Considerable sequencing cost savings can be achieved by enriching samples for mitochondrial (relative to nuclear DNA. Reduction in nuclear DNA (nDNA content can also help to avoid false positive variants resulting from nuclear mitochondrial sequences (numts. We isolate intact mitochondrial organelles from both human cell lines and blood components using two separate methods: a magnetic bead binding protocol and differential centrifugation. DNA is extracted and further enriched for mitochondrial DNA (mtDNA by an enzyme digest. Only 1 ng of the purified DNA is necessary for library preparation and next generation sequence (NGS analysis. Enrichment methods are assessed and compared using mtDNA (versus nDNA content as a metric, measured by using real-time quantitative PCR and NGS read analysis. Among the various strategies examined, the optimal is differential centrifugation isolation followed by exonuclease digest. This strategy yields >35% mtDNA reads in blood and cell lines, which corresponds to hundreds-fold enrichment over baseline. The strategy also avoids false variant calls that, as we show, can be induced by the long-range PCR approaches that are the current standard in enrichment procedures. This optimization procedure allows mtDNA enrichment for efficient and accurate massively parallel sequencing, enabling NGS from samples with small amounts of starting material. This will decrease costs by increasing the number of samples that may be multiplexed, ultimately facilitating efforts to better understand mitochondria-related diseases.

  5. Camera pose refinement by matching uncertain 3D building models with thermal infrared image sequences for high quality texture extraction

    Science.gov (United States)

    Iwaszczuk, Dorota; Stilla, Uwe

    2017-10-01

    Thermal infrared (TIR) images are often used to picture damaged and weak spots in the insulation of the building hull, which is widely used in thermal inspections of buildings. Such inspection in large-scale areas can be carried out by combining TIR imagery and 3D building models. This combination can be achieved via texture mapping. Automation of texture mapping avoids time consuming imaging and manually analyzing each face independently. It also provides a spatial reference for façade structures extracted in the thermal textures. In order to capture all faces, including the roofs, façades, and façades in the inner courtyard, an oblique looking camera mounted on a flying platform is used. Direct geo-referencing is usually not sufficient for precise texture extraction. In addition, 3D building models have also uncertain geometry. In this paper, therefore, methodology for co-registration of uncertain 3D building models with airborne oblique view images is presented. For this purpose, a line-based model-to-image matching is developed, in which the uncertainties of the 3D building model, as well as of the image features are considered. Matched linear features are used for the refinement of the exterior orientation parameters of the camera in order to ensure optimal co-registration. Moreover, this study investigates whether line tracking through the image sequence supports the matching. The accuracy of the extraction and the quality of the textures are assessed. For this purpose, appropriate quality measures are developed. The tests showed good results on co-registration, particularly in cases where tracking between the neighboring frames had been applied.

  6. De novo assembly of human genomes with massively parallel short read sequencing

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Zhu, Hongmei; Ruan, Jue

    2010-01-01

    genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities...... for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way....

  7. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

    Science.gov (United States)

    Nowrousian, Minou; Stajich, Jason E; Chu, Meiling; Engh, Ines; Espagne, Eric; Halliday, Karen; Kamerewerd, Jens; Kempken, Frank; Knab, Birgit; Kuo, Hsiao-Che; Osiewacz, Heinz D; Pöggeler, Stefanie; Read, Nick D; Seiler, Stephan; Smith, Kristina M; Zickler, Denise; Kück, Ulrich; Freitag, Michael

    2010-04-08

    Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb) with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data can be used for

  8. De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.

    Directory of Open Access Journals (Sweden)

    Minou Nowrousian

    2010-04-01

    Full Text Available Filamentous fungi are of great importance in ecology, agriculture, medicine, and biotechnology. Thus, it is not surprising that genomes for more than 100 filamentous fungi have been sequenced, most of them by Sanger sequencing. While next-generation sequencing techniques have revolutionized genome resequencing, e.g. for strain comparisons, genetic mapping, or transcriptome and ChIP analyses, de novo assembly of eukaryotic genomes still presents significant hurdles, because of their large size and stretches of repetitive sequences. Filamentous fungi contain few repetitive regions in their 30-90 Mb genomes and thus are suitable candidates to test de novo genome assembly from short sequence reads. Here, we present a high-quality draft sequence of the Sordaria macrospora genome that was obtained by a combination of Illumina/Solexa and Roche/454 sequencing. Paired-end Solexa sequencing of genomic DNA to 85-fold coverage and an additional 10-fold coverage by single-end 454 sequencing resulted in approximately 4 Gb of DNA sequence. Reads were assembled to a 40 Mb draft version (N50 of 117 kb with the Velvet assembler. Comparative analysis with Neurospora genomes increased the N50 to 498 kb. The S. macrospora genome contains even fewer repeat regions than its closest sequenced relative, Neurospora crassa. Comparison with genomes of other fungi showed that S. macrospora, a model organism for morphogenesis and meiosis, harbors duplications of several genes involved in self/nonself-recognition. Furthermore, S. macrospora contains more polyketide biosynthesis genes than N. crassa. Phylogenetic analyses suggest that some of these genes may have been acquired by horizontal gene transfer from a distantly related ascomycete group. Our study shows that, for typical filamentous fungi, de novo assembly of genomes from short sequence reads alone is feasible, that a mixture of Solexa and 454 sequencing substantially improves the assembly, and that the resulting data

  9. Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.

    Science.gov (United States)

    Huson, Daniel H; Tappu, Rewati; Bazinet, Adam L; Xie, Chao; Cummings, Michael P; Nieselt, Kay; Williams, Rohan

    2017-01-25

    Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. However, for some questions, only specific genes of interest need to be assembled. This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes. We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. Genes are assembled on the fly, based on the alignment of all reads against a protein reference database such as NCBI-nr. Specifically, the user selects a gene family based on a classification such as KEGG and all reads binned to that gene family are assembled. Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered. Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way.

  10. TagDust2: a generic method to extract reads from sequencing data.

    Science.gov (United States)

    Lassmann, Timo

    2015-01-28

    Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads produced by sequencing instruments. The presence of barcodes, adaptors and artifacts subject to sequencing errors makes this step non-trivial. Here I present TagDust2, a generic approach utilizing a library of hidden Markov models (HMM) to accurately extract reads from a wide array of possible read architectures. TagDust2 extracts more reads of higher quality compared to other approaches. Processing of multiplexed single, paired end and libraries containing unique molecular identifiers is fully supported. Two additional post processing steps are included to exclude known contaminants and filter out low complexity sequences. Finally, TagDust2 can automatically detect the library type of sequenced data from a predefined selection. Taken together TagDust2 is a feature rich, flexible and adaptive solution to go from raw to mappable NGS reads in a single step. The ability to recognize and record the contents of raw reads will help to automate and demystify the initial, and often poorly documented, steps in NGS data analysis pipelines. TagDust2 is freely available at: http://tagdust.sourceforge.net .

  11. Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

    Directory of Open Access Journals (Sweden)

    Trimble William L

    2012-07-01

    Full Text Available Abstract Background Gene prediction algorithms (or gene callers are an essential tool for analyzing shotgun nucleic acid sequence data. Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume of data by identifying the most likely reading frame for a fragment, permitting the out-of-frame translations to be ignored. In this study we evaluate five widely used ab initio gene-calling algorithms—FragGeneScan, MetaGeneAnnotator, MetaGeneMark, Orphelia, and Prodigal—for accuracy on short (75–1000 bp fragments containing sequence error from previously published artificial data and “real” metagenomic datasets. Results While gene prediction tools have similar accuracies predicting genes on error-free fragments, in the presence of sequencing errors considerable differences between tools become evident. For error-containing short reads, FragGeneScan finds more prokaryotic coding regions than does MetaGeneAnnotator, MetaGeneMark, Orphelia, or Prodigal. This improved detection of genes in error-containing fragments, however, comes at the cost of much lower (50% specificity and overprediction of genes in noncoding regions. Conclusions Ab initio gene callers offer a significant reduction in the computational burden of annotating individual nucleic acid reads and are used in many metagenomic annotation systems. For predicting reading frames on raw reads, we find the hidden Markov model approach in FragGeneScan is more sensitive than other gene prediction tools, while Prodigal, MGA, and MGM are better suited for higher-quality sequences such as assembled contigs.

  12. Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads

    Directory of Open Access Journals (Sweden)

    Chengxi Ye

    2016-06-01

    Full Text Available Motivation. The third generation sequencing (3GS technology generates long sequences of thousands of bases. However, its current error rates are estimated in the range of 15–40%, significantly higher than those of the prevalent next generation sequencing (NGS technologies (less than 1%. Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high-quality sequences that need to be extracted from these long but erroneous 3GS sequences. Results. We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly. Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region. The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence. Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency. Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies. With only 30× PacBio data, Sparc can reach a consensus with error rate <0.5%. With the more challenging Oxford Nanopore data, Sparc can also achieve similar error rate when combined with NGS data. Compared with the existing approaches, Sparc calculates the consensus with higher accuracy, and uses approximately 80% less memory and time. Availability. The source code is available for download at https://github.com/yechengxi/Sparc.

  13. Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.

    Directory of Open Access Journals (Sweden)

    Matt J Cahill

    Full Text Available BACKGROUND: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. METHODOLOGY/PRINCIPAL FINDINGS: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. CONCLUSIONS: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length.

  14. Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

    KAUST Repository

    Cahill, Matt J.

    2010-07-12

    Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.

  15. Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

    KAUST Repository

    Cahill, Matt J.; Kö ser, Claudio U.; Ross, Nicholas E.; Archer, John A.C.

    2010-01-01

    Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.

  16. Complete Genome Sequence of Bacillus subtilis Strain DKU_NT_03, Isolated from a Traditional Korean Food Using Soybean (Chung-gook-jang) for High-Quality Nattokinase Activity.

    Science.gov (United States)

    Jeong, Hee-Won; Bang, Man-Seok; Lee, Yea-Jin; Lee, Su Ji; Lee, Sang-Cheol; Shin, Jang-In; Oh, Chung-Hun

    2018-06-21

    We present here the complete genome sequence of Bacillus subtilis strain DKU_NT_03 isolated from the traditional Korean food chung-gook-jang, which is made from soybeans. This strain was chosen to identify genetic factors with high-quality nattokinase activity. Copyright © 2018 Jeong et al.

  17. SeqEntropy: genome-wide assessment of repeats for short read sequencing.

    Directory of Open Access Journals (Sweden)

    Hsueh-Ting Chu

    Full Text Available BACKGROUND: Recent studies on genome assembly from short-read sequencing data reported the limitation of this technology to reconstruct the entire genome even at very high depth coverage. We investigated the limitation from the perspective of information theory to evaluate the effect of repeats on short-read genome assembly using idealized (error-free reads at different lengths. METHODOLOGY/PRINCIPAL FINDINGS: We define a metric H(k to be the entropy of sequencing reads at a read length k and use the relative loss of entropy ΔH(k to measure the impact of repeats for the reconstruction of whole-genome from sequences of length k. In our experiments, we found that entropy loss correlates well with de-novo assembly coverage of a genome, and a score of ΔH(k>1% indicates a severe loss in genome reconstruction fidelity. The minimal read lengths to achieve ΔH(k<1% are different for various organisms and are independent of the genome size. For example, in order to meet the threshold of ΔH(k<1%, a read length of 60 bp is needed for the sequencing of human genome (3.2 10(9 bp and 320 bp for the sequencing of fruit fly (1.8×10(8 bp. We also calculated the ΔH(k scores for 2725 prokaryotic chromosomes and plasmids at several read lengths. Our results indicate that the levels of repeats in different genomes are diverse and the entropy of sequencing reads provides a measurement for the repeat structures. CONCLUSIONS/SIGNIFICANCE: The proposed entropy-based measurement, which can be calculated in seconds to minutes in most cases, provides a rapid quantitative evaluation on the limitation of idealized short-read genome sequencing. Moreover, the calculation can be parallelized to scale up to large euakryotic genomes. This approach may be useful to tune the sequencing parameters to achieve better genome assemblies when a closely related genome is already available.

  18. An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq.

    Science.gov (United States)

    Yuan, Yongxian; Xu, Huaiqian; Leung, Ross Ka-Kit

    2016-05-26

    Previous studies compared running cost, time and other performance measures of popular sequencing platforms. However, comprehensive assessment of library construction and analysis protocols for Proton sequencing platform remains unexplored. Unlike Illumina sequencing platforms, Proton reads are heterogeneous in length and quality. When sequencing data from different platforms are combined, this can result in reads with various read length. Whether the performance of the commonly used software for handling such kind of data is satisfactory is unknown. By using universal human reference RNA as the initial material, RNaseIII and chemical fragmentation methods in library construction showed similar result in gene and junction discovery number and expression level estimated accuracy. In contrast, sequencing quality, read length and the choice of software affected mapping rate to a much larger extent. Unspliced aligner TMAP attained the highest mapping rate (97.27 % to genome, 86.46 % to transcriptome), though 47.83 % of mapped reads were clipped. Long reads could paradoxically reduce mapping in junctions. With reference annotation guide, the mapping rate of TopHat2 significantly increased from 75.79 to 92.09 %, especially for long (>150 bp) reads. Sailfish, a k-mer based gene expression quantifier attained highly consistent results with that of TaqMan array and highest sensitivity. We provided for the first time, the reference statistics of library preparation methods, gene detection and quantification and junction discovery for RNA-Seq by the Ion Proton platform. Chemical fragmentation performed equally well with the enzyme-based one. The optimal Ion Proton sequencing options and analysis software have been evaluated.

  19. Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.

    Directory of Open Access Journals (Sweden)

    Laurent Gautier

    Full Text Available Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet, perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc.

  20. Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

    Science.gov (United States)

    Gautier, Laurent; Lund, Ole

    2013-01-01

    Cheap DNA sequencing may soon become routine not only for human genomes but also for practically anything requiring the identification of living organisms from their DNA: tracking of infectious agents, control of food products, bioreactors, or environmental samples. We propose a novel general approach to the analysis of sequencing data where a reference genome does not have to be specified. Using a distributed architecture we are able to query a remote server for hints about what the reference might be, transferring a relatively small amount of data. Our system consists of a server with known reference DNA indexed, and a client with raw sequencing reads. The client sends a sample of unidentified reads, and in return receives a list of matching references. Sequences for the references can be retrieved and used for exhaustive computation on the reads, such as alignment. To demonstrate this approach we have implemented a web server, indexing tens of thousands of publicly available genomes and genomic regions from various organisms and returning lists of matching hits from query sequencing reads. We have also implemented two clients: one running in a web browser, and one as a python script. Both are able to handle a large number of sequencing reads and from portable devices (the browser-based running on a tablet), perform its task within seconds, and consume an amount of bandwidth compatible with mobile broadband networks. Such client-server approaches could develop in the future, allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc. PMID:24391826

  1. Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads

    DEFF Research Database (Denmark)

    Mourier, Tobias; Mollerup, Sarah; Vinner, Lasse

    2015-01-01

    From Illumina sequencing of DNA from brain and liver tissue from the lion, Panthera leo, and tumor samples from the pike-perch, Sander lucioperca, we obtained two assembled sequence contigs with similarity to known retroviruses. Phylogenetic analyses suggest that the pike-perch retrovirus belongs...... to the epsilonretroviruses, and the lion retrovirus to the gammaretroviruses. To determine if these novel retroviral sequences originate from an endogenous retrovirus or from a recently integrated exogenous retrovirus, we assessed the genetic diversity of the parental sequences from which the short Illumina reads...

  2. BarraCUDA - a fast short read sequence aligner using graphics processing units

    Directory of Open Access Journals (Sweden)

    Klus Petr

    2012-01-01

    Full Text Available Abstract Background With the maturation of next-generation DNA sequencing (NGS technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU, extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http://seqbarracuda.sf.net

  3. BarraCUDA - a fast short read sequence aligner using graphics processing units

    LENUS (Irish Health Repository)

    Klus, Petr

    2012-01-13

    Abstract Background With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. Findings Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. Conclusions BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available from http:\\/\\/seqbarracuda.sf.net

  4. Extraction of High Molecular Weight DNA from Fungal Rust Spores for Long Read Sequencing.

    Science.gov (United States)

    Schwessinger, Benjamin; Rathjen, John P

    2017-01-01

    Wheat rust fungi are complex organisms with a complete life cycle that involves two different host plants and five different spore types. During the asexual infection cycle on wheat, rusts produce massive amounts of dikaryotic urediniospores. These spores are dikaryotic (two nuclei) with each nucleus containing one haploid genome. This dikaryotic state is likely to contribute to their evolutionary success, making them some of the major wheat pathogens globally. Despite this, most published wheat rust genomes are highly fragmented and contain very little haplotype-specific sequence information. Current long-read sequencing technologies hold great promise to provide more contiguous and haplotype-phased genome assemblies. Long reads are able to span repetitive regions and phase structural differences between the haplomes. This increased genome resolution enables the identification of complex loci and the study of genome evolution beyond simple nucleotide polymorphisms. Long-read technologies require pure high molecular weight DNA as an input for sequencing. Here, we describe a DNA extraction protocol for rust spores that yields pure double-stranded DNA molecules with molecular weight of >50 kilo-base pairs (kbp). The isolated DNA is of sufficient purity for PacBio long-read sequencing, but may require additional purification for other sequencing technologies such as Nanopore and 10× Genomics.

  5. Centroid based clustering of high throughput sequencing reads based on n-mer counts.

    Science.gov (United States)

    Solovyov, Alexander; Lipkin, W Ian

    2013-09-08

    Many problems in computational biology require alignment-free sequence comparisons. One of the common tasks involving sequence comparison is sequence clustering. Here we apply methods of alignment-free comparison (in particular, comparison using sequence composition) to the challenge of sequence clustering. We study several centroid based algorithms for clustering sequences based on word counts. Study of their performance shows that using k-means algorithm with or without the data whitening is efficient from the computational point of view. A higher clustering accuracy can be achieved using the soft expectation maximization method, whereby each sequence is attributed to each cluster with a specific probability. We implement an open source tool for alignment-free clustering. It is publicly available from github: https://github.com/luscinius/afcluster. We show the utility of alignment-free sequence clustering for high throughput sequencing analysis despite its limitations. In particular, it allows one to perform assembly with reduced resources and a minimal loss of quality. The major factor affecting performance of alignment-free read clustering is the length of the read.

  6. Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

    Science.gov (United States)

    Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Cornelissen, Marion; Kellam, Paul; Reiss, Peter

    2018-01-01

    Abstract Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also

  7. Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle

    DEFF Research Database (Denmark)

    Mesbah-Uddin, Md; Guldbrandtsen, Bernt; Lund, Mogens Sandø

    2018-01-01

    We presented a deletion genotyping (copy-number estimation) method that leverages population-scale whole genome sequence variants data from 1K bull genomes project (1KBGP) to build reference panel for imputation. To estimate deletion-genotype likelihood, we extracted read-depth (RD) data of all...

  8. Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads.

    Directory of Open Access Journals (Sweden)

    Jovan Rebolledo-Mendez

    Full Text Available The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight's half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects' and Twilight's genome or due to errors in the reference. EquCab2 is regarded as "The Twilight Assembly." The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies

  9. Accurate estimation of short read mapping quality for next-generation genome sequencing

    Science.gov (United States)

    Ruffalo, Matthew; Koyutürk, Mehmet; Ray, Soumya; LaFramboise, Thomas

    2012-01-01

    Motivation: Several software tools specialize in the alignment of short next-generation sequencing reads to a reference sequence. Some of these tools report a mapping quality score for each alignment—in principle, this quality score tells researchers the likelihood that the alignment is correct. However, the reported mapping quality often correlates weakly with actual accuracy and the qualities of many mappings are underestimated, encouraging the researchers to discard correct mappings. Further, these low-quality mappings tend to correlate with variations in the genome (both single nucleotide and structural), and such mappings are important in accurately identifying genomic variants. Approach: We develop a machine learning tool, LoQuM (LOgistic regression tool for calibrating the Quality of short read mappings, to assign reliable mapping quality scores to mappings of Illumina reads returned by any alignment tool. LoQuM uses statistics on the read (base quality scores reported by the sequencer) and the alignment (number of matches, mismatches and deletions, mapping quality score returned by the alignment tool, if available, and number of mappings) as features for classification and uses simulated reads to learn a logistic regression model that relates these features to actual mapping quality. Results: We test the predictions of LoQuM on an independent dataset generated by the ART short read simulation software and observe that LoQuM can ‘resurrect’ many mappings that are assigned zero quality scores by the alignment tools and are therefore likely to be discarded by researchers. We also observe that the recalibration of mapping quality scores greatly enhances the precision of called single nucleotide polymorphisms. Availability: LoQuM is available as open source at http://compbio.case.edu/loqum/. Contact: matthew.ruffalo@case.edu. PMID:22962451

  10. High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea

    KAUST Repository

    Ngugi, David

    2018-05-09

    Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in deep hypersaline anoxic brines around the globe. Recently, the genome sequences of two cultivated representatives from hypersaline soda lake sediments were published. Here, we present a single-cell genome sequence from Nereus Deep in the Red Sea that represents a putatively novel family within SA1.

  11. High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea

    KAUST Repository

    Ngugi, David; Stingl, Ulrich

    2018-01-01

    Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in deep hypersaline anoxic brines around the globe. Recently, the genome sequences of two cultivated representatives from hypersaline soda lake sediments were published. Here, we present a single-cell genome sequence from Nereus Deep in the Red Sea that represents a putatively novel family within SA1.

  12. MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.

    Science.gov (United States)

    Pericard, Pierre; Dufresne, Yoann; Couderc, Loïc; Blanquart, Samuel; Touzet, Hélène

    2018-02-15

    Advances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution. We designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered fractions and is suitable to provide improved assemblies for precise taxonomic assignments. https://github.com/bonsai-team/matam. pierre.pericard@gmail.com or helene.touzet@univ-lille1.fr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  13. Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

    Energy Technology Data Exchange (ETDEWEB)

    White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya; Zucker, Jeremy D.; Brislawn, Colin J.; Nicora, Carrie D.; Fansler, Sarah J.; Glaesemann, Kurt R.; Glass, Kevin; Jansson, Janet K.; Langille, Morgan

    2016-06-28

    ABSTRACT

    Soil metagenomics has been touted as the “grand challenge” for metagenomics, as the high microbial diversity and spatial heterogeneity of soils make them unamenable to current assembly platforms. Here, we aimed to improve soil metagenomic sequence assembly by applying the Moleculo synthetic long-read sequencing technology. In total, we obtained 267 Gbp of raw sequence data from a native prairie soil; these data included 109.7 Gbp of short-read data (~100 bp) from the Joint Genome Institute (JGI), an additional 87.7 Gbp of rapid-mode read data (~250 bp), plus 69.6 Gbp (>1.5 kbp) from Moleculo sequencing. The Moleculo data alone yielded over 5,600 reads of >10 kbp in length, and over 95% of the unassembled reads mapped to contigs of >1.5 kbp. Hybrid assembly of all data resulted in more than 10,000 contigs over 10 kbp in length. We mapped three replicate metatranscriptomes derived from the same parent soil to the Moleculo subassembly and found that 95% of the predicted genes, based on their assignments to Enzyme Commission (EC) numbers, were expressed. The Moleculo subassembly also enabled binning of >100 microbial genome bins. We obtained via direct binning the first complete genome, that of “CandidatusPseudomonas sp. strain JKJ-1” from a native soil metagenome. By mapping metatranscriptome sequence reads back to the bins, we found that several bins corresponding to low-relative-abundanceAcidobacteriawere highly transcriptionally active, whereas bins corresponding to high-relative-abundanceVerrucomicrobiawere not. These results demonstrate that Moleculo sequencing provides a significant advance for resolving complex soil microbial communities.

    IMPORTANCESoil microorganisms carry out key processes for life on our planet, including cycling of carbon and other nutrients and supporting growth of plants. However, there is poor molecular-level understanding of their

  14. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.

    Science.gov (United States)

    Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo; Zhu, Shilin; Shi, Daihu; McDill, Joshua; Yang, Linfeng; Hawkins, Simon; Neutelings, Godfrey; Datla, Raju; Lambert, Georgina; Galbraith, David W; Grassa, Christopher J; Geraldes, Armando; Cronk, Quentin C; Cullis, Christopher; Dash, Prasanta K; Kumar, Polumetla A; Cloutier, Sylvie; Sharpe, Andrew G; Wong, Gane K-S; Wang, Jun; Deyholos, Michael K

    2012-11-01

    Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  15. Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias

    DEFF Research Database (Denmark)

    Karst, Søren Michael; Dueholm, Morten Simonsen; McIlroy, Simon Jon

    2018-01-01

    Small subunit ribosomal RNA (SSU rRNA) genes, 16S in bacteria and 18S in eukaryotes, have been the standard phylogenetic markers used to characterize microbial diversity and evolution for decades. However, the reference databases of full-length SSU rRNA gene sequences are skewed to well-studied e...

  16. Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses.

    Directory of Open Access Journals (Sweden)

    Arthur W Pightling

    Full Text Available The wide availability of whole-genome sequencing (WGS and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i depth of sequencing coverage, ii choice of reference-guided short-read sequence assembler, iii choice of reference genome, and iv whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT, using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming. We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers

  17. SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.

    Science.gov (United States)

    Tsuchiya, Mariko; Amano, Kojiro; Abe, Masaya; Seki, Misato; Hase, Sumitaka; Sato, Kengo; Sakakibara, Yasubumi

    2016-06-15

    Deep sequencing of the transcripts of regulatory non-coding RNA generates footprints of post-transcriptional processes. After obtaining sequence reads, the short reads are mapped to a reference genome, and specific mapping patterns can be detected called read mapping profiles, which are distinct from random non-functional degradation patterns. These patterns reflect the maturation processes that lead to the production of shorter RNA sequences. Recent next-generation sequencing studies have revealed not only the typical maturation process of miRNAs but also the various processing mechanisms of small RNAs derived from tRNAs and snoRNAs. We developed an algorithm termed SHARAKU to align two read mapping profiles of next-generation sequencing outputs for non-coding RNAs. In contrast with previous work, SHARAKU incorporates the primary and secondary sequence structures into an alignment of read mapping profiles to allow for the detection of common processing patterns. Using a benchmark simulated dataset, SHARAKU exhibited superior performance to previous methods for correctly clustering the read mapping profiles with respect to 5'-end processing and 3'-end processing from degradation patterns and in detecting similar processing patterns in deriving the shorter RNAs. Further, using experimental data of small RNA sequencing for the common marmoset brain, SHARAKU succeeded in identifying the significant clusters of read mapping profiles for similar processing patterns of small derived RNA families expressed in the brain. The source code of our program SHARAKU is available at http://www.dna.bio.keio.ac.jp/sharaku/, and the simulated dataset used in this work is available at the same link. Accession code: The sequence data from the whole RNA transcripts in the hippocampus of the left brain used in this work is available from the DNA DataBank of Japan (DDBJ) Sequence Read Archive (DRA) under the accession number DRA004502. yasu@bio.keio.ac.jp Supplementary data are available

  18. Improving transcriptome assembly through error correction of high-throughput sequence reads

    Directory of Open Access Journals (Sweden)

    Matthew D. MacManes

    2013-07-01

    Full Text Available The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on and, while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated and empiric dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, and should be applied to all datasets. A complete collection of commands which will allow for the production of Reptile corrected reads is available at https://github.com/macmanes/error_correction/tree/master/scripts and as File S1.

  19. A tale of two sequences: microRNA-target chimeric reads.

    Science.gov (United States)

    Broughton, James P; Pasquinelli, Amy E

    2016-04-04

    In animals, a functional interaction between a microRNA (miRNA) and its target RNA requires only partial base pairing. The limited number of base pair interactions required for miRNA targeting provides miRNAs with broad regulatory potential and also makes target prediction challenging. Computational approaches to target prediction have focused on identifying miRNA target sites based on known sequence features that are important for canonical targeting and may miss non-canonical targets. Current state-of-the-art experimental approaches, such as CLIP-seq (cross-linking immunoprecipitation with sequencing), PAR-CLIP (photoactivatable-ribonucleoside-enhanced CLIP), and iCLIP (individual-nucleotide resolution CLIP), require inference of which miRNA is bound at each site. Recently, the development of methods to ligate miRNAs to their target RNAs during the preparation of sequencing libraries has provided a new tool for the identification of miRNA target sites. The chimeric, or hybrid, miRNA-target reads that are produced by these methods unambiguously identify the miRNA bound at a specific target site. The information provided by these chimeric reads has revealed extensive non-canonical interactions between miRNAs and their target mRNAs, and identified many novel interactions between miRNAs and noncoding RNAs.

  20. When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality.

    Science.gov (United States)

    Lonardi, Stefano; Mirebrahim, Hamid; Wanamaker, Steve; Alpert, Matthew; Ciardo, Gianfranco; Duma, Denisa; Close, Timothy J

    2015-09-15

    As the invention of DNA sequencing in the 70s, computational biologists have had to deal with the problem of de novo genome assembly with limited (or insufficient) depth of sequencing. In this work, we investigate the opposite problem, that is, the challenge of dealing with excessive depth of sequencing. We explore the effect of ultra-deep sequencing data in two domains: (i) the problem of decoding reads to bacterial artificial chromosome (BAC) clones (in the context of the combinatorial pooling design we have recently proposed), and (ii) the problem of de novo assembly of BAC clones. Using real ultra-deep sequencing data, we show that when the depth of sequencing increases over a certain threshold, sequencing errors make these two problems harder and harder (instead of easier, as one would expect with error-free data), and as a consequence the quality of the solution degrades with more and more data. For the first problem, we propose an effective solution based on 'divide and conquer': we 'slice' a large dataset into smaller samples of optimal size, decode each slice independently, and then merge the results. Experimental results on over 15 000 barley BACs and over 4000 cowpea BACs demonstrate a significant improvement in the quality of the decoding and the final assembly. For the second problem, we show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencing data. Python scripts to process slices and resolve decoding conflicts are available from http://goo.gl/YXgdHT; software Hashfilter can be downloaded from http://goo.gl/MIyZHs stelo@cs.ucr.edu or timothy.close@ucr.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. RNA-Seq analysis and gene discovery of Andrias davidianus using Illumina short read sequencing.

    Directory of Open Access Journals (Sweden)

    Fenggang Li

    Full Text Available The Chinese giant salamander, Andrias davidianus, is an important species in the course of evolution; however, there is insufficient genomic data in public databases for understanding its immunologic mechanisms. High-throughput transcriptome sequencing is necessary to generate an enormous number of transcript sequences from A. davidianus for gene discovery. In this study, we generated more than 40 million reads from samples of spleen and skin tissue using the Illumina paired-end sequencing technology. De novo assembly yielded 87,297 transcripts with a mean length of 734 base pairs (bp. Based on the sequence similarities, searching with known proteins, 38,916 genes were identified. Gene enrichment analysis determined that 981 transcripts were assigned to the immune system. Tissue-specific expression analysis indicated that 443 of transcripts were specifically expressed in the spleen and skin. Among these transcripts, 147 transcripts were found to be involved in immune responses and inflammatory reactions, such as fucolectin, β-defensins and lymphotoxin beta. Eight tissue-specific genes were selected for validation using real time reverse transcription quantitative PCR (qRT-PCR. The results showed that these genes were significantly more expressed in spleen and skin than in other tissues, suggesting that these genes have vital roles in the immune response. This work provides a comprehensive genomic sequence resource for A. davidianus and lays the foundation for future research on the immunologic and disease resistance mechanisms of A. davidianus and other amphibians.

  2. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

    DEFF Research Database (Denmark)

    Wang, Zhiwen; Hobson, Neil; Galindo, Leonardo

    2012-01-01

    Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp...... these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species....

  3. Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion.

    Science.gov (United States)

    Cohrs, Randall J; Lee, Katherine S; Beach, Addilynn; Sanford, Bridget; Baird, Nicholas L; Como, Christina; Graybill, Chiharu; Jones, Dallas; Tekeste, Eden; Ballard, Mitchell; Chen, Xiaomi; Yalacki, David; Frietze, Seth; Jones, Kenneth; Lenac Rovis, Tihana; Jonjić, Stipan; Haas, Jürgen; Gilden, Don

    2017-10-15

    The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture. IMPORTANCE Viruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiple in vitro passages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture. Copyright © 2017 American Society for Microbiology.

  4. Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing.

    Science.gov (United States)

    Feehan, Joanna M; Scheibel, Katherine E; Bourras, Salim; Underwood, William; Keller, Beat; Somerville, Shauna C

    2017-03-31

    The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum. The protocol described includes mechanical disruption of spores followed by an optimized phenol/chloroform genomic DNA extraction. A typical yield was 7 µg DNA per 150 mg conidia. The genomic DNA that is isolated using this procedure is suitable for long-read sequencing (i.e., > 48.5 kbp). Quality control measures to ensure the size, yield, and purity of the genomic DNA are also described in this method. Sequencing of the genomic DNA of the quality described here will allow for the assembly and comparison of multiple powdery mildew genomes, which in turn will lead to a better understanding and improved control of this agricultural pathogen.

  5. Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment.

    Science.gov (United States)

    Baichoo, Shakuntala; Ouzounis, Christos A

    A multitude of algorithms for sequence comparison, short-read assembly and whole-genome alignment have been developed in the general context of molecular biology, to support technology development for high-throughput sequencing, numerous applications in genome biology and fundamental research on comparative genomics. The computational complexity of these algorithms has been previously reported in original research papers, yet this often neglected property has not been reviewed previously in a systematic manner and for a wider audience. We provide a review of space and time complexity of key sequence analysis algorithms and highlight their properties in a comprehensive manner, in order to identify potential opportunities for further research in algorithm or data structure optimization. The complexity aspect is poised to become pivotal as we will be facing challenges related to the continuous increase of genomic data on unprecedented scales and complexity in the foreseeable future, when robust biological simulation at the cell level and above becomes a reality. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. The role of upstream sequences in selecting the reading frame on tmRNA

    Directory of Open Access Journals (Sweden)

    Dewey Jonathan D

    2008-06-01

    Full Text Available Abstract Background tmRNA acts first as a tRNA and then as an mRNA to rescue stalled ribosomes in eubacteria. Two unanswered questions about tmRNA function remain: how does tmRNA, lacking an anticodon, bypass the decoding machinery and enter the ribosome? Secondly, how does the ribosome choose the proper codon to resume translation on tmRNA? According to the -1 triplet hypothesis, the answer to both questions lies in the unique properties of the three nucleotides upstream of the first tmRNA codon. These nucleotides assume an A-form conformation that mimics the codon-anticodon interaction, leading to recognition by the decoding center and choice of the reading frame. The -1 triplet hypothesis is important because it is the most credible model in which direct binding and recognition by the ribosome sets the reading frame on tmRNA. Results Conformational analysis predicts that 18 triplets cannot form the correct structure to function as the -1 triplet of tmRNA. We tested the tmRNA activity of all possible -1 triplet mutants using a genetic assay in Escherichia coli. While many mutants displayed reduced activity, our findings do not match the predictions of this model. Additional mutagenesis identified sequences further upstream that are required for tmRNA function. An immunoblot assay for translation of the tmRNA tag revealed that certain mutations in U85, A86, and the -1 triplet sequence result in improper selection of the first codon and translation in the wrong frame (-1 or +1 in vivo. Conclusion Our findings disprove the -1 triplet hypothesis. The -1 triplet is not required for accommodation of tmRNA into the ribosome, although it plays a minor role in frame selection. Our results strongly disfavor direct ribosomal recognition of the upstream sequence, instead supporting a model in which the binding of a separate ligand to A86 is primarily responsible for frame selection.

  7. Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.

    Science.gov (United States)

    Sasagawa, Yohei; Danno, Hiroki; Takada, Hitomi; Ebisawa, Masashi; Tanaka, Kaori; Hayashi, Tetsutaro; Kurisaki, Akira; Nikaido, Itoshi

    2018-03-09

    High-throughput single-cell RNA-seq methods assign limited unique molecular identifier (UMI) counts as gene expression values to single cells from shallow sequence reads and detect limited gene counts. We thus developed a high-throughput single-cell RNA-seq method, Quartz-Seq2, to overcome these issues. Our improvements in the reaction steps make it possible to effectively convert initial reads to UMI counts, at a rate of 30-50%, and detect more genes. To demonstrate the power of Quartz-Seq2, we analyzed approximately 10,000 transcriptomes from in vitro embryonic stem cells and an in vivo stromal vascular fraction with a limited number of reads.

  8. ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

    Science.gov (United States)

    Büssow, Konrad; Hoffmann, Steve; Sievert, Volker

    2002-12-19

    Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. A Java program was developed for retrieval of protein and nucleic acid sequences and annotations from NCBI GenBank, using the XML sequence format. Annotations retrieved by ORFer include sequence name, organism and also the completeness of the sequence. The program has a graphical user interface, although it can be used in a non-interactive mode. For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation. ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers. It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosomes. Sequences are either stored with their features in a relational database or can be exported as text files in Fasta or tabulator delimited format. The ORFer program is freely available at http://www.proteinstrukturfabrik.de/orfer. The ORFer program allows for fast retrieval of DNA sequences, protein sequences and their open reading frames and sequence annotations from GenBank. Furthermore, storage of sequences and features in a relational database is supported. Such a database can supplement a laboratory information system (LIMS) with appropriate sequence information.

  9. Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods.

    Science.gov (United States)

    Mu, John C; Tootoonchi Afshar, Pegah; Mohiyuddin, Marghoob; Chen, Xi; Li, Jian; Bani Asadi, Narges; Gerstein, Mark B; Wong, Wing H; Lam, Hugo Y K

    2015-09-28

    A high-confidence, comprehensive human variant set is critical in assessing accuracy of sequencing algorithms, which are crucial in precision medicine based on high-throughput sequencing. Although recent works have attempted to provide such a resource, they still do not encompass all major types of variants including structural variants (SVs). Thus, we leveraged the massive high-quality Sanger sequences from the HuRef genome to construct by far the most comprehensive gold set of a single individual, which was cross validated with deep Illumina sequencing, population datasets, and well-established algorithms. It was a necessary effort to completely reanalyze the HuRef genome as its previously published variants were mostly reported five years ago, suffering from compatibility, organization, and accuracy issues that prevent their direct use in benchmarking. Our extensive analysis and validation resulted in a gold set with high specificity and sensitivity. In contrast to the current gold sets of the NA12878 or HS1011 genomes, our gold set is the first that includes small variants, deletion SVs and insertion SVs up to a hundred thousand base-pairs. We demonstrate the utility of our HuRef gold set to benchmark several published SV detection tools.

  10. Haematobia irritans dataset of raw sequence reads from Illumina-based transcriptome sequencing of specific tissues and life stages

    Science.gov (United States)

    Illumina HiSeq technology was used to sequence the transcriptome from various dissected tissues and life stages from the horn fly, Haematobia irritans. These samples include eggs (0, 2, 4, and 9 hours post-oviposition), adult fly gut, adult fly legs, adult fly malpighian tubule, adult fly ovary, adu...

  11. Low-Bandwidth and Non-Compute Intensive Remote Identification of Microbes from Raw Sequencing Reads

    DEFF Research Database (Denmark)

    Gautier, Laurent; Lund, Ole

    2013-01-01

    , allowing a fully automated processing of sequencing data and routine instant quality check of sequencing runs from desktop sequencers. A web access is available at http://tapir.cbs.dtu.dk. The source code for a python command-line client, a server, and supplementary data are available at http://bit.ly/1aURxkc....

  12. Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

    Directory of Open Access Journals (Sweden)

    Hao Ye

    2015-11-01

    Full Text Available Precision medicine or personalized medicine has been proposed as a modernized and promising medical strategy. Genetic variants of patients are the key information for implementation of precision medicine. Next-generation sequencing (NGS is an emerging technology for deciphering genetic variants. Alignment of raw reads to a reference genome is one of the key steps in NGS data analysis. Many algorithms have been developed for alignment of short read sequences since 2008. Users have to make a decision on which alignment algorithm to use in their studies. Selection of the right alignment algorithm determines not only the alignment algorithm but also the set of suitable parameters to be used by the algorithm. Understanding these algorithms helps in selecting the appropriate alignment algorithm for different applications in precision medicine. Here, we review current available algorithms and their major strategies such as seed-and-extend and q-gram filter. We also discuss the challenges in current alignment algorithms, including alignment in multiple repeated regions, long reads alignment and alignment facilitated with known genetic variants.

  13. A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing.

    Science.gov (United States)

    Chen, Shi-Yi; Deng, Feilong; Jia, Xianbo; Li, Cao; Lai, Song-Jia

    2017-08-09

    It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus). We totally obtain 36,186 high-confidence transcripts from 14,474 genic loci, among which more than 23% of genic loci and 66% of isoforms have not been annotated yet within the current reference genome. Furthermore, about 17% of transcripts are computationally revealed to be non-coding RNAs. Up to 24,797 alternative splicing (AS) and 11,184 alternative polyadenylation (APA) events are detected within this de novo constructed transcriptome, respectively. The results provide a comprehensive set of reference transcripts and hence contribute to the improved annotation of rabbit genome.

  14. Genome sequencing of Deutsch strain of cattle ticks, Rhipicephalus microplus: Raw Pac Bio reads.

    Science.gov (United States)

    Pac Bio RS II whole genome shotgun sequencing technology was used to sequence the genome of the cattle tick, Rhipicephalus microplus. The DNA was derived from 14 day old eggs from the Deutsch Texas outbreak strain reared at the USDA-ARS Cattle Fever Tick Research Laboratory, Edinburg, TX. Each corre...

  15. COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge.

    Science.gov (United States)

    Lu, Yang Young; Chen, Ting; Fuhrman, Jed A; Sun, Fengzhu

    2017-03-15

    The advent of next-generation sequencing technologies enables researchers to sequence complex microbial communities directly from the environment. Because assembly typically produces only genome fragments, also known as contigs, instead of an entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples. The effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison with state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is using L 1 distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT, GroopM, MaxBin and MetaBAT. The software is available at https://github.com/younglululu/COCACOLA . fsun@usc.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  16. Controlling the structure of sequence-defined poly(phosphodiester)s for optimal MS/MS reading of digital information.

    Science.gov (United States)

    Amalian, J-A; Al Ouahabi, A; Cavallo, G; König, N F; Poyer, S; Lutz, J-F; Charles, L

    2017-11-01

    Digital polymers are monodisperse chains with a controlled sequence of co-monomers, defined as letters of an alphabet, and are used to store information at the molecular level. Reading such messages is hence a sequencing task that can be efficiently achieved by tandem mass spectrometry. To improve their readability, structure of sequence-controlled synthetic polymers can be optimized, based on considerations regarding their fragmentation behavior. This strategy is described here for poly(phosphodiester)s, which were synthesized as monodisperse chains with more than 100 units but exhibited extremely complex dissociation spectra. In these polymers, two repeating units that differ by a simple H/CH 3 variation were defined as the 0 and 1 bit of the ASCII code and spaced by a phosphate moiety. They were readily ionized in negative ion mode electrospray but dissociated via cleavage at all phosphate bonds upon collisional activation. Although allowing a complete sequence coverage of digital poly(phosphodiester)s, this fragmentation behavior was not efficient for macromolecules with more than 50 co-monomers, and data interpretation was very tedious. The structure of these polymers was then modified by introducing alkoxyamine linkages at appropriate location throughout the chain. A first design consisted of placing these low dissociation energy bonds between each monomeric bit: while cleavage of this sole bond greatly simplified MS/MS spectra, efficient sequencing was limited to chains with up to about 50 units. In contrast, introduction of alkoxyamine bonds between each byte (i.e. a set of eight co-monomers) was a more successful strategy. Long messages (so far, up to 8 bytes) could be read in MS 3 experiments, where single-byte containing fragments released during the first activation stage were further dissociated for sequencing. The whole sequence of such byte-truncated poly(phosphodiester)s could be easily re-constructed based on a mass tagging system which permits

  17. StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.

    Science.gov (United States)

    Roosaare, Märt; Vaher, Mihkel; Kaplinski, Lauris; Möls, Märt; Andreson, Reidar; Lepamets, Maarja; Kõressaar, Triinu; Naaber, Paul; Kõljalg, Siiri; Remm, Maido

    2017-01-01

    Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. A tool named StrainSeeker was developed that constructs a list of specific k -mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1-2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k -mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker's web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.

  18. Reading Nature- experienced teachers’ reflections on a teaching sequence in ecology: implications for future teacher training

    Directory of Open Access Journals (Sweden)

    Ola Magntorn

    2012-10-01

    Full Text Available This article explores experienced primary teachers views on teaching for ‘reading nature’. The concept ‘reading nature’ has to do with an ability to recognise organisms and relate them to material cycling and energy flow in the specific habitat which is to be read. It has to do with the natural world that we face outside and the tools we have are our experiences from previous learning situations both in and out-of-doors. The teachers were asked to comment on the content of a CD-ROM with teaching sequences from a primary class studying a river ecosystem. Perceptions that teachers held were found to be supportive but complex and varied regarding the possibilities and advantages of implementing this type of teaching design in the everyday classroom. The paper finishes by identifying some implications for teacher training to support fieldwork and ecological literacy in primary schools in the future.

  19. MGmapper: Reference based mapping and taxonomy annotation of metagenomics sequence reads

    DEFF Research Database (Denmark)

    Petersen, Thomas Nordahl; Lukjancenko, Oksana; Thomsen, Martin Christen Frølund

    2017-01-01

    number of false positive species annotations are a problem unless thresholds or post-processing are applied to differentiate between correct and false annotations. MGmapper is a package to process raw next generation sequence data and perform reference based sequence assignment, followed by a post...... pipeline is freely available as a bitbucked package (https://bitbucket.org/genomicepidemiology/mgmapper). A web-version (https://cge.cbs.dtu.dk/services/MGmapper) provides the basic functionality for analysis of small fastq datasets....

  20. Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40.

    Directory of Open Access Journals (Sweden)

    Myco Umemura

    Full Text Available The development of next-generation sequencing (NGS technologies has dramatically increased the throughput, speed, and efficiency of genome sequencing. The short read data generated from NGS platforms, such as SOLiD and Illumina, are quite useful for mapping analysis. However, the SOLiD read data with lengths of <60 bp have been considered to be too short for de novo genome sequencing. Here, to investigate whether de novo sequencing of fungal genomes is possible using only SOLiD short read sequence data, we performed de novo assembly of the Aspergillus oryzae RIB40 genome using only SOLiD read data of 50 bp generated from mate-paired libraries with 2.8- or 1.9-kb insert sizes. The assembled scaffolds showed an N50 value of 1.6 Mb, a 22-fold increase than those obtained using only SOLiD short read in other published reports. In addition, almost 99% of the reference genome was accurately aligned by the assembled scaffold fragments in long lengths. The sequences of secondary metabolite biosynthetic genes and clusters, whose products are of considerable interest in fungal studies due to their potential medicinal, agricultural, and cosmetic properties, were also highly reconstructed in the assembled scaffolds. Based on these findings, we concluded that de novo genome sequencing using only SOLiD short reads is feasible and practical for molecular biological study of fungi. We also investigated the effect of filtering low quality data, library insert size, and k-mer size on the assembly performance, and recommend for the assembly use of mild filtered read data where the N50 was not so degraded and the library has an insert size of ∼2.0 kb, and k-mer size 33.

  1. FMLRC: Hybrid long read error correction using an FM-index.

    Science.gov (United States)

    Wang, Jeremy R; Holt, James; McMillan, Leonard; Jones, Corbin D

    2018-02-09

    Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the continuity and accuracy of genome assemblies. However, the cost and throughput of these technologies limits their application to complex genomes. One solution is to decrease the cost and time to assemble novel genomes by leveraging "hybrid" assemblies that use long reads for scaffolding and short reads for accuracy. We describe a novel method leveraging a multi-string Burrows-Wheeler Transform with auxiliary FM-index to correct errors in long read sequences using a set of complementary short reads. We demonstrate that our method efficiently produces significantly more high quality corrected sequence than existing hybrid error-correction methods. We also show that our method produces more contiguous assemblies, in many cases, than existing state-of-the-art hybrid and long-read only de novo assembly methods. Our method accurately corrects long read sequence data using complementary short reads. We demonstrate higher total throughput of corrected long reads and a corresponding increase in contiguity of the resulting de novo assemblies. Improved throughput and computational efficiency than existing methods will help better economically utilize emerging long read sequencing technologies.

  2. Cytoplasmic male sterility-associated chimeric open reading frames identified by mitochondrial genome sequencing of four Cajanus genotypes.

    Science.gov (United States)

    Tuteja, Reetu; Saxena, Rachit K; Davila, Jaime; Shah, Trushar; Chen, Wenbin; Xiao, Yong-Li; Fan, Guangyi; Saxena, K B; Alverson, Andrew J; Spillane, Charles; Town, Christopher; Varshney, Rajeev K

    2013-10-01

    The hybrid pigeonpea (Cajanus cajan) breeding technology based on cytoplasmic male sterility (CMS) is currently unique among legumes and displays major potential for yield increase. CMS is defined as a condition in which a plant is unable to produce functional pollen grains. The novel chimeric open reading frames (ORFs) produced as a results of mitochondrial genome rearrangements are considered to be the main cause of CMS. To identify these CMS-related ORFs in pigeonpea, we sequenced the mitochondrial genomes of three C. cajan lines (the male-sterile line ICPA 2039, the maintainer line ICPB 2039, and the hybrid line ICPH 2433) and of the wild relative (Cajanus cajanifolius ICPW 29). A single, circular-mapping molecule of length 545.7 kb was assembled and annotated for the ICPA 2039 line. Sequence annotation predicted 51 genes, including 34 protein-coding and 17 RNA genes. Comparison of the mitochondrial genomes from different Cajanus genotypes identified 31 ORFs, which differ between lines within which CMS is present or absent. Among these chimeric ORFs, 13 were identified by comparison of the related male-sterile and maintainer lines. These ORFs display features that are known to trigger CMS in other plant species and to represent the most promising candidates for CMS-related mitochondrial rearrangements in pigeonpea.

  3. Fast High-Quality Noise

    DEFF Research Database (Denmark)

    Frisvad, Jeppe Revall; Wyvill, Geoff

    2007-01-01

    At the moment the noise functions available in a graphics programmer's toolbox are either slow to compute or they involve grid-line artifacts making them of lower quality. In this paper we present a real-time noise computation with no grid-line artifacts or other regularity problems. In other words......, we put a new tool in the box that computes fast high-quality noise. In addition to being free of artifacts, the noise we present does not rely on tabulated data (everything is computed on the fly) and it is easy to adjust quality vs. quantity for the noise. The noise is based on point rendering (like...... spot noise), but it extends to more than two dimensions. The fact that it is based on point rendering makes art direction of the noise much easier....

  4. The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi.

    Science.gov (United States)

    Sakai, Hiroaki; Naito, Ken; Takahashi, Yu; Sato, Toshiyuki; Yamamoto, Toshiya; Muto, Isamu; Itoh, Takeshi; Tomooka, Norihiko

    2016-01-01

    The genus Vigna includes legume crops such as cowpea, mungbean and azuki bean, as well as >100 wild species. A number of the wild species are highly tolerant to severe environmental conditions including high-salinity, acid or alkaline soil; drought; flooding; and pests and diseases. These features of the genus Vigna make it a good target for investigation of genetic diversity in adaptation to stressful environments; however, a lack of genomic information has hindered such research in this genus. Here, we present a genome database of the genus Vigna, Vigna Genome Server ('VigGS', http://viggs.dna.affrc.go.jp), based on the recently sequenced azuki bean genome, which incorporates annotated exon-intron structures, along with evidence for transcripts and proteins, visualized in GBrowse. VigGS also facilitates user construction of multiple alignments between azuki bean genes and those of six related dicot species. In addition, the database displays sequence polymorphisms between azuki bean and its wild relatives and enables users to design primer sequences targeting any variant site. VigGS offers a simple keyword search in addition to sequence similarity searches using BLAST and BLAT. To incorporate up to date genomic information, VigGS automatically receives newly deposited mRNA sequences of pre-set species from the public database once a week. Users can refer to not only gene structures mapped on the azuki bean genome on GBrowse but also relevant literature of the genes. VigGS will contribute to genomic research into plant biotic and abiotic stresses and to the future development of new stress-tolerant crops. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  5. MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Sakakibara, Yasumbumi

    2011-10-13

    Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  6. Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information

    Directory of Open Access Journals (Sweden)

    Siyu Han

    2016-01-01

    Full Text Available More and more studies have demonstrated that long noncoding RNAs (lncRNAs play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Here, we present a novel method for rapid identification of lncRNAs utilizing sequence intrinsic composition features and open reading frame information based on support vector machine model, named as Lncident (LncRNAs identification. The 10-fold cross-validation and ROC curve are used to evaluate the performance of Lncident. The main advantage of Lncident is high speed without the loss of accuracy. Compared with the exiting popular tools, Lncident outperforms Coding-Potential Calculator, Coding-Potential Assessment Tool, Coding-Noncoding Index, and PLEK. Lncident is also much faster than Coding-Potential Calculator and Coding-Noncoding Index. Lncident presents an outstanding performance on microorganism, which offers a great application prospect to the analysis of microorganism. In addition, Lncident can be trained by users’ own collected data. Furthermore, R package and web server are simultaneously developed in order to maximize the convenience for the users. The R package “Lncident” can be easily installed on multiple operating system platforms, as long as R is supported.

  7. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India

    Energy Technology Data Exchange (ETDEWEB)

    Mukherjee, Supratim; Lapidus, Alla; Shapiro, Nicole; Cheng, Jan-Fang; Han, James; Reddy, TBK; Huntemann, Marcel; Ivanova, Natalia; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Spring, Stefan; Göker, Markus; Markowitz, Victor; Woyke, Tanja; Tindall, Brian J.; Klenk, Hans-Peter; Kyrpides, Nikos C.; Pati, Amrita

    2015-01-01

    Pontibacter roseus Suresh et al 2006 is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern and muddy water. Here we describe the features of Pontibacter roseus strain SRC-1T along with its complete genome sequence and annotation from a culture of DSM 17521T. The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project.

  8. Availability of high quality weather data measurements

    DEFF Research Database (Denmark)

    Andersen, Elsa; Johansen, Jakob Berg; Furbo, Simon

    In the period 2016-2017 the project “Availability of high quality weather data measurements” is carried out at Department of Civil Engineering at the Technical University of Denmark. The aim of the project is to establish measured high quality weather data which will be easily available...... for the building energy branch and the solar energy branch in their efforts to achieve energy savings and for researchers and students carrying out projects where measured high quality weather data are needed....

  9. Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly.

    Science.gov (United States)

    Bai, Yongsheng; Kinne, Jeff; Ding, Lizhong; Rath, Ethan C; Cox, Aaron; Naidu, Siva Dharman

    2017-10-03

    It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years next-generation sequencing technologies have revolutionized the field. The "Read-Split-Walk" (RSW) and "Read-Split-Run" (RSR) methods were developed to identify genome-wide non-canonical spliced regions including special events occurring in cytoplasm. As the significant amount of genome/transcriptome data such as, Encyclopedia of DNA Elements (ENCODE) project, have been generated, we have advanced a newer more memory-efficient version of the algorithm, "Read-Split-Fly" (RSF), which can detect non-canonical spliced regions with higher sensitivity and improved speed. The RSF algorithm also outputs the spliced sequences for further downstream biological function analysis. We used open access ENCODE project RNA-Seq data to search spliced intron sequences against the U12-type spliced intron sequence database to examine whether some events could occur as potential signatures of U12-type splicing. The check was performed by searching spliced sequences against 5'ss and 3'ss sequences from the well-known orthologous U12-type spliceosomal intron database U12DB. Preliminary results of searching 70 ENCODE samples indicated that the presence of 5'ss with U12-type signature is more frequent than U2-type and prevalent in non-canonical junctions reported by RSF. The selected spliced sequences have also been further studied using miRBase to elucidate their functionality. Preliminary results from 70 samples of ENCODE datasets show that several miRNAs are prevalent in studied ENCODE samples. Two of these are associated with many diseases as suggested in the literature. Specifically, hsa-miR-1273 and hsa-miR-548 are associated with many diseases and cancers. Our RSF pipeline is able to detect many possible junctions

  10. Diagnostic accuracy of unenhanced, contrast-enhanced perfusion and angiographic MRI sequences for pulmonary embolism diagnosis: results of independent sequence readings

    Energy Technology Data Exchange (ETDEWEB)

    Revel, Marie Pierre [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Hotel-Dieu, Service de Radiologie, Paris (France); Sanchez, Olivier; Meyer, Guy [Hopital Europeen Georges Pompidou, APHP, Respiratory and intensive care and, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM Unite 765, Paris (France); Lefort, Catherine; Couchon, Sophie; Hernigou, Anne; Frija, Guy [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Niarra, Ralph [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Chatellier, Gilles [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM CIC-EC E4, Paris (France)

    2013-09-15

    To independently evaluate unenhanced, contrast-enhanced perfusion and angiographic MR sequences for pulmonary embolism (PE) diagnosis. Prospective investigation, including 274 patients who underwent perfusion, unenhanced 2D steady-state-free-precession (SSFP) and contrast-enhanced 3D angiographic MR sequences on a 1.5-T unit, in addition to CTA (CT angiography). Two independent readers evaluated each sequence independently in random order. Sensitivity, specificity, predictive values and inter-reader agreement were calculated for each sequence, excluding sequences judged inconclusive. Sensitivity was also calculated according to PE location. Contrast-enhanced angiographic sequences showed the highest sensitivity (82.9 and 89.7 %, reader 1 and reader 2, respectively), specificity (98.5 and 100 %) and agreement (kappa value 0.77). Unenhanced angiographic sequences, although less sensitive overall (68.7 and 76.4 %), were sensitive for the detection of proximal PE (92.7 and 100 %) and showed high specificity (96.1 and 99.1 %) and good agreement (kappa value 0.62). Perfusion sequences showed lower sensitivity (75.0 and 79.3 %), specificity (84.8 and 89.7 %) and agreement (kappa value 0.51), and a negative predictive value of 84.8 % at best. Compared with contrast-enhanced angiographic sequences, unenhanced sequences demonstrate lower sensitivity, except for proximal PE, but high specificity and agreement. The negative predictive value of perfusion sequences was insufficient to safely rule out PE. (orig.)

  11. Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.

    Science.gov (United States)

    Jayakumar, Vasanthan; Sakakibara, Yasubumi

    2017-11-03

    Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms. © The Author 2017. Published by Oxford University Press.

  12. Rhipicephalus microplus dataset of nonredundant raw sequence reads from 454 GS FLX sequencing of Cot-selected (Cot = 660) genomic DNA

    Science.gov (United States)

    A reassociation kinetics-based approach was used to reduce the complexity of genomic DNA from the Deutsch laboratory strain of the cattle tick, Rhipicephalus microplus, to facilitate genome sequencing. Selected genomic DNA (Cot value = 660) was sequenced using 454 GS FLX technology, resulting in 356...

  13. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Ye, Jia; Li, Songgang

    2005-01-01

    in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences. Udgivelsesdato: 2005-Sep...

  14. The diploid genome sequence of an Asian individual

    DEFF Research Database (Denmark)

    Wang, Jun; Wang, Wei; Li, Ruiqiang

    2008-01-01

    Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we...... used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual's genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP...... identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J...

  15. De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from total DNA Sequences.

    NARCIS (Netherlands)

    Izan, Shairul; Esselink, G.; Visser, R.G.F.; Smulders, M.J.M.; Borm, T.J.A.

    2017-01-01

    Whole Genome Shotgun (WGS) sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This

  16. GenHtr: a tool for comparative assessment of genetic heterogeneity in microbial genomes generated by massive short-read sequencing

    Directory of Open Access Journals (Sweden)

    Yu GongXin

    2010-10-01

    Full Text Available Abstract Background Microevolution is the study of short-term changes of alleles within a population and their effects on the phenotype of organisms. The result of the below-species-level evolution is heterogeneity, where populations consist of subpopulations with a large number of structural variations. Heterogeneity analysis is thus essential to our understanding of how selective and neutral forces shape bacterial populations over a short period of time. The Solexa Genome Analyzer, a next-generation sequencing platform, allows millions of short sequencing reads to be obtained with great accuracy, allowing for the ability to study the dynamics of the bacterial population at the whole genome level. The tool referred to as GenHtr was developed for genome-wide heterogeneity analysis. Results For particular bacterial strains, GenHtr relies on a set of Solexa short reads on given bacteria pathogens and their isogenic reference genome to identify heterogeneity sites, the chromosomal positions with multiple variants of genes in the bacterial population, and variations that occur in large gene families. GenHtr accomplishes this by building and comparatively analyzing genome-wide heterogeneity genotypes for both the newly sequenced genomes (using massive short-read sequencing and their isogenic reference (using simulated data. As proof of the concept, this approach was applied to SRX007711, the Solexa sequencing data for a newly sequenced Staphylococcus aureus subsp. USA300 cell line, and demonstrated that it could predict such multiple variants. They include multiple variants of genes critical in pathogenesis, e.g. genes encoding a LysR family transcriptional regulator, 23 S ribosomal RNA, and DNA mismatch repair protein MutS. The heterogeneity results in non-synonymous and nonsense mutations, leading to truncated proteins for both LysR and MutS. Conclusion GenHtr was developed for genome-wide heterogeneity analysis. Although it is much more time

  17. Sequence Text Structure Intervention during Interactive Book Reading of Expository Picture Books with Preschool Children with Language Impairment

    Science.gov (United States)

    Breit-Smith, Allison; Olszewski, Arnold; Swoboda, Christopher; Guo, Ying; Prendeville, Jo-Anne

    2017-01-01

    This study explores the outcomes of an interactive book reading intervention featuring expository picture books. This small-group intervention was delivered by four practitioners (two early childhood special education teachers and two speech-language pathologists) three times per week for 8 weeks to 6 preschool-age children (3 years 1 month to 4…

  18. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library.

    Science.gov (United States)

    Hoffberg, Sandra L; Troendle, Nicholas J; Glenn, Travis C; Mahmud, Ousman; Louha, Swarnali; Chalopin, Domitille; Bennetzen, Jeffrey L; Mauricio, Rodney

    2018-04-27

    The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species. Copyright © 2018, G3: Genes, Genomes, Genetics.

  19. A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library

    Directory of Open Access Journals (Sweden)

    Sandra L. Hoffberg

    2018-06-01

    Full Text Available The western mosquitofish, Gambusia affinis, is a freshwater poecilid fish native to the southeastern United States but with a global distribution due to widespread human introduction. Gambusia affinis has been used as a model species for a broad range of evolutionary and ecological studies. We sequenced the genome of a male G. affinis to facilitate genetic studies in diverse fields including invasion biology and comparative genetics. We generated Illumina short read data from paired-end libraries and in vitro proximity-ligation libraries. We obtained 54.9× coverage, N50 contig length of 17.6 kb, and N50 scaffold length of 6.65 Mb. Compared to two other species in the Poeciliidae family, G. affinis has slightly fewer genes that have shorter total, exon, and intron length on average. Using a set of universal single-copy orthologs in fish genomes, we found 95.5% of these genes were complete in the G. affinis assembly. The number of transposable elements in the G. affinis assembly is similar to those of closely related species. The high-quality genome sequence and annotations we report will be valuable resources for scientists to map the genetic architecture of traits of interest in this species.

  20. libgapmis: extending short-read alignments.

    Science.gov (United States)

    Alachiotis, Nikolaos; Berger, Simon; Flouri, Tomáš; Pissis, Solon P; Stamatakis, Alexandros

    2013-01-01

    A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. We present libgapmis, a library for extending pairwise short-read alignments. We

  1. Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

    Directory of Open Access Journals (Sweden)

    Shultz Jeffry

    2008-07-01

    Full Text Available Abstract Background Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS. Here the aim was to use BAC end sequences (BES derived from three minimum tile paths (MTP to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches. Results Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs were single nucleotide polymorphisms (SNPs; 89% and single nucleotide indels (SNIs 10%. Larger indels were rare but present (1%. Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed. Conclusion The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de

  2. The Role of Sequence Markers on Reading and Recall: A Comparison of Native and Nonnative English Speakers

    Science.gov (United States)

    1988-12-15

    ORGANIZATION PEPOPT NVBER S; 6a E O c PEPFC=V’NG CPC;% ZA " ON 6o OrFiCE SYMBOL 7a NAME OF MONITORING ORGANZA - ON 0 University of Califor-ia (If appi cable...readers. Experimental Aging Research, 7, 253-268. McLeod, B., & McLaughlin, B. (1986). Restructuring or automatization? Reading in a second language

  3. Fabrication of high-quality brazed joints

    International Nuclear Information System (INIS)

    Orlov, A.V.

    1980-01-01

    Problem of ensuring of joint high-quality when brazing different parts in power engineering is considered. To obtain high-quality joints it is necessary to correctly design brazed joint and to choose a gap width, overlap length and fillet radius; to clean up carefully the surfaces to be brazed and fix them properly one relative to another; to apply a solder so as to provide its flowing into the gap and sticking in it; to exactly regulate thermal conditions of brazing. High quality and reliability of brazed joints are ensured by the application of solders based on noble metals, and cheap solders based on nickel, manganese and copper. Joints brazed with nickel base solders may operate at temperatures as high as 888 deg C

  4. Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing

    DEFF Research Database (Denmark)

    Skovgaard, Ole; Bak, Mads; Løbner-Olesen, Anders

    2011-01-01

    a combination of WGS and genome copy number analysis, for the identification of mutations that suppress the growth deficiency imposed by excessive initiations from the Escherichia coli origin of replication, oriC. The E. coli chromosome, like the majority of bacterial chromosomes, is circular, and DNA...... replication is initiated by assembling two replication complexes at the origin, oriC. These complexes then replicate the chromosome bidirectionally toward the terminus, ter. In a population of growing cells, this results in a copy number gradient, so that origin-proximal sequences are more frequent than...... origin-distal sequences. Major rearrangements in the chromosome are, therefore, readily identified by changes in copy number, i.e., certain sequences become over- or under-represented. Of the eight mutations analyzed in detail here, six were found to affect a single gene only, one was a large chromosomal...

  5. Producing high-quality slash pine seeds

    Science.gov (United States)

    James Barnett; Sue Varela

    2003-01-01

    Slash pine is a desirable species. It serves many purposes and is well adapted to poorly drained flatwoods and seasonally flooded areas along the lower Coastal Plain of the Southeastern US. The use of high-quality seeds has been shown to produce uniform seedlings for outplanting, which is key to silvicultural success along the Coastal Plain and elsewhere. We present...

  6. RNA sequence determinants of a coupled termination-reinitiation strategy for downstream open reading frame translation in Helminthosporium victoriae virus 190S and other victoriviruses (Family Totiviridae).

    Science.gov (United States)

    Li, Hua; Havens, Wendy M; Nibert, Max L; Ghabrial, Said A

    2011-07-01

    The genome-length, dicistronic mRNA of the double-stranded RNA fungal virus Helminthosporium victoriae virus 190S (genus Victorivirus, family Totiviridae) contains two long open reading frames (ORFs) that overlap in the tetranucleotide AUGA. Translation of the downstream ORF, which encodes the RNA-dependent RNA polymerase (RdRp), has been proposed to depend on ribosomal reinitiation following termination of the upstream ORF, which encodes the capsid protein. In the current study, we examined the RNA sequence determinants for RdRp translation in this virus and demonstrated that a coupled termination-reinitiation (stop-restart) strategy is indeed used. Signals for termination-reinitiation are found within a 32-nucleotide stretch of RNA immediately upstream of the AUGA motif, including a predicted pseudoknot structure. The close proximity in which this predicted structure is followed by the upstream ORF's stop codon appears to be especially important for promoting translation of the downstream ORF. The normal strong preferences for an AUG start codon and the canonical sequence context to favor translation initiation appear somewhat relaxed for the downstream ORF. Similar sequence motifs and predicted RNA structures in other victoriviruses suggest that they all share a related stop-restart strategy for RdRp translation. Members of the genus Victorivirus thus provide new and unique opportunities for exploring the molecular mechanisms of translational coupling, which remain only partly understood in this and other systems.

  7. Reference genome sequence of the model plant Setaria.

    Science.gov (United States)

    Bennetzen, Jeffrey L; Schmutz, Jeremy; Wang, Hao; Percifield, Ryan; Hawkins, Jennifer; Pontaroli, Ana C; Estep, Matt; Feng, Liang; Vaughn, Justin N; Grimwood, Jane; Jenkins, Jerry; Barry, Kerrie; Lindquist, Erika; Hellsten, Uffe; Deshpande, Shweta; Wang, Xuewen; Wu, Xiaomei; Mitros, Therese; Triplett, Jimmy; Yang, Xiaohan; Ye, Chu-Yu; Mauro-Herrera, Margarita; Wang, Lin; Li, Pinghua; Sharma, Manoj; Sharma, Rita; Ronald, Pamela C; Panaud, Olivier; Kellogg, Elizabeth A; Brutnell, Thomas P; Doust, Andrew N; Tuskan, Gerald A; Rokhsar, Daniel; Devos, Katrien M

    2012-05-13

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  8. Reference genome sequence of the model plant Setaria

    Energy Technology Data Exchange (ETDEWEB)

    Bennetzen, Jeffrey L [ORNL; Schmutz, Jeremy [Hudson Alpha Institute of Biotechnology; Wang, Hao [University of Georgia, Athens, GA; Percifield, Ryan [University of Georgia, Athens, GA; Hawkins, Jennifer [University of Georgia, Athens, GA; Pontaroli, Ana C. [University of Georgia, Athens, GA; Estep, Matt [University of Georgia, Athens, GA; Feng, Liang [University of Georgia, Athens, GA; Vaughn, Justin N [ORNL; Grimwood, Jane [Hudson Alpha Institute of Biotechnology; Jenkins, Jerry [Hudson Alpha Institute of Biotechnology; Barry, Kerrie [U.S. Department of Energy, Joint Genome Institute; Lindquist, Erika [U.S. Department of Energy, Joint Genome Institute; Hellsten, Uffe [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Wang, Xuewen [University of Georgia, Athens, GA; Wu, Xiaomei [University of Georgia, Athens, GA; Mitros, Therese [University of California, Berkeley; Triplett, Jimmy [University of Missouri, St. Louis; Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Mauro-Herrera, Margarita [Oklahoma State University; Wang, Lin [Cornell University; Li, Pinghua [Cornell University; Sharma, Manoj [University of California, Davis; Sharma, Rita [University of California, Davis; Ronald, Pamela [University of California, Davis; Panaud, Olivier [Universite de Perpignan, Perpignan, France; Kellogg, Elizabeth A. [University of Missouri, St. Louis; Brutnell, Thomas P. [Cornell University; Doust, Andrew N. [Oklahoma State University; Tuskan, Gerald A [ORNL; Rokhsar, Daniel [U.S. Department of Energy, Joint Genome Institute; Devos, Katrien M [ORNL

    2012-01-01

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  9. Reference genome sequence of the model plant Setaria

    Energy Technology Data Exchange (ETDEWEB)

    Bennetzen, Jeffrey L [ORNL; Yang, Xiaohan [ORNL; Ye, Chuyu [ORNL; Tuskan, Gerald A [ORNL

    2012-01-01

    We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The {approx}400-Mb assembly covers {approx}80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

  10. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

    Science.gov (United States)

    Karamitros, Timokratis; Harrison, Ian; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

    2016-01-01

    Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal.

  11. De novo SNP calling from RAD sequences for a mink (Neovison vison) specific genotyping assay

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Pujolar, José Martin; Larsen, Peter F

    2013-01-01

    mink from Brown and Black color types were obtained. A mean of 49,789,860.2 (± 9,813,587.2) raw reads of high quality per sample were sequenced. SNPs were called using the software pipeline Stacks. The populations program was used to estimate population structure and genetic divergence between the two...

  12. High-quality compressive ghost imaging

    Science.gov (United States)

    Huang, Heyan; Zhou, Cheng; Tian, Tian; Liu, Dongqi; Song, Lijun

    2018-04-01

    We propose a high-quality compressive ghost imaging method based on projected Landweber regularization and guided filter, which effectively reduce the undersampling noise and improve the resolution. In our scheme, the original object is reconstructed by decomposing of regularization and denoising steps instead of solving a minimization problem in compressive reconstruction process. The simulation and experimental results show that our method can obtain high ghost imaging quality in terms of PSNR and visual observation.

  13. De Novo Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences

    Directory of Open Access Journals (Sweden)

    Shairul Izan

    2017-08-01

    Full Text Available Whole Genome Shotgun (WGS sequences of plant species often contain an abundance of reads that are derived from the chloroplast genome. Up to now these reads have generally been identified and assembled into chloroplast genomes based on homology to chloroplasts from related species. This re-sequencing approach may select against structural differences between the genomes especially in non-model species for which no close relatives have been sequenced before. The alternative approach is to de novo assemble the chloroplast genome from total genomic DNA sequences. In this study, we used k-mer frequency tables to identify and extract the chloroplast reads from the WGS reads and assemble these using a highly integrated and automated custom pipeline. Our strategy includes steps aimed at optimizing assemblies and filling gaps which are left due to coverage variation in the WGS dataset. We have successfully de novo assembled three complete chloroplast genomes from plant species with a range of nuclear genome sizes to demonstrate the universality of our approach: Solanum lycopersicum (0.9 Gb, Aegilops tauschii (4 Gb and Paphiopedilum henryanum (25 Gb. We also highlight the need to optimize the choice of k and the amount of data used. This new and cost-effective method for de novo short read assembly will facilitate the study of complete chloroplast genomes with more accurate analyses and inferences, especially in non-model plant genomes.

  14. De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read.

    Science.gov (United States)

    Austin, Christopher M; Tan, Mun Hua; Harrisson, Katherine A; Lee, Yin Peng; Croft, Laurence J; Sunnucks, Paul; Pavlova, Alexandra; Gan, Han Ming

    2017-08-01

    One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ∼1.8 metres in length and live to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation, and management research, as well as to better understand the evolutionary ecology and history of the species. A draft Murray cod genome of 633 Mbp (N50 = 109 974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of 2 fish individuals with an identical maternal lineage; 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were generated from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome, leading to the identification of 26 539 protein-coding genes. We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic, and phylogenetic studies of the Murray cod and more generally other fish species of the Percichthydae family. © The Authors 2017. Published by Oxford University Press.

  15. A not-so-big crisis: re-reading Silurian conodont diversity in a sequence-stratigraphic framework

    Science.gov (United States)

    Jarochowska, Emilia; Munnecke, Axel

    2016-04-01

    Conodonts are extensively used in Ordovician through Triassic biostratigraphy and fossil-based geochemistry. However, their distribution in rock successions is commonly taken at face value, without taking into account their diverse and poorly understood ecology. Multielement taxonomy, ontogenetic and environmental variability, difficulties in extraction, and relative rarity all contribute to the general lack of quantitative studies on conodont stratigraphic distribution and temporal turnover. With respect to Silurian conodonts, the concept of recurrent conodont extinction events - the so called Ireviken, Mulde and Lau events - has become a standard in the stratigraphic literature. The concept has been proposed based on qualitative observations of local extirpations of open-marine pelagic or nekto-benthic taxa and temporary dominance of shallow-water species in the Silurian succession of the Swedish island of Gotland. These changes coincided with positive carbon isotope excursions, abrupt facies shifts, "blooms" of benthic fauna, and changes in reef communities, which have all been combined into a general view of Silurian bio-geochemical events. This view posits a deterministic, reproducible pattern in Silurian conodont diversity, attributed to recurrent ecological or geochemical conditions. The growing body of sequence-stratigraphic interpretations across these events in Gotland and other sections worldwide indicate that in all cases the Silurian "events" are associated with rapid global regressions. This suggests that faunal changes such as the dominance of shallow-water, low-diversity conodont fauna and the increase of benthic invertebrate diversity and abundance represent predictable consequences of the variation in the completeness of the rock record and preservation potential of different environments. Our studies in Poland and Ukraine indicate that the magnitude of change in the taxonomic composition of conodont assemblages across the middle Silurian global

  16. High quality transportation fuels from renewable feedstock

    Energy Technology Data Exchange (ETDEWEB)

    Lindfors, Lars Peter

    2010-09-15

    Hydrotreating of vegetable oils is novel process for producing high quality renewable diesel. Hydrotreated vegetable oils (HVO) are paraffinic hydrocarbons. They are free of aromatics, have high cetane numbers and reduce emissions. HVO can be used as component or as such. HVO processes can also be modified to produce jet fuel. GHG savings by HVO use are significant compared to fossil fuels. HVO is already in commercial production. Neste Oil is producing its NExBTL diesel in two plants. Production of renewable fuels will be limited by availability of sustainable feedstock. Therefore R and D efforts are made to expand feedstock base further.

  17. Boiling curve in high quality flow boiling

    International Nuclear Information System (INIS)

    Shiralkar, B.S.; Hein, R.A.; Yadigaroglu, G.

    1980-01-01

    The post dry-out heat transfer regime of the flow boiling curve was investigated experimentally for high pressure water at high qualities. The test section was a short round tube located downstream of a hot patch created by a temperature controlled segment of tubing. Results from the experiment showed that the distance from the dryout point has a significant effect on the downstream temperatures and there was no unique boiling curve. The heat transfer coefficients measured sufficiently downstream of the dryout point could be correlated using the Heineman correlation for superheated steam, indicating that the droplet deposition effects could be neglected in this region

  18. Oxford Nanopore MinION Sequencing and Genome Assembly

    Directory of Open Access Journals (Sweden)

    Hengyun Lu

    2016-10-01

    Full Text Available The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS technology. The third-generation sequencing (TGS technology, led by Pacific Biosciences (PacBio, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT. MinION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.

  19. Teaching Reading

    Science.gov (United States)

    Day, Richard R.

    2013-01-01

    "Teaching Reading" uncovers the interactive processes that happen when people learn to read and translates them into a comprehensive easy-to-follow guide on how to teach reading. Richard Day's revelations on the nature of reading, reading strategies, reading fluency, reading comprehension, and reading objectives make fascinating…

  20. Method for synthesis of high quality graphene

    Science.gov (United States)

    Lanzara, Alessandra [Piedmont, CA; Schmid, Andreas K [Berkeley, CA; Yu, Xiaozhu [Berkeley, CA; Hwang, Choonkyu [Albany, CA; Kohl, Annemarie [Beneditkbeuern, DE; Jozwiak, Chris M [Oakland, CA

    2012-03-27

    A method is described herein for the providing of high quality graphene layers on silicon carbide wafers in a thermal process. With two wafers facing each other in close proximity, in a first vacuum heating stage, while maintained at a vacuum of around 10.sup.-6 Torr, the wafer temperature is raised to about 1500.degree. C., whereby silicon evaporates from the wafer leaving a carbon rich surface, the evaporated silicon trapped in the gap between the wafers, such that the higher vapor pressure of silicon above each of the wafers suppresses further silicon evaporation. As the temperature of the wafers is raised to about 1530.degree. C. or more, the carbon atoms self assemble themselves into graphene.

  1. Breeding and maintaining high-quality insects

    DEFF Research Database (Denmark)

    Jensen, Kim; Kristensen, Torsten Nygård; Heckmann, Lars-Henrik

    2017-01-01

    Insects have a large potential for sustainably enhancing global food and feed production, and commercial insect production is a rising industry of high economic value. Insects suitable for production typically have fast growth, short generation time, efficient nutrient utilization, high...... reproductive potential, and thrive at high density. Insects may cost-efficiently convert agricultural and industrial food by-products into valuable protein once the technology is finetuned. However, since insect mass production is a new industry, the technology needed to efficiently farm these animals is still...... in a starting phase. Here, we discuss the challenges and precautions that need to be considered when breeding and maintaining high-quality insect populations for food and feed. This involves techniques typically used in domestic animal breeding programs including maintaining genetically healthy populations...

  2. High Quality Virtual Reality for Architectural Exhibitions

    DEFF Research Database (Denmark)

    Kreutzberg, Anette

    2016-01-01

    This paper will summarise the findings from creating and implementing a visually high quality Virtual Reality (VR) experiment as part of an international architecture exhibition. It was the aim to represent the architectural spatial qualities as well as the atmosphere created from combining natural...... and artificial lighting in a prominent not yet built project. The outcome is twofold: Findings concerning the integration of VR in an exhibition space and findings concerning the experience of the virtual space itself. In the exhibition, an important aspect was the unmanned exhibition space, requiring the VR...... experience to be self-explanatory. Observations of different visitor reactions to the unmanned VR experience compared with visitor reactions at guided tours with personal instructions are evaluated. Data on perception of realism, spatial quality and light in the VR model were collected with qualitative...

  3. Molecular typing of methicillin-resistant Staphylococcus aureus: Comparison of PCR-based open reading frame typing, multilocus sequence typing, and Staphylococcus protein A gene typing.

    Science.gov (United States)

    Ogihara, Shinji; Saito, Ryoichi; Sawabe, Etsuko; Kozakai, Takahiro; Shima, Mari; Aiso, Yoshibumi; Fujie, Toshihide; Nukui, Yoko; Koike, Ryuji; Hagihara, Michio; Tohda, Shuji

    2018-04-01

    The recently developed PCR-based open reading frame typing (POT) method is a useful molecular typing tool. Here, we evaluated the performance of POT for molecular typing of methicillin-resistant Staphylococcus aureus (MRSA) isolates and compared its performance to those of multilocus sequence typing (MLST) and Staphylococcus protein A gene typing (spa typing). Thirty-seven MRSA isolates were collected between July 2012 and May 2015. MLST, spa typing, and POT were performed, and their discriminatory powers were evaluated using Simpson's index analysis. The MRSA isolates were classified into 11, 18, and 33 types by MLST, spa typing, and POT, respectively. The predominant strains identified by MLST, spa typing, and POT were ST8 and ST764, t002, and 93-191-127, respectively. The discriminatory power of MLST, spa typing, and POT was 0.853, 0.875, and 0.992, respectively, indicating that POT had the highest discriminatory power. Moreover, the results of MLST and spa were available after 2 days, whereas that of POT was available in 5 h. Furthermore, POT is rapid and easy to perform and interpret. Therefore, POT is a superior molecular typing tool for monitoring nosocomial transmission of MRSA. Copyright © 2017 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  4. Animated Cell Biology: A Quick and Easy Method for Making Effective, High-Quality Teaching Animations

    Science.gov (United States)

    O'Day, Danton H.

    2006-01-01

    There is accumulating evidence that animations aid learning of dynamic concepts in cell biology. However, existing animation packages are expensive and difficult to learn, and the subsequent production of even short animations can take weeks to months. Here I outline the principles and sequence of steps for producing high-quality PowerPoint…

  5. Optical studies of high quality synthetic diamond

    International Nuclear Information System (INIS)

    Sharp, S.J.

    1999-01-01

    This thesis is concerned with the study of fundamental and defect induced optical properties of synthetic diamond grown using high pressure, high temperature (HPHT) synthesis or chemical vapour deposition (CVD). The primary technique used for investigation is cathodoluminescence (including imaging and decay-time measurements) in addition to other forms of optical spectroscopy. This thesis is timely in that the crystallinity and purity of synthetic diamond has increased ten fold over the last few years. The diamond exciton emission, which is easily quenched by the presence of defects, is studied in high quality samples in detail. In addition the ability now exists to engineer the isotopic content of synthetic diamond to a high degree of accuracy. The experimental chapters are divided as follows: Chapter 2: High resolution, low temperature spectra reveal a splitting of the free-exciton phonon recombination emission peaks and the bound-exciton zero phonon line. Included are measurements of the variation in intensity and decay-time as a function of temperature. Chapter 3: The shift in energy of the phonon-assisted free-exciton phonon replicas with isotopic content has been measured. The shift is in agreement with the results of interatomic force model for phonon scattering due to isotope disorder. Chapter 4: A study of the shift in energy with isotopic content of the diamond of the GR1 band due to the neutral vacancy has allowed a verification of the theoretical predictions due to the Jahn Teller effect. Chapter 5: The spatial distribution of the free-exciton luminescence is studied in HPHT synthetic and CVD diamond. A variation in intensity with distance from the surface is interpreted as a significant non-radiative loss of excitons to the surface. Chapter 6: The decay-times of all known self-interstitial related centres have been measured in order to calculate the concentration of these centres present in electron irradiated diamond. (author)

  6. High Quality Data for Grid Integration Studies

    Energy Technology Data Exchange (ETDEWEB)

    Clifton, Andrew; Draxl, Caroline; Sengupta, Manajit; Hodge, Bri-Mathias

    2017-01-22

    As variable renewable power penetration levels increase in power systems worldwide, renewable integration studies are crucial to ensure continued economic and reliable operation of the power grid. The existing electric grid infrastructure in the US in particular poses significant limitations on wind power expansion. In this presentation we will shed light on requirements for grid integration studies as far as wind and solar energy are concerned. Because wind and solar plants are strongly impacted by weather, high-resolution and high-quality weather data are required to drive power system simulations. Future data sets will have to push limits of numerical weather prediction to yield these high-resolution data sets, and wind data will have to be time-synchronized with solar data. Current wind and solar integration data sets are presented. The Wind Integration National Dataset (WIND) Toolkit is the largest and most complete grid integration data set publicly available to date. A meteorological data set, wind power production time series, and simulated forecasts created using the Weather Research and Forecasting Model run on a 2-km grid over the continental United States at a 5-min resolution is now publicly available for more than 126,000 land-based and offshore wind power production sites. The National Solar Radiation Database (NSRDB) is a similar high temporal- and spatial resolution database of 18 years of solar resource data for North America and India. The need for high-resolution weather data pushes modeling towards finer scales and closer synchronization. We also present how we anticipate such datasets developing in the future, their benefits, and the challenges with using and disseminating such large amounts of data.

  7. Reading faster

    Directory of Open Access Journals (Sweden)

    Paul Nation

    2009-12-01

    Full Text Available This article describes the visual nature of the reading process as it relates to reading speed. It points out that there is a physical limit on normal reading speed and beyond this limit the reading process will be different from normal reading where almost every word is attended to. The article describes a range of activities for developing reading fluency, and suggests how the development of fluency can become part of a reading programme.

  8. An Evaluation of Verbal, Spatial, and Numerical Sequencing Scores in the WISC and WISC-R, with Special Reference to Children with Reading Difficulties.

    Science.gov (United States)

    Moseley, David

    1980-01-01

    Proposes a grouping of subtests corresponding to the three-factor pattern of the Wechsler Intelligence Scale for Children (WISC) and its revised form, WISC-R, for use with children with reading difficulties. (FL)

  9. An improved filtering algorithm for big read datasets and its application to single-cell assembly.

    Science.gov (United States)

    Wedemeyer, Axel; Kliemann, Lasse; Srivastav, Anand; Schielke, Christian; Reusch, Thorsten B; Rosenstiel, Philip

    2017-07-03

    For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers. We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep. We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm. We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm .

  10. Reading: Time

    NARCIS (Netherlands)

    Annemarie Wennekers; Frank Huysmans; Jos de Haan

    2018-01-01

    Original title: Lees:Tijd The amount of time that Dutch people spend reading has been declining steadily since the 1950s. This decline in reading time contrasts starkly with the positive personal and social benefits that can be derived from reading, according to lots of research. The Reading:

  11. Reading Comics

    Science.gov (United States)

    Tilley, Carol L.

    2008-01-01

    Many adults, even librarians who willingly add comics to their collections, often dismiss the importance of comics. Compared to reading "real" books, reading comics appears to be a simple task and compared to reading no books, reading comics might be preferable. After all, comics do have words, but the plentiful pictures seem to carry most of the…

  12. Evaluating a Brief Measure of Reading Comprehension for Narrative and Expository Text: The Convergent and Predictive Validity of the Reading Retell Rubric

    Science.gov (United States)

    Thomas, Lisa B.

    2012-01-01

    Reading comprehension is a critical aspect of the reading process. Children who experience significant problems in reading comprehension are at risk for long-term academic and social problems. High-quality measures are needed for early, efficient, and effective identification of children in need of remediation in reading comprehension. Substantial…

  13. GapMis: a tool for pairwise sequence alignment with a single gap.

    Science.gov (United States)

    Flouri, Tomás; Frousios, Kimon; Iliopoulos, Costas S; Park, Kunsoo; Pissis, Solon P; Tischler, German

    2013-08-01

    Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality part of the read allowing a number of mismatches and the insertion of a single gap in the alignment. We present GapMis, a tool for pairwise sequence alignment with a single gap. It is based on a simple algorithm, which computes a different version of the traditional dynamic programming matrix. The presented experimental results demonstrate that GapMis is more suitable and efficient than most popular tools for this task.

  14. High Quality Unigenes and Microsatellite Markers from Tissue Specific Transcriptome and Development of a Database in Clusterbean (Cyamopsis tetragonoloba, L. Taub

    Directory of Open Access Journals (Sweden)

    Hukam C. Rawal

    2017-11-01

    Full Text Available Clusterbean (Cyamopsis tetragonoloba L. Taub, is an important industrial, vegetable and forage crop. This crop owes its commercial importance to the presence of guar gum (galactomannans in its endosperm which is used as a lubricant in a range of industries. Despite its relevance to agriculture and industry, genomic resources available in this crop are limited. Therefore, the present study was undertaken to generate RNA-Seq based transcriptome from leaf, shoot, and flower tissues. A total of 145 million high quality Illumina reads were assembled using Trinity into 127,706 transcripts and 48,007 non-redundant high quality (HQ unigenes. We annotated 79% unigenes against Plant Genes from the National Center for Biotechnology Information (NCBI, Swiss-Prot, Pfam, gene ontology (GO and KEGG databases. Among the annotated unigenes, 30,020 were assigned with 116,964 GO terms, 9984 with EC and 6111 with 137 KEGG pathways. At different fragments per kilobase of transcript per millions fragments sequenced (FPKM levels, genes were found expressed higher in flower tissue followed by shoot and leaf. Additionally, we identified 8687 potential simple sequence repeats (SSRs with an average frequency of one SSR per 8.75 kb. A total of 28 amplified SSRs in 21 clusterbean genotypes resulted in polymorphism in 13 markers with average polymorphic information content (PIC of 0.21. We also constructed a database named ‘ClustergeneDB’ for easy retrieval of unigenes and the microsatellite markers. The tissue specific genes identified and the molecular marker resources developed in this study is expected to aid in genetic improvement of clusterbean for its end use.

  15. Analysis of high-quality modes in open chaotic microcavities

    International Nuclear Information System (INIS)

    Fang, W.; Yamilov, A.; Cao, H.

    2005-01-01

    We present a numerical study of the high-quality modes in two-dimensional dielectric stadium microcavities. Although the classical ray mechanics is fully chaotic in a stadium billiard, all of the high-quality modes show a 'strong scar' around unstable periodic orbits. When the deformation (ratio of the length of the straight segments over the diameter of the half circles) is small, the high-quality modes correspond to whispering-gallery-type trajectories and their quality factors decrease monotonically with increasing deformation. At large deformation, each high-quality mode is associated with multiple unstable periodic orbits. Its quality factor changes nonmonotonically with the deformation, and there exists an optimal deformation for each mode at which its quality factor reaches a local maximum. This unusual behavior is attributed to the interference of waves propagating along different constituent orbits that could minimize light leakage out of the cavity

  16. Innovative and high quality education through Open Education and OER

    OpenAIRE

    Stracke, Christian M.

    2017-01-01

    Online presentation and webinar by Stracke, C. M. (2017, 18 December) on "Innovative and high quality education through Open Education and OER" for the Belt and Road Open Education Learning Week by the Beijing Normal University, China.

  17. Improving high quality, equitable maternal health services in Malawi ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Improving high quality, equitable maternal health services in Malawi (IMCHA) ... In response, the Ministry of Health implemented a Standards-Based Management and Recognition for Reproductive Health initiative to improve ... Total funding.

  18. High Quality Education and Learning for All through Open Education

    NARCIS (Netherlands)

    Stracke, Christian M.

    2016-01-01

    Keynote at the International Lensky Education Forum 2016, Yakutsk, Republic of Sakha, Russian Federation, by Stracke, C. M. (2016, 16 August): "High Quality Education and Learning for All through Open Education"

  19. Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.

    Science.gov (United States)

    Delong, Allison K; Wu, Mingham; Bennett, Diane; Parkin, Neil; Wu, Zhijin; Hogan, Joseph W; Kantor, Rami

    2012-08-01

    Access to antiretroviral therapy is increasing globally and drug resistance evolution is anticipated. Currently, protease (PR) and reverse transcriptase (RT) sequence generation is increasing, including the use of in-house sequencing assays, and quality assessment prior to sequence analysis is essential. We created a computational HIV PR/RT Sequence Quality Analysis Tool (SQUAT) that runs in the R statistical environment. Sequence quality thresholds are calculated from a large dataset (46,802 PR and 44,432 RT sequences) from the published literature ( http://hivdb.Stanford.edu ). Nucleic acid sequences are read into SQUAT, identified, aligned, and translated. Nucleic acid sequences are flagged if with >five 1-2-base insertions; >one 3-base insertion; >one deletion; >six PR or >18 RT ambiguous bases; >three consecutive PR or >four RT nucleic acid mutations; >zero stop codons; >three PR or >six RT ambiguous amino acids; >three consecutive PR or >four RT amino acid mutations; >zero unique amino acids; or 15% genetic distance from another submitted sequence. Thresholds are user modifiable. SQUAT output includes a summary report with detailed comments for troubleshooting of flagged sequences, histograms of pairwise genetic distances, neighbor joining phylogenetic trees, and aligned nucleic and amino acid sequences. SQUAT is a stand-alone, free, web-independent tool to ensure use of high-quality HIV PR/RT sequences in interpretation and reporting of drug resistance, while increasing awareness and expertise and facilitating troubleshooting of potentially problematic sequences.

  20. SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing.

    Science.gov (United States)

    Sato, Yukuto; Kojima, Kaname; Nariai, Naoki; Yamaguchi-Kabata, Yumi; Kawai, Yosuke; Takahashi, Mamoru; Mimori, Takahiro; Nagasaki, Masao

    2014-08-08

    Next-generation sequencers (NGSs) have become one of the main tools for current biology. To obtain useful insights from the NGS data, it is essential to control low-quality portions of the data affected by technical errors such as air bubbles in sequencing fluidics. We develop a software SUGAR (subtile-based GUI-assisted refiner) which can handle ultra-high-throughput data with user-friendly graphical user interface (GUI) and interactive analysis capability. The SUGAR generates high-resolution quality heatmaps of the flowcell, enabling users to find possible signals of technical errors during the sequencing. The sequencing data generated from the error-affected regions of a flowcell can be selectively removed by automated analysis or GUI-assisted operations implemented in the SUGAR. The automated data-cleaning function based on sequence read quality (Phred) scores was applied to a public whole human genome sequencing data and we proved the overall mapping quality was improved. The detailed data evaluation and cleaning enabled by SUGAR would reduce technical problems in sequence read mapping, improving subsequent variant analysis that require high-quality sequence data and mapping results. Therefore, the software will be especially useful to control the quality of variant calls to the low population cells, e.g., cancers, in a sample with technical errors of sequencing procedures.

  1. Tablet—next generation sequence assembly visualization

    Science.gov (United States)

    Milne, Iain; Bayer, Micha; Cardle, Linda; Shaw, Paul; Stephen, Gordon; Wright, Frank; Marshall, David

    2010-01-01

    Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine. Availability: Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions. Contact: tablet@scri.ac.uk PMID:19965881

  2. Multicultural Reading

    Science.gov (United States)

    Veltze, Linda

    2004-01-01

    Multicultural reading advocates believe in the power of literature to transform and to change people's lives. They take seriously the arguments that racism and prejudice can be lessened through multicultural reading, and also that children from undervalued societal groups who read books that depict people like themselves in a positive light will…

  3. Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

    Directory of Open Access Journals (Sweden)

    Yu-Chih Tsai

    2016-02-01

    Full Text Available Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation.

  4. Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing

    Science.gov (United States)

    Tsai, Yu-Chih; Deming, Clayton; Segre, Julia A.; Kong, Heidi H.; Korlach, Jonas

    2016-01-01

    ABSTRACT Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool for de novo reconstruction of genomes from these communities. However, the resultant “genomes” are typically fragmented and incomplete due to the limited ability of short-read sequence data to assemble complex or low-coverage regions. Here, we use single-molecule, real-time (SMRT) sequencing to reconstruct a high-quality, closed genome of a previously uncharacterized Corynebacterium simulans and its companion bacteriophage from a skin metagenomic sample. Considerable improvement in assembly quality occurs in hybrid approaches incorporating short-read data, with even relatively small amounts of long-read data being sufficient to improve metagenome reconstruction. Using short-read data to evaluate strain variation of this C. simulans in its skin community at single-nucleotide resolution, we observed a dominant C. simulans strain with moderate allelic heterozygosity throughout the population. We demonstrate the utility of SMRT sequencing and hybrid approaches in metagenome quantitation, reconstruction, and annotation. PMID:26861018

  5. RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads

    Czech Academy of Sciences Publication Activity Database

    Novák, Petr; Neumann, Pavel; Pech, Jiří; Steinhaisl, J.; Macas, Jiří

    2013-01-01

    Roč. 29, č. 6 (2013), s. 792-793 ISSN 1367-4803 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) OC10037 Institutional support: RVO:60077344 Keywords : repetitiveDNA * computational analysis * next generation sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.621, year: 2013

  6. Concrete Waste Recycling Process for High Quality Aggregate

    International Nuclear Information System (INIS)

    Ishikura, Takeshi; Fujii, Shin-ichi

    2008-01-01

    Large amount of concrete waste generates during nuclear power plant (NPP) dismantling. Non-contaminated concrete waste is assumed to be disposed in a landfill site, but that will not be the solution especially in the future, because of decreasing tendency of the site availability and natural resources. Concerning concrete recycling, demand for roadbeds and backfill tends to be less than the amount of dismantled concrete generated in a single rural site, and conventional recycled aggregate is limited of its use to non-structural concrete, because of its inferior quality to ordinary natural aggregate. Therefore, it is vital to develop high quality recycled aggregate for general uses of dismantled concrete. If recycled aggregate is available for high structural concrete, the dismantling concrete is recyclable as aggregate for industry including nuclear field. Authors developed techniques on high quality aggregate reclamation for large amount of concrete generated during NPP decommissioning. Concrete of NPP buildings has good features for recycling aggregate; large quantity of high quality aggregate from same origin, record keeping of the aggregate origin, and little impurities in dismantled concrete such as wood and plastics. The target of recycled aggregate in this development is to meet the quality criteria for NPP concrete as prescribed in JASS 5N 'Specification for Nuclear Power Facility Reinforced Concrete' and JASS 5 'Specification for Reinforced Concrete Work'. The target of recycled aggregate concrete is to be comparable performance with ordinary aggregate concrete. The high quality recycled aggregate production techniques are assumed to apply for recycling for large amount of non-contaminated concrete. These techniques can also be applied for slightly contaminated concrete dismantled from radiological control area (RCA), together with free release survey. In conclusion: a technology on dismantled concrete recycling for high quality aggregate was developed

  7. Learning Disabilities and Achieving High-Quality Education Standards

    Science.gov (United States)

    Gartland, Debi; Strosnider, Roberta

    2017-01-01

    This is an official document of the National Joint Committee on Learning Disabilities (NJCLD), of which Council for Learning Disabilities is a long-standing, active member. With this position paper, NJCLD advocates for the implementation of high-quality education standards (HQES) for students with learning disabilities (LD) and outlines the…

  8. extraction of high quality dna from polysaccharides-secreting ...

    African Journals Online (AJOL)

    cistvr

    A DNA extraction method using CTAB was used for the isolation of genomic DNA from ten. Xanthomonas campestris pathovars, ten isolates of Xanthomonas albilineans and one isolate of. Pseudomonas rubrisubalbicans. High quality DNA was obtained that was ideal for molecular analy- ses. Extracellular polysaccharides ...

  9. Negative Binomial charts for monitoring high-quality processes

    NARCIS (Netherlands)

    Albers, Willem/Wim

    Good control charts for high quality processes are often based on the number of successes between failures. Geometric charts are simplest in this respect, but slow in recognizing moderately increased failure rates p. Improvement can be achieved by waiting until r > 1 failures have occurred, i.e. by

  10. Adoption and impact of high quality bambara flour (HQBF ...

    African Journals Online (AJOL)

    Adoption and impact of high quality bambara flour (HQBF) technology in the ... consumer acceptability/quality of products, credit, availability of raw materials, and ... as a result of 12.5 per cent increase in demand for bambara-based products.

  11. Synthesis and spectroscopic study of high quality alloy Cdx S ...

    Indian Academy of Sciences (India)

    Wintec

    In the present study, we report the synthesis of high quality CdxZn1–xS nanocrystals alloy at. 150°C with .... (XRD) using a Siemens model D 500, powder X-ray ... decays were analysed using IBH DAS6 software. 3. ... This alloying process is.

  12. Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

    Science.gov (United States)

    Dasgupta, Modhumita Ghosh; Dharanishanthi, Veeramuthu; Agarwal, Ishangi; Krutovsky, Konstantin V.

    2015-01-01

    The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus. PMID:25602379

  13. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing.

    Directory of Open Access Journals (Sweden)

    Modhumita Ghosh Dasgupta

    Full Text Available The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs and insertions/ deletions (InDels were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family- based QTL and association analysis in Eucalyptus.

  14. QuASAR: quantitative allele-specific analysis of reads.

    Science.gov (United States)

    Harvey, Chris T; Moyerbrailean, Gregory A; Davis, Gordon O; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

    2015-04-15

    Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. http://github.com/piquelab/QuASAR. fluca@wayne.edu or rpique@wayne.edu Supplementary Material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.

    Science.gov (United States)

    Straub, Shannon C K; Parks, Matthew; Weitemier, Kevin; Fishbein, Mark; Cronn, Richard C; Liston, Aaron

    2012-02-01

    Just as Sanger sequencing did more than 20 years ago, next-generation sequencing (NGS) is poised to revolutionize plant systematics. By combining multiplexing approaches with NGS throughput, systematists may no longer need to choose between more taxa or more characters. Here we describe a genome skimming (shallow sequencing) approach for plant systematics. Through simulations, we evaluated optimal sequencing depth and performance of single-end and paired-end short read sequences for assembly of nuclear ribosomal DNA (rDNA) and plastomes and addressed the effect of divergence on reference-guided plastome assembly. We also used simulations to identify potential phylogenetic markers from low-copy nuclear loci at different sequencing depths. We demonstrated the utility of genome skimming through phylogenetic analysis of the Sonoran Desert clade (SDC) of Asclepias (Apocynaceae). Paired-end reads performed better than single-end reads. Minimum sequencing depths for high quality rDNA and plastome assemblies were 40× and 30×, respectively. Divergence from the reference significantly affected plastome assembly, but relatively similar references are available for most seed plants. Deeper rDNA sequencing is necessary to characterize intragenomic polymorphism. The low-copy fraction of the nuclear genome was readily surveyed, even at low sequencing depths. Nearly 160000 bp of sequence from three organelles provided evidence of phylogenetic incongruence in the SDC. Adoption of NGS will facilitate progress in plant systematics, as whole plastome and rDNA cistrons, partial mitochondrial genomes, and low-copy nuclear markers can now be efficiently obtained for molecular phylogenetics studies.

  16. Comparison of reading speed with 3 different log-scaled reading charts.

    Science.gov (United States)

    Buari, Noor Halilah; Chen, Ai-Hong; Musa, Nuraini

    2014-01-01

    A reading chart that resembles real reading conditions is important to evaluate the quality of life in terms of reading performance. The purpose of this study was to compare the reading speed of UiTM Malay related words (UiTM-Mrw) reading chart with MNread Acuity Chart and Colenbrander Reading Chart. Fifty subjects with normal sight were randomly recruited through randomized sampling in this study (mean age=22.98±1.65 years). Subjects were asked to read three different near charts aloud and as quickly as possible at random sequence. The charts were the UiTM-Mrw Reading Chart, MNread Acuity Chart and Colenbrander Reading Chart, respectively. The time taken to read each chart was recorded and any errors while reading were noted. Reading performance was quantified in terms of reading speed as words per minute (wpm). The mean reading speed for UiTM-Mrw Reading Chart, MNread Acuity Chart and Colenbrander Reading Chart was 200±30wpm, 196±28wpm and 194±31wpm, respectively. Comparison of reading speed between UiTM-Mrw Reading Chart and MNread Acuity Chart showed no significant difference (t=-0.73, p=0.72). The same happened with the reading speed between UiTM-Mrw Reading Chart and Colenbrander Reading Chart (t=-0.97, p=0.55). Bland and Altman plot showed good agreement between reading speed of UiTM-Mrw Reading Chart with MNread Acuity Chart with the Colenbrander Reading Chart. UiTM-Mrw Reading Chart in Malay language is highly comparable with standardized charts and can be used for evaluating reading speed. Copyright © 2013 Spanish General Council of Optometry. Published by Elsevier Espana. All rights reserved.

  17. Reading Evaluation

    Science.gov (United States)

    Fagan, W. T.

    1978-01-01

    The Canadian Institute for Research in Behavioral and Social Sciences of Calgary was awarded a contract by the Provincial Government of Alberta to assess student skills and knowledge in reading and written composition. Here evaluation is defined and the use of standardized and criterion referenced tests for evaluating reading performance are…

  18. High quality voice synthesis middle ware; Kohinshitsu onsei gosei middle war

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-03-01

    Toshiba Corp. newly developed a natural voice synthesis system, TOS Drive TTS (TOtally speaker Driven Text-To-Speech) system, in which natural high-quality read-aloud is greatly improved, and also developed as its application a voice synthesis middle ware. In the newly developed system, using as a model a narrator's voice recorded preliminarily, a metrical control dictionary is automatically learned that reproduces the characteristics of metrical patters such as intonation or rhythm of a human voice, as is a voice bases dictionary that reproduces the characteristics of a voice quality, enabling natural voice synthesis to be realized that picks up human voice characteristics. The system is high quality and also very compact, while the voice synthesis middle ware utilizing this technology is adaptable to various platforms such as MPU or OS. The system is very suitable for audio response in the ITS field having car navigation systems as the core; besides, expanded application is expected to an audio response system that used to employ a sound recording and reproducing system. (translated by NEDO)

  19. How Reading Volume Affects both Reading Fluency and Reading Achievement

    Directory of Open Access Journals (Sweden)

    Richard L. ALLINGTON

    2014-10-01

    Full Text Available Long overlooked, reading volume is actually central to the development of reading proficiencies, especially in the development of fluent reading proficiency. Generally no one in schools monitors the actual volume of reading that children engage in. We know that the commonly used commercial core reading programs provide only material that requires about 15 minutes of reading activity daily. The remaining 75 minute of reading lessons is filled with many other activities such as completing workbook pages or responding to low-level literal questions about what has been read. Studies designed to enhance the volume of reading that children do during their reading lessons demonstrate one way to enhance reading development. Repeated readings have been widely used in fostering reading fluency but wide reading options seem to work faster and more broadly in developing reading proficiencies, including oral reading fluency.

  20. Next Generation High Quality Videoconferencing Service for the LHC

    CERN Multimedia

    CERN. Geneva

    2012-01-01

    In recent times, we have witnessed an explosion of video initiatives in the industry worldwide. Several advancements in video technology are currently improving the way we interact and collaborate. These advancements are forcing tendencies and overall experiences: any device in any network can be used to collaborate, in most cases with an overall high quality. To cope with this technology progresses, CERN IT Department has taken the leading role to establish strategies and directions to improve the user experience in remote dispersed meetings and remote collaboration at large in the worldwide LHC communities. Due to the high rate of dispersion in the LHC user communities, these are critically dependent of videoconferencing technology, with a need of robustness and high quality for the best possible user experience. We will present an analysis of the factors that influenced the technical and strategic choices to improve the reliability, efficiency and overall quality of the LHC remote sessions. In particular, ...

  1. Wellbeing Understanding in High Quality Healthcare Informatics and Telepractice.

    Science.gov (United States)

    Fiorini, Rodolfo A; De Giacomo, Piero; L'Abate, Luciano

    2016-01-01

    The proper use of healthcare informatics technology and multidimensional conceptual clarity are fundamental to create and boost outstanding clinical and telepractice results. Avoiding even terminology ambiguities is mandatory for high quality of care service. For instance, well-being or wellbeing is a different way to write the same concept only, or there is a good deal of ambiguity around the meanings of these terms the way they are written. In personal health, healthcare and healthcare informatics, this kind of ambiguity and lack of conceptual clarity has been called out repeatedly over the past 50 years. It is time to get the right, terse scenario. We present a brief review to develop and achieve ultimate wellbeing understanding for practical high quality healthcare informatics and telepractice application. This article presents an innovative point of view on deeper wellbeing understanding towards its increased clinical effective application.

  2. Promoting preschool reading

    OpenAIRE

    Istenič, Vesna

    2013-01-01

    The thesis titled Promoting preschool reading consists of a theoretiral and an empirical part. In the theoretical part I wrote about reading, the importance of reading, types of reading, about reading motivation, promoting reading motivation, internal and external motivation, influence of reading motivation on the child's reading activity, reading and familial literacy, the role of adults in promotion reading literacy, reading to a child and promoting reading in pre-school years, where I ...

  3. Methods and systems for fabricating high quality superconducting tapes

    Science.gov (United States)

    Majkic, Goran; Selvamanickam, Venkat

    2018-02-13

    An MOCVD system fabricates high quality superconductor tapes with variable thicknesses. The MOCVD system can include a gas flow chamber between two parallel channels in a housing. A substrate tape is heated and then passed through the MOCVD housing such that the gas flow is perpendicular to the tape's surface. Precursors are injected into the gas flow for deposition on the substrate tape. In this way, superconductor tapes can be fabricated with variable thicknesses, uniform precursor deposition, and high critical current densities.

  4. Process to Continuously Melt, Refine and Cast High Quality Steel

    Energy Technology Data Exchange (ETDEWEB)

    None

    2005-09-01

    The purpose of this project is to conduct research and development targeted at designing a revolutionary steelmaking process. This process will deliver high quality steel from scrap to the casting mold in one continuous process and will be safer, more productive, and less capital intensive to build and operate than conventional steelmaking. The new process will produce higher quality steel faster than traditional batch processes while consuming less energy and other resources.

  5. High-quality uniform dry transfer of graphene to polymers.

    Science.gov (United States)

    Lock, Evgeniya H; Baraket, Mira; Laskoski, Matthew; Mulvaney, Shawn P; Lee, Woo K; Sheehan, Paul E; Hines, Daniel R; Robinson, Jeremy T; Tosado, Jacob; Fuhrer, Michael S; Hernández, Sandra C; Walton, Scott G

    2012-01-11

    In this paper we demonstrate high-quality, uniform dry transfer of graphene grown by chemical vapor deposition on copper foil to polystyrene. The dry transfer exploits an azide linker molecule to establish a covalent bond to graphene and to generate greater graphene-polymer adhesion compared to that of the graphene-metal foil. Thus, this transfer approach provides a novel alternative route for graphene transfer, which allows for the metal foils to be reused. © 2011 American Chemical Society

  6. High quality digital holographic reconstruction on analog film

    Science.gov (United States)

    Nelsen, B.; Hartmann, P.

    2017-05-01

    High quality real-time digital holographic reconstruction, i.e. at 30 Hz frame rates, has been at the forefront of research and has been hailed as the holy grail of display systems. While these efforts have produced a fascinating array of computer algorithms and technology, many applications of reconstructing high quality digital holograms do not require such high frame rates. In fact, applications such as 3D holographic lithography even require a stationary mask. Typical devices used for digital hologram reconstruction are based on spatial-light-modulator technology and this technology is great for reconstructing arbitrary holograms on the fly; however, it lacks the high spatial resolution achievable by its analog counterpart, holographic film. Analog holographic film is therefore the method of choice for reconstructing highquality static holograms. The challenge lies in taking a static, high-quality digitally calculated hologram and effectively writing it to holographic film. We have developed a theoretical system based on a tunable phase plate, an intensity adjustable high-coherence laser and a slip-stick based piezo rotation stage to effectively produce a digitally calculated hologram on analog film. The configuration reproduces the individual components, both the amplitude and phase, of the hologram in the Fourier domain. These Fourier components are then individually written on the holographic film after interfering with a reference beam. The system is analogous to writing angularly multiplexed plane waves with individual component phase control.

  7. Long quantum channels for high-quality entanglement transfer

    International Nuclear Information System (INIS)

    Banchi, L; Apollaro, T J G; Cuccoli, A; Verrucchi, P; Vaia, R

    2011-01-01

    High-quality quantum-state and entanglement transfer can be achieved in an unmodulated spin bus operating in the ballistic regime, which occurs when the endpoint qubits A and B are nonperturbatively coupled to the chain by a suitable exchange interaction j 0 . Indeed, the transition amplitude characterizing the transfer quality exhibits a maximum for a finite optimal value j opt 0 (N), where N is the channel length. We show that j opt 0 (N) scales as N -1/6 for large N and that it ensures a high-quality entanglement transfer even in the limit of arbitrarily long channels, almost independently of the channel initialization. For instance, for any chain length the average quantum-state transmission fidelity exceeds 90% and decreases very little in a broad neighbourhood of j opt 0 (N). We emphasize that, taking the reverse point of view, should j 0 be experimentally constrained, high-quality transfer can still be obtained by adjusting the channel length to its optimal value. (paper)

  8. High-quality cardiopulmonary resuscitation: current and future directions.

    Science.gov (United States)

    Abella, Benjamin S

    2016-06-01

    Cardiopulmonary resuscitation (CPR) represents the cornerstone of cardiac arrest resuscitation care. Prompt delivery of high-quality CPR can dramatically improve survival outcomes; however, the definitions of optimal CPR have evolved over several decades. The present review will discuss the metrics of CPR delivery, and the evidence supporting the importance of CPR quality to improve clinical outcomes. The introduction of new technologies to quantify metrics of CPR delivery has yielded important insights into CPR quality. Investigations using CPR recording devices have allowed the assessment of specific CPR performance parameters and their relative importance regarding return of spontaneous circulation and survival to hospital discharge. Additional work has suggested new opportunities to measure physiologic markers during CPR and potentially tailor CPR delivery to patient requirements. Through recent laboratory and clinical investigations, a more evidence-based definition of high-quality CPR continues to emerge. Exciting opportunities now exist to study quantitative metrics of CPR and potentially guide resuscitation care in a goal-directed fashion. Concepts of high-quality CPR have also informed new approaches to training and quality improvement efforts for cardiac arrest care.

  9. Integration study of high quality teaching resources in universities

    Directory of Open Access Journals (Sweden)

    Honglu Liu

    2012-12-01

    Full Text Available Purpose: The development level and quality of education depend on the merits and efficiency in the use of teaching resources, especially in the case of obvious contradiction between the demand and supply of teaching resources. So to integrate teaching resources, improve the efficiency in the use of high quality teaching resources, and take the road of content development to enhance the competitiveness of education has become very important and urgent.Design/methodology/approach: On the basis of analysis on the teaching resources of universities and the problems they faced, this paper introduced the basic concepts of cloud storage, and built the integration architecture of high quality teaching resources in universities based on the cloud storage.Findings and Originality/value: The HDFS-based cloud storage proposed in this paper is a dynamically adjustable and Internet-based storage solution, and the users can access storage targets using the network through a common and easy-to-use protocol and application programming interfaces. This new technology is useful for end users benefits. With the continuous development and improvement of cloud storage, it will necessarily result in more and more applications in the institutions of higher learning and education network.Originality/value: This paper introduced the cloud storage into the integration of high quality teaching resources in universities first and as a new form of service, it can be a good solution.

  10. High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond

    DEFF Research Database (Denmark)

    Gong, Xianzhe; Skrivergaard, Stig; Korsgaard, Benjamin

    2017-01-01

    denitrification, and fermentation. The draft genome of strain S3-2T has a size of ~5.8 Mbp and contains 5,297 genes, including 115 RNA genes. Based on the phenotypic properties of the strain, the low in silico DNA-DNA hybridization (DDH) values with related genomes (

  11. Reading Aloud.

    Science.gov (United States)

    Giorgis, Cyndi; Johnson, Nancy J.

    1999-01-01

    Offers brief descriptions of 34 children's books that are excellent for reading aloud: some of them for inviting interaction, for laughing out loud, for prompting discussion, for living vicariously, for lingering over language, and for making curricular connections. (SR)

  12. Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

    Science.gov (United States)

    Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R.; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J.

    2013-01-01

    For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding. PMID:23592960

  13. Combinatorial pooling enables selective sequencing of the barley gene space.

    Directory of Open Access Journals (Sweden)

    Stefano Lonardi

    2013-04-01

    Full Text Available For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

  14. Combinatorial pooling enables selective sequencing of the barley gene space.

    Science.gov (United States)

    Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J

    2013-04-01

    For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

  15. Sequencing and characterization of the guppy (Poecilia reticulata transcriptome

    Directory of Open Access Journals (Sweden)

    Rodd F Helen

    2011-04-01

    Full Text Available Abstract Background Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs, and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA-sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in

  16. Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

    Directory of Open Access Journals (Sweden)

    Haznedaroglu Berat Z

    2012-07-01

    Full Text Available Abstract Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG ortholog identifiers (KOIs, and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly. Results Analyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63. For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs in the assemblies of individual k-mers (k-19 to k-63 that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented. Conclusions This study demonstrated that different k-mer choices result in various quantities

  17. Key factors for a high-quality VR experience

    Science.gov (United States)

    Champel, Mary-Luc; Doré, Renaud; Mollet, Nicolas

    2017-09-01

    For many years, Virtual Reality has been presented as a promising technology that could deliver a truly new experience to users. The media and entertainment industry is now investigating the possibility to offer a video-based VR 360 experience. Nevertheless, there is a substantial risk that VR 360 could have the same fate as 3DTV if it cannot offer more than just being the next fad. The present paper aims at presenting the various quality factors required for a high-quality VR experience. More specifically, this paper will focus on the main three VR quality pillars: visual, audio and immersion.

  18. Anti-Stokes Luminescence in High Quality Quantum Wells

    Science.gov (United States)

    Vinattieri, A.; Bogani, F.; Miotto, A.; Ceccherini, S.

    1997-11-01

    We present a detailed investigation of the anti-Stokes (AS) luminescence which originates from exciton recombination when below gap excitation is used, in a set of high quality quantum well structures. We observe strong excitonic resonances in the AS signal as measured from photoluminescence and photoluminescence excitation spectra. We demonstrate that neither the electromagnetic coupling between the wells nor the morphological disorder can explain this up-conversion effect. Time-resolved luminescence data after ps excitation and fs correlation spectroscopy results provide clear evidence of the occurrence of a two-step absorption which is assisted by the exciton population resonantly excited by the first photon.

  19. Methods and systems for fabricating high quality superconducting tapes

    Energy Technology Data Exchange (ETDEWEB)

    Majkic, Goran; Selvamanickam, Venkat

    2018-02-13

    An MOCVD system fabricates high quality superconductor tapes with variable thicknesses. The MOCVD system can include a gas flow chamber between two parallel channels in a housing. A substrate tape is heated and then passed through the MOCVD housing such that the gas flow is perpendicular to the tape's surface. Precursors are injected into the gas flow for deposition on the substrate tape. In this way, superconductor tapes can be fabricated with variable thicknesses, uniform precursor deposition, and high critical current densities.

  20. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...

  1. Meraculous: De Novo Genome Assembly with Short Paired-End Reads

    Energy Technology Data Exchange (ETDEWEB)

    Chapman, Jarrod A.; Ho, Isaac; Sunkara, Sirisha; Luo, Shujun; Schroth, Gary P.; Rokhsar, Daniel S.; Salzberg, Steven L.

    2011-08-18

    We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ~280 bp or ~3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed.

  2. Percutaneous vertebroplasty with a high-quality rotational angiographic unit

    Energy Technology Data Exchange (ETDEWEB)

    Pedicelli, Alessandro [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: apedicelli@rm.unicatt.it; Rollo, Massimo [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: mrollo@rm.unicatt.it; Piano, Mariangela [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: mariangela.piano@gmail.com; Re, Thomas J. [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: tomjre@gmail.com; Cipriani, Maria C. [Department of Gerontology, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: alexped@yahoo.com; Colosimo, Cesare [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: colosimo@rm.unicatt.it; Bonomo, Lorenzo [Department of Bioimaging and Radiological Sciences, Catholic University of Sacred Heart, Policl. A.Gemelli, l.go Gemelli 1, 00168 Rome (Italy)], E-mail: lbonomo@rm.unicatt.it

    2009-02-15

    We evaluated the reliability of a rotational angiographic unit (RA) with flat-panel detector as a single technique to guide percutaneous vertebroplasty (PVP) and for post-procedure assessment by 2D and 3D reformatted images. Fifty-five consecutive patients (104 vertebral bodies) were treated under RA fluoroscopy. Rotational acquisitions with 2D and 3D reconstruction were obtained in all patients for immediate post-procedure assessment. In complex cases, this technique was also used to evaluate the needle position during the procedure. All patients underwent CT scan after the procedure. RA and CT findings were compared. In all cases, a safe trans-pedicular access and an accurate control of the bone-cement injection were successfully performed with high-quality fluoroscopy, even at the thoracic levels and in case of vertebra plana. 2D and 3D rotational reconstructions permitted CT-like images that clearly showed needle position and were similar to CT findings in depicting intrasomatic implant-distribution. RA detected 40 cement leakages compared to 42 demonstrated by CT and showed overall 95% sensitivity and 100% specificity compared to CT for final post-procedure assessment. Our preliminary results suggest that high-quality RA is reliable and safe as a single technique for PVP guidance, control and post-procedure assessment. It permits fast and cost-effective procedures avoiding multi-modality imaging.

  3. Computer-aided control of high-quality cast iron

    Directory of Open Access Journals (Sweden)

    S. Pietrowski

    2008-04-01

    Full Text Available The study discusses the possibility of control of the high-quality grey cast iron and ductile iron using the author’s genuine computer programs. The programs have been developed with the help of algorithms based on statistical relationships that are said to exist between the characteristic parameters of DTA curves and properties, like Rp0,2, Rm, A5 and HB. It has been proved that the spheroidisation and inoculation treatment of cast iron changes in an important way the characteristic parameters of DTA curves, thus enabling a control of these operations as regards their correctness and effectiveness, along with the related changes in microstructure and mechanical properties of cast iron. Moreover, some examples of statistical relationships existing between the typical properties of ductile iron and its control process were given for cases of the melts consistent and inconsistent with the adopted technology.A test stand for control of the high-quality cast iron and respective melts has been schematically depicted.

  4. High quality electron beams from a laser wakefield accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Wiggins, S M; Issac, R C; Welsh, G H; Brunetti, E; Shanks, R P; Anania, M P; Cipiccia, S; Manahan, G G; Aniculaesei, C; Ersfeld, B; Islam, M R; Burgess, R T L; Vieux, G; Jaroszynski, D A [SUPA, Department of Physics, University of Strathclyde, Glasgow (United Kingdom); Gillespie, W A [SUPA, Division of Electronic Engineering and Physics, University of Dundee, Dundee (United Kingdom); MacLeod, A M [School of Computing and Creative Technologies, University of Abertay Dundee, Dundee (United Kingdom); Van der Geer, S B; De Loos, M J, E-mail: m.wiggins@phys.strath.ac.u [Pulsar Physics, Burghstraat 47, 5614 BC Eindhoven (Netherlands)

    2010-12-15

    High quality electron beams have been produced in a laser-plasma accelerator driven by femtosecond laser pulses with a peak power of 26 TW. Electrons are produced with an energy up to 150 MeV from the 2 mm gas jet accelerator and the measured rms relative energy spread is less than 1%. Shot-to-shot stability in the central energy is 3%. Pepper-pot measurements have shown that the normalized transverse emittance is {approx}1{pi} mm mrad while the beam charge is in the range 2-10 pC. The generation of high quality electron beams is understood from simulations accounting for beam loading of the wakefield accelerating structure. Experiments and self-consistent simulations indicate that the beam peak current is several kiloamperes. Efficient transportation of the beam through an undulator is simulated and progress is being made towards the realization of a compact, high peak brilliance free-electron laser operating in the vacuum ultraviolet and soft x-ray wavelength ranges.

  5. Next-generation sequencing reveals the mutational landscape of clinically diagnosed Usher syndrome: copy number variations, phenocopies, a predominant target for translational read-through, and PEX26 mutated in Heimler syndrome.

    Science.gov (United States)

    Neuhaus, Christine; Eisenberger, Tobias; Decker, Christian; Nagl, Sandra; Blank, Cornelia; Pfister, Markus; Kennerknecht, Ingo; Müller-Hofstede, Cornelie; Charbel Issa, Peter; Heller, Raoul; Beck, Bodo; Rüther, Klaus; Mitter, Diana; Rohrschneider, Klaus; Steinhauer, Ute; Korbmacher, Heike M; Huhle, Dagmar; Elsayed, Solaf M; Taha, Hesham M; Baig, Shahid M; Stöhr, Heidi; Preising, Markus; Markus, Susanne; Moeller, Fabian; Lorenz, Birgit; Nagel-Wolfrum, Kerstin; Khan, Arif O; Bolz, Hanno J

    2017-09-01

    Combined retinal degeneration and sensorineural hearing impairment is mostly due to autosomal recessive Usher syndrome (USH1: congenital deafness, early retinitis pigmentosa (RP); USH2: progressive hearing impairment, RP). Sanger sequencing and NGS of 112 genes (Usher syndrome, nonsyndromic deafness, overlapping conditions), MLPA, and array-CGH were conducted in 138 patients clinically diagnosed with Usher syndrome. A molecular diagnosis was achieved in 97% of both USH1 and USH2 patients, with biallelic mutations in 97% (USH1) and 90% (USH2), respectively. Quantitative readout reliably detected CNVs (confirmed by MLPA or array-CGH), qualifying targeted NGS as one tool for detecting point mutations and CNVs. CNVs accounted for 10% of identified USH2A alleles, often in trans to seemingly monoallelic point mutations. We demonstrate PTC124-induced read-through of the common p.Trp3955* nonsense mutation (13% of detected USH2A alleles), a potential therapy target. Usher gene mutations were found in most patients with atypical Usher syndrome, but the diagnosis was adjusted in case of double homozygosity for mutations in OTOA and NR2E3 , genes implicated in isolated deafness and RP. Two patients with additional enamel dysplasia had biallelic PEX26 mutations, for the first time linking this gene to Heimler syndrome. Targeted NGS not restricted to Usher genes proved beneficial in uncovering conditions mimicking Usher syndrome.

  6. Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

    Science.gov (United States)

    Kisand, Veljo; Lettieri, Teresa

    2013-04-01

    De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize

  7. Multi-line split DNA synthesis: a novel combinatorial method to make high quality peptide libraries

    Directory of Open Access Journals (Sweden)

    Ueno Shingo

    2004-09-01

    Full Text Available Abstract Background We developed a method to make a various high quality random peptide libraries for evolutionary protein engineering based on a combinatorial DNA synthesis. Results A split synthesis in codon units was performed with mixtures of bases optimally designed by using a Genetic Algorithm program. It required only standard DNA synthetic reagents and standard DNA synthesizers in three lines. This multi-line split DNA synthesis (MLSDS is simply realized by adding a mix-and-split process to normal DNA synthesis protocol. Superiority of MLSDS method over other methods was shown. We demonstrated the synthesis of oligonucleotide libraries with 1016 diversity, and the construction of a library with random sequence coding 120 amino acids containing few stop codons. Conclusions Owing to the flexibility of the MLSDS method, it will be able to design various "rational" libraries by using bioinformatics databases.

  8. High quality reference genome of drumstick tree (Moringa oleifera Lam.), a potential perennial crop.

    Science.gov (United States)

    Tian, Yang; Zeng, Yan; Zhang, Jing; Yang, ChengGuang; Yan, Liang; Wang, XuanJun; Shi, ChongYing; Xie, Jing; Dai, TianYi; Peng, Lei; Zeng Huan, Yu; Xu, AnNi; Huang, YeWei; Zhang, JiaJin; Ma, Xiao; Dong, Yang; Hao, ShuMei; Sheng, Jun

    2015-07-01

    The drumstick tree (Moringa oleifera Lam.) is a perennial crop that has gained popularity in certain developing countries for its high-nutrition content and adaptability to arid and semi-arid environments. Here we report a high-quality draft genome sequence of M. oleifera. This assembly represents 91.78% of the estimated genome size and contains 19,465 protein-coding genes. Comparative genomic analysis between M. oleifera and related woody plant genomes helps clarify the general evolution of this species, while the identification of several species-specific gene families and positively selected genes in M. oleifera may help identify genes related to M. oleifera's high protein content, fast-growth, heat and stress tolerance. This reference genome greatly extends the basic research on M. oleifera, and may further promote applying genomics to enhanced breeding and improvement of M. oleifera.

  9. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  10. Reading Letters

    DEFF Research Database (Denmark)

    Beier, Sofie

    2012-01-01

    In our everyday life we constantly encounter a diversity of reading matters, including display types on traffic signage, printed text in novels, newspaper headlines, or our own writing on a computer screen. All these conditions place different demands on the typefaces applied. The book discusses...

  11. Reading Rembrandt

    NARCIS (Netherlands)

    Bal, Mieke

    2006-01-01

    Reading Rembrandt: Beyond the Word-Image Opposition explores the potential for an interdisciplinary methodology between visual art and literature. In a series of close analyses of works by "Rembrandt" - works as we see them today, through all the ways of seeing and commenting that precede - and

  12. High quality diesel fuels by VO-LSGO hydrotreatment

    Energy Technology Data Exchange (ETDEWEB)

    Stanica-Ezeanu, Dorin; Juganaru, Traian [Petroleum and Gas Univ. of Ploiesti (Romania)

    2013-06-01

    The aim of the paper is to obtain a high quality Diesel fuel by hydro-deoxigenation of vegetable oils (VO) mixed with a low sulfur gasoil (LSGO). The process is possible by using a bi-functional catalyst Ni-Mo supported by an activated Al{sub 2}O{sub 3} containing 2% Ultrastable Y-zeolite. The experimental conditions were: T =340 - 380 C, Pressure = 50 bar, LHSV = 1,5 h{sup -1}, H{sub 2}/Feed ratio = 15 mole H{sub 2} /mole liquid feed. The liquid product was separated in two fractions: a light distillate (similar to gasoline) and a heavy distillate (boiling point > 200 C) with very good characteristics for Diesel engines. The reaction chemistry is very complex, but the de-oxygenation process is decisive for the chemical structure of hydrocarbons from final product. Finally, a schema for the reaction mechanism is proposed. (orig.)

  13. Supercapacitors based on high-quality graphene scrolls

    Science.gov (United States)

    Zeng, Fanyan; Kuang, Yafei; Liu, Gaoqin; Liu, Rui; Huang, Zhongyuan; Fu, Chaopeng; Zhou, Haihui

    2012-06-01

    High-quality graphene scrolls (GSS) with a unique scrolled topography are designed using a microexplosion method. Their capacitance properties are investigated by cyclic voltammetry, galvanostatic charge-discharge and electrical impedance spectroscopy. Compared with the specific capacity of 110 F g-1 for graphene sheets, a remarkable capacity of 162.2 F g-1 is obtained at the current density of 1.0 A g-1 in 6 M KOH aqueous solution owing to the unique scrolled structure of GSS. The capacity value is increased by about 50% only because of the topological change of graphene sheets. Meanwhile, GSS exhibit excellent long-term cycling stability along with 96.8% retained after 1000 cycles at 1.0 A g-1. These encouraging results indicate that GSS based on the topological structure of graphene sheets are a kind of promising material for supercapacitors.

  14. High quality flux control system for electron gun evaporation

    International Nuclear Information System (INIS)

    Appelbloom, A.M.; Hadley, P.; van der Marel, D.; Mooij, J.E.

    1991-01-01

    This paper reports on a high quality flux control system for electron gun evaporation developed and tested for the MBE growth of high temperature superconductors. The system can be applied to any electron gun without altering the electron gun itself. Essential elements of the system are a high bandwidth mass spectrometer, control electronics and a high voltage modulator to sweep the electron beam over the melt at high frequencies. the sweep amplitude of the electron beam is used to control the evaporation flux at high frequencies. The feedback loop of the system has a bandwidth of over 100 Hz, which makes it possible to grow superlattices and layered structures in a fast and precisely controlled manner

  15. A roadmap to high quality chemically prepared graphene

    Energy Technology Data Exchange (ETDEWEB)

    Gengler, Regis Y N; Spyrou, Konstantinos; Rudolf, Petra, E-mail: r.gengler@rug.n, E-mail: p.rudolf@rug.n [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747AG Groningen (Netherlands)

    2010-09-22

    Graphene was discovered half a decade ago and proved the existence of a two-dimensional system which becomes stable as a result of 3D corrugation. It appeared very quickly that this exceptional material had truly outstanding electronic, mechanical, thermal and optical properties. Consequently a broad range of applications appeared, as the graphene science speedily moved forward. Since then, a lot of effort has been devoted not only to the study of graphene but also to its fabrication. Here we review the chemical approaches to graphene production, their advantages as well as their downsides. Our aim is to draw a roadmap of today's most reliable path to high quality graphene via chemical preparation.

  16. Quality management manual for production of high quality cassava flour

    DEFF Research Database (Denmark)

    Dziedzoave, Nanam Tay; Abass, Adebayo Busura; Amoa-Awua, Wisdom K.

    The high quality cassava flour (HQCF) industry has just started to evolve in Africa and elsewhere. The sustainability of the growing industry, the profitability of small- and medium-scale enterprises (SMEs) that are active in the industry and good-health of consumers can best be guaranteed through...... the adoption of proper quality and food safety procedures. Cassava processing enterprises involved in the productionof HQCF must therefore be commited to the quality and food safety of the HQCF. They must have the right technology, appropriate processing machhinery, standard testing instruments...... and the necessary technical expertise. This quality manual was therefore developed to guide small- to medium-scale cassava in the design and implematation of Hazard Analysis Critical Control Point (HACCP) system and Good manufacturing Practices (GMP) plans for HQCF production. It describes the HQCF production...

  17. A roadmap to high quality chemically prepared graphene

    International Nuclear Information System (INIS)

    Gengler, Regis Y N; Spyrou, Konstantinos; Rudolf, Petra

    2010-01-01

    Graphene was discovered half a decade ago and proved the existence of a two-dimensional system which becomes stable as a result of 3D corrugation. It appeared very quickly that this exceptional material had truly outstanding electronic, mechanical, thermal and optical properties. Consequently a broad range of applications appeared, as the graphene science speedily moved forward. Since then, a lot of effort has been devoted not only to the study of graphene but also to its fabrication. Here we review the chemical approaches to graphene production, their advantages as well as their downsides. Our aim is to draw a roadmap of today's most reliable path to high quality graphene via chemical preparation.

  18. CHOREOGRAPHIC METHODS FOR CREATING NOVEL, HIGH QUALITY DANCE

    Directory of Open Access Journals (Sweden)

    David Kirsh

    2016-02-01

    Full Text Available We undertook a detailed ethnographic study of the dance creation process of a noted choreographer and his distinguished troupe. All choreographer dancer interactions were videoed, the choreographer and dancers were interviewed extensively each day, as well as other observations and tests performed. The choreographer used three main methods to produce high quality and novel content: showing, making-on, and tasking. We present, analyze and evaluate these methods, and show how these approaches allow the choreographer to increase the creative output of the dancers and him. His methods, although designed for dance, apply more generally to other creative endeavors, especially where brainstorming is involved, and where the creative process is distributed over many individuals. His approach is also a case study in multi-modal direction, owing to the range of mechanisms he uses to communicate and direct.

  19. Biotransformation of Organic Waste into High Quality Fertilizer

    DEFF Research Database (Denmark)

    Bryndum, Sofie

    Agriculture faces several challenges of future provision of nutrients such as limited P reserves and increasing prices of synthetic fertilizers and recycling of nutrients from organic waste can be an important strategy for the long-term sustainability of the agricultural systems. Organically...... and S, is often low; and (3) the unbalanced composition of nutrients rarely matches crop demands. Therefore the objective of this project was to investigate the potential for (1) recycling nutrients from agro-industrial wastes and (2) compost biotransformation into high-quality organic fertilizers...... other uses into fertilizer use would be unlikely. An estimated ~50 % of the total organic waste pool, primarily consisting of animal manure and waste from the processing of sugar cane, coffee, oil palm and oranges, is currently being re-used as “fertilizers”, meaning it is eventually returned...

  20. MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

    Science.gov (United States)

    Brown, Bonnie L; Watson, Mick; Minot, Samuel S; Rivera, Maria C; Franklin, Rima B

    2017-03-01

    Environmental metagenomic analysis is typically accomplished by assigning taxonomy and/or function from whole genome sequencing or 16S amplicon sequences. Both of these approaches are limited, however, by read length, among other technical and biological factors. A nanopore-based sequencing platform, MinION™, produces reads that are ≥1 × 104 bp in length, potentially providing for more precise assignment, thereby alleviating some of the limitations inherent in determining metagenome composition from short reads. We tested the ability of sequence data produced by MinION (R7.3 flow cells) to correctly assign taxonomy in single bacterial species runs and in three types of low-complexity synthetic communities: a mixture of DNA using equal mass from four species, a community with one relatively rare (1%) and three abundant (33% each) components, and a mixture of genomic DNA from 20 bacterial strains of staggered representation. Taxonomic composition of the low-complexity communities was assessed by analyzing the MinION sequence data with three different bioinformatic approaches: Kraken, MG-RAST, and One Codex. Results: Long read sequences generated from libraries prepared from single strains using the version 5 kit and chemistry, run on the original MinION device, yielded as few as 224 to as many as 3497 bidirectional high-quality (2D) reads with an average overall study length of 6000 bp. For the single-strain analyses, assignment of reads to the correct genus by different methods ranged from 53.1% to 99.5%, assignment to the correct species ranged from 23.9% to 99.5%, and the majority of misassigned reads were to closely related organisms. A synthetic metagenome sequenced with the same setup yielded 714 high quality 2D reads of approximately 5500 bp that were up to 98% correctly assigned to the species level. Synthetic metagenome MinION libraries generated using version 6 kit and chemistry yielded from 899 to 3497 2D reads with lengths averaging 5700 bp with up

  1. SNP discovery in the transcriptome of white Pacific shrimp Litopenaeus vannamei by next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Yang Yu

    Full Text Available The application of next generation sequencing technology has greatly facilitated high throughput single nucleotide polymorphism (SNP discovery and genotyping in genetic research. In the present study, SNPs were discovered based on two transcriptomes of Litopenaeus vannamei (L. vannamei generated from Illumina sequencing platform HiSeq 2000. One transcriptome of L. vannamei was obtained through sequencing on the RNA from larvae at mysis stage and its reference sequence was de novo assembled. The data from another transcriptome were downloaded from NCBI and the reads of the two transcriptomes were mapped separately to the assembled reference by BWA. SNP calling was performed using SAMtools. A total of 58,717 and 36,277 SNPs with high quality were predicted from the two transcriptomes, respectively. SNP calling was also performed using the reads of two transcriptomes together, and a total of 96,040 SNPs with high quality were predicted. Among these 96,040 SNPs, 5,242 and 29,129 were predicted as non-synonymous and synonymous SNPs respectively. Characterization analysis of the predicted SNPs in L. vannamei showed that the estimated SNP frequency was 0.21% (one SNP per 476 bp and the estimated ratio for transition to transversion was 2.0. Fifty SNPs were randomly selected for validation by Sanger sequencing after PCR amplification and 76% of SNPs were confirmed, which indicated that the SNPs predicted in this study were reliable. These SNPs will be very useful for genetic study in L. vannamei, especially for the high density linkage map construction and genome-wide association studies.

  2. Automated Theorem Proving in High-Quality Software Design

    Science.gov (United States)

    Schumann, Johann; Swanson, Keith (Technical Monitor)

    2001-01-01

    The amount and complexity of software developed during the last few years has increased tremendously. In particular, programs are being used more and more in embedded systems (from car-brakes to plant-control). Many of these applications are safety-relevant, i.e. a malfunction of hardware or software can cause severe damage or loss. Tremendous risks are typically present in the area of aviation, (nuclear) power plants or (chemical) plant control. Here, even small problems can lead to thousands of casualties and huge financial losses. Large financial risks also exist when computer systems are used in the area of telecommunication (telephone, electronic commerce) or space exploration. Computer applications in this area are not only subject to safety considerations, but also security issues are important. All these systems must be designed and developed to guarantee high quality with respect to safety and security. Even in an industrial setting which is (or at least should be) aware of the high requirements in Software Engineering, many incidents occur. For example, the Warshaw Airbus crash, was caused by an incomplete requirements specification. Uncontrolled reuse of an Ariane 4 software module was the reason for the Ariane 5 disaster. Some recent incidents in the telecommunication area, like illegal "cloning" of smart-cards of D2GSM handies, or the extraction of (secret) passwords from German T-online users show that also in this area serious flaws can happen. Due to the inherent complexity of computer systems, most authors claim that only a rigorous application of formal methods in all stages of the software life cycle can ensure high quality of the software and lead to real safe and secure systems. In this paper, we will have a look, in how far automated theorem proving can contribute to a more widespread application of formal methods and their tools, and what automated theorem provers (ATPs) must provide in order to be useful.

  3. Using high-throughput literature mining to support read-across predictions of skin sensitization (WC)

    Science.gov (United States)

    Read-across predictions require high quality measured data for source analogues. These data are typically retrieved from structured databases, but biomedical literature data are often untapped because current literature mining approaches are resource intensive. Our high-throughpu...

  4. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

    Directory of Open Access Journals (Sweden)

    Blackmon Barbara P

    2011-07-01

    Full Text Available Abstract Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

  5. Does Extensive Reading Promote Reading Speed?

    Science.gov (United States)

    He, Mu

    2014-01-01

    Research has shown a wide range of learning benefits accruing from extensive reading. Not only is there improvement in reading, but also in a wide range of language uses and areas of language knowledge. However, few research studies have examined reading speed. The existing literature on reading speed focused on students' reading speed without…

  6. Characterization of Liaoning cashmere goat transcriptome: sequencing, de novo assembly, functional annotation and comparative analysis.

    Directory of Open Access Journals (Sweden)

    Hongliang Liu

    Full Text Available Liaoning cashmere goat is a famous goat breed for cashmere wool. In order to increase the transcriptome data and accelerate genetic improvement for this breed, we performed de novo transcriptome sequencing to generate the first expressed sequence tag dataset for the Liaoning cashmere goat, using next-generation sequencing technology.Transcriptome sequencing of Liaoning cashmere goat on a Roche 454 platform yielded 804,601 high-quality reads. Clustering and assembly of these reads produced a non-redundant set of 117,854 unigenes, comprising 13,194 isotigs and 104,660 singletons. Based on similarity searches with known proteins, 17,356 unigenes were assigned to 6,700 GO categories, and the terms were summarized into three main GO categories and 59 sub-categories. 3,548 and 46,778 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Comparative analysis revealed that 42,254 unigenes were aligned to 17,532 different sequences in NCBI non-redundant nucleotide databases. 97,236 (82.51% unigenes were mapped to the 30 goat chromosomes. 35,551 (30.17% unigenes were matched to 11,438 reported goat protein-coding genes. The remaining non-matched unigenes were further compared with cattle and human reference genes, 67 putative new goat genes were discovered. Additionally, 2,781 potential simple sequence repeats were initially identified from all unigenes.The transcriptome of Liaoning cashmere goat was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the Liaoning cashmere goat transcriptome. The potential simple sequence repeats provide a material basis for future genetic linkage and quantitative trait loci analyses.

  7. Reading Approach Use Effectiveness And EFL Reading Comprehension In University Muhammadiyah Of Parepare

    Directory of Open Access Journals (Sweden)

    Baharuddin

    2017-10-01

    Full Text Available This study investigated Indonesian EFL learners approach of two reading approaches cognitive and metacognitive their perceived contact on effectiveness and the association between reading approach and effectiveness on their English reading comprehension. Fifty-Three English-major freshmen from University Muhammadiyah of Parepare participated in these lessons. Two principal questions were addressed 1 what is the most frequent use of reading approach reported by individual students 2 Is there any significant association between reading approach and effectiveness on their English reading comprehension To examine the effects of approach instruction on students reading performance a qualitative interview technique and quantitative research methods including a paired-sample t-test and Person Product Moment Correlation were used to estimate the relationship between reading approach use and effectiveness on students reading accomplishment. Significance showed that the most frequent use of reading approach was found to be metacognitive approach followed by the cognitive approach. In addition there was a significant positive connection between reading approach and effectiveness on their English reading comprehension. Reading approach on the other hand was unrelated to reading achievement. Results of interview findings were analyzed to explore in-depth in sequence about the condition of approach used. The implications of these findings for implementing effective reading strategy instruction are discussed.

  8. Draft genome sequence of the silver pomfret fish, Pampus argenteus.

    Science.gov (United States)

    AlMomin, Sabah; Kumar, Vinod; Al-Amad, Sami; Al-Hussaini, Mohsen; Dashti, Talal; Al-Enezi, Khaznah; Akbar, Abrar

    2016-01-01

    Silver pomfret, Pampus argenteus, is a fish species from coastal waters. Despite its high commercial value, this edible fish has not been sequenced. Hence, its genetic and genomic studies have been limited. We report the first draft genome sequence of the silver pomfret obtained using a Next Generation Sequencing (NGS) technology. We assembled 38.7 Gb of nucleotides into scaffolds of 350 Mb with N50 of about 1.5 kb, using high quality paired end reads. These scaffolds represent 63.7% of the estimated silver pomfret genome length. The newly sequenced and assembled genome has 11.06% repetitive DNA regions, and this percentage is comparable to that of the tilapia genome. The genome analysis predicted 16 322 genes. About 91% of these genes showed homology with known proteins. Many gene clusters were annotated to protein and fatty-acid metabolism pathways that may be important in the context of the meat texture and immune system developmental processes. The reference genome can pave the way for the identification of many other genomic features that could improve breeding and population-management strategies, and it can also help characterize the genetic diversity of P. argenteus.

  9. Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples

    Directory of Open Access Journals (Sweden)

    Nezar Noor Al-Hebshi

    2015-09-01

    Full Text Available Background: Usefulness of next-generation sequencing (NGS in assessing bacteria associated with oral squamous cell carcinoma (OSCC has been undermined by inability to classify reads to the species level. Objective: The purpose of this study was to develop a robust algorithm for species-level classification of NGS reads from oral samples and to pilot test it for profiling bacteria within OSCC tissues. Methods: Bacterial 16S V1-V3 libraries were prepared from three OSCC DNA samples and sequenced using 454's FLX chemistry. High-quality, well-aligned, and non-chimeric reads ≥350 bp were classified using a novel, multi-stage algorithm that involves matching reads to reference sequences in revised versions of the Human Oral Microbiome Database (HOMD, HOMD extended (HOMDEXT, and Greengene Gold (GGG at alignment coverage and percentage identity ≥98%, followed by assignment to species level based on top hit reference sequences. Priority was given to hits in HOMD, then HOMDEXT and finally GGG. Unmatched reads were subject to operational taxonomic unit analysis. Results: Nearly, 92.8% of the reads were matched to updated-HOMD 13.2, 1.83% to trusted-HOMDEXT, and 1.36% to modified-GGG. Of all matched reads, 99.6% were classified to species level. A total of 228 species-level taxa were identified, representing 11 phyla; the most abundant were Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria. Thirty-five species-level taxa were detected in all samples. On average, Prevotella oris, Neisseria flava, Neisseria flavescens/subflava, Fusobacterium nucleatum ss polymorphum, Aggregatibacter segnis, Streptococcus mitis, and Fusobacterium periodontium were the most abundant. Bacteroides fragilis, a species rarely isolated from the oral cavity, was detected in two samples. Conclusion: This multi-stage algorithm maximizes the fraction of reads classified to the species level while ensuring reliable classification by giving priority to the

  10. 76 FR 45397 - Export Inspection and Weighing Waiver for High Quality Specialty Grain Transported in Containers

    Science.gov (United States)

    2011-07-29

    ...-AB18 Export Inspection and Weighing Waiver for High Quality Specialty Grain Transported in Containers... permanent a waiver due to expire on July 31, 2012, for high quality specialty grain exported in containers... of high quality specialty grain exported in containers are small entities that up until recently...

  11. Using quality scores and longer reads improves accuracy of Solexa read mapping

    Directory of Open Access Journals (Sweden)

    Xuan Zhenyu

    2008-02-01

    Full Text Available Abstract Background Second-generation sequencing has the potential to revolutionize genomics and impact all areas of biomedical science. New technologies will make re-sequencing widely available for such applications as identifying genome variations or interrogating the oligonucleotide content of a large sample (e.g. ChIP-sequencing. The increase in speed, sensitivity and availability of sequencing technology brings demand for advances in computational technology to perform associated analysis tasks. The Solexa/Illumina 1G sequencer can produce tens of millions of reads, ranging in length from ~25–50 nt, in a single experiment. Accurately mapping the reads back to a reference genome is a critical task in almost all applications. Two sources of information that are often ignored when mapping reads from the Solexa technology are the 3' ends of longer reads, which contain a much higher frequency of sequencing errors, and the base-call quality scores. Results To investigate whether these sources of information can be used to improve accuracy when mapping reads, we developed the RMAP tool, which can map reads having a wide range of lengths and allows base-call quality scores to determine which positions in each read are more important when mapping. We applied RMAP to analyze data re-sequenced from two human BAC regions for varying read lengths, and varying criteria for use of quality scores. RMAP is freely available for downloading at http://rulai.cshl.edu/rmap/. Conclusion Our results indicate that significant gains in Solexa read mapping performance can be achieved by considering the information in 3' ends of longer reads, and appropriately using the base-call quality scores. The RMAP tool we have developed will enable researchers to effectively exploit this information in targeted re-sequencing projects.

  12. High-Quality Seismic Observations of Sonic Booms

    Science.gov (United States)

    Wurman, Gilead; Haering, Edward A., Jr.; Price, Michael J.

    2011-01-01

    The SonicBREWS project (Sonic Boom Resistant Earthquake Warning Systems) is a collaborative effort between Seismic Warning Systems, Inc. and NASA Dryden Flight Research Center. This project aims to evaluate the effects of sonic booms on Earthquake Warning Systems in order to prevent such systems from experiencing false alarms due to sonic booms. The airspace above the Antelope Valley, California includes the High Altitude Supersonic Corridor and the Black Mountain Supersonic Corridor. These corridors are among the few places in the US where supersonic flight is permitted, and sonic booms are commonplace in the Antelope Valley. One result of this project is a rich dataset of high-quality accelerometer records of sonic booms which can shed light on the interaction between these atmospheric phenomena and the solid earth. Nearly 100 sonic booms were recorded with low-noise triaxial MEMS accelerometers recording 1000 samples per second. The sonic booms had peak overpressures ranging up to approximately 10 psf and were recorded in three flight series in 2010 and 2011. Each boom was recorded with up to four accelerometers in various array configurations up to 100 meter baseline lengths, both in the built environment and the free field. All sonic booms were also recorded by nearby microphones. We present the results of the project in terms of the potential for sonic-boom-induced false alarms in Earthquake Warning Systems, and highlight some of the interesting features of the dataset.

  13. Construction of High-Quality Camel Immune Antibody Libraries.

    Science.gov (United States)

    Romão, Ema; Poignavent, Vianney; Vincke, Cécile; Ritzenthaler, Christophe; Muyldermans, Serge; Monsion, Baptiste

    2018-01-01

    Single-domain antibodies libraries of heavy-chain only immunoglobulins from camelids or shark are enriched for high-affinity antigen-specific binders by a short in vivo immunization. Thus, potent binders are readily retrieved from relatively small-sized libraries of 10 7 -10 8 individual transformants, mostly after phage display and panning on a purified target. However, the remaining drawback of this strategy arises from the need to generate a dedicated library, for nearly every envisaged target. Therefore, all the procedures that shorten and facilitate the construction of an immune library of best possible quality are definitely a step forward. In this chapter, we provide the protocol to generate a high-quality immune VHH library using the Golden Gate Cloning strategy employing an adapted phage display vector where a lethal ccdB gene has to be substituted by the VHH gene. With this procedure, the construction of the library can be shortened to less than a week starting from bleeding the animal. Our libraries exceed 10 8 individual transformants and close to 100% of the clones harbor a phage display vector having an insert with the length of a VHH gene. These libraries are also more economic to make than previous standard approaches using classical restriction enzymes and ligations. The quality of the Nanobodies that are retrieved from immune libraries obtained by Golden Gate Cloning is identical to those from immune libraries made according to the classical procedure.

  14. High-quality remote interactive imaging in the operating theatre

    Science.gov (United States)

    Grimstead, Ian J.; Avis, Nick J.; Evans, Peter L.; Bocca, Alan

    2009-02-01

    We present a high-quality display system that enables the remote access within an operating theatre of high-end medical imaging and surgical planning software. Currently, surgeons often use printouts from such software for reference during surgery; our system enables surgeons to access and review patient data in a sterile environment, viewing real-time renderings of MRI & CT data as required. Once calibrated, our system displays shades of grey in Operating Room lighting conditions (removing any gamma correction artefacts). Our system does not require any expensive display hardware, is unobtrusive to the remote workstation and works with any application without requiring additional software licenses. To extend the native 256 levels of grey supported by a standard LCD monitor, we have used the concept of "PseudoGrey" where slightly off-white shades of grey are used to extend the intensity range from 256 to 1,785 shades of grey. Remote access is facilitated by a customized version of UltraVNC, which corrects remote shades of grey for display in the Operating Room. The system is successfully deployed at Morriston Hospital, Swansea, UK, and is in daily use during Maxillofacial surgery. More formal user trials and quantitative assessments are being planned for the future.

  15. Production of high quality water for oil sands application

    Energy Technology Data Exchange (ETDEWEB)

    Beaudette-Hodsman, C.; Macleod, B. [Pall Corp., Mississauga, ON (Canada); Venkatadri, R. [Pall Corp., East Hills, NY (United States)

    2008-10-15

    This paper described a pressurized microfiltration membrane system installed at an oil sands extraction site in Alberta. The system was designed to complement a reverse osmosis (RO) system installed at the site to produce the high quality feed water required by the system's boilers. Groundwater in the region exhibited moderate total suspended solids and high alkalinity and hardness levels, and the RO system required feed water with a silt density index of 3 or less. The conventional pretreatment system used at the site was slowing down production due to the severe fouling of the RO membranes. The new microfiltration system contained an automated PVDF hollow fiber microfiltration membrane system contained in a trailer. Suspended particles and bacteria were captured within the filter, and permeate was sent to the RO unit. Within 6 hours of being installed, the unit was producing water with SDI values in the range of 1.0 to 2.5. It was concluded that the microfiltration system performed reliably regardless of wide variations in feed water quality and flow rates. 3 refs., 1 tab., 8 figs.

  16. CCD Astrophotography High-Quality Imaging from the Suburbs

    CERN Document Server

    Stuart, Adam

    2006-01-01

    This is a reference book for amateur astronomers who have become interested in CCD imaging. Those glorious astronomical images found in astronomy magazines might seem out of reach to newcomers to CCD imaging, but this is not the case. Great pictures are attainable with modest equipment. Adam Stuart’s many beautiful images, reproduced in this book, attest to the quality of – initially – a beginner’s efforts. Chilled-chip astronomical CCD-cameras and software are also wonderful tools for cutting through seemingly impenetrable light-pollution. CCD Astrophotography from the Suburbs describes one man’s successful approach to the problem of getting high-quality astronomical images under some of the most light-polluted conditions. Here is a complete and thoroughly tested program that will help every CCD-beginner to work towards digital imaging of the highest quality. It is equally useful to astronomers who have perfect observing conditions, as to those who have to observe from light-polluted city skies.

  17. Sequencing and analysis of the Mediterranean amphioxus (Branchiostoma lanceolatum transcriptome.

    Directory of Open Access Journals (Sweden)

    Silvan Oulion

    Full Text Available BACKGROUND: The basally divergent phylogenetic position of amphioxus (Cephalochordata, as well as its conserved morphology, development and genetics, make it the best proxy for the chordate ancestor. Particularly, studies using the amphioxus model help our understanding of vertebrate evolution and development. Thus, interest for the amphioxus model led to the characterization of both the transcriptome and complete genome sequence of the American species, Branchiostoma floridae. However, recent technical improvements allowing induction of spawning in the laboratory during the breeding season on a daily basis with the Mediterranean species Branchiostoma lanceolatum have encouraged European Evo-Devo researchers to adopt this species as a model even though no genomic or transcriptomic data have been available. To fill this need we used the pyrosequencing method to characterize the B. lanceolatum transcriptome and then compared our results with the published transcriptome of B. floridae. RESULTS: Starting with total RNA from nine different developmental stages of B. lanceolatum, a normalized cDNA library was constructed and sequenced on Roche GS FLX (Titanium mode. Around 1.4 million of reads were produced and assembled into 70,530 contigs (average length of 490 bp. Overall 37% of the assembled sequences were annotated by BlastX and their Gene Ontology terms were determined. These results were then compared to genomic and transcriptomic data of B. floridae to assess similarities and specificities of each species. CONCLUSION: We obtained a high-quality amphioxus (B. lanceolatum reference transcriptome using a high throughput sequencing approach. We found that 83% of the predicted genes in the B. floridae complete genome sequence are also found in the B. lanceolatum transcriptome, while only 41% were found in the B. floridae transcriptome obtained with traditional Sanger based sequencing. Therefore, given the high degree of sequence conservation

  18. Transcriptome analysis of carnation (Dianthus caryophyllus L.) based on next-generation sequencing technology.

    Science.gov (United States)

    Tanase, Koji; Nishitani, Chikako; Hirakawa, Hideki; Isobe, Sachiko; Tabata, Satoshi; Ohmiya, Akemi; Onozaki, Takashi

    2012-07-02

    Carnation (Dianthus caryophyllus L.), in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST) database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology. We constructed a normalized cDNA library and a 3'-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380) of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO) and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs) in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway. We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

  19. Transcriptome analysis of carnation (Dianthus caryophyllus L. based on next-generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Tanase Koji

    2012-07-01

    Full Text Available Abstract Background Carnation (Dianthus caryophyllus L., in the family Caryophyllaceae, can be found in a wide range of colors and is a model system for studies of flower senescence. In addition, it is one of the most important flowers in the global floriculture industry. However, few genomics resources, such as sequences and markers are available for carnation or other members of the Caryophyllaceae. To increase our understanding of the genetic control of important characters in carnation, we generated an expressed sequence tag (EST database for a carnation cultivar important in horticulture by high-throughput sequencing using 454 pyrosequencing technology. Results We constructed a normalized cDNA library and a 3’-UTR library of carnation, obtaining a total of 1,162,126 high-quality reads. These reads were assembled into 300,740 unigenes consisting of 37,844 contigs and 262,896 singlets. The contigs were searched against an Arabidopsis sequence database, and 61.8% (23,380 of them had at least one BLASTX hit. These contigs were also annotated with Gene Ontology (GO and were found to cover a broad range of GO categories. Furthermore, we identified 17,362 potential simple sequence repeats (SSRs in 14,291 of the unigenes. We focused on gene discovery in the areas of flower color and ethylene biosynthesis. Transcripts were identified for almost every gene involved in flower chlorophyll and carotenoid metabolism and in anthocyanin biosynthesis. Transcripts were also identified for every step in the ethylene biosynthesis pathway. Conclusions We present the first large-scale sequence data set for carnation, generated using next-generation sequencing technology. The large EST database generated from these sequences is an informative resource for identifying genes involved in various biological processes in carnation and provides an EST resource for understanding the genetic diversity of this plant.

  20. Recruiting and retaining high-quality teachers in rural areas.

    Science.gov (United States)

    Monk, David H

    2007-01-01

    In examining recruitment and retention of teachers in rural areas, David Monk begins by noting the numerous possible characteristics of rural communities--small size, sparse settlement, distance from population concentrations, and an economic reliance on agricultural industries that are increasingly using seasonal and immigrant workers to minimize labor costs. Many, though not all, rural areas, he says, are seriously impoverished. Classes in rural schools are relatively small, and teachers tend to report satisfaction with their work environments and relatively few problems with discipline. But teacher turnover is often high, and hiring can be difficult. Monk observes that rural schools have a below-average share of highly trained teachers. Compensation in rural schools tends to be low, perhaps because of a lower fiscal capacity in rural areas, thus complicating efforts to attract and retain teachers. Several student characteristics, including relatively large shares of students with special needs and with limited English skills and lower shares of students attending college, can also make it difficult to recruit and retain high-quality teachers. Other challenges include meeting the needs of highly mobile children of low-income migrant farm workers. With respect to public policy, Monk asserts a need to focus on a subcategory of what might be called hard-to-staff rural schools rather than to develop a blanket set of policies for all rural schools. In particular, he recommends a focus on such indicators as low teacher qualifications, teaching in fields far removed from the area of training, difficulty in hiring, high turnover, a lack of diversity among teachers in the school, and the presence of migrant farm workers' children. Successful efforts to stimulate economic growth in these areas would be highly beneficial. He also calls attention to the potential for modern telecommunication and computing technologies to offset some of the drawbacks associated with teaching

  1. High-quality endoscope reprocessing decreases endoscope contamination.

    Science.gov (United States)

    Decristoforo, P; Kaltseis, J; Fritz, A; Edlinger, M; Posch, W; Wilflingseder, D; Lass-Flörl, C; Orth-Höller, D

    2018-02-24

    Several outbreaks of severe infections due to contamination of gastrointestinal (GI) endoscopes, mainly duodenoscopes, have been described. The rate of microbial endoscope contamination varies dramatically in literature. The aim of this multicentre prospective study was to evaluate the hygiene quality of endoscopes and automated endoscope reprocessors (AERs) in Tyrol/Austria. In 2015 and 2016, a total of 463 GI endoscopes and 105 AERs from 29 endoscopy centres were analysed by a routine (R) and a combined routine and advanced (CRA) sampling procedure and investigated for microbial contamination by culture-based and molecular-based analyses. The contamination rate of GI endoscopes was 1.3%-4.6% according to the national guideline, suggesting that 1.3-4.6 patients out of 100 could have had contacts with hygiene-relevant microorganisms through an endoscopic intervention. Comparison of R and CRA sampling showed 1.8% of R versus 4.6% of CRA failing the acceptance criteria in phase I and 1.3% of R versus 3.0% of CRA samples failing in phase II. The most commonly identified indicator organism was Pseudomonas spp., mainly Pseudomonas oleovorans. None of the tested viruses were detected in 40 samples. While AERs in phase I failed (n = 9, 17.6%) mainly due to technical faults, phase II revealed lapses (n = 6, 11.5%) only on account of microbial contamination of the last rinsing water, mainly with Pseudomonas spp. In the present study the contamination rate of endoscopes was low compared with results from other European countries, possibly due to the high quality of endoscope reprocessing, drying and storage. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  2. Slow Reading: Reading along "Lectio" Lines

    Science.gov (United States)

    Badley, K. Jo-Ann; Badley, Ken

    2011-01-01

    The medieval monastic movement preserved and developed reading practices--lectio--from ancient Greek pedagogy as a slow, mindful approach to reading for formation. This ancient way of reading, now better known as lectio divina, challenges the fast, pragmatic reading so characteristic of our time. We propose that the present moment may be ripe for…

  3. Developing reading literacy by reading badge

    OpenAIRE

    Rejc, Blanka

    2017-01-01

    Reading is a fundamental activity of our society and is present in all areas of a person’s life. Authors who deal with reading define reading with different definitions, some of them I also presented in my master’s degree thesis. The ways of reading, typology of readers and knowledge of different reading models are only some of the important theoretical facts that serve as a basis for the research and defining reading. Reading motivation is an important motivational factor, which encourages a...

  4. A Filtration-based Method of Preparing High-quality Nuclei from Cross-linked Skeletal Muscle for Chromatin Immunoprecipitation.

    Science.gov (United States)

    Nohara, Kazunari; Chen, Zheng; Yoo, Seung-Hee

    2017-07-06

    Chromatin immunoprecipitation (ChIP) is a powerful method to determine protein binding to chromatin DNA. Fiber-rich skeletal muscle, however, has been a challenge for ChIP due to technical difficulty in isolation of high-quality nuclei with minimal contamination of myofibrils. Previous protocols have attempted to purify nuclei before cross-linking, which incurs the risk of altered DNA-protein interaction during the prolonged nuclei preparation process. In the current protocol, we first cross-linked the skeletal muscle tissue collected from mice, and the tissues were minced and sonicated. Since we found that ultracentrifugation was not able to separate nuclei from myofibrils using cross-linked muscle tissue, we devised a sequential filtration procedure to obtain high-quality nuclei devoid of significant myofibril contamination. We subsequently prepared chromatin by using an ultrasonicator, and ChIP assays with anti-BMAL1 antibody revealed robust circadian binding pattern of BMAL1 to target gene promoters. This filtration protocol constitutes an easily applicable method to isolate high-quality nuclei from cross-linked skeletal muscle tissue, allowing consistent sample processing for circadian and other time-sensitive studies. In combination with next-generation sequencing (NGS), our method can be deployed for various mechanistic and genomic studies focusing on skeletal muscle function.

  5. Quantum reading capacity

    International Nuclear Information System (INIS)

    Pirandola, Stefano; Braunstein, Samuel L; Lupo, Cosmo; Mancini, Stefano; Giovannetti, Vittorio

    2011-01-01

    The readout of a classical memory can be modelled as a problem of quantum channel discrimination, where a decoder retrieves information by distinguishing the different quantum channels encoded in each cell of the memory (Pirandola 2011 Phys. Rev. Lett. 106 090504). In the case of optical memories, such as CDs and DVDs, this discrimination involves lossy bosonic channels and can be remarkably boosted by the use of nonclassical light (quantum reading). Here we generalize these concepts by extending the model of memory from single-cell to multi-cell encoding. In general, information is stored in a block of cells by using a channel-codeword, i.e. a sequence of channels chosen according to a classical code. Correspondingly, the readout of data is realized by a process of ‘parallel’ channel discrimination, where the entire block of cells is probed simultaneously and decoded via an optimal collective measurement. In the limit of a large block we define the quantum reading capacity of the memory, quantifying the maximum number of readable bits per cell. This notion of capacity is nontrivial when we suitably constrain the physical resources of the decoder. For optical memories (encoding bosonic channels), such a constraint is energetic and corresponds to fixing the mean total number of photons per cell. In this case, we are able to prove a separation between the quantum reading capacity and the maximum information rate achievable by classical transmitters, i.e. arbitrary classical mixtures of coherent states. In fact, we can easily construct nonclassical transmitters that are able to outperform any classical transmitter, thus showing that the advantages of quantum reading persist in the optimal multi-cell scenario. (paper)

  6. Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels

    Directory of Open Access Journals (Sweden)

    Bibby Kyle

    2011-03-01

    Full Text Available Abstract Background Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production. Results Next generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons were subjected to BLAST similarity searches and annotated with Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG orthology (KO identifiers. These analyses identified the majority of lipid and starch biosynthesis and catabolism pathways in D. tertiolecta. Conclusions The construction of metabolic pathways involved in the biosynthesis and catabolism of fatty acids, triacylglycrols, and starch in D. tertiolecta as well as the assembled transcriptome provide a foundation for the molecular genetics and functional genomics required to direct metabolic engineering efforts that seek to enhance the quantity and character of microalgae-based biofuel feedstock.

  7. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  8. New developments in high quality grey cast irons

    Directory of Open Access Journals (Sweden)

    Iulian Riposan

    2014-07-01

    Full Text Available The paper reviews original data obtained by the present authors, revealed in recent separate publications, describing specific procedures for high quality grey irons, and reflecting the forecast needs of the worldwide iron foundry industry. High power, medium frequency coreless induction furnaces are commonly used in electric melting grey iron foundries. This has resulted in low sulphur (1,500 °C, contributing to unfavourable conditions for graphite nucleation. Thin wall castings are increasingly produced by these electric melt shops with a risk of greater eutectic undercooling during solidification. The paper focused on two groups of grey cast irons and their specific problems: carbides and graphite morphology control in lower carbon equivalent high strength irons (CE=3.4%-3.8%, and austenite dendrite promotion in eutectic and slightly hypereutectic irons (CE=4.1%-4.5%, in order to increase their strength characteristics. There are 3 stages and 3 steps involving graphite formation, iron chemistry and iron processing that appear to be important. The concept in the present paper sustains a threestage model for nucleating flake graphite [(Mn,XS type nuclei]. There are three important groups of elements (deoxidizer, Mn/S, and inoculant and three technological stages in electric melting of iron (superheat, pre-conditioning of base iron, final inoculation. Attention is drawn to a control factor (%Mn x (%S ensuring it equals to 0.03 – 0.06, accompanied by 0.005wt.%–0.010wt.% Al and/or Zr content in inoculated irons. It was found that iron powder addition promotes austenite dendrite formation in eutectic and slightly eutectic, acting as reinforcement for the eutectic cells. But, there is an accompanying possible negative influence on the characteristics of the (Mn,XS type graphite nuclei (change the morphology of nuclei from polygonal compact to irregular polygonal, and therefore promote chill tendency in treated irons. A double addition (iron

  9. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  10. High quality mask storage in an advanced Logic-Fab

    Science.gov (United States)

    Jähnert, Carmen; Fritsche, Silvio

    2012-02-01

    High efficient mask logistics as well as safe and high quality mask storage are essential requirements within an advanced lithography area of a modern logic waferfab. Fast operational availability of the required masks at the exposure tool with excellent mask condition requires a safe mask handling, safeguarding of high mask quality over the whole mask usage time without any quality degradation and an intelligent mask logistics. One big challenge is the prevention of haze on high advanced phase shift masks used in a high volume production line for some thousands of 248nm or 193nm exposures. In 2008 Infineon Dresden qualified a customer specific developed semi-bare mask storage system from DMSDynamic Micro Systems in combination with a high advanced mask handling and an interconnected complex logistic system. This high-capacity mask storage system DMS M1900.22 for more than 3000 masks with fully automated mask and box handling as well as full-blown XCDA purge has been developed and adapted to the Infineon Lithotoollandscape using Nikon and SMIF reticle cases. Advanced features for ESD safety and mask security, mask tracking via RFID and interactions with the exposure tools were developed and implemented. The stocker is remote controlled by the iCADA-RSM system, ordering of the requested mask directly from the affected exposure tool allows fast access. This paper discusses the advantages and challenges for this approach as well as the practical experience gained during the implementation of the new system which improves the fab performance with respect to mask quality, security and throughput. Especially the realization of an extremely low and stable humidity level in addition with a well controlled air flow at each mask surface, preventing masks from haze degradation and particle contamination, turns out to be a notable technical achievement. The longterm stability of haze critical masks has been improved significantly. Relevant environmental parameters like

  11. The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.

    Science.gov (United States)

    Mao, Qing; Ciotlos, Serban; Zhang, Rebecca Yu; Ball, Madeleine P; Chin, Robert; Carnevali, Paolo; Barua, Nina; Nguyen, Staci; Agarwal, Misha R; Clegg, Tom; Connelly, Abram; Vandewege, Ward; Zaranek, Alexander Wait; Estep, Preston W; Church, George M; Drmanac, Radoje; Peters, Brock A

    2016-10-11

    Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.

  12. Supporting read-across using biological data.

    Science.gov (United States)

    Zhu, Hao; Bouhifd, Mounir; Donley, Elizabeth; Egnash, Laura; Kleinstreuer, Nicole; Kroese, E Dinant; Liu, Zhichao; Luechtefeld, Thomas; Palmer, Jessica; Pamies, David; Shen, Jie; Strauss, Volker; Wu, Shengde; Hartung, Thomas

    2016-01-01

    Read-across, i.e. filling toxicological data gaps by relating to similar chemicals, for which test data are available, is usually done based on chemical similarity. Besides structure and physico-chemical properties, however, biological similarity based on biological data adds extra strength to this process. In the context of developing Good Read-Across Practice guidance, a number of case studies were evaluated to demonstrate the use of biological data to enrich read-across. In the simplest case, chemically similar substances also show similar test results in relevant in vitro assays. This is a well-established method for the read-across of e.g. genotoxicity assays. Larger datasets of biological and toxicological properties of hundreds and thousands of substances become increasingly available enabling big data approaches in read-across studies. Several case studies using various big data sources are described in this paper. An example is given for the US EPA's ToxCast dataset allowing read-across for high quality uterotrophic assays for estrogenic endocrine disruption. Similarly, an example for REACH registration data enhancing read-across for acute toxicity studies is given. A different approach is taken using omics data to establish biological similarity: Examples are given for stem cell models in vitro and short-term repeated dose studies in rats in vivo to support read-across and category formation. These preliminary biological data-driven read-across studies highlight the road to the new generation of read-across approaches that can be applied in chemical safety assessment.

  13. mpscan: Fast Localisation of Multiple Reads in Genomes

    Science.gov (United States)

    Rivals, Eric; Salmela, Leena; Kiiskinen, Petteri; Kalsi, Petri; Tarhio, Jorma

    With Next Generation Sequencers, sequence based transcriptomic or epigenomic assays yield millions of short sequence reads that need to be mapped back on a reference genome. The upcoming versions of these sequencers promise even higher sequencing capacities; this may turn the read mapping task into a bottleneck for which alternative pattern matching approaches must be experimented. We present an algorithm and its implementation, called mpscan, which uses a sophisticated filtration scheme to match a set of patterns/reads exactly on a sequence. mpscan can search for millions of reads in a single pass through the genome without indexing its sequence. Moreover, we show that mpscan offers an optimal average time complexity, which is sublinear in the text length, meaning that it does not need to examine all sequence positions. Comparisons with BLAT-like tools and with six specialised read mapping programs (like bowtie or zoom) demonstrate that mpscan also is the fastest algorithm in practice for exact matching. Our accuracy and scalability comparisons reveal that some tools are inappropriate for read mapping. Moreover, we provide evidence suggesting that exact matching may be a valuable solution in some read mapping applications. As most read mapping programs somehow rely on exact matching procedures to perform approximate pattern mapping, the filtration scheme we experimented may reveal useful in the design of future algorithms. The absence of genome index gives mpscan its low memory requirement and flexibility that let it run on a desktop computer and avoids a time-consuming genome preprocessing.

  14. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

    Directory of Open Access Journals (Sweden)

    Benkman Craig W

    2010-03-01

    Full Text Available Abstract Background Massively parallel sequencing of cDNA is now an efficient route for generating enormous sequence collections that represent expressed genes. This approach provides a valuable starting point for characterizing functional genetic variation in non-model organisms, especially where whole genome sequencing efforts are currently cost and time prohibitive. The large and complex genomes of pines (Pinus spp. have hindered the development of genomic resources, despite the ecological and economical importance of the group. While most genomic studies have focused on a single species (P. taeda, genomic level resources for other pines are insufficiently developed to facilitate ecological genomic research. Lodgepole pine (P. contorta is an ecologically important foundation species of montane forest ecosystems and exhibits substantial adaptive variation across its range in western North America. Here we describe a sequencing study of expressed genes from P. contorta, including their assembly and annotation, and their potential for molecular marker development to support population and association genetic studies. Results We obtained 586,732 sequencing reads from a 454 GS XLR70 Titanium pyrosequencer (mean length: 306 base pairs. A combination of reference-based and de novo assemblies yielded 63,657 contigs, with 239,793 reads remaining as singletons. Based on sequence similarity with known proteins, these sequences represent approximately 17,000 unique genes, many of which are well covered by contig sequences. This sequence collection also included a surprisingly large number of retrotransposon sequences, suggesting that they are highly transcriptionally active in the tissues we sampled. We located and characterized thousands of simple sequence repeats and single nucleotide polymorphisms as potential molecular markers in our assembled and annotated sequences. High quality PCR primers were designed for a substantial number of the SSR loci

  15. Rearing a reading habit

    OpenAIRE

    Sridhar, M. S.

    2009-01-01

    Discusses the importance and ways of inculcating reading habit in children at the right age, describes the five reading phases in children along with interest and the material to satiate the need, explains how four deterministic factors affect the reading habit of children, enlists motivations that are behind the reading process with tips to improve reading habit of children.

  16. Manufacturing High-Quality Carbon Nanotubes at Lower Cost

    Science.gov (United States)

    Benavides, Jeanette M.; Lidecker, Henning

    2004-01-01

    A modified electric-arc welding process has been developed for manufacturing high-quality batches of carbon nanotubes at relatively low cost. Unlike in some other processes for making carbon nanotubes, metal catalysts are not used and, consequently, it is not necessary to perform extensive cleaning and purification. Also, unlike some other processes, this process is carried out at atmospheric pressure under a hood instead of in a closed, pressurized chamber; as a result, the present process can be implemented more easily. Although the present welding-based process includes an electric arc, it differs from a prior electric-arc nanotube-production process. The welding equipment used in this process includes an AC/DC welding power source with an integral helium-gas delivery system and circulating water for cooling an assembly that holds one of the welding electrodes (in this case, the anode). The cathode is a hollow carbon (optionally, graphite) rod having an outside diameter of 2 in. (approximately equal to 5.1 cm) and an inside diameter of 5/8 in. (approximately equal to 1.6 cm). The cathode is partly immersed in a water bath, such that it protrudes about 2 in. (about 5.1 cm) above the surface of the water. The bottom end of the cathode is held underwater by a clamp, to which is connected the grounding cable of the welding power source. The anode is a carbon rod 1/8 in. (approximately equal to 0.3 cm) in diameter. The assembly that holds the anode includes a thumbknob- driven mechanism for controlling the height of the anode. A small hood is placed over the anode to direct a flow of helium downward from the anode to the cathode during the welding process. A bell-shaped exhaust hood collects the helium and other gases from the process. During the process, as the anode is consumed, the height of the anode is adjusted to maintain an anode-to-cathode gap of 1 mm. The arc-welding process is continued until the upper end of the anode has been lowered to a specified height

  17. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  18. Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Users.

    Science.gov (United States)

    Carugo, Oliviero; Djinović-Carugo, Kristina

    2016-01-01

    It is often necessary to build subsets of the Protein Data Bank to extract structural trends and average values. For this purpose it is mandatory that the subsets are non-redundant and of high quality. The first problem can be solved relatively easily at the sequence level or at the structural level. The second, on the contrary, needs special attention. It is not sufficient, in fact, to consider the crystallographic resolution and other feature must be taken into account: the absence of strings of residues from the electron density maps and from the files deposited in the Protein Data Bank; the B-factor values; the appropriate validation of the structural models; the quality of the electron density maps, which is not uniform; and the temperature of the diffraction experiments. More stringent criteria produce smaller subsets, which can be enlarged with more tolerant selection criteria. The incessant growth of the Protein Data Bank and especially of the number of high-resolution structures is allowing the use of more stringent selection criteria, with a consequent improvement of the quality of the subsets of the Protein Data Bank.

  19. Teolenn: an efficient and customizable workflow to design high-quality probes for microarray experiments

    Science.gov (United States)

    Jourdren, Laurent; Duclos, Aurélie; Brion, Christian; Portnoy, Thomas; Mathis, Hugues; Margeot, Antoine; Le Crom, Stéphane

    2010-01-01

    Despite the development of new high-throughput sequencing techniques, microarrays are still attractive tools to study small genome organisms, thanks to sample multiplexing and high-feature densities. However, the oligonucleotide design remains a delicate step for most users. A vast array of software is available to deal with this problem, but each program is developed with its own strategy, which makes the choice of the best solution difficult. Here we describe Teolenn, a universal probe design workflow developed with a flexible and customizable module organization allowing fixed or variable length oligonucleotide generation. In addition, our software is able to supply quality scores for each of the designed probes. In order to assess the relevance of these scores, we performed a real hybridization using a tiling array designed against the Trichoderma reesei fungus genome. We show that our scoring pipeline correlates with signal quality for 97.2% of all the designed probes, allowing for a posteriori comparisons between quality scores and signal intensities. This result is useful in discarding any bad scoring probes during the design step in order to get high-quality microarrays. Teolenn is available at http://transcriptome.ens.fr/teolenn/. PMID:20176570

  20. Genetic and geochemical signatures to prevent frauds and counterfeit of high-quality asparagus and pistachio.

    Science.gov (United States)

    Zannella, Carmela; Carucci, Francesca; Aversano, Riccardo; Prohaska, Thomas; Vingiani, Simona; Carputo, Domenico; Adamo, Paola

    2017-12-15

    A fingerprinting strategy based on genetic (simple sequence repeat) and geochemical (multielement and 87 Sr/ 86 Sr ratio) analysis was tested to prove the geographical origin of high-quality Italian products "White Asparagus from Bassano del Grappa" and "Green Pistachio from Bronte". Genetic analysis generated many polymorphic alleles and different specific amplified fragments in both agriproducts. In addition, a core set of markers was defined. According to variability within production soils and products, potential candidate elements linking asparagus (Zn, P, Cr, Mg, B, K) and pistachio (Mn, P, Cr, Mg, Ti, B, K, Sc, S) to the production areas were identified. The Sr isotopic signature was an excellent marker when Italian asparagus was compared with literature data for Hungarian and Peruvian asparagus. This work reinforces the use of Sr isotope composition in the soil bioavailable fraction, as assessed by 1mol/L NH 4 NO 3 , to distinguish white asparagus and pistachio originating from different geographical areas. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

    KAUST Repository

    Zhang, Runxuan

    2017-04-05

    Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

  2. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

    KAUST Repository

    Zhang, Runxuan; Calixto, Cristiane  P.  G.; Marquez, Yamile; Venhuizen, Peter; Tzioutziou, Nikoleta A.; Guo, Wenbin; Spensley, Mark; Entizne, Juan Carlos; Lewandowska, Dominika; ten  Have, Sara; Frei  dit  Frey, Nicolas; Hirt, Heribert; James, Allan B.; Nimmo, Hugh G.; Barta, Andrea; Kalyna, Maria; Brown, John  W.  S.

    2017-01-01

    Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.

  3. Unveiling the dynamics of reading

    International Nuclear Information System (INIS)

    Posner, M.; Abdullaev, Y.

    1996-01-01

    What happens in our brain when we read isolated words? Are some particular areas of cortex stimulated when these words make sense? Does the reading practice induce others areas? And what about the new senses research? Some studies carried out for a century show that two regions of the left cerebral hemisphere: the Broca and the Wernicke areas are involved. By visualizing in vivo an elementary thought as what is for instance the function of a hammer, the functional cerebral imagery (positron computed tomography, NMR imaging, electro-encephalography) allows to deepen and to explain the analysis. It reveals an areas network called semantic, in the right hemisphere too. Their activation would take place according to a very fast sequence in order to direct the eye movements during the reading. (O.M.)

  4. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  5. Publishing high-quality climate data on the semantic web

    Science.gov (United States)

    Woolf, Andrew; Haller, Armin; Lefort, Laurent; Taylor, Kerry

    2013-04-01

    The effort over more than a decade to establish the semantic web [Berners-Lee et. al., 2001] has received a major boost in recent years through the Open Government movement. Governments around the world are seeking technical solutions to enable more open and transparent access to Public Sector Information (PSI) they hold. Existing technical protocols and data standards tend to be domain specific, and so limit the ability to publish and integrate data across domains (health, environment, statistics, education, etc.). The web provides a domain-neutral platform for information publishing, and has proven itself beyond expectations for publishing and linking human-readable electronic documents. Extending the web pattern to data (often called Web 3.0) offers enormous potential. The semantic web applies the basic web principles to data [Berners-Lee, 2006]: using URIs as identifiers (for data objects and real-world 'things', instead of documents) making the URIs actionable by providing useful information via HTTP using a common exchange standard (serialised RDF for data instead of HTML for documents) establishing typed links between information objects to enable linking and integration Leading examples of 'linked data' for publishing PSI may be found in both the UK (http://data.gov.uk/linked-data) and US (http://www.data.gov/page/semantic-web). The Bureau of Meteorology (BoM) is Australia's national meteorological agency, and has a new mandate to establish a national environmental information infrastructure (under the National Plan for Environmental Information, NPEI [BoM, 2012a]). While the initial approach is based on the existing best practice Spatial Data Infrastructure (SDI) architecture, linked-data is being explored as a technological alternative that shows great promise for the future. We report here the first trial of government linked-data in Australia under data.gov.au. In this initial pilot study, we have taken BoM's new high-quality reference surface

  6. Dialogic Reading Aloud to Promote Extensive Reading

    Science.gov (United States)

    Jacobs, George M.

    2016-01-01

    How can teachers motivate students to read extensively in a second language? One strategy is for teachers to read aloud to students to promote the joys of reading generally, to build students' language skills and to introduce students to specific authors, book series, genres, websites, etc. This article begins by discussing why teachers might want…

  7. Enhancing academic reading skills through extensive reading ...

    African Journals Online (AJOL)

    Abstract. The current study explores the feasibility of an extensive reading programme in the context of a low-income country (Mozambique), as well as the influence of extensive reading on academic reading. The programme took over 4 months and was conducted among 30 students majoring in Journalism at the Eduardo ...

  8. Transcriptome sequencing and de novo analysis of the copepod Calanus sinicus using 454 GS FLX.

    Directory of Open Access Journals (Sweden)

    Juan Ning

    Full Text Available BACKGROUND: Despite their species abundance and primary economic importance, genomic information about copepods is still limited. In particular, genomic resources are lacking for the copepod Calanus sinicus, which is a dominant species in the coastal waters of East Asia. In this study, we performed de novo transcriptome sequencing to produce a large number of expressed sequence tags for the copepod C. sinicus. RESULTS: Copepodid larvae and adults were used as the basic material for transcriptome sequencing. Using 454 pyrosequencing, a total of 1,470,799 reads were obtained, which were assembled into 56,809 high quality expressed sequence tags. Based on their sequence similarity to known proteins, about 14,000 different genes were identified, including members of all major conserved signaling pathways. Transcripts that were putatively involved with growth, lipid metabolism, molting, and diapause were also identified among these genes. Differentially expressed genes related to several processes were found in C. sinicus copepodid larvae and adults. We detected 284,154 single nucleotide polymorphisms (SNPs that provide a resource for gene function studies. CONCLUSION: Our data provide the most comprehensive transcriptome resource available for C. sinicus. This resource allowed us to identify genes associated with primary physiological processes and SNPs in coding regions, which facilitated the quantitative analysis of differential gene expression. These data should provide foundation for future genetic and genomic studies of this and related species.

  9. Inequality in Preschool Quality? Community-Level Disparities in Access to High-Quality Learning Environments

    Science.gov (United States)

    Bassok, Daphna; Galdo, Eva

    2016-01-01

    In recent years, unequal access to high-quality preschool has emerged as a growing public policy concern. Because of data limitations, it is notoriously difficult to measure disparities in access to early learning opportunities across communities and particularly challenging to quantify gaps in access to "high-quality" programs. Research…

  10. Genome survey sequencing and genetic background characterization of Gracilariopsis lemaneiformis (Rhodophyta) based on next-generation sequencing.

    Science.gov (United States)

    Zhou, Wei; Hu, Yiyi; Sui, Zhenghong; Fu, Feng; Wang, Jinguo; Chang, Lianpeng; Guo, Weihua; Li, Binbin

    2013-01-01

    Gracilariopsis lemaneiformis has a high economic value and is one of the most important aquaculture species in China. Despite it is economic importance, it has remained largely unstudied at the genomic level. In this study, we conducted a genome survey of Gp. lemaneiformis using next-generation sequencing (NGS) technologies. In total, 18.70 Gb of high-quality sequence data with an estimated genome size of 97 Mb were obtained by HiSeq 2000 sequencing for Gp. lemaneiformis. These reads were assembled into 160,390 contigs with a N50 length of 3.64 kb, which were further assembled into 125,685 scaffolds with a total length of 81.17 Mb. Genome analysis predicted 3490 genes and a GC% content of 48%. The identified genes have an average transcript length of 1,429 bp, an average coding sequence size of 1,369 bp, 1.36 exons per gene, exon length of 1,008 bp, and intron length of 191 bp. From the initial assembled scaffold, transposable elements constituted 54.64% (44.35 Mb) of the genome, and 7737 simple sequence repeats (SSRs) were identified. Among these SSRs, the trinucleotide repeat type was the most abundant (up to 73.20% of total SSRs), followed by the di- (17.41%), tetra- (5.49%), hexa- (2.90%), and penta- (1.00%) nucleotide repeat type. These characteristics suggest that Gp. lemaneiformis is a model organism for genetic study. This is the first report of genome-wide characterization within this taxon.

  11. Genome Survey Sequencing and Genetic Background Characterization of Gracilariopsis lemaneiformis (Rhodophyta) Based on Next-Generation Sequencing

    Science.gov (United States)

    Sui, Zhenghong; Fu, Feng; Wang, Jinguo; Chang, Lianpeng; Guo, Weihua; Li, Binbin

    2013-01-01

    Gracilariopsis lemaneiformis has a high economic value and is one of the most important aquaculture species in China. Despite it is economic importance, it has remained largely unstudied at the genomic level. In this study, we conducted a genome survey of Gp. lemaneiformis using next-generation sequencing (NGS) technologies. In total, 18.70 Gb of high-quality sequence data with an estimated genome size of 97 Mb were obtained by HiSeq 2000 sequencing for Gp. lemaneiformis. These reads were assembled into 160,390 contigs with a N50 length of 3.64 kb, which were further assembled into 125,685 scaffolds with a total length of 81.17 Mb. Genome analysis predicted 3490 genes and a GC% content of 48%. The identified genes have an average transcript length of 1,429 bp, an average coding sequence size of 1,369 bp, 1.36 exons per gene, exon length of 1,008 bp, and intron length of 191 bp. From the initial assembled scaffold, transposable elements constituted 54.64% (44.35 Mb) of the genome, and 7737 simple sequence repeats (SSRs) were identified. Among these SSRs, the trinucleotide repeat type was the most abundant (up to 73.20% of total SSRs), followed by the di- (17.41%), tetra- (5.49%), hexa- (2.90%), and penta- (1.00%) nucleotide repeat type. These characteristics suggest that Gp. lemaneiformis is a model organism for genetic study. This is the first report of genome-wide characterization within this taxon. PMID:23875008

  12. Short Communication An efficient method for simultaneous extraction of high-quality RNA and DNA from various plant tissues.

    Science.gov (United States)

    Oliveira, R R; Viana, A J C; Reátegui, A C E; Vincentz, M G A

    2015-12-29

    Determination of gene expression is an important tool to study biological processes and relies on the quality of the extracted RNA. Changes in gene expression profiles may be directly related to mutations in regulatory DNA sequences or alterations in DNA cytosine methylation, which is an epigenetic mark. Correlation of gene expression with DNA sequence or epigenetic mark polymorphism is often desirable; for this, a robust protocol to isolate high-quality RNA and DNA simultaneously from the same sample is required. Although commercial kits and protocols are available, they are mainly optimized for animal tissues and, in general, restricted to RNA or DNA extraction, not both. In the present study, we describe an efficient and accessible method to extract both RNA and DNA simultaneously from the same sample of various plant tissues, using small amounts of starting material. The protocol was efficient in the extraction of high-quality nucleic acids from several Arabidopsis thaliana tissues (e.g., leaf, inflorescence stem, flower, fruit, cotyledon, seedlings, root, and embryo) and from other tissues of non-model plants, such as Avicennia schaueriana (Acanthaceae), Theobroma cacao (Malvaceae), Paspalum notatum (Poaceae), and Sorghum bicolor (Poaceae). The obtained nucleic acids were used as templates for downstream analyses, such as mRNA sequencing, quantitative real time-polymerase chain reaction, bisulfite treatment, and others; the results were comparable to those obtained with commercial kits. We believe that this protocol could be applied to a broad range of plant species, help avoid technical and sampling biases, and facilitate several RNA- and DNA-dependent analyses.

  13. Generation and annotation of lodgepole pine and oleoresin-induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a Mountain Pine Beetle-associated pathogen.

    Science.gov (United States)

    DiGuistini, Scott; Ralph, Steven G; Lim, Young W; Holt, Robert; Jones, Steven; Bohlmann, Jörg; Breuil, Colette

    2007-02-01

    Ophiostoma clavigerum is a destructive pathogen of lodgepole pine (Pinus contorta) forests in western North America. It is therefore a relevant system for a genomics analysis of fungi vectored by bark beetles. To begin characterizing molecular interactions between the pathogen and its conifer host, we created an expressed sequence tag (EST) collection for O. clavigerum. Lodgepole pine sawdust and oleoresin media were selected to stimulate gene expression that would be specific to this host interaction. Over 6500 cDNA clones, derived from four normalized cDNA libraries, were single-pass sequenced from the 3' end. After quality screening, we identified 5975 high-quality reads with an average PHRED 20 of greater than 750 bp. Clustering and assembly of this high-quality EST set resulted in the identification of 2620 unique putative transcripts. BLASTX analysis revealed that only 67% of these unique transcripts could be matched to known or predicted protein sequences in public databases. Functional classification of these sequences provided initial insights into the transcriptome of O. clavigerum. Of particular interest, our ESTs represent an extensive collection of cytochrome P450 s, ATP-binding-cassette-type transporters and genes involved in 1,8-dihydroxynaphthalene-melanin biosynthesis. These results are discussed in the context of detoxification of conifer oleoresins and fungal pathogenesis.

  14. Theme: Parents and Reading.

    Science.gov (United States)

    Jund, Suzanne, Ed.

    1977-01-01

    This journal issue concentrates on the theme "Parents and Reading." It presents articles on sharing books with young children, using public relations in a reading program, guiding preschool learning, assessing language readiness, working with reading problems, and teaching reading readiness in Wisconsin kindergartens. Resources and a review of…

  15. Psychometric Research in Reading.

    Science.gov (United States)

    Davis, Frederick B.

    This review of psychometric research in reading analyzes the factors which seem related to reading comprehension skills. Experimental analysis of reading comprehension by L. E. Thorndike revealed two major components: knowledge of word meanings and verbal reasoning abilities. Subsequent analysis of experimental studies of reading comprehension…

  16. Peak reading detector circuit

    International Nuclear Information System (INIS)

    Courtin, E.; Grund, K.; Traub, S.; Zeeb, H.

    1975-01-01

    The peak reading detector circuit serves for picking up the instants during which peaks of a given polarity occur in sequences of signals in which the extreme values, their time intervals, and the curve shape of the signals vary. The signal sequences appear in measuring the foetal heart beat frequence from amplitude-modulated ultrasonic, electrocardiagram, and blood pressure signals. In order to prevent undesired emission of output signals from, e. g., disturbing intermediate extreme values, the circuit consists of the series connections of a circuit to simulate an ideal diode, a strong unit, a discriminator for the direction of charging current, a time-delay circuit, and an electronic switch lying in the decharging circuit of the storage unit. The time-delay circuit thereby causes storing of a preliminary maximum value being used only after a certain time delay for the emission of the output signal. If a larger extreme value occurs during the delay time the preliminary maximum value is cleared and the delay time starts running anew. (DG/PB) [de

  17. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

    Science.gov (United States)

    Gao, Song; Sung, Wing-Kin; Nagarajan, Niranjan

    2011-11-01

    Scaffolding, the problem of ordering and orienting contigs, typically using paired-end reads, is a crucial step in the assembly of high-quality draft genomes. Even as sequencing technologies and mate-pair protocols have improved significantly, scaffolding programs still rely on heuristics, with no guarantees on the quality of the solution. In this work, we explored the feasibility of an exact solution for scaffolding and present a first tractable solution for this problem (Opera). We also describe a graph contraction procedure that allows the solution to scale to large scaffolding problems and demonstrate this by scaffolding several large real and synthetic datasets. In comparisons with existing scaffolders, Opera simultaneously produced longer and more accurate scaffolds demonstrating the utility of an exact approach. Opera also incorporates an exact quadratic programming formulation to precisely compute gap sizes (Availability: http://sourceforge.net/projects/operasf/ ).

  18. High Quality Draft Genomes of the Type Strains Geobacillus thermocatenulatus DSM 730T, G. uzenensis DSM 23175T And Parageobacillus galactosidasius DSM 18751T.

    Science.gov (United States)

    Ramaloko, Winnie Thabisa; Koen, Nadine; Polliack, Shamara; Aliyu, Habibu; Lebre, Pedro Humberto; Mohr, Teresa; Oswald, Florian; Zwick, Michaela; Zeigler, Daniel Ray; Neumann, Anke; Syldatk, Christoph; Cowan, Don Arthur; De Maayer, Pieter

    2018-01-01

    The thermophilic 'Geobacilli' are important sources of thermostable enzymes and other biotechnologically relevant macromolecules. The present work reports the high quality draft genome sequences of previously unsequenced type strains of Geobacillus uzenensis (DSM 23175 T ), G. thermocatenulatus (DSM 730 T ) and Parageobacillus galactosidasius (DSM 18751 T ). Phylogenomic analyses revealed that DSM 18751 T and DSM 23175 T represent later heterotypic synonyms of P. toebii and G. subterraneus , respectively, while DSM 730 T represents the type strain for the species G. thermocatenulatus . These genome sequences will contribute towards a deeper understanding of the ecological and biological diversity and the biotechnological exploitation of the 'geobacilli'.

  19. RNA sequencing analysis to capture the transcriptome landscape during skin ulceration syndrome progression in sea cucumber Apostichopus japonicus.

    Science.gov (United States)

    Yang, Aifu; Zhou, Zunchun; Pan, Yongjia; Jiang, Jingwei; Dong, Ying; Guan, Xiaoyan; Sun, Hongjuan; Gao, Shan; Chen, Zhong

    2016-06-14

    Sea cucumber Apostichopus japonicus is an important economic species in China, which is affected by various diseases; skin ulceration syndrome (SUS) is the most serious. In this study, we characterized the transcriptomes in A. japonicus challenged with Vibrio splendidus to elucidate the changes in gene expression throughout the three stages of SUS progression. RNA sequencing of 21 cDNA libraries from various tissues and developmental stages of SUS-affected A. japonicus yielded 553 million raw reads, of which 542 million high-quality reads were generated by deep-sequencing using the Illumina HiSeq™ 2000 platform. The reference transcriptome comprised a combination of the Illumina reads, 454 sequencing data and Sanger sequences obtained from the public database to generate 93,163 unigenes (average length, 1,052 bp; N50 = 1,575 bp); 33,860 were annotated. Transcriptome comparisons between healthy and SUS-affected A. japonicus revealed greater differences in gene expression profiles in the body walls (BW) than in the intestines (Int), respiratory trees (RT) and coelomocytes (C). Clustering of expression models revealed stable up-regulation as the main pattern occurring in the BW throughout the three stages of SUS progression. Significantly affected pathways were associated with signal transduction, immune system, cellular processes, development and metabolism. Ninety-two differentially expressed genes (DEGs) were divided into four functional categories: attachment/pathogen recognition (17), inflammatory reactions (38), oxidative stress response (7) and apoptosis (30). Using quantitative real-time PCR, twenty representative DEGs were selected to validate the sequencing results. The Pearson's correlation coefficient (R) of the 20 DEGs ranged from 0.811 to 0.999, which confirmed the consistency and accuracy between these two approaches. Dynamic changes in global gene expression occur during SUS progression in A. japonicus. Elucidation of these changes is important

  20. 501 reading comprehension questions

    CERN Document Server

    2014-01-01

    This updated edition offers the most extensive and varied practice for all types of questions students might face on standardized and in-class tests. With this guide, students will learn to develop expert reading strategies, understand how to read faster and with greater comprehension, overcome reading anxiety, and increase appreciation of reading for pleasure. This book's step-by-step approach provides graduated coverage that moves from the basics to more advanced reading.

  1. Real-World Solutions for Developing High-Quality PHP Frameworks and Applications

    CERN Document Server

    Bergmann, Sebastian

    2011-01-01

    Learn to develop high-quality applications and frameworks in PHP Packed with in-depth information and step-by-step guidance, this book escorts you through the process of creating, maintaining and extending sustainable software of high quality with PHP. World-renowned PHP experts present real-world case studies for developing high-quality applications and frameworks in PHP that can easily be adapted to changing business requirements. . They offer different approaches to solving  typical development and quality assurance problems that every developer needs to know and master.Details the process

  2. Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform.

    Science.gov (United States)

    Rutvisuttinunt, Wiriya; Chinnawirotpisan, Piyawan; Simasathien, Sriluck; Shrestha, Sanjaya K; Yoon, In-Kyu; Klungthong, Chonticha; Fernandez, Stefan

    2013-11-01

    Active global surveillance and characterization of influenza viruses are essential for better preparation against possible pandemic events. Obtaining comprehensive information about the influenza genome can improve our understanding of the evolution of influenza viruses and emergence of new strains, and improve the accuracy when designing preventive vaccines. This study investigated the use of deep sequencing by the next-generation sequencing (NGS) Illumina MiSeq Platform to obtain complete genome sequence information from influenza virus isolates. The influenza virus isolates were cultured from 6 respiratory acute clinical specimens collected in Thailand and Nepal. DNA libraries obtained from each viral isolate were mixed and all were sequenced simultaneously. Total information of 2.6 Gbases was obtained from a 455±14 K/mm2 density with 95.76% (8,571,655/8,950,724 clusters) of the clusters passing quality control (QC) filters. Approximately 93.7% of all sequences from Read1 and 83.5% from Read2 contained high quality sequences that were ≥Q30, a base calling QC score standard. Alignments analysis identified three seasonal influenza A H3N2 strains, one 2009 pandemic influenza A H1N1 strain and two influenza B strains. The nearly entire genomes of all six virus isolates yielded equal or greater than 600-fold sequence coverage depth. MiSeq Platform identified seasonal influenza A H3N2, 2009 pandemic influenza A H1N1and influenza B in the DNA library mixtures efficiently. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Transcriptome sequencing and De Novo analysis of Youngia japonica using the illumina platform.

    Directory of Open Access Journals (Sweden)

    Yulan Peng

    Full Text Available Youngia japonica, a weed species distributed worldwide, has been widely used in traditional Chinese medicine. It is an ideal plant for studying the evolution of Asteraceae plants because of its short life history and abundant source. However, little is known about its evolution and genetic diversity. In this study, de novo transcriptome sequencing was conducted for the first time for the comprehensive analysis of the genetic diversity of Y. japonica. The Y. japonica transcriptome was sequenced using Illumina paired-end sequencing technology. We produced 21,847,909 high-quality reads for Y. japonica and assembled them into contigs. A total of 51,850 unigenes were identified, among which 46,087 were annotated in the NCBI non-redundant protein database and 41,752 were annotated in the Swiss-Prot database. We mapped 9,125 unigenes onto 163 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. In addition, 3,648 simple sequence repeats (SSRs were detected. Our data provide the most comprehensive transcriptome resource currently available for Y. japonica. C4 photosynthesis unigenes were found in the biological process of Y. japonica. There were 5596 unigenes related to defense response and 1344 ungienes related to signal transduction mechanisms (10.95%. These data provide insights into the genetic diversity of Y. japonica. Numerous SSRs contributed to the development of novel markers. These data may serve as a new valuable resource for genomic studies on Youngia and, more generally, Cichoraceae.

  4. Identifying suitable substrates for high-quality graphene-based heterostructures

    Science.gov (United States)

    Banszerus, L.; Janssen, H.; Otto, M.; Epping, A.; Taniguchi, T.; Watanabe, K.; Beschoten, B.; Neumaier, D.; Stampfer, C.

    2017-06-01

    We report on a scanning confocal Raman spectroscopy study investigating the strain-uniformity and the overall strain and doping of high-quality chemical vapour deposited (CVD) graphene-based heterostuctures on a large number of different substrate materials, including hexagonal boron nitride (hBN), transition metal dichalcogenides, silicon, different oxides and nitrides, as well as polymers. By applying a hBN-assisted, contamination free, dry transfer process for CVD graphene, high-quality heterostructures with low doping densities and low strain variations are assembled. The Raman spectra of these pristine heterostructures are sensitive to substrate-induced doping and strain variations and are thus used to probe the suitability of the substrate material for potential high-quality graphene devices. We find that the flatness of the substrate material is a key figure for gaining, or preserving high-quality graphene.

  5. Production of high quality sodium iodide preparations labelled with carrier free iodine-125

    International Nuclear Information System (INIS)

    Abdukayumov, M.N.; Chistyakov, P.G.; Shilin, E.A.

    2001-01-01

    Work is related to the problem of high-quality Sodium Iodide preparation production and to the choice of the peptids iodination methods with the purpose of control test developing to determine the Biological activity of the above mentioned preparation

  6. The Role of Dosimetry in High-Quality EMI Risk Assessment

    National Research Council Canada - National Science Library

    2006-01-01

    The Final Proceedings for The role of EMF dosimetry in high quality risk assessment 13 September 2006 - 15 September 2006 In the last three decades the use of devices that emit electromagnetic fields (EMF...

  7. Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing

    Directory of Open Access Journals (Sweden)

    Gang Nie

    2017-01-01

    Full Text Available Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly. Furthermore, 95,897 (83.57% unigenes were annotated to at least one database including NR, Swiss-Prot, KEGG, COG, GO, and NT, supporting that the sequences obtained were annotated properly. Differentially expressed gene analysis indicates that drought stress 15 days could be a critical period for M. sinensis response to drought stress. The high-throughput transcriptome sequencing of M. sinensis under drought stress has greatly enriched the current genomic available resources. The comparison of DEGs under different periods of drought stress identified a wealth of candidate genes involved in drought tolerance regulatory networks, which will facilitate further genetic improvement and molecular studies of the M. sinensis.

  8. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.

    OpenAIRE

    Aljanabi, S M; Martinez, I

    1997-01-01

    A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley, potato, beans, pear and almond leaves as well as fungi, insects and shrimps' fresh tissue) without any modification. The method does not require expensive and environmentally hazardous reagents and equipment. It can be performed even i...

  9. [Quality management is associated with high quality services in health care].

    Science.gov (United States)

    Nielsen, Tenna Hassert; Riis, Allan; Mainz, Jan; Jensen, Anne-Louise Degn

    2013-12-09

    In these years, quality management has been the focus in order to meet high quality services for the patients in Danish health care. This article provides information on quality management and quality improvement and it evaluates its effectiveness in achieving better organizational structures, processes and results in Danish health-care organizations. Our findings generally support that quality management is associated with high quality services in health care.

  10. Fluency First: Reversing the Traditional ESL Sequence.

    Science.gov (United States)

    MacGowan-Gilhooly, Adele

    1991-01-01

    Describes an ESL department's whole language approach to writing and reading, replacing its traditional grammar-based ESL instructional sequence. Reports the positive quantitative and qualitative results of the first three years of using the new approach. (KEH)

  11. Reading Disabilities and PASS Reading Enhancement Programme

    Science.gov (United States)

    Mahapatra, Shamita

    2016-01-01

    Children experience difficulties in reading either because they fail to decode the words and thus are unable to comprehend the text or simply fail to comprehend the text even if they are able to decode the words and read them out. Failure in word decoding results from a failure in phonological coding of written information, whereas reading…

  12. To read or not to read

    NARCIS (Netherlands)

    Mol, Suzanne Elizabeth

    2010-01-01

    There is a widely held belief that reading (story)books makes us smarter and helps promote success in life. Does scientific evidence support this notion? The three meta-analyses in this thesis comprise 146 studies between 1988 and 2010 (N=10,308 participants) that addressed the role of book reading

  13. Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

    Directory of Open Access Journals (Sweden)

    Shan Wei

    2018-05-01

    Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

  14. Adaptive Basis Selection for Exponential Family Smoothing Splines with Application in Joint Modeling of Multiple Sequencing Samples

    OpenAIRE

    Ma, Ping; Zhang, Nan; Huang, Jianhua Z.; Zhong, Wenxuan

    2017-01-01

    Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments in parallel. After the resulting sequences (short reads) are mapped to the genome, one gets a sequence of short read counts along the genome. Effective extraction of signals in these short read counts is the key to the success of sequencing technologies. No...

  15. A Pedagogical Route for the Reading of the Press Opinion Article

    Directory of Open Access Journals (Sweden)

    Niura Maria Fontana

    2011-07-01

    Full Text Available A teaching sequence for the university level, focusing on the press opinion article as a genre, based on genre assumptions (Bakhtin, 1992, Bronckart, 2003 and on teaching sequences (Dolz, Noverraz e Schneuwly, 2004, comprehends the following activities: pre-reading (previous knowledge activation; hypotheses raising; reading (production conditions; constitution of text meaning; reading strategies; post-reading (relationships between text and reality; critical awareness. These were followed by chain genres production (press opinion article and related genres, promoting interaction among text, reader and writer, complemented by metacognitive reflection. Applied to two groups of freshmen, the sequence showed statistically significant results in the development of reading competence.

  16. Construction of high-quality recombination maps with low-coverage genomic sequencing for joint linkage analysis in maize

    Science.gov (United States)

    A genome-wide association study (GWAS) is the foremost strategy used for finding genes that control human diseases and agriculturally important traits, but it often reports false positives. In contrast, its complementary method, linkage analysis, provides direct genetic confirmation, but with limite...

  17. High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot

    OpenAIRE

    Aberg, Karolina A.; Xie, Lin Y.; Nerella, Srilaxmi; Copeland, William E.; Costello, E. Jane; van den Oord, Edwin J.C.G.

    2013-01-01

    The potential importance of DNA methylation in the etiology of complex diseases has led to interest in the development of methylome-wide association studies (MWAS) aimed at interrogating all methylation sites in the human genome. When using blood as biomaterial for a MWAS the DNA is typically extracted directly from fresh or frozen whole blood that was collected via venous puncture. However, DNA extracted from dry blood spots may also be an alternative starting material. In the present study,...

  18. Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.).

    Science.gov (United States)

    Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

    2016-01-01

    Mango (Mangifera indica L.) is called "king of fruits" due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties 'Neelam', 'Dashehari' and their hybrid 'Amrapali' using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.

  19. Guided Reading and Motivation

    Science.gov (United States)

    Hauptman, Allyson L.

    2012-01-01

    The purpose of this study was to determine the relationship between Guided Reading and student motivation to read across fourth, fifth, and sixth grades. The study defined literacy motivation as: (a) task value; (b) self-perceived competence; (c) students' perceptions of the Guided Reading format. Factor analysis and repeated measures ANOVAs were…

  20. Readability and Reading Ability.

    Science.gov (United States)

    Wright, Benjamin D.; Stenner, A. Jackson

    This document discusses the measurement of reading ability and the readability of books by application of the Lexile framework. It begins by stating the importance of uniform measures. It then discusses the history of reading ability testing, based on the assumption that no researcher has been able to measure more than one kind of reading ability.…

  1. Reading and Empathy

    Science.gov (United States)

    McCreary, John J.; Marchant, Gregory J.

    2017-01-01

    The relationship between reading and empathy was explored. Controlling for GPA and gender, reading variables were hypothesized as related to empathy; the relationship was expected to differ for males and females. For the complete sample, affective components were related to GPA but not reading. Perspective taking was related to reading…

  2. Free Reading Is UTOPIA

    Science.gov (United States)

    LeCrone, Nancy

    2010-01-01

    In high school students get tied up in extracurricular activities and have little time for pleasure reading. It is true that with rigorous academic schedules they have little time for pleasure reading. Thus began a conversation with a sophomore English teacher at the author's high school. As they were discussing the plight of free reading he was…

  3. Reading: United States.

    Science.gov (United States)

    Weber, Rose-Marie

    1983-01-01

    An exploration of the increasingly important role of linguistics in literacy research and instruction reviews literature on reading comprehension, written language, orthography, metalinguistics, classroom language use, reading disabilities, native tongues, nonstandard dialects, bilingual education, adult literacy, and second-language reading. (86…

  4. Teaching Reading with Puppets.

    Science.gov (United States)

    Bennett, Ruth

    The use of traditional stories in American Indian language programs connects students' reading to their lives and familiarizes learners with the rhythms of the oral language. Puppet performances are one way of connecting reading programs to the Native oral tradition. A high school reading lesson in a first-year Hupa language class uses many…

  5. 100 articles every ecologist should read.

    Science.gov (United States)

    Courchamp, Franck; Bradshaw, Corey J A

    2018-02-01

    Reading scientific articles is a valuable and major part of the activity of scientists. Yet, with the upsurge of currently available articles and the increasing specialization of scientists, it becomes difficult to identify, let alone read, important papers covering topics not directly related to one's own specific field of research, or that are older than a few years. Our objective was to propose a list of seminal papers deemed to be of major importance in ecology, thus providing a general 'must-read' list for any new ecologist, regardless of particular topic or expertise. We generated a list of 544 papers proposed by 147 ecology experts (journal editorial members) and subsequently ranked via random-sample voting by 368 of 665 contacted ecology experts, covering 6 article types, 6 approaches and 17 fields. Most of the recommended papers were not published in the highest-ranking journals, nor did they have the highest number of mean annual citations. The articles proposed through the collective recommendation of several hundred experienced researchers probably do not represent an 'ultimate', invariant list, but they certainly contain many high-quality articles that are undoubtedly worth reading-regardless of the specific field of interest in ecology-to foster the understanding, knowledge and inspiration of early-career scientists.

  6. Lenses on Reading An Introduction to Theories and Models

    CERN Document Server

    Tracey, Diane H

    2012-01-01

    This widely adopted text explores key theories and models that frame reading instruction and research. Readers learn why theory matters in designing and implementing high-quality instruction and research; how to critically evaluate the assumptions and beliefs that guide their own work; and what can be gained by looking at reading through multiple theoretical lenses. For each theoretical model, classroom applications are brought to life with engaging vignettes and teacher reflections. Research applications are discussed and illustrated with descriptions of exemplary studies. New to This Edition

  7. Developmental relations between reading comprehension and reading strategies

    OpenAIRE

    Muijselaar, M.M.L.; Swart, N.M.; Steenbeek-Planting, E.G.; Droop, W.; Verhoeven, L.T.W.; Jong, P.F. de

    2017-01-01

    We examined the developmental relations between knowledge of reading strategies and reading comprehension in a longitudinal study of 312 Dutch children from the beginning of fourth grade to the end of fifth grade. Measures for reading comprehension, reading strategies, reading fluency, vocabulary, and working memory were administered. A structural equation model was constructed to estimate the unique relations between reading strategies and reading comprehension, while controlling for reading...

  8. High-Throughput Sequencing of Microbial Community Diversity and Dynamics during Douchi Fermentation

    Science.gov (United States)

    Tu, Zong-cai; Wang, Xiao-lan

    2016-01-01

    Douchi is a type of Chinese traditional fermented food that is an important source of protein and is used in flavouring ingredients. The end product is affected by the microbial community present during fermentation, but exactly how microbes influence the fermentation process remains poorly understood. We used an Illumina MiSeq approach to investigate bacterial and fungal community diversity during both douchi-koji making and fermentation. A total of 181,443 high quality bacterial 16S rRNA sequences and 221,059 high quality fungal internal transcribed spacer reads were used for taxonomic classification, revealing eight bacterial and three fungal phyla. Firmicutes, Actinobacteria and Proteobacteria were the dominant bacterial phyla, while Ascomycota and Zygomycota were the dominant fungal phyla. At the genus level, Staphylococcus and Weissella were the dominant bacteria, while Aspergillus and Lichtheimia were the dominant fungi. Principal coordinate analysis showed structural separation between the composition of bacteria in koji making and fermentation. However, multivariate analysis of variance based on unweighted UniFrac distances did identify distinct differences (p fermentation. This is the first investigation to integrate douchi fermentation and koji making and fermentation processes through this technological approach. The results provide insight into the microbiome of the douchi fermentation process, and reveal a structural separation that may be stratified by the environment during the production of this traditional fermented food. PMID:27992473

  9. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

    Science.gov (United States)

    Senol Cali, Damla; Kim, Jeremie S; Ghose, Saugata; Alkan, Can; Mutlu, Onur

    2018-04-02

    Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious

  10. Reading Comprehension Strategies

    Directory of Open Access Journals (Sweden)

    Unal Ulker

    2017-12-01

    Full Text Available The academic success of the university students greatly depends on the mastery of an academic reading skill. However, students as well as teachers, take the learning of this skill for granted, as they tend to presuppose that reading skill is acquired as a part of their secondary education. As a result, most first-year students employ non university strategies to read academic texts, which leads to a surface approach to reading and prevents students from a better understanding of the material. This paper will discuss the strategies that involve students in taking a deep approach to reading academic texts.

  11. Reading use in preschool

    OpenAIRE

    Laísa Cristina dos Santos Guilherme; Rodrigo Ferreira Daverni

    2016-01-01

    Abstract: Reading in preschool is a time of awakening the taste and pleasure in reading, it is also a source of reflection, discovery and learn to listen. It is then necessary that the contact with the reading start from pre-school, with a variety of texts and the teacher also has the habit of reading in their daily lives. Therefore, this study aimed to investigate the benefits of daily reading in the classroom pre-school life of a student, which the characteristics of a player and teacher re...

  12. What oral text reading fluency can reveal about reading comprehension

    NARCIS (Netherlands)

    Veenendaal, N.J.; Groen, M.A.; Verhoeven, L.T.W.

    2015-01-01

    Text reading fluency – the ability to read quickly, accurately and with a natural intonation – has been proposed as a predictor of reading comprehension. In the current study, we examined the role of oral text reading fluency, defined as text reading rate and text reading prosody, as a contributor

  13. Isolation of high quality RNA from pistachio (Pistacia vera L.) and other woody plants high in secondary metabolites.

    Science.gov (United States)

    Moazzam Jazi, Maryam; Rajaei, Saideh; Seyedi, Seyed Mahdi

    2015-10-01

    The quality and quantity of RNA are critical for successful downstream transcriptome-based studies such as microarrays and RNA sequencing (RNA-Seq). RNA isolation from woody plants, such as Pistacia vera, with very high amounts of polyphenols and polysaccharides is an enormous challenge. Here, we describe a highly efficient protocol that overcomes the limitations posed by poor quality and low yield of isolated RNA from pistachio and various recalcitrant woody plants. The key factors that resulted in a yield of 150 μg of high quality RNA per 200 mg of plant tissue include the elimination of phenol from the extraction buffer, raising the concentration of β-mercaptoethanol, long time incubation at 65 °C, and nucleic acid precipitation with optimized volume of NaCl and isopropyl alcohol. Also, the A260/A280 and A260/A230 of extracted RNA were about 1.9-2.1and 2.2-2.3, respectively, revealing the high purity. Since the isolated RNA passed highly stringent quality control standards for sensitive reactions, including RNA sequencing and real-time PCR, it can be considered as a reliable and cost-effective method for RNA extraction from woody plants.

  14. Isolation of high-quality total RNA from rumen anaerobic bacteria and fungi, and subsequent detection of glycoside hydrolases.

    Science.gov (United States)

    Wang, Pan; Qi, Meng; Barboza, Perry; Leigh, Mary Beth; Ungerfeld, Emilio; Selinger, L Brent; McAllister, Tim A; Forster, Robert J

    2011-07-01

    The rumen is one of the most powerful fibrolytic fermentation systems known. Gene expression analyses, such as reverse transcription PCR (RT-PCR), microarrays, and metatranscriptomics, are techniques that could significantly expand our understanding of this ecosystem. The ability to isolate and stabilize representative RNA samples is critical to obtaining reliable results with these procedures. In this study, we successfully isolated high-quality total RNA from the solid phase of ruminal contents by using an improved RNA extraction method. This method is based on liquid nitrogen grinding of whole ruminal solids without microbial detachment and acid guanidinium - phenol - chloroform extraction combined with column purification. Yields of total RNA were as high as 150 µg per g of fresh ruminal content. The typical large subunit/small subunit rRNA ratio ranged from 1.8 to 2.0 with an RNA integrity number (Agilent Technologies) greater than 8.5. By eliminating the detachment step, the resulting RNA was more representative of the complete ecosystem. Our improved method removed a major barrier limiting analysis of rumen microbial function from a gene expression perspective. The polyA-tailed eukaryotic mRNAs obtained have successfully been applied to next-generation sequencing, and metatranscriptomic analysis of the solid fraction of rumen contents revealed abundant sequences related to rumen fungi.

  15. Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.

    Directory of Open Access Journals (Sweden)

    Dario Cantu

    Full Text Available BACKGROUND: The wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130. METHODOLOGY/PRINCIPAL FINDINGS: We obtained nearly 80 million high quality paired-end reads (>50x coverage that were assembled into 29,178 contigs (64.8 Mb, which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase. CONCLUSIONS/SIGNIFICANCE: The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for

  16. Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology.

    Science.gov (United States)

    Sasaki, Katsutomo; Mitsuda, Nobutaka; Nashima, Kenji; Kishimoto, Kyutaro; Katayose, Yuichi; Kanamori, Hiroyuki; Ohmiya, Akemi

    2017-09-04

    Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits. To obtain useful information about molecular bases for floral traits of chrysanthemums, we read expressed sequence tags (ESTs) of chrysanthemums by high-throughput sequencing using the 454 pyrosequencing technology. We constructed normalized cDNA libraries, consisting of full-length, 3'-UTR, and 5'-UTR cDNAs derived from various tissues of chrysanthemums. These libraries produced a total number of 3,772,677 high-quality reads, which were assembled into 213,204 contigs. By comparing the data obtained with those of full genome-sequenced species, we confirmed that our chrysanthemum contig set contained the majority of all expressed genes, which was sufficient for further molecular analysis in chrysanthemums. We confirmed that our chrysanthemum EST set (contigs) contained a number of contigs that encoded transcription factors and enzymes involved in pigment and aroma compound metabolism that was comparable to that of other species. This information can serve as an informative resource for identifying genes involved in various biological processes in chrysanthemums. Moreover, the findings of our study will contribute to a better understanding of the floral characteristics of chrysanthemums including the myriad cultivars at the molecular level.

  17. High Quality RNA Isolation from Leaf, Shell, Root Tissues and Callus of Hazelnut (Corylus avellana L.

    Directory of Open Access Journals (Sweden)

    Hossein Khosravi

    2017-12-01

    Full Text Available Extraction of high quality RNA is a critical step in molecular genetics studies. Hazelnut is one of the most important nuts plants in the world. The presence of the taxol and other taxanes in hazelnut plant necessitates explaining their biosynthesis pathway and identifying the candidate genes. Therefore, an easy and practical method is necessary for RNA extraction from hazelnuts. Hazelnut has high levels of phenolic compounds. High amounts of polyphenolic and polysaccharide compounds in plants could be causing problems in RNA extraction procedures.  To avoid these problems, a simple and efficient method can be used based on cetyltrimethylammonium bromide (CTAB extraction buffer and lithium chloride for extraction of high quality RNA from different parts of hazelnut plant. Using this method, a high-quality RNA sample (light absorbed in the A260/A280 was 2.04

  18. Development of a high-quality cut-off wall using electrophoresis

    International Nuclear Information System (INIS)

    Kawachi, T.; Murahashi, H.

    1991-01-01

    Techniques to build a high-quality cut-off wall have been developed for storage facilities of low-level radioactive waste (LLW) as an emergency measures to prevent leakages. The cut-off wall is highly impermeable, nucleid-adsorptive and have long-term durability. Electrophoresis is used to form impermeable membrane of bentonite as main features of the cut-off wall. First of all, laboratory tests have been conducted to study ways of building barriers on site and to collect data on the barriers properties. Afterwards, on-site construction tests of a high-quality cut-off wall have been carried out. In this paper, we describe the process and results on the studies of the high-quality cut-off wall using electrophoresis

  19. Stainless steel fabrication for high quality requirements in the nuclear industry

    International Nuclear Information System (INIS)

    Wareing, A.J.

    1990-01-01

    In this paper the author explains the welding procedures and practices adopted within the nuclear industry to achieve the high quality and standards of welds required. The changeover to mechanised welding, orbital TIG welding and synergic MIG welding, has resulted in consistent achievement of high quality standards as well as optimising the productivity. However, the use of mechanised welding machines does require the welder operating them to be fully trained and qualified. The formally organised training courses are described and the cost savings and production rates achieved by utilising the mechanised method are discussed. (author)

  20. Comparative transcriptome sequencing and de novo analysis of Vaccinium corymbosum during fruit and color development.

    Science.gov (United States)

    Li, Lingli; Zhang, Hehua; Liu, Zhongshuai; Cui, Xiaoyue; Zhang, Tong; Li, Yanfang; Zhang, Lingyun

    2016-10-12

    Blueberry is an economically important fruit crop in Ericaceae family. The substantial quantities of flavonoids in blueberry have been implicated in a broad range of health benefits. However, the information regarding fruit development and flavonoid metabolites based on the transcriptome level is still limited. In the present study, the transcriptome and gene expression profiling over berry development, especially during color development were initiated. A total of approximately 13.67 Gbp of data were obtained and assembled into 186,962 transcripts and 80,836 unigenes from three stages of blueberry fruit and color development. A large number of simple sequence repeats (SSRs) and candidate genes, which are potentially involved in plant development, metabolic and hormone pathways, were identified. A total of 6429 sequences containing 8796 SSRs were characterized from 15,457 unigenes and 1763 unigenes contained more than one SSR. The expression profiles of key genes involved in anthocyanin biosynthesis were also studied. In addition, a comparison between our dataset and other published results was carried out. Our high quality reads produced in this study are an important advancement and provide a new resource for the interpretation of high-throughput data for blueberry species whether regarding sequencing data depth or species extension. The use of this transcriptome data will serve as a valuable public information database for the studies of blueberry genome and would greatly boost the research of fruit and color development, flavonoid metabolisms and regulation and breeding of more healthful blueberries.

  1. DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

    Science.gov (United States)

    Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

    2016-01-01

    The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

  2. [EST-SSR identification, markers development of Ligusticum chuanxiong based on Ligusticum chuanxiong transcriptome sequences].

    Science.gov (United States)

    Yuan, Can; Peng, Fang; Yang, Ze-Mao; Zhong, Wen-Juan; Mou, Fang-Sheng; Gong, Yi-Yun; Ji, Pei-Cheng; Pu, De-Qiang; Huang, Hai-Yan; Yang, Xiao; Zhang, Chao

    2017-09-01

    Ligusticum chuanxiong is a well-known traditional Chinese medicine plant. The study on its molecular markers development and germplasm resources is very important. In this study, we obtained 24 422 unigenes by assembling transcriptome sequencing reads of L. chuanxiong root. EST-SSR was detected and 4 073 SSR loci were identified. EST-SSR distribution and characteristic analysis results showed that the mono-nucleotide repeats were the main repeat types, accounting for 41.0%. In addition, the sequences containing SSR were functionally annotated in Gene Ontology (GO) and KEGG pathway and were assigned to 49 GO categories, 242 KEGG pathways, among them 2 201 sequences were annotated against Nr database. By validating 235 EST-SSRs,74 primer pairs were ultimately proved to have high quality amplification. Subsequently, genetic diversity analysis, UPGMA cluster analysis, PCoA analysis and population structure analysis of 34 L. chuanxiong germplasm resources were carried out with 74 primer pairs. In both UPGMA tree and PCoA results, L. chuanxiong resources were clustered into two groups, which are believed to be partial related to their geographical distribution. In this study, EST-SSRs in L. chuanxiong was firstly identified, and newly developed molecular markers would contribute significantly to further genetic diversity study, the purity detection, gene mapping, and molecular breeding. Copyright© by the Chinese Pharmaceutical Association.

  3. Rapid development of microsatellite markers for Callosobruchus chinensis using Illumina paired-end sequencing.

    Directory of Open Access Journals (Sweden)

    Can-Xing Duan

    Full Text Available BACKGROUND: The adzuki bean weevil, Callosobruchus chinensis L., is one of the most destructive pests of stored legume seeds such as mungbean, cowpea, and adzuki bean, which usually cause considerable loss in the quantity and quality of stored seeds during transportation and storage. However, a lack of genetic information of this pest results in a series of genetic questions remain largely unknown, including population genetic structure, kinship, biotype abundance, and so on. Co-dominant microsatellite markers offer a great resolving power to determine these events. Here, we report rapid microsatellite isolation from C. chinensis via high-throughput sequencing. PRINCIPAL FINDINGS: In this study, 94,560,852 quality-filtered and trimmed reads were obtained for the assembly of genome using Illumina paired-end sequencing technology. In total, the genome with total length of 497,124,785 bp, comprising 403,113 high quality contigs was generated with de novo assembly. More than 6800 SSR loci were detected and a suit of 6303 primer pair sequences were designed and 500 of them were randomly selected for validation. Of these, 196 pair of primers, i.e. 39.2%, produced reproducible amplicons that were polymorphic among 8 C. chinensis genotypes collected from different geographical regions. Twenty out of 196 polymorphic SSR markers were used to analyze the genetic diversity of 18 C. chinensis populations. The results showed the twenty SSR loci were highly polymorphic among these populations. CONCLUSIONS: This study presents a first report of genome sequencing and de novo assembly for C. chinensis and demonstrates the feasibility of generating a large scale of sequence information and SSR loci isolation by Illumina paired-end sequencing. Our results provide a valuable resource for C. chinensis research. These novel markers are valuable for future genetic mapping, trait association, genetic structure and kinship among C. chinensis.

  4. Exploring the Relationship between Adolescent's Reading Skills, Reading Motivation and Reading Habits

    Science.gov (United States)

    McGeown, Sarah P.; Duncan, Lynne G.; Griffiths, Yvonne M.; Stothard, Sue E.

    2015-01-01

    The present study examines the extent to which adolescents' reading affect (reading motivation) and behaviour (reading habits) predict different components of reading (word reading, comprehension, summarisation and text reading speed) and also adds to the limited research examining group differences (gender, age, ability) in adolescents' reading…

  5. Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

    Directory of Open Access Journals (Sweden)

    Marais Gabriel AB

    2011-07-01

    Full Text Available Abstract Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO terms, and thousands of single-nucleotide polymorphisms (SNPs were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49% that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to

  6. Comparative high-throughput transcriptome sequencing and development of SiESTa, the Silene EST annotation database

    Science.gov (United States)

    2011-01-01

    Background The genus Silene is widely used as a model system for addressing ecological and evolutionary questions in plants, but advances in using the genus as a model system are impeded by the lack of available resources for studying its genome. Massively parallel sequencing cDNA has recently developed into an efficient method for characterizing the transcriptomes of non-model organisms, generating massive amounts of data that enable the study of multiple species in a comparative framework. The sequences generated provide an excellent resource for identifying expressed genes, characterizing functional variation and developing molecular markers, thereby laying the foundations for future studies on gene sequence and gene expression divergence. Here, we report the results of a comparative transcriptome sequencing study of eight individuals representing four Silene and one Dianthus species as outgroup. All sequences and annotations have been deposited in a newly developed and publicly available database called SiESTa, the Silene EST annotation database. Results A total of 1,041,122 EST reads were generated in two runs on a Roche GS-FLX 454 pyrosequencing platform. EST reads were analyzed separately for all eight individuals sequenced and were assembled into contigs using TGICL. These were annotated with results from BLASTX searches and Gene Ontology (GO) terms, and thousands of single-nucleotide polymorphisms (SNPs) were characterized. Unassembled reads were kept as singletons and together with the contigs contributed to the unigenes characterized in each individual. The high quality of unigenes is evidenced by the proportion (49%) that have significant hits in similarity searches with the A. thaliana proteome. The SiESTa database is accessible at http://www.siesta.ethz.ch. Conclusion The sequence collections established in the present study provide an important genomic resource for four Silene and one Dianthus species and will help to further develop Silene as a

  7. Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA.

    Science.gov (United States)

    Marine, Rachel; Polson, Shawn W; Ravel, Jacques; Hatfull, Graham; Russell, Daniel; Sullivan, Matthew; Syed, Fraz; Dumas, Michael; Wommack, K Eric

    2011-11-01

    Construction of DNA fragment libraries for next-generation sequencing can prove challenging, especially for samples with low DNA yield. Protocols devised to circumvent the problems associated with low starting quantities of DNA can result in amplification biases that skew the distribution of genomes in metagenomic data. Moreover, sample throughput can be slow, as current library construction techniques are time-consuming. This study evaluated Nextera, a new transposon-based method that is designed for quick production of DNA fragment libraries from a small quantity of DNA. The sequence read distribution across nine phage genomes in a mock viral assemblage met predictions for six of the least-abundant phages; however, the rank order of the most abundant phages differed slightly from predictions. De novo genome assemblies from Nextera libraries provided long contigs spanning over half of the phage genome; in four cases where full-length genome sequences were available for comparison, consensus sequences were found to match over 99% of the genome with near-perfect identity. Analysis of areas of low and high sequence coverage within phage genomes indicated that GC content may influence coverage of sequences from Nextera libraries. Comparisons of phage genomes prepared using both Nextera and a standard 454 FLX Titanium library preparation protocol suggested that the coverage biases according to GC content observed within the Nextera libraries were largely attributable to bias in the Nextera protocol rather than to the 454 sequencing technology. Nevertheless, given suitable sequence coverage, the Nextera protocol produced high-quality data for genomic studies. For metagenomics analyses, effects of GC amplification bias would need to be considered; however, the library preparation standardization that Nextera provides should benefit comparative metagenomic analyses.

  8. Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina.

    Directory of Open Access Journals (Sweden)

    Tingcai Cheng

    Full Text Available The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG and posterior silk gland (PSG. Three sericin genes (sericin 1, sericin 2, and sericin 3 were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25 were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs and 361 insertion-deletions (INDELs were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research.

  9. Reading in developmental prosopagnosia

    DEFF Research Database (Denmark)

    Starrfelt, Randi; Klargaard, Solja K; Petersen, Anders

    2018-01-01

    exposure durations (targeting the word superiority effect), and d) text reading. RESULTS: Participants with developmental prosopagnosia performed strikingly similar to controls across the four reading tasks. Formal analysis revealed a significant dissociation between word and face recognition......, that is, impaired reading in developmental prosopagnosia. METHOD: We tested 10 adults with developmental prosopagnosia and 20 matched controls. All participants completed the Cambridge Face Memory Test, the Cambridge Face Perception test and a Face recognition questionnaire used to quantify everyday face...... recognition experience. Reading was measured in four experimental tasks, testing different levels of letter, word, and text reading: (a) single word reading with words of varying length,(b) vocal response times in single letter and short word naming, (c) recognition of single letters and short words at brief...

  10. INTEREST AND READING MOTIVATION

    Directory of Open Access Journals (Sweden)

    Alhamdu Alhamdu

    2016-05-01

    Full Text Available The purpose of this study is to examine the relationship between interest and reading motivation based on literature review. The concept of the interest portrayed as a psychological state that occurs during interaction between individual and specific topic, object or activity including process of willingness, increased attention, concentration and positive feeling to the topic, object or activity. Meanwhile reading motivation emphasized to mental readiness, willingness and refers to beliefs and perception of individual to engage in reading activity. Some researchers were identified factors that influenced reading motivation such as intrinsic and extrinsic factors, self-concept and value of reading, and interest. In general, the literature review described that have positive relationship between interest and reading motivation.

  11. Motivational reading on education, meaningful reading realisation

    Directory of Open Access Journals (Sweden)

    Adriana Qafa

    2017-07-01

    Full Text Available In this study I will present some ideas on today’s educational practice for motivation, the realization of the meaningful reading. There is a special place for the methodical ranking of the reading process, starting in school. Main requests of this reading, consist of the deep meaning of the subject, exploration of the idea, and other elements of the subject, implementation of the technique’s rules of the expressive reading, such as breathing, voice, diction, intonation, spelling, stoppages, logical emphasizes, emotional expressions, temper, timber, gesticulations, and mimic. There is also highlighted the fact that the used method comes from the pupils’ results and depends on the capability and level of the teacher, from the programming’s scale, the tools that are put into disposition, the age and the level of the pupils, and from the environment that the teacher creates during courses. At the end there are some practical guidelines for the realization of the expressive reading in the literature subject.

  12. Evaluating approaches to find exon chains based on long reads.

    Science.gov (United States)

    Kuosmanen, Anna; Norri, Tuukka; Mäkinen, Veli

    2018-05-01

    Transcript prediction can be modeled as a graph problem where exons are modeled as nodes and reads spanning two or more exons are modeled as exon chains. Pacific Biosciences third-generation sequencing technology produces significantly longer reads than earlier second-generation sequencing technologies, which gives valuable information about longer exon chains in a graph. However, with the high error rates of third-generation sequencing, aligning long reads correctly around the splice sites is a challenging task. Incorrect alignments lead to spurious nodes and arcs in the graph, which in turn lead to incorrect transcript predictions. We survey several approaches to find the exon chains corresponding to long reads in a splicing graph, and experimentally study the performance of these methods using simulated data to allow for sensitivity/precision analysis. Our experiments show that short reads from second-generation sequencing can be used to significantly improve exon chain correctness either by error-correcting the long reads before splicing graph creation, or by using them to create a splicing graph on which the long-read alignments are then projected. We also study the memory and time consumption of various modules, and show that accurate exon chains lead to significantly increased transcript prediction accuracy. The simulated data and in-house scripts used for this article are available at http://www.cs.helsinki.fi/group/gsa/exon-chains/exon-chains-bib.tar.bz2.

  13. Improve your reading

    CERN Document Server

    Fry, Ron

    2012-01-01

    Help your students discover the practical solution to their reading frustrations, with Improve Your Reading. Written by bestselling author and education advocate Ron Fry, this book avoids gimmicks and tricks in favor of proven strategies that will help your students better retain and comprehend what they've read in any textbook, in any course, at any academic level. Endlessly adaptable to each student's individual learning needs, the text focuses on fundamental skills students can carry beyond the classroom.

  14. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  15. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  16. Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study.

    Directory of Open Access Journals (Sweden)

    Emeline Deleury

    Full Text Available Our present understanding of the functioning and evolutionary history of invertebrate innate immunity derives mostly from studies on a few model species belonging to ecdysozoa. In particular, the characterization of signaling pathways dedicated to specific responses towards fungi and Gram-positive or Gram-negative bacteria in Drosophila melanogaster challenged our original view of a non-specific immunity in invertebrates. However, much remains to be elucidated from lophotrochozoan species. To investigate the global specificity of the immune response in the fresh-water snail Biomphalaria glabrata, we used massive Illumina sequencing of 5'-end cDNAs to compare expression profiles after challenge by Gram-positive or Gram-negative bacteria or after a yeast challenge. 5'-end cDNA sequencing of the libraries yielded over 12 millions high quality reads. To link these short reads to expressed genes, we prepared a reference transcriptomic database through automatic assembly and annotation of the 758,510 redundant sequences (ESTs, mRNAs of B. glabrata available in public databases. Computational analysis of Illumina reads followed by multivariate analyses allowed identification of 1685 candidate transcripts differentially expressed after an immune challenge, with a two fold ratio between transcripts showing a challenge-specific expression versus a lower or non-specific differential expression. Differential expression has been validated using quantitative PCR for a subset of randomly selected candidates. Predicted functions of annotated candidates (approx. 700 unisequences belonged to a large extend to similar functional categories or protein types. This work significantly expands upon previous gene discovery and expression studies on B. glabrata and suggests that responses to various pathogens may involve similar immune processes or signaling pathways but different genes belonging to multigenic families. These results raise the question of the importance

  17. Producing high-quality negatives from ERTS black-and-white transparancies

    Science.gov (United States)

    Richard J. Myhre

    1973-01-01

    A method has been devised for producing high-quality black-and-white negatives quickly and efficiently from dense transparencies orgininating from Earth Resources Technology Satellite imagery. Transparencies are evaluated on a standard light source to determine exposure and processing information needed for making negatives. A “System ASA Rating” was developed by...

  18. Study on the Introduction of High-Quality Educational Resources for Sino-Foreign Cooperative Education

    Science.gov (United States)

    Jinhui, Lin

    2016-01-01

    In Sino-foreign cooperative education, high-quality introduced educational resources must benefit the growth and development of students, facilitate the school's capacity building and the improvement of overall educational standards, and promote national socioeconomic development. It is necessary to establish and perfect the various working…

  19. High quality ion channels recordings on an injection molded polymer chip

    DEFF Research Database (Denmark)

    Tanzi, Simone

    In this thesis we demonstrate high quality recordings of the ion channel activity across the cell membrane in a biological cell by employing the so called patch clamping technique on an injection molded polymer microfluidic device. Such recordings are traditionally made using glass micropipettes,...

  20. High-quality bulk hybrid perovskite single crystals within minutes by inverse temperature crystallization

    KAUST Repository

    Saidaminov, Makhsud I.; Abdelhady, Ahmed L.; Banavoth, Murali; Alarousu, Erkki; Burlakov, Victor M.; Peng, Wei; Dursun, Ibrahim; Wang, Lingfei; He, Yao; Maculan, Giacomo; Goriely, Alain; Wu, Tao; Mohammed, Omar F.; Bakr, Osman

    2015-01-01

    Single crystals of methylammonium lead trihalide perovskites (MAPbX3; MA=CH3NH3+, X=Br− or I−) have shown remarkably low trap density and charge transport properties; however, growth of such high-quality semiconductors is a time-consuming process

  1. Emotional Experience, Expression, and Regulation of High-Quality Japanese Elementary School Teachers

    Science.gov (United States)

    Hosotani, Rika; Imai-Matsumura, Kyoko

    2011-01-01

    The present study investigates the emotional experience, expression, and regulation processes of high-quality Japanese elementary school teachers while they interact with children, in terms of teachers' emotional competence. Qualitative analysis of interview data demonstrated that teachers had various emotional experiences including self-elicited…

  2. High quality factor GaAs microcavity with buried bullseye defects

    DEFF Research Database (Denmark)

    Winkler, K.; Gregersen, Niels; Hayrynen, T.

    2018-01-01

    The development of high quality factor solid-state microcavities with low mode volumes has paved the way towards on-chip cavity quantum electrodynamics experiments and the development of high-performance nanophotonic devices. Here, we report on the implementation of a new kind of solid...

  3. 75 FR 41693 - Export Inspection and Weighing Waiver for High Quality Specialty Grains Transported in Containers

    Science.gov (United States)

    2010-07-19

    ... Specialty Grains Transported in Containers AGENCY: Grain Inspection, Packers and Stockyards Administration... rule to potentially make permanent the current waiver for high quality grain exported in containers... exported in containers that was established by a final rule on December 13, 2005 (70 FR 73556). This...

  4. A safe inexpensive method to isolate high quality plant and fungal ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-08-18

    Aug 18, 2008 ... quality DNA from plant and fungal species. This method uses potassium acetate to remove proteins and polysaccharides in an SDS extraction buffer. Further DNA purification is achieved using a low salt. CTAB treatment. This SDS/CTAB protocol was used to isolate high quality genomic DNA subject to.

  5. Student Writing Accepted as High-Quality Responses to Analytic Text-Based Writing Tasks

    Science.gov (United States)

    Wang, Elaine; Matsumura, Lindsay Clare; Correnti, Richard

    2018-01-01

    Literacy standards increasingly emphasize the importance of analytic text-based writing. Little consensus exists, however, around what high-quality student responses should look like in this genre. In this study, we investigated fifth-grade students' writing in response to analytic text-based writing tasks (15 teachers, 44 writing tasks, 88 pieces…

  6. Toward High Quality Family Day Care for Infants and Toddlers. Final Report.

    Science.gov (United States)

    Rauch, Marian D.; Crowell, Doris C.

    Reported were the results of a project which established a cluster of family day care homes in Hawaii in which caregivers were selected, trained, and provided with supportive services and salaries. The primary objective of the program was to provide a replicable, high quality program for preschool children that would maximize social, emotional,…

  7. Optimization of nitridation conditions for high quality inter-polysilicon dielectric layers

    NARCIS (Netherlands)

    Klootwijk, J.H.; Bergveld, H.J.; van Kranenburg, H.; Woerlee, P.H.; Wallinga, Hans

    1996-01-01

    Nitridation of deposited high temperature oxides (HTO) was studied to form high quality inter-polysilicon dielectric layers for embedded non volatile memories. Good quality dielectric layers were obtained earlier by using an optimized deposition of polysilicon and by performing a post-dielectric

  8. 10 Principles for Building a High-Quality System of Assessments

    Science.gov (United States)

    Jobs for the Future, 2018

    2018-01-01

    Many states and districts are working toward developing and implementing high-quality systems that align assessments with each other, and to college and career readiness, and a comprehensive set of higher-order thinking skills. In order to support states, districts, and communities in this, the following 10 principles as guidance and common…

  9. Access, Participation, and Supports: The Defining Features of High-Quality Inclusion

    Science.gov (United States)

    Buysse, Virginia

    2011-01-01

    This article describes current knowledge about early childhood inclusion, summarizing research and the DEC/NAEYC joint position statement on inclusion. The article also describes effective or promising educational practices that promote access, participation, and supports--the defining features of high-quality inclusion. Future efforts to improve…

  10. Integrated Pathology Informatics Enables High-Quality Personalized and Precision Medicine: Digital Pathology and Beyond.

    Science.gov (United States)

    Volynskaya, Zoya; Chow, Hung; Evans, Andrew; Wolff, Alan; Lagmay-Traya, Cecilia; Asa, Sylvia L

    2018-03-01

    - The critical role of pathology in diagnosis, prognosis, and prediction demands high-quality subspecialty diagnostics that integrates information from multiple laboratories. - To identify key requirements and to establish a systematic approach to providing high-quality pathology in a health care system that is responsible for services across a large geographic area. - This report focuses on the development of a multisite pathology informatics platform to support high-quality surgical pathology and hematopathology using a sophisticated laboratory information system and whole slide imaging for histology and immunohistochemistry, integrated with ancillary tools, including electron microscopy, flow cytometry, cytogenetics, and molecular diagnostics. - These tools enable patients in numerous geographic locations access to a model of subspecialty pathology that allows reporting of every specimen by the right pathologist at the right time. The use of whole slide imaging for multidisciplinary case conferences enables better communication among members of patient care teams. The system encourages data collection using a discrete data synoptic reporting module, has implemented documentation of quality assurance activities, and allows workload measurement, providing examples of additional benefits that can be gained by this electronic approach to pathology. - This approach builds the foundation for accurate big data collection and high-quality personalized and precision medicine.

  11. A Novel Approach to High-Quality Postmortem Tissue Procurement: The GTEx Project

    NARCIS (Netherlands)

    Carithers, Latarsha J.; Ardlie, Kristin; Barcus, Mary; Branton, Philip A.; Britton, Angela; Buia, Stephen A.; Compton, Carolyn C.; Deluca, David S.; Peter-Demchok, Joanne; Gelfand, Ellen T.; Guan, Ping; Korzeniewski, Greg E.; Lockhart, Nicole C.; Rabiner, Chana A.; Rao, Abhi K.; Robinson, Karna L.; Roche, Nancy V.; Sawyer, Sherilyn J.; Segrè, Ayellet V.; Shive, Charles E.; Smith, Anna M.; Sobin, Leslie H.; Undale, Anita H.; Valentino, Kimberly M.; Vaught, Jim; Young, Taylor R.; Moore, Helen M.; Barker, Laura; Basile, Margaret; Battle, Alexis; Boyer, Joy; Bradbury, Debra; Bridge, Jason P.; Brown, Amanda; Burges, Robin; Choi, Christopher; Colantuoni, Deborah; Cox, Nancy; Dermitzakis, Emmanouil T.; Derr, Leslie K.; Dinsmore, Michael J.; Erickson, Kenyon; Fleming, Johnelle; Flutre, Timothée; Foster, Barbara A.; Gamazon, Eric R.; Getz, Gad; Gillard, Bryan M.; Guigo, Roderic; Hambright, Kenneth W.; Hariharan, Pushpa; Hasz, Rick; Im, Hae K.; Jewell, Scott; Karasik, Ellen; Kellis, Manolis; Kheradpour, Pouya; Koester, Susan; Koller, Daphne; Konkashbaev, Anuar; Lappalainen, Tuuli; Little, Roger; Liu, Jun; Lo, Edmund; Lonsdale, John T.; Lu, Chunrong; MacArthur, Daniel G.; Magazine, Harold; Maller, Julian B.; Marcus, Yvonne; Mash, Deborah C.; McCarthy, Mark I.; McLean, Jeffrey; Mestichelli, Bernadette; Miklos, Mark; Monlong, Jean; Mosavel, Magboeba; Moser, Michael T.; Mostafavi, Sara; Nicolae, Dan L.; Pritchard, Jonathan; Qi, Liqun; Ramsey, Kimberly; Rivas, Manuel A.; Robles, Barnaby E.; Rohrer, Daniel C.; Salvatore, Mike; Sammeth, Michael; Seleski, John; Shad, Saboor; Siminoff, Laura A.; Stephens, Matthew; Struewing, Jeff; Sullivan, Timothy; Sullivan, Susan; Syron, John; Tabor, David; Taherian, Mehran; Tejada, Jorge; Temple, Gary F.; Thomas, Jeffrey A.; Thomson, Alexander W.; Tidwell, Denee; Traino, Heather M.; Tu, Zhidong; Valley, Dana R.; Volpi, Simona; Walters, Gary D.; Ward, Lucas D.; Wen, Xiaoquan; Winckler, Wendy; Wu, Shenpei; Zhu, Jun

    2015-01-01

    The Genotype-Tissue Expression (GTEx) project, sponsored by the NIH Common Fund, was established to study the correlation between human genetic variation and tissue-specific gene expression in non-diseased individuals. A significant challenge was the collection of high-quality biospecimens for

  12. High quality data: An evaluation of AIM data quality and data quality procedures

    Science.gov (United States)

    The goal of every monitoring program is to collect high-quality data which can then be used to provide information to decision makers. The Bureau of Land Management (BLM) Assessment, Inventory, and Monitoring (AIM) program is one such data set which provides rangeland status, condition, and trend in...

  13. Timing of high-quality child care and cognitive, language, and preacademic development.

    Science.gov (United States)

    Li, Weilin; Farkas, George; Duncan, Greg J; Burchinal, Margaret R; Vandell, Deborah Lowe

    2013-08-01

    The effects of high- versus low-quality child care during 2 developmental periods (infant-toddlerhood and preschool) were examined using data from the National Institute of Child Health and Human Development Study of Early Child Care. Propensity score matching was used to account for differences in families who used different combinations of child care quality during the 2 developmental periods. Findings indicated that cognitive, language, and preacademic skills prior to school entry were highest among children who experienced high-quality care in both the infant-toddler and preschool periods, somewhat lower among children who experienced high-quality child care during only 1 of these periods, and lowest among children who experienced low-quality care during both periods. Irrespective of the care received during infancy-toddlerhood, high-quality preschool care was related to better language and preacademic outcomes at the end of the preschool period; high-quality infant-toddler care, irrespective of preschool care, was related to better memory skills at the end of the preschool period. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  14. From journal to headline: the accuracy of climate science news in Danish high quality newspapers

    DEFF Research Database (Denmark)

    Vestergård, Gunver Lystbæk

    2011-01-01

    analysis to examine the accuracy of Danish high quality newspapers in quoting scientific publications from 1997 to 2009. Out of 88 articles, 46 contained inaccuracies though the majority was found to be insignificant and random. The study concludes that Danish broadsheet newspapers are ‘moderately...

  15. Dare to share? How people share high-quality knowledge in online communities

    NARCIS (Netherlands)

    Rotundo, Enrico; Blank, M.; Moser, C.; Leopold, H.

    The Internet has fundamentally changed how work gets done in the 21st century. For example, people increasingly spend time on the Internet where they share and develop knowledge in online communities. Yet, little is known about how high-quality knowledge comes about in these communities. This is

  16. Emblems of Quality in Higher Education. Developing and Sustaining High-Quality Programs.

    Science.gov (United States)

    Haworth, Jennifer Grant; Conrad, Clifton F.

    This book proposes an "engagement" theory of program quality to evaluate and improve higher education programs at all degree levels. Based on interviews with 781 participants in a national study of Masters degree programs, it focuses on the interactive roles of students, faculty, and administrators in developing high-quality programs…

  17. Reading disorders and dyslexia.

    Science.gov (United States)

    Hulme, Charles; Snowling, Margaret J

    2016-12-01

    We review current knowledge about the nature of reading development and disorders, distinguishing between the processes involved in learning to decode print, and the processes involved in reading comprehension. Children with decoding difficulties/dyslexia experience deficits in phoneme awareness, letter-sound knowledge and rapid automatized naming in the preschool years and beyond. These phonological/language difficulties appear to be proximal causes of the problems in learning to decode print in dyslexia. We review data from a prospective study of children at high risk of dyslexia to show that being at family risk of dyslexia is a primary risk factor for poor reading and children with persistent language difficulties at school entry are more likely to develop reading problems. Early oral language difficulties are strong predictors of later difficulties in reading comprehension. There are two distinct forms of reading disorder in children: dyslexia (a difficulty in learning to translate print into speech) and reading comprehension impairment. Both forms of reading problem appear to be predominantly caused by deficits in underlying oral language skills. Implications for screening and for the delivery of robust interventions for language and reading are discussed.

  18. ConDeTri--a content dependent read trimmer for Illumina data.

    Science.gov (United States)

    Smeds, Linnéa; Künstner, Axel

    2011-01-01

    During the last few years, DNA and RNA sequencing have started to play an increasingly important role in biological and medical applications, especially due to the greater amount of sequencing data yielded from the new sequencing machines and the enormous decrease in sequencing costs. Particularly, Illumina/Solexa sequencing has had an increasing impact on gathering data from model and non-model organisms. However, accurate and easy to use tools for quality filtering have not yet been established. We present ConDeTri, a method for content dependent read trimming for next generation sequencing data using quality scores of each individual base. The main focus of the method is to remove sequencing errors from reads so that sequencing reads can be standardized. Another aspect of the method is to incorporate read trimming in next-generation sequencing data processing and analysis pipelines. It can process single-end and paired-end sequence data of arbitrary length and it is independent from sequencing coverage and user interaction. ConDeTri is able to trim and remove reads with low quality scores to save computational time and memory usage during de novo assemblies. Low coverage or large genome sequencing projects will especially gain from trimming reads. The method can easily be incorporated into preprocessing and analysis pipelines for Illumina data. Freely available on the web at http://code.google.com/p/condetri.

  19. ConDeTri--a content dependent read trimmer for Illumina data.

    Directory of Open Access Journals (Sweden)

    Linnéa Smeds

    Full Text Available UNLABELLED: During the last few years, DNA and RNA sequencing have started to play an increasingly important role in biological and medical applications, especially due to the greater amount of sequencing data yielded from the new sequencing machines and the enormous decrease in sequencing costs. Particularly, Illumina/Solexa sequencing has had an increasing impact on gathering data from model and non-model organisms. However, accurate and easy to use tools for quality filtering have not yet been established. We present ConDeTri, a method for content dependent read trimming for next generation sequencing data using quality scores of each individual base. The main focus of the method is to remove sequencing errors from reads so that sequencing reads can be standardized. Another aspect of the method is to incorporate read trimming in next-generation sequencing data processing and analysis pipelines. It can process single-end and paired-end sequence data of arbitrary length and it is independent from sequencing coverage and user interaction. ConDeTri is able to trim and remove reads with low quality scores to save computational time and memory usage during de novo assemblies. Low coverage or large genome sequencing projects will especially gain from trimming reads. The method can easily be incorporated into preprocessing and analysis pipelines for Illumina data. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://code.google.com/p/condetri.

  20. Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis

    Directory of Open Access Journals (Sweden)

    Qian Ding

    2015-01-01

    Full Text Available Simple sequence repeats (SSRs are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%, amplicons were successfully generated with high quality. Seventeen (89.5% showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.

  1. A Narrative Review of High-Quality Literature on the Effects of Resident Duty Hours Reforms.

    Science.gov (United States)

    Lin, Henry; Lin, Emery; Auditore, Stephanie; Fanning, Jon

    2016-01-01

    To summarize current high-quality studies evaluating the effect and efficacy of resident duty hours reforms (DHRs) on patient safety and resident education and well-being. The authors searched PubMed and Medline in August 2012 and again in May 2013 for literature (1987-2013) about the effects of DHRs. They assessed the quality of articles using the Medical Education Research Study Quality Instrument (MERSQI) scoring system. They considered randomized controlled trials (RCTs), partial RCTs, and all studies with a MERSQI score ≥ 14 to be "high-quality" methodology studies. A total of 72 high-quality studies met inclusion criteria. Most studies showed no change or slight improvement in mortality and complication rates after DHRs. Resident well-being was generally improved, but there was a perceived negative impact on education (knowledge acquisition, skills, and cognitive performance) following DHRs. Eleven high-quality studies assessed the impact of DHR interventions; all reported a neutral to positive impact. Seven high-quality studies assessed costs associated with DHRs and demonstrated an increase in hospital costs. The results of most studies that allow enough time for DHR interventions to take effect suggest a benefit to patient safety and resident well-being, but the effect on the quality of training remains unknown. Additional methodologically sound studies on the impact of DHRs are necessary. Priorities for future research include approaches to optimizing education and clinical proficiency and studies on the effect of intervention strategies on both education and patient safety. Such studies will provide additional information to help improve duty hours policies.

  2. Providing high-quality care in primary care settings: how to make trade-offs.

    Science.gov (United States)

    Beaulieu, Marie-Dominique; Geneau, Robert; Del Grande, Claudio; Denis, Jean-Louis; Hudon, Eveline; Haggerty, Jeannie L; Bonin, Lucie; Duplain, Réjean; Goudreau, Johanne; Hogg, William

    2014-05-01

    To gain a deeper understanding of how primary care (PC) practices belonging to different models manage resources to provide high-quality care. Multiple-case study embedded in a cross-sectional study of a random sample of 37 practices. Three regions of Quebec. Health care professionals and staff of 5 PC practices. Five cases showing above-average results on quality-of-care indicators were purposefully selected to contrast on region, practice size, and PC model. Data were collected using an organizational questionnaire; the Team Climate Inventory, which was completed by health care professionals and staff; and 33 individual interviews. Detailed case histories were written and thematic analysis was performed. The core common feature of these practices was their ongoing effort to make trade-offs to deliver services that met their vision of high-quality care. These compromises involved the same 3 areas, but to varying degrees depending on clinic characteristics: developing a shared vision of high-quality care; aligning resource use with that vision; and balancing professional aspirations and population needs. The leadership of the physician lead was crucial. The external environment was perceived as a source of pressure and dilemmas rather than as a source of support in these matters. Irrespective of their models, PC practices' pursuit of high-quality care is based on a vision in which accessibility is a key component, balanced by appropriate management of available resources and of external environment expectations. Current PC reforms often create tensions rather than support PC practices in their pursuit of high-quality care. Copyright© the College of Family Physicians of Canada.

  3. Isolation of high-quality total RNA from leaves of Myrciaria dubia "CAMU CAMU".

    Science.gov (United States)

    Gómez, Juan Carlos Castro; Reátegui, Alina Del Carmen Egoavil; Flores, Julián Torres; Saavedra, Roberson Ramírez; Ruiz, Marianela Cobos; Correa, Sixto Alfredo Imán

    2013-01-01

    Myrciaria dubia is a main source of vitamin C for people in the Amazon region. Molecular studies of M. dubia require high-quality total RNA from different tissues. So far, no protocols have been reported for total RNA isolation from leaves of this species. The objective of this research was to develop protocols for extracting high-quality total RNA from leaves of M. dubia. Total RNA was purified following two modified protocols developed for leaves of other species (by Zeng and Yang, and by Reid et al.) and one modified protocol developed for fruits of the studied species (by Silva). Quantity and quality of purified total RNA were assessed by spectrophotometric and electrophoretic analysis. Additionally, quality of total RNA was evaluated with reverse-transcription polymerase chain reaction (RT-PCR). With these three modified protocols we were able to isolate high-quality RNA (A260nm/A280nm >1.9 and A260nm/A230nm >2.0). Highest yield was produced with the Zeng and Yang modified protocol (384±46µg ARN/g fresh weight). Furthermore, electrophoretic analysis showed the integrity of isolated RNA and the absence of DNA. Another proof of the high quality of our purified RNA was the successful cDNA synthesis and amplification of a segment of the M. dubia actin 1 gene. We report three modified protocols for isolation total RNA from leaves of M. dubia. The modified protocols are easy, rapid, low in cost, and effective for high-quality and quantity total RNA isolation suitable for cDNA synthesis and polymerase chain reaction.

  4. Separating metagenomic short reads into genomes via clustering

    Directory of Open Access Journals (Sweden)

    Tanaseichuk Olga

    2012-09-01

    Full Text Available Abstract Background The metagenomics approach allows the simultaneous sequencing of all genomes in an environmental sample. This results in high complexity datasets, where in addition to repeats and sequencing errors, the number of genomes and their abundance ratios are unknown. Recently developed next-generation sequencing (NGS technologies significantly improve the sequencing efficiency and cost. On the other hand, they result in shorter reads, which makes the separation of reads from different species harder. Among the existing computational tools for metagenomic analysis, there are similarity-based methods that use reference databases to align reads and composition-based methods that use composition patterns (i.e., frequencies of short words or l-mers to cluster reads. Similarity-based methods are unable to classify reads from unknown species without close references (which constitute the majority of reads. Since composition patterns are preserved only in significantly large fragments, composition-based tools cannot be used for very short reads, which becomes a significant limitation with the development of NGS. A recently proposed algorithm, AbundanceBin, introduced another method that bins reads based on predicted abundances of the genomes sequenced. However, it does not separate reads from genomes of similar abundance levels. Results In this work, we present a two-phase heuristic algorithm for separating short paired-end reads from different genomes in a metagenomic dataset. We use the observation that most of the l-mers belong to unique genomes when l is sufficiently large. The first phase of the algorithm results in clusters of l-mers each of which belongs to one genome. During the second phase, clusters are merged based on l-mer repeat information. These final clusters are used to assign reads. The algorithm could handle very short reads and sequencing errors. It is initially designed for genomes with similar abundance levels and then

  5. Promoting Active Learning of Graduate Student by Deep Reading in Biochemistry and Microbiology Pharmacy Curriculum

    Science.gov (United States)

    Peng, Ren

    2017-01-01

    To promote graduate students' active learning, deep reading of high quality papers was done by graduate students enrolled in biochemistry and microbiology pharmacy curriculum offered by college of life science, Jiangxi Normal University from 2013 to 2015. The number of graduate students, who participated in the course in 2013, 2014, and 2015 were…

  6. End-of-Kindergarten Spelling Outcomes: How Can Spelling Error Analysis Data Inform Beginning Reading Instruction?

    Science.gov (United States)

    Lee, Julia Ai Cheng; Al Otaiba, Stephanie

    2017-01-01

    In this study, we examined the spelling performance of 430 kindergartners, which included a high-risk sample, to determine the relations between end-of-kindergarten reading and spelling in a high-quality language arts setting. We described, analyzed, and compared spelling outcomes, including spelling errors, between good and poor readers. The…

  7. Next generation sequencing (NGS)technologies and applications

    Energy Technology Data Exchange (ETDEWEB)

    Vuyisich, Momchilo [Los Alamos National Laboratory

    2012-09-11

    NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

  8. Developmental Relations Between Reading Comprehension and Reading Strategies

    NARCIS (Netherlands)

    Muijselaar, M.; Swart, N.M.; Steenbeek-Planting, E.G,.; Droop, M.; Verhoeven, L.; de Jong, P.F.

    2017-01-01

    We examined the developmental relations between knowledge of reading strategies and reading comprehension in a longitudinal study of 312 Dutch children from the beginning of fourth grade to the end of fifth grade. Measures for reading comprehension, reading strategies, reading fluency, vocabulary,

  9. LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning

    Directory of Open Access Journals (Sweden)

    Ruibang Luo

    Full Text Available Linked-read sequencing, using highly-multiplexed genome partitioning and barcoding, can span hundreds of kilobases to improve de novo assembly, haplotype phasing, and other applications. Based on our analysis of 14 datasets, we introduce LRSim that simulates linked-reads by emulating the library preparation and sequencing process with fine control over variants, linked-read characteristics, and the short-read profile. We conclude from the phasing and assembly of multiple datasets, recommendations on coverage, fragment length, and partitioning when sequencing genomes of different sizes and complexities. These optimizations improve results by orders of magnitude, and enable the development of novel methods. LRSim is available at https://github.com/aquaskyline/LRSIM. Keywords: Linked-read, Molecular barcoding, Reads partitioning, Phasing, Reads simulation, Genome assembly, 10X Genomics

  10. CSAF Reading List 2014

    Science.gov (United States)

    ... Undaunted Zero Dark Thirty 101109-F-RH756-737 Raptor's Reveille Featured Books Featured Films Featured Art House To House House To House by David Bellavia and John Bruning One of the great heroes of the Iraq War /McMillan/Switzler Read More... Fearless Book: Fearless by Eric Blehm Read More... Zero Dark Thirty Zero

  11. Reading Patterns Changing

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Modern life is changing the way people read April 23 was the 16th World Book and Copyright Day,also known as the World Book Day.Reading-related problems have once again attracted people’s attention.Today,living a life with an increasingly rapid pace,most people are

  12. VISION AND READING ABILITY.

    Science.gov (United States)

    MANGRUM, CHARLES T.

    SIGNIFICANT RESEARCH ON THE PHYSIOLOGICAL AND FUNCTIONAL ASPECTS OF VISION AND READING DISABILITY IS SURVEYED. CONCLUSIONS BASED ON THE LITERATURE IN THE FIELD ARE DISCUSSED. A BIBLIOGRAPHY OF 70 REFERENCES AND A GLOSSARY OF TERMS ARE APPENDED. A TABLE SUMMARIZING REFRACTIVE ERRORS AND EYE DEFECTS CONTRIBUTING TO READING DISABILITY IS INCLUDED.…

  13. Reading and Working Memory

    Science.gov (United States)

    Baddeley, Alan

    1984-01-01

    Outlines the concept of working memory, with particular reference to a hypothetical subcomponent, the articulatory loop. Discusses the role of the loop in fluent adult reading, then examines the reading performance of adults with deficits in auditory verbal memory, showing that a capacity to articulate is not necessary for the effective…

  14. How Knowledge Powers Reading

    Science.gov (United States)

    Lemov, Doug

    2017-01-01

    Recent research shows that reading comprehension relies heavily on prior knowledge. Far more than generic "reading skills" like drawing inferences, making predictions, and knowing the function of subheads, how well students learn from a nonfiction text depends on their background knowledge of the text's subject matter. And in a cyclical…

  15. Science Fiction: Serious Reading, Critical Reading

    Science.gov (United States)

    Zigo, Diane; Moore, Michael T.

    2004-01-01

    Science fiction deserves a greater respect, serious and critical reading and a better place in high school literature classes. Some of the science fiction books by Isaac Asimov, Alfred Bester, Ray Bradbury and Octavia L. Butler and various activities for incorporating science fiction into the English language arts instruction classroom are…

  16. TEACHING READING USING MAGAZINE

    Directory of Open Access Journals (Sweden)

    Henny Uswatun Hasanah

    2013-11-01

    Full Text Available Teaching is a process of communication. It has to be created through the way of teaching and exchanging the message or information by every teacher and student. The message can be knowledge, skills, ideas, experiences, and many others. Through the process of communication, the people can receive the message or information. To avoid misunderstanding in the process of communication, media are needed in the process of teaching. Magazine can be other alternative as reading material in the classroom. Magazine as reading material has appeal for the students. To make the students get information from magazine, the teacher can ask the students to observe table of content and giving the students training to use it. Like, what is done on text book. Distinguishing informative reading material with fictive reading, important to know students in reading magazine. Like analyzing advertisements to detect propaganda.

  17. Delivering high quality hip fracture rehabilitation: the perspective of occupational and physical therapy practitioners.

    Science.gov (United States)

    Leland, Natalie E; Lepore, Michael; Wong, Carin; Chang, Sun Hwa; Freeman, Lynn; Crum, Karen; Gillies, Heather; Nash, Paul

    2018-03-01

    The majority of post-acute hip fracture rehabilitation in the US is delivered in skilled nursing facilities (SNFs). Currently, there are limited guidelines that equip occupational and physical therapy practitioners with a summary of what constitutes evidence-based high quality rehabilitation. Thus, this study aimed to identify rehabilitation practitioners' perspectives on the practices that constitute high quality hip fracture rehabilitation. Focus groups were conducted with 99 occupational and physical therapy practitioners working in SNFs in southern California. Purposive sampling of facilities was conducted to capture variation in key characteristics known to impact care delivery for this patient population (e.g., financial resources, staffing, and patient case-mix). Questions aimed to elicit practitioners' perspectives on high quality hip fracture rehabilitation practices. Each session was audio-recorded and transcribed. Data were systematically analyzed using a modified grounded theory approach. Seven themes emerged: objectives of care; first 72 h; positioning, pain, and precautions; use of standardized assessments; episode of care practices; facilitating insight into progress; and interdisciplinary collaboration. Clinical guidelines are critical tools to facilitate clinical decision-making and achieve desired patient outcomes. The findings of this study highlight the practitioners' perspective on what constitutes high quality hip fracture rehabilitation. This work provides critical information to advance the development of stakeholder-driven rehabilitation clinical guidelines. Future research is needed to verify the findings from other stakeholders (e.g., patients), ensure the alignment of our findings with current evidence, and develop measures for evaluating their delivery and relationship to desired outcomes. Implications for Rehabilitation This study highlights occupational and physiotherapy therapy practitioners' perspectives on the cumulative best

  18. Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)

    Science.gov (United States)

    Mahato, Ajay Kumar; Sharma, Nimisha; Singh, Akshay; Srivastav, Manish; Jaiprakash; Singh, Sanjay Kumar; Singh, Anand Kumar; Sharma, Tilak Raj; Singh, Nagendra Kumar

    2016-01-01

    Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango. PMID:27736892

  19. Transcriptome sequencing of the Microarray Quality Control (MAQC RNA reference samples using next generation sequencing

    Directory of Open Access Journals (Sweden)

    Thierry-Mieg Danielle

    2009-06-01

    Full Text Available Abstract Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.

  20. Improvement of the banana "Musa acuminata" reference sequence using NGS data and semi-automated bioinformatics methods.

    Science.gov (United States)

    Martin, Guillaume; Baurens, Franc-Christophe; Droc, Gaëtan; Rouard, Mathieu; Cenci, Alberto; Kilian, Andrzej; Hastie, Alex; Doležel, Jaroslav; Aury, Jean-Marc; Alberti, Adriana; Carreel, Françoise; D'Hont, Angélique

    2016-03-16

    Recent advances in genomics indicate functional significance of a majority of genome sequences and their long range interactions. As a detailed examination of genome organization and function requires very high quality genome sequence, the objective of this study was to improve reference genome assembly of banana (Musa acuminata). We have developed a modular bioinformatics pipeline to improve genome sequence assemblies, which can handle various types of data. The pipeline comprises several semi-automated tools. However, unlike classical automated tools that are based on global parameters, the semi-automated tools proposed an expert mode for a user who can decide on suggested improvements through local compromises. The pipeline was used to improve the draft genome sequence of Musa acuminata. Genotyping by sequencing (GBS) of a segregating population and paired-end sequencing were used to detect and correct scaffold misassemblies. Long insert size paired-end reads identified scaffold junctions and fusions missed by automated assembly methods. GBS markers were used to anchor scaffolds to pseudo-molecules with a new bioinformatics approach that avoids the tedious step of marker ordering during genetic map construction. Furthermore, a genome map was constructed and used to assemble scaffolds into super scaffolds. Finally, a consensus gene annotation was projected on the new assembly from two pre-existing annotations. This approach reduced the total Musa scaffold number from 7513 to 1532 (i.e. by 80%), with an N50 that increased from 1.3 Mb (65 scaffolds) to 3.0 Mb (26 scaffolds). 89.5% of the assembly was anchored to the 11 Musa chromosomes compared to the previous 70%. Unknown sites (N) were reduced from 17.3 to 10.0%. The release of the Musa acuminata reference genome version 2 provides a platform for detailed analysis of banana genome variation, function and evolution. Bioinformatics tools developed in this work can be used to improve genome sequence assemblies in

  1. Marine Corps Contract Supply Model for High Quality Male Enlistment Contracts at the Recruiting Sub Station Level

    National Research Council Canada - National Science Library

    Welsh, Brian K

    2008-01-01

    .... This research develops contract production models at the Recruiting Sub Station level to estimate the effects of local economic conditions, demographics, and recruiting resources on new high quality...

  2. A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source.

    Science.gov (United States)

    Atwood, Robert C; Bodey, Andrew J; Price, Stephen W T; Basham, Mark; Drakopoulos, Michael

    2015-06-13

    Tomographic datasets collected at synchrotrons are becoming very large and complex, and, therefore, need to be managed efficiently. Raw images may have high pixel counts, and each pixel can be multidimensional and associated with additional data such as those derived from spectroscopy. In time-resolved studies, hundreds of tomographic datasets can be collected in sequence, yielding terabytes of data. Users of tomographic beamlines are drawn from various scientific disciplines, and many are keen to use tomographic reconstruction software that does not require a deep understanding of reconstruction principles. We have developed Savu, a reconstruction pipeline that enables users to rapidly reconstruct data to consistently create high-quality results. Savu is designed to work in an 'orthogonal' fashion, meaning that data can be converted between projection and sinogram space throughout the processing workflow as required. The Savu pipeline is modular and allows processing strategies to be optimized for users' purposes. In addition to the reconstruction algorithms themselves, it can include modules for identification of experimental problems, artefact correction, general image processing and data quality assessment. Savu is open source, open licensed and 'facility-independent': it can run on standard cluster infrastructure at any institution.

  3. Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase

    International Nuclear Information System (INIS)

    Guo, Min; Shapiro, Ryan; Schimmel, Paul; Yang, Xiang-Lei

    2010-01-01

    E. coli alanyl-tRNA synthetase is recalcitrant to crystallization. A group of leucine substitutions has transformed the protein. Although Escherichia coli alanyl-tRNA synthetase was among the first tRNA synthetases to be sequenced and extensively studied by functional analysis, it has proved to be recalcitrant to crystallization. This challenge remained even for crystallization of the catalytic fragment. By mutationally introducing three stacked leucines onto the solvent-exposed side of an α-helix, an engineered catalytic fragment of the synthetase was obtained that yielded multiple high-quality crystals and cocrystals with different ligands. The engineered α-helix did not form a leucine zipper that interlocked with the same α-helix from another molecule. Instead, using the created hydrophobic spine, it interacted with other surfaces of the protein as a leucine half-zipper (LHZ) to enhance the crystal lattice interactions. The LHZ made crystal lattice contacts in all crystals of different space groups. These results illustrate the power of introducing an LHZ into helices to facilitate crystallization. The authors propose that the method can be unified with surface-entropy reduction and can be broadly used for protein-surface optimization in crystallization

  4. Attempt at cloning high-quality goldfish breed 'Ranchu' by fin-cultured cell nuclear transplantation.

    Science.gov (United States)

    Tanaka, Daisuke; Takahashi, Akito; Takai, Akinori; Ohta, Hiromi; Ueno, Koichi

    2012-02-01

    The viability of ornamental fish culture relies on the maintenance of high-quality breeds. To improve the profitability of culture operations we attempted to produce cloned fish from the somatic nucleus of the high-quality Japanese goldfish (Carassius auratus auratus) breed 'Ranchu'. We transplanted the nucleus of a cultured fin-cell from an adult Ranchu into the non-enucleated egg of the original goldfish breed 'Wakin'. Of the 2323 eggs we treated, 802 underwent cleavage, 321 reached the blastula stage, and 51 reached the gastrula stage. Two of the gastrulas developed until the hatching stage. A considerable number of nuclear transplants retained only the donor nucleus. Some of these had only a 2n nucleus derived from the same donor fish. Our results provide insights into the process of somatic cell nuclear transplantation in teleosts, and the cloning of Ranchu.

  5. (-201) β-Gallium oxide substrate for high quality GaN materials

    KAUST Repository

    Roqan, Iman S.

    2015-03-13

    (-201) oriented β-Ga2O3 has the potential to be used as a transparent and conductive substrate for GaN-growth. The key advantages of Ga2O3 are its small lattice mismatches (4.7%), appropriate structural, thermal and electrical properties and a competitive price compared to other substrates. Optical characterization show that GaN layers grown on (-201) oriented β-Ga2O3 are dominated by intense bandedge emission with a high luminescence efficiency. Atomic force microscopy studies show a modest threading dislocation density of ~108 cm-2, while complementary Raman spectroscopy indicates that the GaN epilayer is of high quality with slight compressive strain. Room temperature time-findings suggest that the limitation of the photoluminescence lifetime (~500 ps) is due to nonradiative recombination arising from threading dislocation. Therefore, by optimizing the growth conditions, high quality material with significant optical efficiency can be obtained.

  6. A design technique of low cost but high quality peak stretcher

    Energy Technology Data Exchange (ETDEWEB)

    Lo, H Y; Su, C S; Hsu, J Y; Wang, L

    1981-03-01

    This paper presents the design of low cost but high quality pulse peak stretcher incorporated with a LSI of 12 bit ADC and SKD-85 microcomputer. The conflict between the capacitor high charging speed and longer holding time for realizing a high quality stretcher is discussed and solved. For a lager number of channels available in a dual ramp Wilkinson-type ADC, two-stage stretchers connected in series are designed. The first stage is a fast-discharge to keep the output stretched pulse follow-up the input quickly and the second-stage (main stretcher) is a slow-discharge to keep the transient of the circuit minimum. Both of these two peak stretchers are described and the experiment results are photographically recorded.

  7. High quality atomically thin PtSe2 films grown by molecular beam epitaxy

    Science.gov (United States)

    Yan, Mingzhe; Wang, Eryin; Zhou, Xue; Zhang, Guangqi; Zhang, Hongyun; Zhang, Kenan; Yao, Wei; Lu, Nianpeng; Yang, Shuzhen; Wu, Shilong; Yoshikawa, Tomoki; Miyamoto, Koji; Okuda, Taichi; Wu, Yang; Yu, Pu; Duan, Wenhui; Zhou, Shuyun

    2017-12-01

    Atomically thin PtSe2 films have attracted extensive research interests for potential applications in high-speed electronics, spintronics and photodetectors. Obtaining high quality thin films with large size and controlled thickness is critical. Here we report the first successful epitaxial growth of high quality PtSe2 films by molecular beam epitaxy. Atomically thin films from 1 ML to 22 ML have been grown and characterized by low-energy electron diffraction, Raman spectroscopy and x-ray photoemission spectroscopy. Moreover, a systematic thickness dependent study of the electronic structure is revealed by angle-resolved photoemission spectroscopy (ARPES), and helical spin texture is revealed by spin-ARPES. Our work provides new opportunities for growing large size single crystalline films to investigate the physical properties and potential applications of PtSe2.

  8. Recent developments in high-quality drying of vegetables, fruits, and aquatic products.

    Science.gov (United States)

    Zhang, Min; Chen, Huizhi; Mujumdar, Arun S; Tang, Juming; Miao, Song; Wang, Yuchuan

    2017-04-13

    Fresh foods like vegetables, fruits, and aquatic products have high water activity and they are highly heat-sensitive and easily degradable. Dehydration is one of the most common methods used to improve food shelf-life. However, drying methods used for food dehydration must not only be efficient and economic but also yield high-quality products based on flavor, nutrients, color, rehydration, uniformity, appearance, and texture. This paper reviews some new drying technologies developed for dehydration of vegetables, fruits, and aquatic products. These include: infrared drying, microwave drying, radio frequency drying, electrohydrodynamic drying, etc., as well as hybrid drying methods combining two or more different drying techniques. A comprehensive review of recent developments in high-quality drying of vegetables, fruits and aquatic products is presented and recommendations are made for future research.

  9. Formation of a high quality electron beam using photo cathode RF electron gun

    International Nuclear Information System (INIS)

    Washio, Masakazu

    2000-01-01

    Formation of a high quality electron beam using photo cathode RF electron gun is expected for formation of a next generation high brilliant X-ray beam and a source for electron and positron collider. And, on a field of material science, as is possible to carry out an experiment under ultra short pulse and extremely high precision in time, it collects large expectation. Recently, formation of high quality beam possible to develop for multi directions and to use by everyone in future has been able to realize. Here were explained on electron beam source, principle and component on RF electron gun, working features on RF gun, features and simulation of RF gun under operation, and some views in near future. (G.K.)

  10. Selection of process parameters for producing high quality defatted sesame flour at pilot scale.

    Science.gov (United States)

    Manikantan, M R; Sharma, Rajiv; Yadav, D N; Gupta, R K

    2015-03-01

    The present work was undertaken to study the effect of pearling duration, soaking time, steaming duration and drying temperature on the quality of sesame seeds and mechanically extracted partially defatted sesame cake. On the basis of quality attributes i.e. high protein, low crude fibre, low residual oil and low oxalic acid, the optimum process parameters were selected. The combination of 20 min of pearling duration, 15 min of soaking, 15 min of steaming at 100 kPa pressure and drying at 50 °C yielded high quality partially defatted protein rich sesame flour as compared to untreated defatted sesame flour. The developed high quality partially defatted protein rich sesame flour may be used in various food applications as a vital ingredient to increase the nutritional significance of the prepared foodstuffs.

  11. The Barriers to High-Quality Inpatient Pain Management: A Qualitative Study.

    Science.gov (United States)

    Lin, Richard J; Reid, M Carrington; Liu, Lydia L; Chused, Amy E; Evans, Arthur T

    2015-09-01

    The current literature suggests deficiencies in the quality of acute pain management among general medical inpatients. The aim of this qualitative study is to identify potential barriers to high-quality acute pain management among general medical inpatients at an urban academic medical center during a 2-year period. Data are collected using retrospective chart reviews, survey questionnaires, and semistructured, open-ended interviews of 40 general medical inpatients who have experienced pain during their hospitalization. Our results confirm high prevalence and disabling impacts of pain and significant patient- and provider-related barriers to high-quality acute pain management. We also identify unique system-related barriers such as time delay and pain management culture. Efforts to improve the pain management experience of general medical inpatients will need to address all these barriers. © The Author(s) 2014.

  12. High quality junctions by interpenetration of vapor liquid solid grown nanostructures for microchip integration

    Energy Technology Data Exchange (ETDEWEB)

    Jebril, Seid; Kuhlmann, Hanna; Adelung, Rainer [Funktionale Nanomaterialien, CAU Kiel (Germany); Mueller, Sven [Nanowires and Thin Films, II. Physikalisches Institut, Goettingen (Germany); Ronning, Carsten [Institute for Solid State Physics, Universitaet Jena (Germany); Kienle, Lorenz [Synthese und Realstruktur, CAU Kiel (Germany); Duppel, Viola [MPI fuer Festkoerperforschung, Stuttgart (Germany)

    2009-07-01

    The usability of nanostructures in electrical devices like gas sensors depends critically on the ability to form high quality contacts and junctions. For the fabrication of various nanostructures, vapor-liquid-solid (VLS) growth is a wide spread and very efficient technique. However, forming contacts with the VLS grown structures to utilize them in a device is still tedious, because either the substrate has to be epitaxial to the VLS material or a manual alignment is necessary. Here we demonstrate the contact formation by simply using the ability of individual crystals to interpenetrate each other during the straight forward VLS growth. This allows growing VLS structures directly on two neighboring gold circuit paths of a microchip; bridges over predefined gaps will be formed. Moreover, TEM investigations confirm the high quality of the crystalline junctions that allow demonstrations as UV and hydrogen-sensor. The VLS devices are compared with conventional produced.

  13. Forecasting Reading Anxiety for Promoting English-Language Reading Performance Based on Reading Annotation Behavior

    Science.gov (United States)

    Chen, Chih-Ming; Wang, Jung-Ying; Chen, Yong-Ting; Wu, Jhih-Hao

    2016-01-01

    To reduce effectively the reading anxiety of learners while reading English articles, a C4.5 decision tree, a widely used data mining technique, was used to develop a personalized reading anxiety prediction model (PRAPM) based on individual learners' reading annotation behavior in a collaborative digital reading annotation system (CDRAS). In…

  14. Optimisation of transgene action at the post-transcriptional level: high quality parthenocarpic fruits in industrial tomatoes

    Directory of Open Access Journals (Sweden)

    Defez Roberto

    2002-01-01

    Full Text Available Abstract Background Genetic engineering of parthenocarpy confers to horticultural plants the ability to produce fruits under environmental conditions that curtail fruit productivity and quality. The DefH9-iaaM transgene, whose predicted action is to confer auxin synthesis specifically in the placenta, ovules and derived tissues, has been shown to confer parthenocarpy to several plant species (tobacco, eggplant, tomato and varieties. Results UC82 tomato plants, a typical cultivar used by the processing industry, transgenic for the DefH9-iaaM gene produce parthenocarpic fruits that are malformed. UC82 plants transgenic for the DefH9-RI-iaaM, a DefH9-iaaM derivative gene modified in its 5'ULR by replacing 53 nucleotides immediately upstream of the AUG initiation codon with an 87 nucleotides-long sequence derived from the rolA intron sequence, produce parthenocarpic fruits of high quality. In an in vitro translation system, the iaaM mRNA, modified in its 5'ULR is translated 3–4 times less efficiently than the original transcript. An optimal expressivity of parthenocarpy correlates with a reduced transgene mRNA steady state level in DefH9-RI-iaaM flower buds in comparison to DefH9-iaaM flower buds. Consistent with the known function of the iaaM gene, flower buds transgenic for the DefH9-RI-iaaM gene contain ten times more IAA than control untransformed flower buds, but five times less than DefH9-iaaM flower buds. Conclusions By using an auxin biosynthesis transgene downregulated at the post-transcriptional level, an optimal expressivity of parthenocarpy has been achieved in a genetic background not suitable for the original transgene. Thus, the method allows the generation of a wider range of expressivity of the desired trait in transgenic plants.

  15. Lip-reading enhancement for law enforcement

    Science.gov (United States)

    Theobald, Barry J.; Harvey, Richard; Cox, Stephen J.; Lewis, Colin; Owen, Gari P.

    2006-09-01

    Accurate lip-reading techniques would be of enormous benefit for agencies involved in counter-terrorism and other law-enforcement areas. Unfortunately, there are very few skilled lip-readers, and it is apparently a difficult skill to transmit, so the area is under-resourced. In this paper we investigate the possibility of making the lip-reading task more amenable to a wider range of operators by enhancing lip movements in video sequences using active appearance models. These are generative, parametric models commonly used to track faces in images and video sequences. The parametric nature of the model allows a face in an image to be encoded in terms of a few tens of parameters, while the generative nature allows faces to be re-synthesised using the parameters. The aim of this study is to determine if exaggerating lip-motions in video sequences by amplifying the parameters of the model improves lip-reading ability. We also present results of lip-reading tests undertaken by experienced (but non-expert) adult subjects who claim to use lip-reading in their speech recognition process. The results, which are comparisons of word error-rates on unprocessed and processed video, are mixed. We find that there appears to be the potential to improve the word error rate but, for the method to improve the intelligibility there is need for more sophisticated tracking and visual modelling. Our technique can also act as an expression or visual gesture amplifier and so has applications to animation and the presentation of information via avatars or synthetic humans.

  16. Production of high-quality polydisperse construction mixes for additive 3D technologies.

    Science.gov (United States)

    Gerasimov, M. D.; Brazhnik, Yu V.; Gorshkov, P. S.; Latyshev, S. S.

    2018-03-01

    The paper describes a new design of a mixer allowing production of high quality polydisperse powders, used in additive 3D technologies. A new principle of dry powder particle mixing is considered, implementing a possibility of a close-to-ideal distribution of such particles in common space. A mathematical model of the mixer is presented, allowing evaluating quality indicators of the produced mixture. Experimental results are shown and rational values of process parameters of the mixer are obtained.

  17. Project outline of high quality electron beam generation at Waseda University

    Energy Technology Data Exchange (ETDEWEB)

    Washio, M.; Hama, Y.; Kashiwagi, S.; Kuroda, R.; Kobuki, T. [Waseda Univ., Advanced Research Institute for Science and Engineering, Shinjuku, Tokyo (Japan); Hirose, T. [Tokyo Metropolitan Univ. (Japan). Dept. of Physics

    2000-03-01

    High quality electron beam generation project has been started at Waseda University under the grant of Ministry of Education, named High-Tech Research Center Project. In the project, we will install a laser photo-cathode RF Gun system with 1.6 accelerating structure cells of s-band and a stabilized RF power source. This RF Gun is expected to produce single electron bunch up to 1 or 2nC with around 10ps pulse duration. (author)

  18. Project outline of high quality electron beam generation at Waseda University

    International Nuclear Information System (INIS)

    Washio, M.; Hama, Y.; Kashiwagi, S.; Kuroda, R.; Kobuki, T.; Hirose, T.

    2000-01-01

    High quality electron beam generation project has been started at Waseda University under the grant of Ministry of Education, named High-Tech Research Center Project. In the project, we will install a laser photo-cathode RF Gun system with 1.6 accelerating structure cells of s-band and a stabilized RF power source. This RF Gun is expected to produce single electron bunch up to 1 or 2nC with around 10ps pulse duration. (author)

  19. Fabrication of high quality GaN nanopillar arrays by dry and wet chemical etching

    OpenAIRE

    Paramanik, Dipak; Motayed, Abhishek; King, Matthew; Ha, Jong-Yoon; Kryluk, Sergi; Davydov, Albert V.; Talin, Alec

    2013-01-01

    We study strain relaxation and surface damage of GaN nanopillar arrays fabricated using inductively coupled plasma (ICP) etching and post etch wet chemical treatment. We controlled the shape and surface damage of such nanopillar structures through selection of etching parameters. We compared different substrate temperatures and different chlorine-based etch chemistries to fabricate high quality GaN nanopillars. Room temperature photoluminescence and Raman scattering measurements were carried ...

  20. Teaching Surgical Procedures with Movies: Tips for High-quality Video Clips

    OpenAIRE

    Jacquemart, Mathieu; Bouletreau, Pierre; Breton, Pierre; Mojallal, Ali; Sigaux, Nicolas

    2016-01-01

    Summary: Video must now be considered as a precious tool for learning surgery. However, the medium does present production challenges, and currently, quality movies are not always accessible. We developed a series of 7 surgical videos and made them available on a publicly accessible internet website. Our videos have been viewed by thousands of people worldwide. High-quality educational movies must respect strategic and technical points to be reliable.

  1. Teaching Surgical Procedures with Movies: Tips for High-quality Video Clips.

    Science.gov (United States)

    Jacquemart, Mathieu; Bouletreau, Pierre; Breton, Pierre; Mojallal, Ali; Sigaux, Nicolas

    2016-09-01

    Video must now be considered as a precious tool for learning surgery. However, the medium does present production challenges, and currently, quality movies are not always accessible. We developed a series of 7 surgical videos and made them available on a publicly accessible internet website. Our videos have been viewed by thousands of people worldwide. High-quality educational movies must respect strategic and technical points to be reliable.

  2. Characteristics of primary care practices associated with high quality of care.

    Science.gov (United States)

    Beaulieu, Marie-Dominique; Haggerty, Jeannie; Tousignant, Pierre; Barnsley, Janet; Hogg, William; Geneau, Robert; Hudon, Éveline; Duplain, Réjean; Denis, Jean-Louis; Bonin, Lucie; Del Grande, Claudio; Dragieva, Natalyia

    2013-09-03

    No primary practice care model has been shown to be superior in achieving high-quality primary care. We aimed to identify the organizational characteristics of primary care practices that provide high-quality primary care. We performed a cross-sectional observational study involving a stratified random sample of 37 primary care practices from 3 regions of Quebec. We recruited 1457 patients who had 1 of 2 chronic care conditions or 1 of 6 episodic care conditions. The main outcome was the overall technical quality score. We measured organizational characteristics by use of a validated questionnaire and the Team Climate Inventory. Statistical analyses were based on multilevel regression modelling. The following characteristics were strongly associated with overall technical quality of care score: physician remuneration method (27.0; 95% confidence interval [CI] 19.0-35.0), extent of sharing of administrative resources (7.6; 95% CI 0.8-14.4), presence of allied health professionals (15.3; 95% CI 5.4-25.2) and/or specialist physicians (19.6; 95% CI 8.3-30.9), the presence of mechanisms for maintaining or evaluating competence (7.7; 95% CI 3.0-12.4) and average organizational access to the practice (4.9; 95% CI 2.6-7.2). The number of physicians (1.2; 95% CI 0.6-1.8) and the average Team Climate Inventory score (1.3; 95% CI 0.1-2.5) were modestly associated with high-quality care. We identified a common set of organizational characteristics associated with high-quality primary care. Many of these characteristics are amenable to change through practice-level organizational changes.

  3. Quantitative Analysis of High-Quality Officer Selection by Commandants Career-Level Education Board

    Science.gov (United States)

    2017-03-01

    impact on the organization and allocate resources to improve the human capital of this select group. From 2011 onward, CCLEB revamped the application...ANALYSIS OF HIGH-QUALITY OFFICER SELECTION BY COMMANDANT’S CAREER - LEVEL EDUCATION BOARD by Clifton N. Rateike March 2017 Thesis Advisor...of Management and Budget, Paperwork Reduction Project (0704-0188) Washington, DC 20503. 1. AGENCY USE ONLY (Leave blank) 2. REPORT DATE March

  4. High-quality AlN films grown on chemical vapor-deposited graphene films

    Directory of Open Access Journals (Sweden)

    Chen Bin-Hao

    2016-01-01

    Full Text Available We report the growth of high-quality AlN films on graphene. The graphene films were synthesized by CVD and then transferred onto silicon substrates. Epitaxial aluminum nitride films were deposited by DC magnetron sputtering on both graphene as an intermediate layer and silicon as a substrate. The structural characteristics of the AlN films and graphene were investigated. Highly c-axis-oriented AlN crystal structures are investigated based on the XRDpatterns observations.

  5. Burnout in boiling heat transfer. Part III. High-quality forced-convection systems

    International Nuclear Information System (INIS)

    Bergles, A.E.

    1979-01-01

    This is the final part of a review of burnout during boiling heat transfer. The status of burnout in high-quality forced-convection systems is reviewed, and recent developments are summarized in detail. A general guide to the considerable literature is given. Parametric effects and correlations for water in circular and noncircular ducts are presented. Other topics discussed include transients, steam-generator applications, correlations for other fluids, fouling, and augmentation

  6. High-quality poly-dispersed mixtures applied in additive 3D technologies.

    Science.gov (United States)

    Gerasimov, M. D.; Brazhnik, Yu V.; Gorshkov, P. S.; Latyshev, S. S.

    2018-03-01

    The paper describes the new mixer design to obtain high-quality poly-dispersed powders applied in additive 3D technologies. It also considers a new mixing principle of dry powder particles ensuring the distribution of such particles in the total volume, which is close to ideal. The paper presents the mathematical model of mixer operation providing for the quality assessment of the ready mixtures. Besides, it demonstrates experimental results and obtained rational values of mixer process parameters.

  7. Generating high-quality single droplets for optical particle characterization with an easy setup

    Science.gov (United States)

    Xu, Jie; Ge, Baozhen; Meng, Rui

    2018-06-01

    The high-performance and micro-sized single droplet is significant for optical particle characterization. We develop a single-droplet generator (SDG) based on a piezoelectric inkjet technique with advantages of low cost and easy setup. By optimizing the pulse parameters, we achieve various size single droplets. Further investigations reveal that SDG generates single droplets of high quality, demonstrating good sphericity, monodispersity and a stable length of several millimeters.

  8. Fast Batch Production of High-Quality Graphene Films in a Sealed Thermal Molecular Movement System.

    Science.gov (United States)

    Xu, Jianbao; Hu, Junxiong; Li, Qi; Wang, Rubing; Li, Weiwei; Guo, Yufen; Zhu, Yongbo; Liu, Fengkui; Ullah, Zaka; Dong, Guocai; Zeng, Zhongming; Liu, Liwei

    2017-07-01

    Chemical vapor deposition (CVD) growth of high-quality graphene has emerged as the most promising technique in terms of its integrated manufacturing. However, there lacks a controllable growth method for producing high-quality and a large-quantity graphene films, simultaneously, at a fast growth rate, regardless of roll-to-roll (R2R) or batch-to-batch (B2B) methods. Here, a stationary-atmospheric-pressure CVD (SAPCVD) system based on thermal molecular movement, which enables fast B2B growth of continuous and uniform graphene films on tens of stacked Cu(111) foils, with a growth rate of 1.5 µm s -1 , is demonstrated. The monolayer graphene of batch production is found to nucleate from arrays of well-aligned domains, and the films possess few defects and exhibit high carrier mobility up to 6944 cm 2 V -1 s -1 at room temperature. The results indicate that the SAPCVD system combined with single-domain Cu(111) substrates makes it possible to realize fast batch-growth of high-quality graphene films, which opens up enormous opportunities to use this unique 2D material for industrial device applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. I read, you read, we read: the history of reading in Slovenia

    Directory of Open Access Journals (Sweden)

    Anja Dular

    2013-03-01

    Full Text Available ABSTRACTPurpose: The aim of the article is to research reading habits in Slovenia in the period between 16th and 19th century and to find similarities with Austria and other European countries of that time.Methodology/approach: For the purpose of the analysis different resources were used – study books, catechisms, prayer books and manuals. We were focused on introductions in which readers are advised how to read, explaining to whom the work is intended and emphasizing the importance of meditation on the texts.Results: Historically the laud reading was prefered, as to continue the folk tradition. However, the 16th century texts were transmitted by women while the folk tradition was narrated by males. In the 18th century the higher level of literacy and greater book production and availability caused that the books were not a privilege of a few. At that time more texts were intended for silent, individual reading. Interestingly, the authors emphasized the importance of meditation on the texts, too. It was also advised when to read – it wasrecommedend to read in leisure time on Sundays, and on holidays. The role of books was also to breakaway with the reality and to forget everyday problems. Due to the overproduction of books in the 17th centrury it was concerned that books are misleading the crowds. The church considered the reading of books as inappropriate, and criticized fiction, novels and adventure stories mostly read by women.Research limitation: The study is based on Slovenian texts only, although the foreign literature, especially in German, was generally available, too.Originality/practical implications: The study is fullfiling the gap in the history of reading in Slovenia.

  10. What can we learn about lyssavirus genomes using 454 sequencing?

    Science.gov (United States)

    Höper, Dirk; Finke, Stefan; Freuling, Conrad M; Hoffmann, Bernd; Beer, Martin

    2012-01-01

    The main task of the individual project number four"Whole genome sequencing, virus-host adaptation, and molecular epidemiological analyses of lyssaviruses "within the network" Lyssaviruses--a potential re-emerging public health threat" is to provide high quality complete genome sequences from lyssaviruses. These sequences are analysed in-depth with regard to the diversity of the viral populations as to both quasi-species and so-called defective interfering RNAs. Moreover, the sequence data will facilitate further epidemiological analyses, will provide insight into the evolution of lyssaviruses and will be the basis for the design of novel nucleic acid based diagnostics. The first results presented here indicate that not only high quality full-length lyssavirus genome sequences can be generated, but indeed efficient analysis of the viral population gets feasible.

  11. Mapping RNA-seq Reads with STAR.

    Science.gov (United States)

    Dobin, Alexander; Gingeras, Thomas R

    2015-09-03

    Mapping of large sets of high-throughput sequencing reads to a reference genome is one of the foundational steps in RNA-seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA-seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. Copyright © 2015 John Wiley & Sons, Inc.

  12. The recurrence sequences via Sylvester matrices

    Science.gov (United States)

    Karaduman, Erdal; Deveci, Ömür

    2017-07-01

    In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

  13. Reading and company

    DEFF Research Database (Denmark)

    Kuzmičová, Anežka; Dias, Patrícia; Vogrinčič Čepič, Ana

    2017-01-01

    in the environment where one engages in individual silent reading. The primary goal of the study was to explore the role and possible associations of a number of variables (text type, purpose, device) in selecting generic (e.g. indoors vs outdoors) as well as specific (e.g. home vs library) reading environments....... Across all six samples included in the study, participants spontaneously attested to varied, and partly surprising, forms of sensitivity to company and social space in their daily efforts to align body with mind for reading. The article reports these emergent trends and discusses their potential...

  14. Enhanced throughput for infrared automated DNA sequencing

    Science.gov (United States)

    Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

    1995-04-01

    Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

  15. Use of a Social Annotation Platform for Pre-Class Reading Assignments in a Flipped Introductory Physics Class

    Directory of Open Access Journals (Sweden)

    Kelly Miller

    2018-03-01

    Full Text Available In this paper, we illustrate the successful implementation of pre-class reading assignments through a social learning platform that allows students to discuss the reading online with their classmates. We show how the platform can be used to understand how students are reading before class. We find that, with this platform, students spend an above average amount of time reading (compared to that reported in the literature and that most students complete their reading assignments before class. We identify specific reading behaviors that are predictive of in-class exam performance. We also demonstrate ways that the platform promotes active reading strategies and produces high-quality learning interactions between students outside class. Finally, we compare the exam performance of two cohorts of students, where the only difference between them is the use of the platform; we show that students do significantly better on exams when using the platform.

  16. Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Cannon Charles H

    2011-07-01

    Full Text Available Abstract Background Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants. Results We sequenced transcriptomes of A. auriculiformis and A. mangium from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. De novo assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for A. auriculiformis and A. mangium respectively. The assemblies of A. auriculiformis and A. mangium had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3-MYB proteins in other plant species that are involved in transcriptional regulation of secondary cell wall formation and lignin deposition. We searched the contigs against public microRNA database and predicted the stem-loop structures of six highly conserved microRNA families (miR319, miR396, miR160, miR172, miR162 and miR168 and one legume-specific family (miR2086. Three microRNA target genes were predicted to be involved in wood formation and flavonoid biosynthesis. By using the assemblies as a reference, we discovered 16,648 and 9,335 high quality putative Single Nucleotide Polymorphisms (SNPs in the transcriptomes of A. auriculiformis and A. mangium

  17. Understanding Blood Pressure Readings

    Science.gov (United States)

    ... Venous Thromboembolism Aortic Aneurysm More Understanding Blood Pressure Readings Updated:Jun 1,2018 What do your blood ... and Live Our Interactive Cardiovascular Library has detailed animations and illustrations to help you learn about conditions, ...

  18. Reading the Tourist Guidebook

    DEFF Research Database (Denmark)

    Therkelsen, Anette; Sørensen, Anders

    2005-01-01

    of information sought, amount of information read and level of involvement displayed, indicating a three-pronged typology of guidebook readers. The guidebook reader typology thus constructed may be regarded as a first step in understanding the effect of guidebooks on tourists’ behaviour and their experience......This article investigates tourists’ ways of reading their guidebooks on the basis of qualitative interviews with tourists visiting Copenhagen, Denmark. Tourist guidebooks have only been dealt with sporadically by tourism scholars. The relatively few studies that focus on guidebooks either present...... a historical perspective on the guidebook or centre on content analyses of place representation, whereas virtually no research exists on the way in which tourists read and use their guidebooks. This study reveals that tourists read the same guidebooks in a number of different ways regarding types...

  19. What Are Reading Disorders?

    Science.gov (United States)

    ... and language-based learning disabilities are commonly called dyslexia . These disorders are present from a young age ... information about these problems. Types of Reading Disorders Dyslexia is a brain-based type of learning disability ...

  20. Textbook Reading Levels

    Science.gov (United States)

    Hopkins, Charles R.; Kim, Paul Y.

    1974-01-01

    Since the reading abilities of general business students vary from one individual to the next, the author's report on the readability of three general business textbooks to guide business teachers in their selection of textbooks. (AG)

  1. Reading-Boxing Class

    Science.gov (United States)

    Kravitz, Richard; Shapiro, Marvin

    1969-01-01

    The physical education department of the Pennsylvania Advancement School of Philadelphia has established a reading and communication skill project that uses the appeal of sports to help students improve their basic skills. (Author)

  2. Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

    Science.gov (United States)

    Desai, Aarti; Marwah, Veer Singh; Yadav, Akshay; Jha, Vineet; Dhaygude, Kishor; Bangar, Ujwala; Kulkarni, Vivek; Jere, Abhay

    2013-01-01

    Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. Currently, NGS systems generate sequence data as short reads and de novo genome assembly using these short reads is computationally very intensive. Due to lower cost of sequencing and higher throughput, NGS systems now provide the ability to sequence genomes at high depth. However, currently no report is available highlighting the impact of high sequence depth on genome assembly using real data sets and multiple assembly algorithms. Recently, some studies have evaluated the impact of sequence coverage, error rate and average read length on genome assembly using multiple assembly algorithms, however, these evaluations were performed using simulated datasets. One limitation of using simulated datasets is that variables such as error rates, read length and coverage which are known to impact genome assembly are carefully controlled. Hence, this study was undertaken to identify the minimum depth of sequencing required for de novo assembly for different sized genomes using graph based assembly algorithms and real datasets. Illumina reads for E.coli (4.6 MB) S.kudriavzevii (11.18 MB) and C.elegans (100 MB) were assembled using SOAPdenovo, Velvet, ABySS, Meraculous and IDBA-UD. Our analysis shows that 50X is the optimum read depth for assembling these genomes using all assemblers except Meraculous which requires 100X read depth. Moreover, our analysis shows that de novo assembly from 50X read data requires only 6-40 GB RAM depending on the genome size and assembly algorithm used. We believe that this information can be extremely valuable for researchers in designing experiments and multiplexing which will enable optimum utilization of sequencing as well as analysis resources.

  3. 75 FR 70289 - Certain Coated Paper Suitable For High-Quality Print Graphics Using Sheet-Fed Presses From China...

    Science.gov (United States)

    2010-11-17

    ...)] Certain Coated Paper Suitable For High-Quality Print Graphics Using Sheet-Fed Presses From China and... paper suitable for high-quality print graphics using sheet-fed presses (``certain coated paper'') from... paper industry is materially injured by reason of imports of the subject merchandise from China and...

  4. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

    DEFF Research Database (Denmark)

    Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam

    2013-01-01

    Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition–independent approach to recover high-quality microbial genomes from deeply sequenced metageno......Reference genomes are required to understand the diverse roles of microorganisms in ecology, evolution, human and animal health, but most species remain uncultured. Here we present a sequence composition–independent approach to recover high-quality microbial genomes from deeply sequenced...

  5. The Swiss-Prot protein knowledgebase and ExPASy: providing the plant community with high quality proteomic data and tools.

    Science.gov (United States)

    Schneider, Michel; Tognolli, Michael; Bairoch, Amos

    2004-12-01

    The Swiss-Prot protein knowledgebase provides manually annotated entries for all species, but concentrates on the annotation of entries from model organisms to ensure the presence of high quality annotation of representative members of all protein families. A specific Plant Protein Annotation Program (PPAP) was started to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Its main goal is the annotation of proteins from the model plant organism Arabidopsis thaliana. In addition to bibliographic references, experimental results, computed features and sometimes even contradictory conclusions, direct links to specialized databases connect amino acid sequences with the current knowledge in plant sciences. As protein families and groups of plant-specific proteins are regularly reviewed to keep up with current scientific findings, we hope that the wealth of information of Arabidopsis origin accumulated in our knowledgebase, and the numerous software tools provided on the Expert Protein Analysis System (ExPASy) web site might help to identify and reveal the function of proteins originating from other plants. Recently, a single, centralized, authoritative resource for protein sequences and functional information, UniProt, was created by joining the information contained in Swiss-Prot, Translation of the EMBL nucleotide sequence (TrEMBL), and the Protein Information Resource-Protein Sequence Database (PIR-PSD). A rising problem is that an increasing number of nucleotide sequences are not being submitted to the public databases, and thus the proteins inferred from such sequences will have difficulties finding their way to the Swiss-Prot or TrEMBL databases.

  6. Small Open Reading Frames

    Indian Academy of Sciences (India)

    enormous growth in whole genome sequencing. Hence today, genome sequence ... Similarly, during the embryo development of zebrafish, 58 aa long toddler polypeptide produced by a short ORF within a lncRNA, regulates cell migration ...

  7. Developing New Reading Assessments to Promote Beginning Reading in Singapore

    Science.gov (United States)

    Koh, Kim H.; Paris, Scott G.

    2011-01-01

    Effective reading instruction and intervention are rooted in effective assessments of children's developing skills in reading. The article aims to describe the development of new reading assessments to help promote beginning reading in Singapore primary schools. We begin with an introduction to the educational landscape and policies before…

  8. Reading Every Single Day: A Journey to Authentic Reading

    Science.gov (United States)

    Hudson, Alida K.; Williams, Joan A.

    2015-01-01

    This article details one teacher's implementation of reading workshop in her second grade classroom. She provided a framework for authentic reading using the five components of reading workshop: time, choice, response, community, and structure. She found that reading workshop is a highly effective practice for not only increasing students'…

  9. Exploring Students' Reading Profiles to Guide a Reading Intervention Programme

    Science.gov (United States)

    Boakye, Naomi A. N. Y.

    2017-01-01

    There have been a number of studies on reading interventions to improve students' reading proficiency, yet the majority of these interventions are undertaken with the assumption that students' reading challenges are obvious and generic in nature. The interventions do not take into consideration the diversity in students' reading backgrounds and…

  10. "Read the Text, as if!"The Reading Retention Strategy

    Science.gov (United States)

    Divoll, Kent; Browning, Sandra

    2013-01-01

    Students do not always read what is expected in college courses (Berry, Cook, Hill, & Stevens, 2010; Phillips & Phillips, 2007; Sikorski et al., 2002) or they read to cram for an exam or quiz (Clump, Bauer, & Bradley, 2004). The Reading Retention Strategy (RRS) is designed to motivate students to read and assist students in…

  11. Child-centered reading intervention: See, talk, dictate, read, write!

    Directory of Open Access Journals (Sweden)

    Muhammet BAŞTUĞ

    2016-06-01

    Full Text Available Poor reading achievement of children in elementary schools has been one of the major concerns in education. The aim of this study is to examine the effectiveness of a child-centered reading intervention in eliminating the reading problems of a student with poor reading achievement. The research was conducted with a student having difficulty in reading. A reading intervention was designed that targeted multiple areas of reading and aimed to improve reading skills through the use of multiple strategies. This intervention is child-centered and includes visual aids, talking, dictating, reading and writing stages. The study was performed in 35 sessions consisting of stages of a single sentence (5 sessions, two sentences (5 sessions, three sentences (20 sessions and the text stage (5 sessions. The intervention sessions were audio-taped. These recordings and the written responses to the reading comprehension questions provided the data for analysis. The findings on the reading intervention revealed positive outcomes. The student exhibited certain improvements at the levels of reading, reading rate and reading comprehension. These results were discussed in the literature and the findings suggest that child-centered reading strategies such as talking, dictating and writing should be the main focus of instruction for students with low reading literacy achievement to enable these students to meet the demands of the curriculum.

  12. Use of Non-Normalized, Non-Amplified cDNA for 454-Based RNA Sequencing of Fleshy Melon Fruit

    Directory of Open Access Journals (Sweden)

    Vitaly Portnoy

    2011-03-01

    Full Text Available The melon ( L. fruit is an important crop and model system for the genomic study of both fleshy fruit development and the Cucurbitaceae family. To obtain an accurate representation of the melon fruit transcriptome based on expressed sequence tag (EST abundance in 454-pyrosequencing data, we prepared double-stranded complementary DNA (cDNA of melon without the usual amplification and normalization steps. A purification step was also included to eliminate small fragments. Complementary DNAs were obtained from 14 individual fruit libraries derived from two genotypes, separated into flesh and peel tissues, and sampled throughout fruit development. Pyrosequencing was performed using Genome Sequencer FLX (GS FLX technology, resulting in 1,215,359 reads, with mean length of >200 nucleotides. The global digital expression data was validated by comparative reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR of 40 selected genes and expression patterns were similar for the two methods. The results indicate that high-quality, nonbiased cDNA for next-generation sequencing can be prepared from mature, fleshy fruit, which are notorious for difficulties in ribonucleic acid (RNA preparation.

  13. Transcriptome sequencing and differential gene expression analysis in Viola yedoensis Makino (Fam. Violaceae) responsive to cadmium (Cd) pollution

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Jian [Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan (China); Luo, Mao [Drug Discovery Research Center of Luzhou Medical College, Luzhou, Sichuan (China); Zhu, Ye; He, Ying; Wang, Qin [Department of Pharmacy of Luzhou Medical College, Luzhou, Sichuan (China); Zhang, Chun, E-mail: zc83good@126.com [Department of Pharmacy of Luzhou Medical College, Luzhou, Sichuan (China)

    2015-03-27

    Viola yedoensis Makino is an important Chinese traditional medicine plant adapted to cadmium (Cd) pollution regions. Illumina sequencing technology was used to sequence the transcriptome of V. yedoensis Makino. We sequenced Cd-treated (VIYCd) and untreated (VIYCK) samples of V. yedoensis, and obtained 100,410,834 and 83,587,676 high quality reads, respectively. After de novo assembly and quantitative assessment, 109,800 unigenes were finally generated with an average length of 661 bp. We then obtained functional annotations by aligning unigenes with public protein databases including NR, NT, SwissProt, KEGG and COG. In addition, 892 differentially expressed genes (DEGs) were investigated between the two libraries of untreated (VIYCK) and Cd-treated (VIYCd) plants. Moreover, 15 randomly selected DEGs were further validated with qRT-PCR and the results were highly accordant with the Solexa analysis. This study firstly generated a successful global analysis of the V. yedoensis transcriptome and it will provide for further studies on gene expression, genomics, and functional genomics in Violaceae. - Highlights: • A de novo assembly generated 109,800 unigenes and 5,4479 of them were annotated. • 31,285 could be classified into 26 COG categories. • 263 biosynthesis pathways were predicted and classified into five categories. • 892 DEGs were detected and 15 of them were validated by qRT-PCR.

  14. Transcriptome sequencing and differential gene expression analysis in Viola yedoensis Makino (Fam. Violaceae) responsive to cadmium (Cd) pollution

    International Nuclear Information System (INIS)

    Gao, Jian; Luo, Mao; Zhu, Ye; He, Ying; Wang, Qin; Zhang, Chun

    2015-01-01

    Viola yedoensis Makino is an important Chinese traditional medicine plant adapted to cadmium (Cd) pollution regions. Illumina sequencing technology was used to sequence the transcriptome of V. yedoensis Makino. We sequenced Cd-treated (VIYCd) and untreated (VIYCK) samples of V. yedoensis, and obtained 100,410,834 and 83,587,676 high quality reads, respectively. After de novo assembly and quantitative assessment, 109,800 unigenes were finally generated with an average length of 661 bp. We then obtained functional annotations by aligning unigenes with public protein databases including NR, NT, SwissProt, KEGG and COG. In addition, 892 differentially expressed genes (DEGs) were investigated between the two libraries of untreated (VIYCK) and Cd-treated (VIYCd) plants. Moreover, 15 randomly selected DEGs were further validated with qRT-PCR and the results were highly accordant with the Solexa analysis. This study firstly generated a successful global analysis of the V. yedoensis transcriptome and it will provide for further studies on gene expression, genomics, and functional genomics in Violaceae. - Highlights: • A de novo assembly generated 109,800 unigenes and 5,4479 of them were annotated. • 31,285 could be classified into 26 COG categories. • 263 biosynthesis pathways were predicted and classified into five categories. • 892 DEGs were detected and 15 of them were validated by qRT-PCR

  15. STUDENTS’ READING PRACTICES AND ENVIRONMENTS

    Directory of Open Access Journals (Sweden)

    Aiza Johari

    2013-07-01

    Full Text Available Abstract: The challenges of reading are indeed apparent in most teaching and learning processes in ESL classrooms. As a result, this study is conducted to resolve the issues of students who seem to find reading to be unbearable. Many of them have limited ability to read well and hence, possess insufficient reading habits to become competent readers, particularly out-of-school context. Besides, poor home literacy environments also contribute to their shortcomings in reading. The main objectives of this study are to identify the students’ reasons for reading as well as to find out their home reading environments (reading backgrounds and habits; reading attitudes and motivation; reading exposure and supports. To identify these, questionnaires were distributed to 120 secondary school students (Form 4: 16 years old from one of the urban schools in Sarawak, Malaysia. The findings indicate that the students read to gain information and knowledge though many chose reading as a hobby as their last choice in explaining their motives of reading. Besides, they preferred non-academic reading materials, mainly lighter forms reading materials such as comics, story books and magazines. Though the students acknowledged the importance of reading in their daily lives, their average reading habits, attitude, motivation, exposure and support within the home domain had suggested otherwise. They mainly read for instrumental purposes while reading for pleasure seemed not to be given priority. Besides, the respondents acknowledge that their parents and themselves did not read much at home. As an implication, it is vital for students to improve their reading perceptions, abilities and practices to achieve personal, societal and national progress. On a final note, parents’ early and continuous efforts to be involved in their children’s literacy events in an out-of-school context are believed to be vital to inculcate positive reading environments, habits and culture

  16. IMPROVING STUDENTS’ READING COMPREHENSION THROUGH IINTERACTIVE READ-ALOUD TECHNIQUE

    Directory of Open Access Journals (Sweden)

    Edi Santoso

    2015-10-01

    Full Text Available Abstract: The present study, entitled Improving Students’ Reading Comprehension through Interactive Read-Aloud, attempts to unlock problems found in teaching and reading comprehension through interactive read-aloud in a Senior High School of Sport (SMAN Olah Raga Lampung, in Metro. The findings revealed that students’ reading comprehension improved through interactive read-aloud. The improvement can be seen from the increase of test results, meaning construction, and motivation. The process of reading activities showed that the teacher’s gesture and body language, 20 questions, explain and guess activities were proven to help the students construct meaning from the given texts. In addition, interactive read-aloud is effective to boost students’ motivation to comprehend the texts.   Key words: Reading comprehension, interactive read-aloud.

  17. De novo sequencing and analysis of the transcriptome during the browning of fresh-cut Luffa cylindrica 'Fusi-3' fruits

    Science.gov (United States)

    Chen, Mindong; Wang, Bin; Zhang, Qianrong; Xue, Zhuzheng

    2017-01-01

    Fresh-cut luffa (Luffa cylindrica) fruits commonly undergo browning. However, little is known about the molecular mechanisms regulating this process. We used the RNA-seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut fruits from luffa cultivar ‘Fusi-3’. Over 90 million high-quality reads were assembled into 58,073 Unigenes, and 60.86% of these were annotated based on sequences in four public databases. We detected 35,282 Unigenes with significant hits to sequences in the NCBInr database, and 24,427 Unigenes encoded proteins with sequences that were similar to those of known proteins in the Swiss-Prot database. Additionally, 20,546 and 13,021 Unigenes were similar to existing sequences in the Eukaryotic Orthologous Groups of proteins and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Furthermore, 27,301 Unigenes were differentially expressed during the browning of fresh-cut luffa fruits (i.e., after 1–6 h). Moreover, 11 genes from five gene families (i.e., PPO, PAL, POD, CAT, and SOD) identified as potentially associated with enzymatic browning as well as four WRKY transcription factors were observed to be differentially regulated in fresh-cut luffa fruits. With the assistance of rapid amplification of cDNA ends technology, we obtained the full-length sequences of the 15 Unigenes. We also confirmed these Unigenes were expressed by quantitative real-time polymerase chain reaction analysis. This study provides a comprehensive transcriptome sequence resource, and may facilitate further studies aimed at identifying genes affecting luffa fruit browning for the exploitation of the underlying mechanism. PMID:29145430

  18. De novo sequencing and analysis of the transcriptome during the browning of fresh-cut Luffa cylindrica 'Fusi-3' fruits.

    Directory of Open Access Journals (Sweden)

    Haisheng Zhu

    Full Text Available Fresh-cut luffa (Luffa cylindrica fruits commonly undergo browning. However, little is known about the molecular mechanisms regulating this process. We used the RNA-seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut fruits from luffa cultivar 'Fusi-3'. Over 90 million high-quality reads were assembled into 58,073 Unigenes, and 60.86% of these were annotated based on sequences in four public databases. We detected 35,282 Unigenes with significant hits to sequences in the NCBInr database, and 24,427 Unigenes encoded proteins with sequences that were similar to those of known proteins in the Swiss-Prot database. Additionally, 20,546 and 13,021 Unigenes were similar to existing sequences in the Eukaryotic Orthologous Groups of proteins and Kyoto Encyclopedia of Genes and Genomes databases, respectively. Furthermore, 27,301 Unigenes were differentially expressed during the browning of fresh-cut luffa fruits (i.e., after 1-6 h. Moreover, 11 genes from five gene families (i.e., PPO, PAL, POD, CAT, and SOD identified as potentially associated with enzymatic browning as well as four WRKY transcription factors were observed to be differentially regulated in fresh-cut luffa fruits. With the assistance of rapid amplification of cDNA ends technology, we obtained the full-length sequences of the 15 Unigenes. We also confirmed these Unigenes were expressed by quantitative real-time polymerase chain reaction analysis. This study provides a comprehensive transcriptome sequence resource, and may facilitate further studies aimed at identifying genes affecting luffa fruit browning for the exploitation of the underlying mechanism.

  19. Deep sequencing-based identification of small regulatory RNAs in Synechocystis sp. PCC 6803.

    Directory of Open Access Journals (Sweden)

    Wen Xu

    Full Text Available Synechocystis sp. PCC 6803 is a genetically tractable model organism for photosynthesis research. The genome of Synechocystis sp. PCC 6803 consists of a circular chromosome and seven plasmids. The importance of small regulatory RNAs (sRNAs as mediators of a number of cellular processes in bacteria has begun to be recognized. However, little is known regarding sRNAs in Synechocystis sp. PCC 6803. To provide a comprehensive overview of sRNAs in this model organism, the sRNAs of Synechocystis sp. PCC 6803 were analyzed using deep sequencing, and 7,951,189 reads were obtained. High quality mapping reads (6,127,890 were mapped onto the genome and assembled into 16,192 transcribed regions (clusters based on read overlap. A total number of 5211 putative sRNAs were revealed from the genome and the 4 megaplasmids, and 27 of these molecules, including four from plasmids, were confirmed by RT-PCR. In addition, possible target genes regulated by all of the putative sRNAs identified in this study were predicted by IntaRNA and analyzed for functional categorization and biological pathways, which provided evidence that sRNAs are indeed involved in many different metabolic pathways, including basic metabolic pathways, such as glycolysis/gluconeogenesis, the citrate cycle, fatty acid metabolism and adaptations to environmentally stress-induced changes. The information from this study provides a valuable reservoir for understanding the sRNA-mediated regulation of the complex physiology and metabolic processes of cyanobacteria.

  20. Transcriptome sequence analysis of an ornamental plant, Ananas comosus var. bracteatus, revealed the potential unigenes involved in terpenoid and phenylpropanoid biosynthesis.

    Science.gov (United States)

    Ma, Jun; Kanakala, S; He, Yehua; Zhang, Junli; Zhong, Xiaolan

    2015-01-01

    Ananas comosus var. bracteatus (Red Pineapple) is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies. The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis. The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

  1. Transcriptome sequence analysis of an ornamental plant, Ananas comosus var. bracteatus, revealed the potential unigenes involved in terpenoid and phenylpropanoid biosynthesis.

    Directory of Open Access Journals (Sweden)

    Jun Ma

    Full Text Available Ananas comosus var. bracteatus (Red Pineapple is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies.The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis.The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

  2. Zseq: An Approach for Preprocessing Next-Generation Sequencing Data.

    Science.gov (United States)

    Alkhateeb, Abedalrhman; Rueda, Luis

    2017-08-01

    Next-generation sequencing technology generates a huge number of reads (short sequences), which contain a vast amount of genomic data. The sequencing process, however, comes with artifacts. Preprocessing of sequences is mandatory for further downstream analysis. We present Zseq, a linear method that identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. Zseq finds the complexity of the sequences by counting the number of unique k-mers in each sequence as its corresponding score and also takes into the account other factors such as ambiguous nucleotides or high GC-content percentage in k-mers. Based on a z-score threshold, Zseq sweeps through the sequences again and filters those with a z-score less than the user-defined threshold. Zseq algorithm is able to provide a better mapping rate; it reduces the number of ambiguous bases significantly in comparison with other methods. Evaluation of the filtered reads has been conducted by aligning the reads and assembling the transcripts using the reference genome as well as de novo assembly. The assembled transcripts show a better discriminative ability to separate cancer and normal samples in comparison with another state-of-the-art method. Moreover, de novo assembled transcripts from the reads filtered by Zseq have longer genomic sequences than other tested methods. Estimating the threshold of the cutoff point is introduced using labeling rules with optimistic results.

  3. Sequencing of BAC pools by different next generation sequencing platforms and strategies

    Directory of Open Access Journals (Sweden)

    Scholz Uwe

    2011-10-01

    Full Text Available Abstract Background Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs improve the assemblies by scaffolding and whether barcoding of BACs is dispensable. Results Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library. Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%. Conclusion Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.

  4. High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin; Wang, Zhigang C.; Richardson, Andrea L.; Warren, Robert; Walther, Axel; Bondy, Melissa; Sahin, Aysegul; Krahe, Ralf; Tuna, Musaffe; Thompson, Patricia A.; Spellman, Paul T.; Gray, Joe W.; Mills, Gordon B.; Faham, Malek

    2009-02-24

    A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.

  5. Reading in a Digital Age

    Science.gov (United States)

    Baron, Naomi S.

    2017-01-01

    The many advantages of reading digitally also bring with them implications for how we learn differently when we read differently. The author suggests that new contemporary technologies are changing the very notion of what it means to read. Even millennials acknowledge that their attention is more focused when they read print rather than online.…

  6. Early Reading and Concrete Operations.

    Science.gov (United States)

    Polk, Cindy L. Howes; Goldstein, David

    1980-01-01

    Indicated that early readers are more likely to be advanced in cognitive development than are nonearly-reading peers. After one year of formal reading instruction, early readers maintained their advantage in reading achievement. Measures of concrete operations were found to predict reading achievement for early and nonearly readers. (Author/DB)

  7. Repeat-aware modeling and correction of short read errors.

    Science.gov (United States)

    Yang, Xiao; Aluru, Srinivas; Dorman, Karin S

    2011-02-15

    High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome resequencing, and digital gene expression analysis. Short read error detection is typically carried out by counting the observed frequencies of kmers in reads and validating those with frequencies exceeding a threshold. In case of genomes with high repeat content, an erroneous kmer may be frequently observed if it has few nucleotide differences with valid kmers with multiple occurrences in the genome. Error detection and correction were mostly applied to genomes with low repeat content and this remains a challenging problem for genomes with high repeat content. We develop a statistical model and a computational method for error detection and correction in the presence of genomic repeats. We propose a method to infer genomic frequencies of kmers from their observed frequencies by analyzing the misread relationships among observed kmers. We also propose a method to estimate the threshold useful for validating kmers whose estimated genomic frequency exceeds the threshold. We demonstrate that superior error detection is achieved using these methods. Furthermore, we break away from the common assumption of uniformly distributed errors within a read, and provide a framework to model position-dependent error occurrence frequencies common to many short read platforms. Lastly, we achieve better error correction in genomes with high repeat content. The software is implemented in C++ and is freely available under GNU GPL3 license and Boost Software V1.0 license at "http://aluru-sun.ece.iastate.edu/doku.php?id = redeem". We introduce a statistical framework to model sequencing errors in next-generation reads, which led to promising results in detecting and correcting errors

  8. De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae.

    Directory of Open Access Journals (Sweden)

    Mukesh Kumar

    Full Text Available The cereal cyst nematode (CCN, Heterodera avenae is a major pest of wheat (Triticum spp that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy revealed fewer glycoside hydrolases (GHs but more glycosyl transferases (GTs and carbohydrate esterases (CEs when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction.

  9. De novo transcriptome sequencing and analysis of the cereal cyst nematode, Heterodera avenae.

    Science.gov (United States)

    Kumar, Mukesh; Gantasala, Nagavara Prasad; Roychowdhury, Tanmoy; Thakur, Prasoon Kumar; Banakar, Prakash; Shukla, Rohit N; Jones, Michael G K; Rao, Uma

    2014-01-01

    The cereal cyst nematode (CCN, Heterodera avenae) is a major pest of wheat (Triticum spp) that reduces crop yields in many countries. Cyst nematodes are obligate sedentary endoparasites that reproduce by amphimixis. Here, we report the first transcriptome analysis of two stages of H. avenae. After sequencing extracted RNA from pre parasitic infective juvenile and adult stages of the life cycle, 131 million Illumina high quality paired end reads were obtained which generated 27,765 contigs with N50 of 1,028 base pairs, of which 10,452 were annotated. Comparative analyses were undertaken to evaluate H. avenae sequences with those of other plant, animal and free living nematodes to identify differences in expressed genes. There were 4,431 transcripts common to H. avenae and the free living nematode Caenorhabditis elegans, and 9,462 in common with more closely related potato cyst nematode, Globodera pallida. Annotation of H. avenae carbohydrate active enzymes (CAZy) revealed fewer glycoside hydrolases (GHs) but more glycosyl transferases (GTs) and carbohydrate esterases (CEs) when compared to M. incognita. 1,280 transcripts were found to have secretory signature, presence of signal peptide and absence of transmembrane. In a comparison of genes expressed in the pre-parasitic juvenile and feeding female stages, expression levels of 30 genes with high RPKM (reads per base per kilo million) value, were analysed by qRT-PCR which confirmed the observed differences in their levels of expression levels. In addition, we have also developed a user-friendly resource, Heterodera transcriptome database (HATdb) for public access of the data generated in this study. The new data provided on the transcriptome of H. avenae adds to the genetic resources available to study plant parasitic nematodes and provides an opportunity to seek new effectors that are specifically involved in the H. avenae-cereal host interaction.

  10. Open Reading Frame Phylogenetic Analysis on the Cloud

    Directory of Open Access Journals (Sweden)

    Che-Lun Hung

    2013-01-01

    Full Text Available Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus.

  11. Preparation of high-quality iodine-125-labeled pituitary luteinizing hormone for radioimmunoassay

    International Nuclear Information System (INIS)

    Pinto, H.; Wajchenberg, B.L.; Higa, O.Z.; Toledo e Souza, I.T. de; Werner, R.S.; Pieroni, R.R.

    1974-01-01

    High quality pituitary luteinizing hormone labeled with 125 I was obtained after separating out the more heavily iodinated fractions, through starch gel electrophoresis, using the cathodal component (fraction 1) which was further purified on Sephadex G-100, with the obtention of an almost pure 125 I-LH preparation, presenting excellent immunoreactivity and low levels of damage on incubation in plasma. The quality control of the steps of the technique was done with plasma-coated talc (200 mg) which compared favorably, as far indicating undamaged labeled LH, with the more time-consuming chromatoelectrophoresis

  12. Production of high-quality marketing applications: strategies for biotechnology companies working with contract research organizations.

    Science.gov (United States)

    Hecker, Sandra J; Preston, Christopher; Foote, MaryAnn

    2003-01-01

    Many biotechnology and pharmaceutical companies use clinical research organizations (CROs) to assist in the writing and preparation of clinical documents intended for submission to health authorities. Start-up companies often require the expertise of a CRO to prepare their first regulatory documents. Larger or more experienced companies often require CRO staff to assist at times of multiple simultaneous submissions. The timely production of high-quality new drug marketing applications requires close collaborations between the drug company and the CRO. The views of both CRO and industry in ensuring best practices are discussed.

  13. Growth of high quality large area MgB2 thin films by reactive evaporation

    OpenAIRE

    Moeckly, Brian H.; Ruby, Ward S.

    2006-01-01

    We report a new in-situ reactive deposition thin film growth technique for the production of MgB2 thin films which offers several advantages over all existing methods and is the first deposition method to enable the production of high-quality MgB2 films for real-world applications. We have used this growth method, which incorporates a rotating pocket heater, to deposit MgB2 films on a variety of substrates, including single-crystalline, polycrystalline, metallic, and semiconductor materials u...

  14. Joining forces: collaborating internationally to deliver high-quality, online postgraduate education in pain management.

    Science.gov (United States)

    Devonshire, Elizabeth; Siddall, Philip

    2011-01-01

    The effective management of pain is a complex and costly global issue, requiring a range of innovative educational strategies to enable culturally appropriate and high-quality health care provision. In response to this issue, the Pain Management Research Institute at the University of Sydney (Sydney, Australia) has established several strategic alliances with other overseas universities to deliver online postgraduate education in pain management. The present article discusses the rationale for joining forces, and the approach adopted in creating and maintaining these alliances. It also provides insights into the benefits, challenges and opportunities associated with collaborative educational initiatives of this nature, from institutional, academic and student perspectives.

  15. Isolation of high quality graphene from Ru by solution phase intercalation

    Science.gov (United States)

    Koren, E.; Sutter, E.; Bliznakov, S.; Ivars-Barcelo, F.; Sutter, P.

    2013-09-01

    We introduce a method for isolating graphene grown on epitaxial Ru(0001)/α-Al2O3. The strong graphene/Ru(0001) coupling is weakened by electrochemically driven intercalation of hydrogen underpotentially deposited in aqueous KOH solution, which allows the penetration of water molecules at the graphene/Ru(0001) interface. Following these electrochemically driven processes, the graphene can be isolated by electrochemical hydrogen evolution and transferred to arbitrary supports. Raman and transport measurements demonstrate the high quality of the transferred graphene. Our results show that intercalation, typically carried out in vacuum, can be extended to solution environments for graphene processing under ambient conditions.

  16. Experience in melting of high-quality chromium-nickel-molybdenum steel in oxygen converter

    Energy Technology Data Exchange (ETDEWEB)

    Kosoi, L F; Yaburov, S I; Shul' kin, M L; Vedernikov, G G; Bragin, E D; Filork' yan, B K

    1978-10-01

    Technology of melting high-quality medium-carbon constructional chromium-nickel-molybdenum steel has been developed and tested in 130-t converters. The technology envisages metal refinement in a casting laddle using synthetic lime-aluminous slag and argon blowing, as well as liquid ferroallys (master alloys) for steel deoxidation and alloying. Due to a smaller content of sulfur, phosphorus, arsenic and sulphide inclusions, and to a smaller grain size (N 11-12), the steel, produced according to this technology possesses higher plastic properties and impact strength than conventional open-hearth furnace metal after heat treatment for the same strength.

  17. Availability and Price of High Quality Day Care and Female Employment

    DEFF Research Database (Denmark)

    Simonsen, Marianne

    In this paper I analyse to what degree availability and price of high quality publicly subsidised childcare affects female employment for women living in couples following maternity leave. The results show that unrestricted access to day care has a significantly positive effct on female employment.......The price effect is significantly negative: An increase in the price of child care of C=1 will decrease the female employment with 0.08% corresponding to a price elasticity of −0.17. This effect prevails during the first 12 months after childbirth....

  18. Low-cost high-quality crystalline germanium based flexible devices

    KAUST Repository

    Nassar, Joanna M.

    2014-06-16

    High performance flexible electronics promise innovative future technology for various interactive applications for the pursuit of low-cost, light-weight, and multi-functional devices. Thus, here we show a complementary metal oxide semiconductor (CMOS) compatible fabrication of flexible metal-oxide-semiconductor capacitors (MOSCAPs) with high-κ/metal gate stack, using a physical vapor deposition (PVD) cost-effective technique to obtain a high-quality Ge channel. We report outstanding bending radius ~1.25 mm and semi-transparency of 30%.

  19. Facilitating the openEHR approach - organizational structures for defining high-quality archetypes.

    Science.gov (United States)

    Kohl, Christian Dominik; Garde, Sebastian; Knaup, Petra

    2008-01-01

    Using openEHR archetypes to establish an electronic patient record promises rapid development and system interoperability by using or adopting existing archetypes. However, internationally accepted, high quality archetypes which enable a comprehensive semantic interoperability require adequate development and maintenance processes. Therefore, structures have to be created involving different health professions. In the following we present a model which facilitates and governs distributed but cooperative development and adoption of archetypes by different professionals including peer reviews. Our model consists of a hierarchical structure of professional committees and descriptions of the archetype development process considering these different committees.

  20. Assessment of bird populations in a high quality savanna/woodland: a banding approach

    Science.gov (United States)

    Wilmore, Sandra L.; Glowacki, Gary A.; Grundel, Ralph

    2005-01-01

    Between 1999 and 2004, Save the Dunes Conservation Fund's Miller Woods Bird Banding Program monitored migrating and breeding bird populations within a high quality black oak, dry-mesic sand savanna/woodland with ridge and swale topography. The objectives of this program were to collect consistent and reliable demographic and abundance data on the bird populations, to investigate long-term population trends, and to contribute to improved land management decisions at regional and national scales. The technique employed involved capturing birds in mist nets that were deployed for set periods of time at 17 net sites in two banding areas in Miller Woods.

  1. Low-cost high-quality crystalline germanium based flexible devices

    KAUST Repository

    Nassar, Joanna M.; Hussain, Aftab M.; Rojas, Jhonathan Prieto; Hussain, Muhammad Mustafa

    2014-01-01

    High performance flexible electronics promise innovative future technology for various interactive applications for the pursuit of low-cost, light-weight, and multi-functional devices. Thus, here we show a complementary metal oxide semiconductor (CMOS) compatible fabrication of flexible metal-oxide-semiconductor capacitors (MOSCAPs) with high-κ/metal gate stack, using a physical vapor deposition (PVD) cost-effective technique to obtain a high-quality Ge channel. We report outstanding bending radius ~1.25 mm and semi-transparency of 30%.

  2. Fast Synthesis of High Quality Biodiesel from ‘Waste Fish Oil’ by Single Step Transesterification

    Directory of Open Access Journals (Sweden)

    Yogesh C. Sharma

    2014-09-01

    Full Text Available A large volume of fish wastes is produced on a daily basis in the Indian sub-continent. This abundant waste source could serve as an economic feedstock for bioenergy generation. In the present study, oil extracted from discarded fish parts was used for high quality biodiesel production. More specifically, a single step transesterification of ‘waste fishoil’ with methanol using sodium methoxide (CH3ONa as homogeneous catalyst under moderate operational conditions resulted in highly pure biodiesel of > 98% of fatty acid methyl ester (FAME content. Characterization was performed by Fourier Transform-Nuclear Magnetic Resonance (FT-NMR.

  3. HIGH QUALITY FACADE SEGMENTATION BASED ON STRUCTURED RANDOM FOREST, REGION PROPOSAL NETWORK AND RECTANGULAR FITTING

    Directory of Open Access Journals (Sweden)

    K. Rahmani

    2018-05-01

    Full Text Available In this paper we present a pipeline for high quality semantic segmentation of building facades using Structured Random Forest (SRF, Region Proposal Network (RPN based on a Convolutional Neural Network (CNN as well as rectangular fitting optimization. Our main contribution is that we employ features created by the RPN as channels in the SRF.We empirically show that this is very effective especially for doors and windows. Our pipeline is evaluated on two datasets where we outperform current state-of-the-art methods. Additionally, we quantify the contribution of the RPN and the rectangular fitting optimization on the accuracy of the result.

  4. ATR-FTIR as a potential tool for controlling high quality vinegar categories

    DEFF Research Database (Denmark)

    Ríos-Reina, Rocío; Callejón, Raquel M.; Oliver-Pozo, Celia

    2017-01-01

    potential as a rapid, cost-effective and non-destructive tool for characterizing different categories of high-quality vinegars. Spectra from 67 wine vinegars belonging to the PDOs “Vinagre de Jerez” and “Vinagre Condado de Huelva”, including their different established categories, were analyzed in the 4000......–600 cm−1 infrared region. Changes associated to categories were observed in the region 1800–900 cm−1. These changes were assigned to certain compounds that increase during aging (e.g. acetic acids, alcohols, esters) or are characteristic of Pedro Ximenez category (e.g. sugars, furfural). Principal...

  5. High-quality fiber fabrication in buffered hydrofluoric acid solution with ultrasonic agitation.

    Science.gov (United States)

    Zhong, Nianbing; Liao, Qiang; Zhu, Xun; Wang, Yongzhong; Chen, Rong

    2013-03-01

    An etching method for preparing high-quality fiber-optic sensors using a buffered etchant with ultrasonic agitation is proposed. The effects of etching conditions on the etch rate and surface morphology of the etched fibers are investigated. The effect of surface roughness is discussed on the fibers' optical properties. Linear etching behavior and a smooth fiber surface can be repeatedly obtained by adjusting the ultrasonic power and etchant pH. The fibers' spectral quality is improved as the ratio of the pit depth to size decreases, and the fibers with smooth surfaces are more sensitive to a bacterial suspension than those with rough surfaces.

  6. THE ACADEMIC PERSONNEL MOTIVATION - A FACTOR FOR HIGH QUALITY EDUCATIONAL PRODUCT

    Directory of Open Access Journals (Sweden)

    Viara Slavianska

    2014-06-01

    Full Text Available The present paper consecutively puts an accent on 1 the quality of higher education as a national priority, 2 the qualification and motivation of the academic staff as factors for offering an educational product of high quality, 3 the strategies, policies and practices for motivating the academic personnel. The necessity of education improvement is adduced, the strategies and politics in the field of academic personnel training are presented, and the possible effects from a wrong approach to employees’ motivation in academic environment are commented.

  7. Low index contrast heterostructure photonic crystal cavities with high quality factors and vertical radiation coupling

    Science.gov (United States)

    Ge, Xiaochen; Minkov, Momchil; Fan, Shanhui; Li, Xiuling; Zhou, Weidong

    2018-04-01

    We report here design and experimental demonstration of heterostructure photonic crystal cavities resonating near the Γ point with simultaneous strong lateral confinement and highly directional vertical radiation patterns. The lateral confinement is provided by a mode gap originating from a gradual modulation of the hole radii. High quality factor resonance is realized with a low index contrast between silicon nitride and quartz. The near surface-normal directional emission is preserved when the size of the core region is scaled down. The influence of the cavity size parameters on the resonant modes is also investigated theoretically and experimentally.

  8. High quality-factor fano metasurface comprising a single resonator unit cell

    Science.gov (United States)

    Sinclair, Michael B.; Warne, Larry K.; Basilio, Lorena I.; Langston, William L.; Campione, Salvatore; Brener, Igal; Liu, Sheng

    2017-06-20

    A new monolithic resonator metasurface design achieves ultra-high Q-factors while using only one resonator per unit cell. The metasurface relies on breaking the symmetry of otherwise highly symmetric resonators to induce intra-resonator mixing of bright and dark modes (rather than inter-resonator couplings), and is scalable from the near-infrared to radio frequencies and can be easily implemented in dielectric materials. The resulting high-quality-factor Fano metasurface can be used in many sensing, spectral filtering, and modulation applications.

  9. A hybrid plasmonic microresonator with high quality factor and small mode volume

    International Nuclear Information System (INIS)

    Lu, Qijing; Chen, Daru; Wu, Genzhu; Peng, Baojin; Xu, Jiancheng

    2012-01-01

    We propose a novel hybrid plasmonic microcavity which is composed of a silver nanoring and a silica toroidal microcavity. The hybrid mode of the proposed hybrid plasmonic microcavity due to the coupling between the surface plasmon polaritons (SPPs) and the dielectric mode is demonstrated with a high quality factor (>1000) and an ultrasmall mode volume (∼0.8 μm 3 ). This microcavity shows great potential in fundamental studies of nonlinear optics and cavity quantum electrodynamics (cQED) and applications in low-threshold plasmonic microlasers. (paper)

  10. Noncoding sequence classification based on wavelet transform analysis: part I

    Science.gov (United States)

    Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

    2017-09-01

    DNA sequences in human genome can be divided into the coding and noncoding ones. Coding sequences are those that are read during the transcription. The identification of coding sequences has been widely reported in literature due to its much-studied periodicity. Noncoding sequences represent the majority of the human genome. They play an important role in gene regulation and differentiation among the cells. However, noncoding sequences do not exhibit periodicities that correlate to their functions. The ENCODE (Encyclopedia of DNA elements) and Epigenomic Roadmap Project projects have cataloged the human noncoding sequences into specific functions. We study characteristics of noncoding sequences with wavelet analysis of genomic signals.

  11. Consed: a graphical editor for next-generation sequencing

    OpenAIRE

    Gordon, David; Green, Phil

    2013-01-01

    Summary: The rapid growth of DNA sequencing throughput in recent years implies that graphical interfaces for viewing and correcting errors must now handle large numbers of reads, efficiently pinpoint regions of interest and automate as many tasks as possible. We have adapted consed to reflect this. To allow full-feature editing of large datasets while keeping memory requirements low, we developed a viewer, bamScape, that reads billion-read BAM files, identifies and displays problem areas for ...

  12. Monitoring Progress toward Independent Silent Reading.

    Science.gov (United States)

    Franc, Lillian H.; Hildebrandt, Jeannette

    1984-01-01

    Concludes, among other things, that fluent oral reading is an important step toward reading for meaning and independent silent reading and that silent reading should be encouraged from the beginning of reading instruction. (FL)

  13. DeepSimulator: a deep simulator for Nanopore sequencing

    KAUST Repository

    Li, Yu; Han, Renmin; Bi, Chongwei; Li, Mo; Wang, Sheng; Gao, Xin

    2017-01-01

    or assembled contigs, we simulate the electrical current signals by a context-dependent deep learning model, followed by a base-calling procedure to yield simulated reads. This workflow mimics the sequencing procedure more naturally. The thorough experiments

  14. Factors Influencing Early Adolescents' Mathematics Achievement: High-Quality Teaching Rather than Relationships

    Science.gov (United States)

    Winheller, Sandra; Hattie, John A.; Brown, Gavin T. L.

    2013-01-01

    This study used data from the Assessment Tools for Teaching and Learning project, which involved data on the academic performance of more than 90,000 New Zealand students in six subjects (i.e. reading, writing and mathematics in two languages). Two sub-samples of this dataset were included for detailed re-analysis to test the general applicability…

  15. An improved multi-exposure approach for high quality holographic femtosecond laser patterning

    International Nuclear Information System (INIS)

    Zhang, Chenchu; Hu, Yanlei; Li, Jiawen; Lao, Zhaoxin; Ni, Jincheng; Chu, Jiaru; Huang, Wenhao; Wu, Dong

    2014-01-01

    High efficiency two photon polymerization through single exposure via spatial light modulator (SLM) has been used to decrease the fabrication time and rapidly realize various micro/nanostructures, but the surface quality remains a big problem due to the speckle noise of optical intensity distribution at the defocused plane. Here, a multi-exposure approach which used tens of computer generate holograms successively loaded on SLM is presented to significantly improve the optical uniformity without losing efficiency. By applying multi-exposure, we found that the uniformity at the defocused plane was increased from ∼0.02 to ∼0.6 according to our simulation. The fabricated two series of letters “HELLO” and “USTC” under single-and multi-exposure in our experiment also verified that the surface quality was greatly improved. Moreover, by this method, several kinds of beam splitters with high quality, e.g., 2 × 2, 5 × 5 Daman, and complex nonseperate 5 × 5, gratings were fabricated with both of high quality and short time (<1 min, 95% time-saving). This multi-exposure SLM-two-photon polymerization method showed the promising prospect in rapidly fabricating and integrating various binary optical devices and their systems

  16. High-quality GaN nanowires grown on Si and porous silicon by thermal evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Shekari, L., E-mail: lsg09_phy089@student.usm.my [Nano-Optoelectronics Research and Technology Laboratory, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Ramizy, A.; Omar, K.; Hassan, H. Abu; Hassan, Z. [Nano-Optoelectronics Research and Technology Laboratory, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer A new kind of substrate (porous silicon) was used. Black-Right-Pointing-Pointer Also this research introduces an easy and safe method to grow high quality GaN NWs. Black-Right-Pointing-Pointer This is a new growth process to decrease the cost, complexity of growth of GaN NWs. Black-Right-Pointing-Pointer It is a controllable method to synthesize GaN NWs by thermal evaporation. - Abstract: Nanowires (NWs) of GaN thin films were prepared on as-grown Si (1 1 1) and porous silicon (PS) substrates using thermal evaporation method. The film growth produced high-quality wurtzite GaN NWs. The size, morphology, and nanostructures of the crystals were investigated through scanning electron microscopy, high-resolution X-ray diffraction and photoluminescence spectroscopy. The NWs grown on porous silicon were thinner, longer and denser compared with those on as-grown Si. The energy band gap of the NWs grown on PS was larger than that of NWs on as-grown Si. This is due to the greater quantum confinement effects of the crystalline structure of the NWs grown on PS.

  17. Achieving graphical excellence: suggestions and methods for creating high-quality visual displays of experimental data.

    Science.gov (United States)

    Schriger, D L; Cooper, R J

    2001-01-01

    Graphics are an important means of communicating experimental data and results. There is evidence, however, that many of the graphics printed in scientific journals contain errors, redundancies, and lack clarity. Perhaps more important, many graphics fail to portray data at an appropriate level of detail, presenting summary statistics rather than underlying distributions. We seek to aid investigators in the production of high-quality graphics that do their investigations justice by providing the reader with optimum access to the relevant aspects of the data. The depiction of by-subject data, the signification of pairing when present, and the use of symbolic dimensionality (graphing different symbols to identify relevant subgroups) and small multiples (the presentation of an array of similar graphics each depicting one group of subjects) to portray stratification are stressed. Step-by-step instructions for the construction of high-quality graphics are offered. We hope that authors will incorporate these suggestions when developing graphics to accompany their manuscripts and that this process will lead to improvements in the graphical literacy of scientific journals. We also hope that journal editors will keep these principles in mind when refereeing manuscripts submitted for peer review.

  18. The perspective awareness model - Eliciting multiple perspectives to formulate high quality decisions

    International Nuclear Information System (INIS)

    Boucher, Laurel

    2013-01-01

    A great deal of attention is given to the importance of communication in environmental remediation and radioactive waste management. However, very little attention is given to eliciting multiple perspectives so as to formulate high quality decisions. Plans that are based on a limited number of perspectives tend to be narrowly focused whereas those that are based on a wide variety of perspectives tend to be comprehensive, higher quality, and more apt to be put into application. In addition, existing methods of dialogue have built-in limitations in that they typically draw from the predominant thinking patterns which focus in some areas but ignore others. This can result in clarity but a lack of comprehensiveness. This paper presents a Perspective Awareness Model which helps groups such as partnering teams, interagency teams, steering committees, and working groups elicit a wide net of perspectives and viewpoints. The paper begins by describing five factors that makes cooperation among such groups challenging. Next, a Perspective Awareness Model that makes it possible to manage these five factors is presented. The two primary components of this model --- the eight 'Thinking Directions' and the 'Shared Documentation' --- are described in detail. Several examples are given to illustrate how the Perspective Awareness Model can be used to elicit multiple perspectives to formulate high quality decisions in the area of environmental remediation and radioactive waste management. (authors)

  19. High-quality ZnO growth, doping, and polarization effect

    Science.gov (United States)

    Kun, Tang; Shulin, Gu; Jiandong, Ye; Shunming, Zhu; Rong, Zhang; Youdou, Zheng

    2016-03-01

    The authors have reported their recent progress in the research field of ZnO materials as well as the corresponding global advance. Recent results regarding (1) the development of high-quality epitaxy techniques, (2) the defect physics and the Te/N co-doping mechanism for p-type conduction, and (3) the design, realization, and properties of the ZnMgO/ZnO hetero-structures have been shown and discussed. A complete technology of the growth of high-quality ZnO epi-films and nano-crystals has been developed. The co-doping of N plus an iso-valent element to oxygen has been found to be the most hopeful path to overcome the notorious p-type hurdle. High mobility electrons have been observed in low-dimensional structures utilizing the polarization of ZnMgO and ZnO. Very different properties as well as new physics of the electrons in 2DEG and 3DES have been found as compared to the electrons in the bulk. Project supported by the National Natural Science Foundation of China (Nos. 61025020, 61274058, 61322403, 61504057, 61574075), the Natural Science Foundation of Jiangsu Province (Nos. BK2011437, BK20130013, BK20150585), the Priority Academic Program Development of Jiangsu Higher Education Institutions, and the Fundamental Research Funds for the Central Universities.

  20. Development of a biotechnological process for the production of high quality linen fibers.

    Science.gov (United States)

    Valladares Juárez, Ana Gabriela; Rost, Gernot; Heitmann, Uwe; Heger, Egon; Müller, Rudolf

    2011-10-01

    A novel biotechnological process for the production of high-quality flax fibers was developed. In this process, decorticated fibers from green flax were washed with 0.5% soda solution and treated with the pectinolytic strain Geobacillus thermoglucosidasius PB94A. Before drying the fibers, they were treated with the textile softener Adulcinol BUN. If the fibers contained contaminant shives, a bleaching step with hydrogen peroxide was performed before the softener treatment. In experiments where fibers were treated by the new process, and in which the bacterial solutions were reused seven times, the fiber quality was similar in all batches. The resolution of the treated fibers was 2.7 ± 0.4 and the fineness was 11.1 ± 1.1 dtex, while the starting material had a resolution of 7.3 and a fineness of 37 dtex. The new biotechnological treatment eliminates the weather-associated risks of the traditional fiber retting completely and produces consistently high-quality fibers that can be used to produce fine linen yarns.

  1. Different paths to high-quality care: three archetypes of top-performing practice sites.

    Science.gov (United States)

    Feifer, Chris; Nemeth, Lynne; Nietert, Paul J; Wessell, Andrea M; Jenkins, Ruth G; Roylance, Loraine; Ornstein, Steven M

    2007-01-01

    Primary care practices use different approaches in their quest for high-quality care. Previous work in the Practice Partner Research Network (PPRNet) found that improved outcomes are associated with strategies to prioritize performance, involve staff, redesign elements of the delivery system, make patients active partners in guideline adherence, and use tools embedded in the electronic medical record. The aim of this study was to examine variations in the adoption of improvements among sites achieving the best outcomes. This study used an observational case study design. A practice-level measure of adherence to clinical guidelines was used to identify the highest performing practices in a network of internal and family medicine practices participating in a national demonstration project. We analyzed qualitative and quantitative information derived from project documents, field notes, and evaluation questionnaires to develop and compare case studies. Nine cases are described. All use many of the same improvement strategies. Differences in the way improvements are organized define 3 distinct archetypes: the Technophiles, the Motivated Team, and the Care Enterprise. There is no single approach that explains the superior performance of high-performing practices, though each has adopted variations of PPRNet's improvement model. Practices will vary in their path to high-quality care. The archetypes could prove to be a useful guide to other practices selecting an overall quality improvement approach.

  2. Angle-resolved reflection spectroscopy of high-quality PMMA opal crystal

    Science.gov (United States)

    Nemtsev, Ivan V.; Tambasov, Igor A.; Ivanenko, Alexander A.; Zyryanov, Victor Ya.

    2018-02-01

    PMMA opal crystal was prepared by a simple hybrid method, which includes sedimentation, meniscus formation and evaporation. We investigated three surfaces of this crystal by angle-resolved reflective light spectroscopy and SEM study. The angle-resolved reflective measurements were carried out in the 400-1100 nm range. We have determined the high-quality ordered surface of the crystal region. Narrow particle size distribution of the surface has been revealed. The average particle diameter obtained with SEM was nearly 361 nm. The most interesting result was that reflectivity of the surface turned out up to 98% at normal light incidence. Using a fit of dependences of the maximum reflectivity wavelength from an angle based on the Bragg-Snell law, the wavelength of maximum 0° reflectivity, the particle diameter and the fill factor have been determined. For the best surface maximum reflectivity wavelength of a 0° angle was estimated to be 869 nm. The particle diameter and fill factor were calculated as 372 nm and 0.8715, respectively. The diameter obtained by fitting is in excellent agreement with the particle diameter obtained with SEM. The reflectivity maximum is assumed to increase significantly when increasing the fill factor. We believe that using our simple approach to manufacture PMMA opal crystals will significantly increase the fabrication of high-quality photonic crystal templates and thin films.

  3. Comparison of reduced sugar high quality chocolates sweetened with stevioside and crude stevia 'green' extract.

    Science.gov (United States)

    Torri, Luisa; Frati, Alessandra; Ninfali, Paolino; Mantegna, Stefano; Cravotto, Giancarlo; Morini, Gabriella

    2017-06-01

    The demand for zero and reduced-sugar food products containing cocoa is expanding continuously. The present study was designed to evaluate the feasibility of producing high-quality chocolate sweetened with a crude extract of Stevia rebaudiana (Bertoni) prepared by a green microwave-assisted water-steam extraction procedure. Seven approximately isosweet chocolate formulations were developed, mixing cocoa paste, sucrose, commercial stevioside, crude green extract and maltitol in different proportions. All samples were analyzed for the determination of polyphenol and flavonoid content, antioxidant activity, and sensory acceptability. The use of a crude stevia extract allowed low-sugar, high-quality chocolates to be obtained that were also acceptable by consumers and had a significant increased antioxidant activity. Moreover, consumers' segmentation revealed a cluster of consumers showing the same overall liking for the sample with 50% sucrose replaced by the stevia crude extract as that obtained with the commercial stevioside and the control sample (without sucrose replacement). The results provide information that can contribute to promoting the development of sweet food products, with advantages in terms of an improved nutritional value (reduced sugar content and increased antioxidant activity) and a reduced impact of the production process on the environment. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  4. Effect of osmotic dehydration and vacuum-frying parameters to produce high-quality mango chips.

    Science.gov (United States)

    Nunes, Yolanda; Moreira, Rosana G

    2009-09-01

    Mango (Mangifera indica L.) is a fruit rich in flavor and nutritional values, which is an excellent candidate for producing chips. The objective of this study was to develop high-quality mango chips using vacuum frying. Mango ("Tommy Atkins") slices were pretreated with different maltodextrin concentrations (40, 50, and 65, w/v), osmotic dehydration times (45, 60, and 70 min), and solution temperatures (22 and 40 degrees C). Pretreated slices were vacuum fried at 120, 130, and 138 degrees C and product quality attributes (oil content, texture, color, carotenoid content) determined. The effect of frying temperatures at optimum osmotic dehydration times (65 [w/v] at 40 degrees C) was assessed. All samples were acceptable (scores > 5) to consumer panelists. The best mango chips were those pretreated with 65 (w/v) concentration for 60 min and vacuum fried at 120 degrees C. Mango chips under atmospheric frying had less carotenoid retention (32%) than those under vacuum frying (up to 65%). These results may help further optimize vacuum-frying processing of high-quality fruit-based snacks.

  5. Fabrication of high-quality single-crystal Cu thin films using radio-frequency sputtering.

    Science.gov (United States)

    Lee, Seunghun; Kim, Ji Young; Lee, Tae-Woo; Kim, Won-Kyung; Kim, Bum-Su; Park, Ji Hun; Bae, Jong-Seong; Cho, Yong Chan; Kim, Jungdae; Oh, Min-Wook; Hwang, Cheol Seong; Jeong, Se-Young

    2014-08-29

    Copper (Cu) thin films have been widely used as electrodes and interconnection wires in integrated electronic circuits, and more recently as substrates for the synthesis of graphene. However, the ultra-high vacuum processes required for high-quality Cu film fabrication, such as molecular beam epitaxy (MBE), restricts mass production with low cost. In this work, we demonstrated high-quality Cu thin films using a single-crystal Cu target and radio-frequency (RF) sputtering technique; the resulting film quality was comparable to that produced using MBE, even under unfavorable conditions for pure Cu film growth. The Cu thin film was epitaxially grown on an Al2O3 (sapphire) (0001) substrate, and had high crystalline orientation along the (111) direction. Despite the 10(-3) Pa vacuum conditions, the resulting thin film was oxygen free due to the high chemical stability of the sputtered specimen from a single-crystal target; moreover, the deposited film had >5× higher adhesion force than that produced using a polycrystalline target. This fabrication method enabled Cu films to be obtained using a simple, manufacturing-friendly process on a large-area substrate, making our findings relevant for industrial applications.

  6. Catalytic pyrolysis of microalgae to high-quality liquid bio-fuels

    International Nuclear Information System (INIS)

    Babich, I.V.; Hulst, M. van der; Lefferts, L.; Moulijn, J.A.; O'Connor, P.; Seshan, K.

    2011-01-01

    The pyrolytic conversion of chlorella algae to liquid fuel precursor in presence of a catalyst (Na 2 CO 3 ) has been studied. Thermal decomposition studies of the algae samples were performed using TGA coupled with MS. Liquid oil samples were collected from pyrolysis experiments in a fixed-bed reactor and characterized for water content and heating value. The oil composition was analyzed by GC-MS. Pretreatment of chlorella with Na 2 CO 3 influences the primary conversion of chlorella by shifting the decomposition temperature to a lower value. In the presence of Na 2 CO 3 , gas yield increased and liquid yield decreased when compared with non-catalytic pyrolysis at the same temperatures. However, pyrolysis oil from catalytic runs carries higher heating value and lower acidity. Lower content of acids in the bio-oil, higher aromatics, combined with higher heating value show promise for production of high-quality bio-oil from algae via catalytic pyrolysis, resulting in energy recovery in bio-oil of 40%. -- Highlights: → The pyrolytic catalytic conversion of chlorella algae to liquid fuel precursor. → Na 2 CO 3 as a catalyst for the primary conversion of chlorella. → Pyrolysis oil from catalytic runs carries higher heating value and lower acidity. → High-quality bio-oil from algae via catalytic pyrolysis with energy recovery in bio-oil of 40%.

  7. An improved multi-exposure approach for high quality holographic femtosecond laser patterning

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Chenchu; Hu, Yanlei, E-mail: huyl@ustc.edu.cn, E-mail: jwl@ustc.edu.cn; Li, Jiawen, E-mail: huyl@ustc.edu.cn, E-mail: jwl@ustc.edu.cn; Lao, Zhaoxin; Ni, Jincheng; Chu, Jiaru; Huang, Wenhao; Wu, Dong [Department of Precision Machinery and Precision Instrumentation, University of Science and Technology of China, Hefei 230026 (China)

    2014-12-01

    High efficiency two photon polymerization through single exposure via spatial light modulator (SLM) has been used to decrease the fabrication time and rapidly realize various micro/nanostructures, but the surface quality remains a big problem due to the speckle noise of optical intensity distribution at the defocused plane. Here, a multi-exposure approach which used tens of computer generate holograms successively loaded on SLM is presented to significantly improve the optical uniformity without losing efficiency. By applying multi-exposure, we found that the uniformity at the defocused plane was increased from ∼0.02 to ∼0.6 according to our simulation. The fabricated two series of letters “HELLO” and “USTC” under single-and multi-exposure in our experiment also verified that the surface quality was greatly improved. Moreover, by this method, several kinds of beam splitters with high quality, e.g., 2 × 2, 5 × 5 Daman, and complex nonseperate 5 × 5, gratings were fabricated with both of high quality and short time (<1 min, 95% time-saving). This multi-exposure SLM-two-photon polymerization method showed the promising prospect in rapidly fabricating and integrating various binary optical devices and their systems.

  8. Frequency of chromosomal aneuploidy in high quality embryos from young couples using preimplantation genetic screening

    Directory of Open Access Journals (Sweden)

    Farzaneh Fesahat

    2017-09-01

    Full Text Available Background: Selection of the best embryo for transfer is very important in assisted reproductive technology (ART. Using morphological assessment for this selection demonstrated that the correlation between embryo morphology and implantation potential is relatively weak. On the other hand, aneuploidy is a key genetic factor that can influence human reproductive success in ART. Objective: The aim of this lab trial study was to evaluate the incidence of aneuploidies in five chromosomes in the morphologically high-quality embryos from young patients undergoing ART for sex selection. Materials and Methods: A total of 97 high quality embryos from 23 women at the age of 37or younger years that had previously undergone preimplantation genetic screening for sex selection were included in this study. After washing, the slides of blastomeres from embryos of patients were reanalyzed by fluorescence in-situ hybridization for chromosomes 13, 18 and 21. Results: There was a significant rate of aneuploidy determination in the embryos using preimplantation genetic screening for both sex and three evaluated autosomal chromosomes compared to preimplantation genetic screening for only sex chromosomes (62.9% vs. 24.7%, p=0.000. The most frequent detected chromosomal aneuploidy was trisomy or monosomy of chromosome 13. Conclusion: There is considerable numbers of chromosomal abnormalities in embryos generated in vitro which cause in vitro fertilization failure and it seems that morphological characterization of embryos is not a suitable method for choosing the embryos without these abnormalities

  9. The use of citation indicators to identify and support high-quality research in Poland.

    Science.gov (United States)

    Pilc, Andrzej

    2008-01-01

    In large, mostly English-speaking countries, where the "critical mass" of scientists working in different subfields of science is achieved, the peer review system may be sufficient to assess the quality of scientific research. However, in smaller countries, outside the Anglo-American circle, it is important to introduce different systems to identify research of high quality. In Poland, a parametric system for assessing the quality of research has been introduced. It was largely based on the impact factor of scientific journals. While the use of this indicator to assess research quality is highly questionable, the implementation of the system in the Polish reality is even worse. Therefore it is important to change and improve the system currently used by the Ministry of Science and Higher Education to both evaluate and, more importantly, finance science in Poland. Here, a system based on three factors, i.e. the impact factor, the institutional h-index, and the institutional number of citations, is proposed. The scientific quality of institutions in Division VI: Medical Sciences of the Polish Academy of Sciences were evaluated and the results were compared with the existing system. Moreover, a method to identify high-quality researchers and institutions at the national level based on the quantity of highly cited papers is shown. Additionally, an attempt to identify the highest quality Polish research on an international level is proposed. This is based on the number of individual citations, the individual h-index, the number of publications, and the priority of the discovery.

  10. Identify High-Quality Protein Structural Models by Enhanced K-Means.

    Science.gov (United States)

    Wu, Hongjie; Li, Haiou; Jiang, Min; Chen, Cheng; Lv, Qiang; Wu, Chuang

    2017-01-01

    Background. One critical issue in protein three-dimensional structure prediction using either ab initio or comparative modeling involves identification of high-quality protein structural models from generated decoys. Currently, clustering algorithms are widely used to identify near-native models; however, their performance is dependent upon different conformational decoys, and, for some algorithms, the accuracy declines when the decoy population increases. Results. Here, we proposed two enhanced K -means clustering algorithms capable of robustly identifying high-quality protein structural models. The first one employs the clustering algorithm SPICKER to determine the initial centroids for basic K -means clustering ( SK -means), whereas the other employs squared distance to optimize the initial centroids ( K -means++). Our results showed that SK -means and K -means++ were more robust as compared with SPICKER alone, detecting 33 (59%) and 42 (75%) of 56 targets, respectively, with template modeling scores better than or equal to those of SPICKER. Conclusions. We observed that the classic K -means algorithm showed a similar performance to that of SPICKER, which is a widely used algorithm for protein-structure identification. Both SK -means and K -means++ demonstrated substantial improvements relative to results from SPICKER and classical K -means.

  11. A Systematic Process for Developing High Quality SaaS Cloud Services

    Science.gov (United States)

    La, Hyun Jung; Kim, Soo Dong

    Software-as-a-Service (SaaS) is a type of cloud service which provides software functionality through Internet. Its benefits are well received in academia and industry. To fully utilize the benefits, there should be effective methodologies to support the development of SaaS services which provide high reusability and applicability. Conventional approaches such as object-oriented methods do not effectively support SaaS-specific engineering activities such as modeling common features, variability, and designing quality services. In this paper, we present a systematic process for developing high quality SaaS and highlight the essentiality of commonality and variability (C&V) modeling to maximize the reusability. We first define criteria for designing the process model and provide a theoretical foundation for SaaS; its meta-model and C&V model. We clarify the notion of commonality and variability in SaaS, and propose a SaaS development process which is accompanied with engineering instructions. Using the proposed process, SaaS services with high quality can be effectively developed.

  12. Key elements of high-quality practice organisation in primary health care: a systematic review.

    Science.gov (United States)

    Crossland, Lisa; Janamian, Tina; Jackson, Claire L

    2014-08-04

    To identify elements that are integral to high-quality practice and determine considerations relating to high-quality practice organisation in primary care. A narrative systematic review of published and grey literature. Electronic databases (PubMed, CINAHL, the Cochrane Library, Embase, Emerald Insight, PsycInfo, the Primary Health Care Research and Information Service website, Google Scholar) were searched in November 2013 and used to identify articles published in English from 2002 to 2013. Reference lists of included articles were searched for relevant unpublished articles and reports. Data were configured at the study level to allow for the inclusion of findings from a broad range of study types. Ten elements were most often included in the existing organisational assessment tools. A further three elements were identified from an inductive thematic analysis of descriptive articles, and were noted as important considerations in effective quality improvement in primary care settings. Although there are some validated tools available to primary care that identify and build quality, most are single-strategy approaches developed outside health care settings. There are currently no validated organisational improvement tools, designed specifically for primary health care, which combine all elements of practice improvement and whose use does not require extensive external facilitation.

  13. High-quality PVD graphene growth by fullerene decomposition on Cu foils.

    Science.gov (United States)

    Azpeitia, J; Otero-Irurueta, G; Palacio, I; Martinez, J I; Del Árbol, N Ruiz; Santoro, G; Gutiérrez, A; Aballe, L; Foerster, M; Kalbac, M; Vales, V; Mompeán, F J; García-Hernández, M; Martín-Gago, J A; Munuera, C; López, M F

    2017-08-01

    We present a new protocol to grow large-area, high-quality single-layer graphene on Cu foils at relatively low temperatures. We use C 60 molecules evaporated in ultra high vacuum conditions as carbon source. This clean environment results in a strong reduction of oxygen-containing groups as depicted by X-ray photoelectron spectroscopy (XPS). Unzipping of C 60 is thermally promoted by annealing the substrate at 800ºC during evaporation. The graphene layer extends over areas larger than the Cu crystallite size, although it is changing its orientation with respect to the surface in the wrinkles and grain boundaries, producing a modulated ring in the low energy electron diffraction (LEED) pattern. This protocol is a self-limiting process leading exclusively to one single graphene layer. Raman spectroscopy confirms the high quality of the grown graphene. This layer exhibits an unperturbed Dirac-cone with a clear n-doping of 0.77 eV, which is caused by the interaction between graphene and substrate. Density functional theory (DFT) calculations show that this interaction can be induced by a coupling between graphene and substrate at specific points of the structure leading to a local sp 3 configuration, which also contribute to the D-band in the Raman spectra.

  14. High quality TmIG films with perpendicular magnetic anisotropy grown by sputtering

    Science.gov (United States)

    Wu, C. N.; Tseng, C. C.; Yeh, S. L.; Lin, K. Y.; Cheng, C. K.; Fanchiang, Y. T.; Hong, M.; Kwo, J.

    Ferrimagnetic thulium iron garnet (TmIG) films grown on gadolinium gallium garnet substrates recently showed stress-induced perpendicular magnetic anisotropy (PMA), attractive for realization of quantum anomalous Hall effect (QAHE) of topological insulator (TI) films via the proximity effect. Moreover, current induced magnetization switching of Pt/TmIG has been demonstrated for the development of room temperature (RT) spintronic devices. In this work, high quality TmIG films (about 25nm) were grown by sputtering at RT followed by post-annealing. We showed that the film composition is tunable by varying the growth parameters. The XRD results showed excellent crystallinity of stoichiometric TmIG films with an out-of-plane lattice constant of 1.2322nm, a narrow film rocking curve of 0.017 degree, and a film roughness of 0.2 nm. The stoichiometric films exhibited PMA and the saturation magnetization at RT was 109 emu/cm3 (RT bulk value 110 emu/cm3) with a coercive field of 2.7 Oe. In contrast, TmIG films of Fe deficiency showed in-plane magnetic anisotropy. The high quality sputtered TmIG films will be applied to heterostructures with TIs or metals with strong spin-orbit coupling for novel spintronics.

  15. High-quality collection and disposal of WEEE: Environmental impacts and resultant issues.

    Science.gov (United States)

    Baxter, John; Lyng, Kari-Anne; Askham, Cecilia; Hanssen, Ole Jørgen

    2016-11-01

    Life cycle assessment of the collection, transport and recycling of various types of waste electrical and electronic equipment (WEEE) in Norway shows that small amounts of critical materials (refrigerants, precious/trace metals) are vital for the overall environmental accounts of the value chains. High-quality recycling ensures that materials and energy are effectively recovered from WEEE. This recovery means that responsible waste handling confers net environmental benefits in terms of global warming potential (GWP), for all types of WEEE analysed. For refrigeration equipment, the potential reduction of GWP by high-quality recycling is so large as to be of national significance. For all waste types, the magnitude of the net benefit from recovering materials and energy exceeds the negative consequences of irresponsible disposal. One outcome of this may be widespread misunderstanding of the need for recycling. Furthermore, framing public communication on recycling in terms of avoiding negative consequences, as is essentially universal, may not convey an appropriate message. The issue is particularly important where the consumer regards products as relatively disposable and environmentally benign, and/or where the "null option" of retaining the product at end-of-life is especially prevalent. The paper highlights the implications of all these issues for policy-makers, waste collectors and recyclers, and consumers. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. High-quality GaN epitaxially grown on Si substrate with serpentine channels

    Science.gov (United States)

    Wei, Tiantian; Zong, Hua; Jiang, Shengxiang; Yang, Yue; Liao, Hui; Xie, Yahong; Wang, Wenjie; Li, Junze; Tang, Jun; Hu, Xiaodong

    2018-06-01

    A novel serpentine-channeled mask was introduced to Si substrate for low-dislocation GaN epitaxial growth and the fully coalesced GaN film on the masked Si substrate was achieved for the first time. Compared with the epitaxial lateral overgrowth (ELOG) growth method, this innovative mask only requires one-step epitaxial growth of GaN which has only one high-dislocation region per mask opening. This new growth method can effectively reduce dislocation density, thus improving the quality of GaN significantly. High-quality GaN with low dislocation density ∼2.4 × 107 cm-2 was obtained, which accounted for about eighty percent of the GaN film in area. This innovative technique is promising for the growth of high-quality GaN templates and the subsequent fabrication of high-performance GaN-based devices like transistors, laser diodes (LDs), and light-emitting diodes (LEDs) on Si substrate.

  17. Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages.

    Science.gov (United States)

    Esplin, Ian N D; Berg, Jordan A; Sharma, Ruchira; Allen, Robert C; Arens, Daniel K; Ashcroft, Cody R; Bairett, Shannon R; Beatty, Nolan J; Bickmore, Madeline; Bloomfield, Travis J; Brady, T Scott; Bybee, Rachel N; Carter, John L; Choi, Minsey C; Duncan, Steven; Fajardo, Christopher P; Foy, Brayden B; Fuhriman, David A; Gibby, Paul D; Grossarth, Savannah E; Harbaugh, Kala; Harris, Natalie; Hilton, Jared A; Hurst, Emily; Hyde, Jonathan R; Ingersoll, Kayleigh; Jacobson, Caitlin M; James, Brady D; Jarvis, Todd M; Jaen-Anieves, Daniella; Jensen, Garrett L; Knabe, Bradley K; Kruger, Jared L; Merrill, Bryan D; Pape, Jenny A; Payne Anderson, Ashley M; Payne, David E; Peck, Malia D; Pollock, Samuel V; Putnam, Micah J; Ransom, Ethan K; Ririe, Devin B; Robinson, David M; Rogers, Spencer L; Russell, Kerri A; Schoenhals, Jonathan E; Shurtleff, Christopher A; Simister, Austin R; Smith, Hunter G; Stephenson, Michael B; Staley, Lyndsay A; Stettler, Jason M; Stratton, Mallorie L; Tateoka, Olivia B; Tatlow, P J; Taylor, Alexander S; Thompson, Suzanne E; Townsend, Michelle H; Thurgood, Trever L; Usher, Brittian K; Whitley, Kiara V; Ward, Andrew T; Ward, Megan E H; Webb, Charles J; Wienclaw, Trevor M; Williamson, Taryn L; Wells, Michael J; Wright, Cole K; Breakwell, Donald P; Hope, Sandra; Grose, Julianne H

    2017-11-16

    Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages. Copyright © 2017 Esplin et al.

  18. The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing

    Directory of Open Access Journals (Sweden)

    Fatemeh Maghuly

    2018-04-01

    handling of GBS data is more difficult and more challenging than the traditional TILLING strategy in mutated plants, since the Jatropha genome sequence is incomplete, which makes alignment and variant analysis of target sequence reads challenging to perform and interpret. Therefore, providing a complete Jatropha reference genome sequence with high quality should be a priority for any breeding program.

  19. The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype.

    Science.gov (United States)

    Sun, Fengming; Fan, Guangyi; Hu, Qiong; Zhou, Yongming; Guan, Mei; Tong, Chaobo; Li, Jiana; Du, Dezhi; Qi, Cunkou; Jiang, Liangcai; Liu, Weiqing; Huang, Shunmou; Chen, Wenbin; Yu, Jingyin; Mei, Desheng; Meng, Jinling; Zeng, Peng; Shi, Jiaqin; Liu, Kede; Wang, Xi; Wang, Xinfa; Long, Yan; Liang, Xinming; Hu, Zhiyong; Huang, Guodong; Dong, Caihua; Zhang, He; Li, Jun; Zhang, Yaolei; Li, Liangwei; Shi, Chengcheng; Wang, Jiahao; Lee, Simon Ming-Yuen; Guan, Chunyun; Xu, Xun; Liu, Shengyi; Liu, Xin; Chalhoub, Boulos; Hua, Wei; Wang, Hanzhong

    2017-11-01

    Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (A r ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with A r , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  20. Reading through Films

    Directory of Open Access Journals (Sweden)

    Madhavi Gayathri Raman

    2016-02-01

    Full Text Available This paper captures the design of a comprehensive curriculum incorporating the four skills based exclusively on the use of parallel audio-visual and written texts. We discuss the use of authentic materials to teach English to Indian undergraduates aged 18 to 20 years. Specifically, we talk about the use of parallel reading (screen-play and audio-visual texts (Shawshank Redemption, and Life is Beautiful, A Few Good Men and Lion King drawn from popular culture in the classroom as an effective teaching medium. Students were gradually introduced to films based on novels with extracts from the original texts (Schindler’s List, Beautiful Mind for extended reading and writing practice. We found that students began to pay more attention to aspects such as pronunciation, intonational variations, discourse markers and vocabulary items (phrasal verbs, synonyms, homophones, and puns. Keywords: Reading, films, popular culture, ESL classroom, language skills