Sample records for accurate short read

  1. Genometa--a fast and accurate classifier for short metagenomic shotgun reads.

    PubMed

    Davenport, Colin F; Neugebauer, Jens; Beckmann, Nils; Friedrich, Benedikt; Kameri, Burim; Kokott, Svea; Paetow, Malte; Siekmann, Björn; Wieding-Drewes, Matthias; Wienhöfer, Markus; Wolf, Stefan; Tümmler, Burkhard; Ahlers, Volker; Sprengel, Frauke

    2012-01-01

    Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer. The Genometa program, a step by step tutorial and Java source code are freely available from http://genomics1.mh-hannover.de/genometa/ and on http://code.google.com/p/genometa/. This program has been tested on Ubuntu Linux and Windows XP/7.

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

    PubMed Central

    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

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

    PubMed

    Wymant, Chris; Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; 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; Berkhout, Ben; Cornelissen, Marion; Kellam, Paul; Reiss, Peter; Fraser, Christophe

    2018-01-01

    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 successfully applied

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

    PubMed Central

    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

  5. Concurrent and Accurate Short Read Mapping on Multicore Processors.

    PubMed

    Martínez, Héctor; Tárraga, Joaquín; Medina, Ignacio; Barrachina, Sergio; Castillo, Maribel; Dopazo, Joaquín; Quintana-Ortí, Enrique S

    2015-01-01

    We introduce a parallel aligner with a work-flow organization for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, HPG Aligner SA (HPG Aligner SA is an open-source application. The software is available at http://www.opencb.org, exploits a suffix array to rapidly map a large fraction of the RNA fragments (reads), as well as leverages the accuracy of the Smith-Waterman algorithm to deal with conflictive reads. The aligner is enhanced with a careful strategy to detect splice junctions based on an adaptive division of RNA reads into small segments (or seeds), which are then mapped onto a number of candidate alignment locations, providing crucial information for the successful alignment of the complete reads. The experimental results on a platform with Intel multicore technology report the parallel performance of HPG Aligner SA, on RNA reads of 100-400 nucleotides, which excels in execution time/sensitivity to state-of-the-art aligners such as TopHat 2+Bowtie 2, MapSplice, and STAR.

  6. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

    PubMed

    Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).

  7. MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

    PubMed Central

    Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair; Stewart, Chip; Garrison, Erik P.; Marth, Gabor T.

    2014-01-01

    MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324

  8. Accurate indel prediction using paired-end short reads

    PubMed Central

    2013-01-01

    Background One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels). Current methods for indel calling assign scores to different types of evidence or counter-evidence for the presence of an indel, such as the number of split read alignments spanning the boundaries of a deletion candidate or reads that map within a putative deletion. Candidates with a score above a manually defined threshold are then predicted to be true indels. As a consequence, structural variants detected in this manner contain many false positives. Results Here, we present a machine learning based method which is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate. Our method identifies indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing. We demonstrate the usefulness of our method with paired-end Illumina reads from 80 genomes of the first phase of the 1001 Genomes Project ( http://www.1001genomes.org) in Arabidopsis thaliana. Conclusion In this work we show that indel classification is a necessary step to reduce the number of false positive candidates. We demonstrate that missing classification may lead to spurious biological interpretations. The software is available at: http://agkb.is.tuebingen.mpg.de/Forschung/SV-M/. PMID:23442375

  9. COPS: A Sensitive and Accurate Tool for Detecting Somatic Copy Number Alterations Using Short-Read Sequence Data from Paired Samples

    PubMed Central

    Krishnan, Neeraja M.; Gaur, Prakhar; Chaudhary, Rakshit; Rao, Arjun A.; Panda, Binay

    2012-01-01

    Copy Number Alterations (CNAs) such as deletions and duplications; compose a larger percentage of genetic variations than single nucleotide polymorphisms or other structural variations in cancer genomes that undergo major chromosomal re-arrangements. It is, therefore, imperative to identify cancer-specific somatic copy number alterations (SCNAs), with respect to matched normal tissue, in order to understand their association with the disease. We have devised an accurate, sensitive, and easy-to-use tool, COPS, COpy number using Paired Samples, for detecting SCNAs. We rigorously tested the performance of COPS using short sequence simulated reads at various sizes and coverage of SCNAs, read depths, read lengths and also with real tumor:normal paired samples. We found COPS to perform better in comparison to other known SCNA detection tools for all evaluated parameters, namely, sensitivity (detection of true positives), specificity (detection of false positives) and size accuracy. COPS performed well for sequencing reads of all lengths when used with most upstream read alignment tools. Additionally, by incorporating a downstream boundary segmentation detection tool, the accuracy of SCNA boundaries was further improved. Here, we report an accurate, sensitive and easy to use tool in detecting cancer-specific SCNAs using short-read sequence data. In addition to cancer, COPS can be used for any disease as long as sequence reads from both disease and normal samples from the same individual are available. An added boundary segmentation detection module makes COPS detected SCNA boundaries more specific for the samples studied. COPS is available at ftp://115.119.160.213 with username “cops” and password “cops”. PMID:23110103

  10. Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.

    PubMed

    Sharon, Itai; Kertesz, Michael; Hug, Laura A; Pushkarev, Dmitry; Blauwkamp, Timothy A; Castelle, Cindy J; Amirebrahimi, Mojgan; Thomas, Brian C; Burstein, David; Tringe, Susannah G; Williams, Kenneth H; Banfield, Jillian F

    2015-04-01

    Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads. © 2015 Sharon et al.; Published by Cold Spring Harbor Laboratory Press.

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

    PubMed

    Li, Ruiqiang; Zhu, Hongmei; Ruan, Jue; Qian, Wubin; Fang, Xiaodong; Shi, Zhongbin; Li, Yingrui; Li, Shengting; Shan, Gao; Kristiansen, Karsten; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

    2010-02-01

    Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large 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.

  12. Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly.

    PubMed

    Garcia, T I; Shen, Y; Catchen, J; Amores, A; Schartl, M; Postlethwait, J; Walter, R B

    2012-01-01

    For many researchers, next generation sequencing data holds the key to answering a category of questions previously unassailable. One of the important and challenging steps in achieving these goals is accurately assembling the massive quantity of short sequencing reads into full nucleic acid sequences. For research groups working with non-model or wild systems, short read assembly can pose a significant challenge due to the lack of pre-existing EST or genome reference libraries. While many publications describe the overall process of sequencing and assembly, few address the topic of how many and what types of reads are best for assembly. The goal of this project was use real world data to explore the effects of read quantity and short read quality scores on the resulting de novo assemblies. Using several samples of short reads of various sizes and qualities we produced many assemblies in an automated manner. We observe how the properties of read length, read quality, and read quantity affect the resulting assemblies and provide some general recommendations based on our real-world data set. Published by Elsevier Inc.

  13. libgapmis: extending short-read alignments

    PubMed Central

    2013-01-01

    Background 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. Results 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. Conclusions We present libgapmis, a library for extending

  14. Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies

    PubMed Central

    Sundquist, Andreas; Ronaghi, Mostafa; Tang, Haixu; Pevzner, Pavel; Batzoglou, Serafim

    2007-01-01

    While recently developed short-read sequencing technologies may dramatically reduce the sequencing cost and eventually achieve the $1000 goal for re-sequencing, their limitations prevent the de novo sequencing of eukaryotic genomes with the standard shotgun sequencing protocol. We present SHRAP (SHort Read Assembly Protocol), a sequencing protocol and assembly methodology that utilizes high-throughput short-read technologies. We describe a variation on hierarchical sequencing with two crucial differences: (1) we select a clone library from the genome randomly rather than as a tiling path and (2) we sample clones from the genome at high coverage and reads from the clones at low coverage. We assume that 200 bp read lengths with a 1% error rate and inexpensive random fragment cloning on whole mammalian genomes is feasible. Our assembly methodology is based on first ordering the clones and subsequently performing read assembly in three stages: (1) local assemblies of regions significantly smaller than a clone size, (2) clone-sized assemblies of the results of stage 1, and (3) chromosome-sized assemblies. By aggressively localizing the assembly problem during the first stage, our method succeeds in assembling short, unpaired reads sampled from repetitive genomes. We tested our assembler using simulated reads from D. melanogaster and human chromosomes 1, 11, and 21, and produced assemblies with large sets of contiguous sequence and a misassembly rate comparable to other draft assemblies. Tested on D. melanogaster and the entire human genome, our clone-ordering method produces accurate maps, thereby localizing fragment assembly and enabling the parallelization of the subsequent steps of our pipeline. Thus, we have demonstrated that truly inexpensive de novo sequencing of mammalian genomes will soon be possible with high-throughput, short-read technologies using our methodology. PMID:17534434

  15. A hybrid short read mapping accelerator

    PubMed Central

    2013-01-01

    Background The rapid growth of short read datasets poses a new challenge to the short read mapping problem in terms of sensitivity and execution speed. Existing methods often use a restrictive error model for computing the alignments to improve speed, whereas more flexible error models are generally too slow for large-scale applications. A number of short read mapping software tools have been proposed. However, designs based on hardware are relatively rare. Field programmable gate arrays (FPGAs) have been successfully used in a number of specific application areas, such as the DSP and communications domains due to their outstanding parallel data processing capabilities, making them a competitive platform to solve problems that are “inherently parallel”. Results We present a hybrid system for short read mapping utilizing both FPGA-based hardware and CPU-based software. The computation intensive alignment and the seed generation operations are mapped onto an FPGA. We present a computationally efficient, parallel block-wise alignment structure (Align Core) to approximate the conventional dynamic programming algorithm. The performance is compared to the multi-threaded CPU-based GASSST and BWA software implementations. For single-end alignment, our hybrid system achieves faster processing speed than GASSST (with a similar sensitivity) and BWA (with a higher sensitivity); for pair-end alignment, our design achieves a slightly worse sensitivity than that of BWA but has a higher processing speed. Conclusions This paper shows that our hybrid system can effectively accelerate the mapping of short reads to a reference genome based on the seed-and-extend approach. The performance comparison to the GASSST and BWA software implementations under different conditions shows that our hybrid design achieves a high degree of sensitivity and requires less overall execution time with only modest FPGA resource utilization. Our hybrid system design also shows that the performance

  16. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications.

    PubMed

    Fungtammasan, Arkarachai; Ananda, Guruprasad; Hile, Suzanne E; Su, Marcia Shu-Wei; Sun, Chen; Harris, Robert; Medvedev, Paul; Eckert, Kristin; Makova, Kateryna D

    2015-05-01

    Short tandem repeats (STRs) are implicated in dozens of human genetic diseases and contribute significantly to genome variation and instability. Yet profiling STRs from short-read sequencing data is challenging because of their high sequencing error rates. Here, we developed STR-FM, short tandem repeat profiling using flank-based mapping, a computational pipeline that can detect the full spectrum of STR alleles from short-read data, can adapt to emerging read-mapping algorithms, and can be applied to heterogeneous genetic samples (e.g., tumors, viruses, and genomes of organelles). We used STR-FM to study STR error rates and patterns in publicly available human and in-house generated ultradeep plasmid sequencing data sets. We discovered that STRs sequenced with a PCR-free protocol have up to ninefold fewer errors than those sequenced with a PCR-containing protocol. We constructed an error correction model for genotyping STRs that can distinguish heterozygous alleles containing STRs with consecutive repeat numbers. Applying our model and pipeline to Illumina sequencing data with 100-bp reads, we could confidently genotype several disease-related long trinucleotide STRs. Utilizing this pipeline, for the first time we determined the genome-wide STR germline mutation rate from a deeply sequenced human pedigree. Additionally, we built a tool that recommends minimal sequencing depth for accurate STR genotyping, depending on repeat length and sequencing read length. The required read depth increases with STR length and is lower for a PCR-free protocol. This suite of tools addresses the pressing challenges surrounding STR genotyping, and thus is of wide interest to researchers investigating disease-related STRs and STR evolution. © 2015 Fungtammasan et al.; Published by Cold Spring Harbor Laboratory Press.

  17. Short-read, high-throughput sequencing technology for STR genotyping

    PubMed Central

    Bornman, Daniel M.; Hester, Mark E.; Schuetter, Jared M.; Kasoji, Manjula D.; Minard-Smith, Angela; Barden, Curt A.; Nelson, Scott C.; Godbold, Gene D.; Baker, Christine H.; Yang, Boyu; Walther, Jacquelyn E.; Tornes, Ivan E.; Yan, Pearlly S.; Rodriguez, Benjamin; Bundschuh, Ralf; Dickens, Michael L.; Young, Brian A.; Faith, Seth A.

    2013-01-01

    DNA-based methods for human identification principally rely upon genotyping of short tandem repeat (STR) loci. Electrophoretic-based techniques for variable-length classification of STRs are universally utilized, but are limited in that they have relatively low throughput and do not yield nucleotide sequence information. High-throughput sequencing technology may provide a more powerful instrument for human identification, but is not currently validated for forensic casework. Here, we present a systematic method to perform high-throughput genotyping analysis of the Combined DNA Index System (CODIS) STR loci using short-read (150 bp) massively parallel sequencing technology. Open source reference alignment tools were optimized to evaluate PCR-amplified STR loci using a custom designed STR genome reference. Evaluation of this approach demonstrated that the 13 CODIS STR loci and amelogenin (AMEL) locus could be accurately called from individual and mixture samples. Sensitivity analysis showed that as few as 18,500 reads, aligned to an in silico referenced genome, were required to genotype an individual (>99% confidence) for the CODIS loci. The power of this technology was further demonstrated by identification of variant alleles containing single nucleotide polymorphisms (SNPs) and the development of quantitative measurements (reads) for resolving mixed samples. PMID:25621315

  18. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

    PubMed Central

    Liao, Yang; Smyth, Gordon K.; Shi, Wei

    2013-01-01

    Read alignment is an ongoing challenge for the analysis of data from sequencing technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and-vote, for mapping reads to a reference genome. The new strategy chooses the mapped genomic location for the read directly from the seeds. It uses a relatively large number of short seeds (called subreads) extracted from each read and allows all the seeds to vote on the optimal location. When the read length is <160 bp, overlapping subreads are used. More conventional alignment algorithms are then used to fill in detailed mismatch and indel information between the subreads that make up the winning voting block. The strategy is fast because the overall genomic location has already been chosen before the detailed alignment is done. It is sensitive because no individual subread is required to map exactly, nor are individual subreads constrained to map close by other subreads. It is accurate because the final location must be supported by several different subreads. The strategy extends easily to find exon junctions, by locating reads that contain sets of subreads mapping to different exons of the same gene. It scales up efficiently for longer reads. PMID:23558742

  19. Reading Abilities and Strategies: A Short Introduction

    ERIC Educational Resources Information Center

    Liu, Feng

    2010-01-01

    This paper gives a short analysis of reading abilities and reading strategies. Much research has been done to investigate the nature of reading, though it's had to exactly define reading abilities and strategies. Different kinds of readings are discussed in this paper and distinctions are made between first language reading and second or foreign…

  20. BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads.

    PubMed

    Hong, Lewis Z; Hong, Shuzhen; Wong, Han Teng; Aw, Pauline P K; Cheng, Yan; Wilm, Andreas; de Sessions, Paola F; Lim, Seng Gee; Nagarajan, Niranjan; Hibberd, Martin L; Quake, Stephen R; Burkholder, William F

    2014-01-01

    We present a method for obtaining long haplotypes, of over 3 kb in length, using a short-read sequencer, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq). BAsE-Seq relies on transposing a template-specific barcode onto random segments of the template molecule and assembling the barcoded short reads into complete haplotypes. We applied BAsE-Seq on mixed clones of hepatitis B virus and accurately identified haplotypes occurring at frequencies greater than or equal to 0.4%, with >99.9% specificity. Applying BAsE-Seq to a clinical sample, we obtained over 9,000 viral haplotypes, which provided an unprecedented view of hepatitis B virus population structure during chronic infection. BAsE-Seq is readily applicable for monitoring quasispecies evolution in viral diseases.

  1. Unlocking Short Read Sequencing for Metagenomics

    DOE PAGES

    Rodrigue, Sébastien; Materna, Arne C.; Timberlake, Sonia C.; ...

    2010-07-28

    We describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.

  2. Accurate Reading with Sequential Presentation of Single Letters

    PubMed Central

    Price, Nicholas S. C.; Edwards, Gemma L.

    2012-01-01

    Rapid, accurate reading is possible when isolated, single words from a sentence are sequentially presented at a fixed spatial location. We investigated if reading of words and sentences is possible when single letters are rapidly presented at the fovea under user-controlled or automatically controlled rates. When tested with complete sentences, trained participants achieved reading rates of over 60 wpm and accuracies of over 90% with the single letter reading (SLR) method and naive participants achieved average reading rates over 30 wpm with greater than 90% accuracy. Accuracy declined as individual letters were presented for shorter periods of time, even when the overall reading rate was maintained by increasing the duration of spaces between words. Words in the lexicon that occur more frequently were identified with higher accuracy and more quickly, demonstrating that trained participants have lexical access. In combination, our data strongly suggest that comprehension is possible and that SLR is a practicable form of reading under conditions in which normal scanning of text is not possible, or for scenarios with limited spatial and temporal resolution such as patients with low vision or prostheses. PMID:23115548

  3. SlideSort: all pairs similarity search for short reads

    PubMed Central

    Shimizu, Kana; Tsuda, Koji

    2011-01-01

    Motivation: Recent progress in DNA sequencing technologies calls for fast and accurate algorithms that can evaluate sequence similarity for a huge amount of short reads. Searching similar pairs from a string pool is a fundamental process of de novo genome assembly, genome-wide alignment and other important analyses. Results: In this study, we designed and implemented an exact algorithm SlideSort that finds all similar pairs from a string pool in terms of edit distance. Using an efficient pattern growth algorithm, SlideSort discovers chains of common k-mers to narrow down the search. Compared to existing methods based on single k-mers, our method is more effective in reducing the number of edit distance calculations. In comparison to backtracking methods such as BWA, our method is much faster in finding remote matches, scaling easily to tens of millions of sequences. Our software has an additional function of single link clustering, which is useful in summarizing short reads for further processing. Availability: Executable binary files and C++ libraries are available at http://www.cbrc.jp/~shimizu/slidesort/ for Linux and Windows. Contact: slidesort@m.aist.go.jp; shimizu-kana@aist.go.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21148542

  4. Auditory short-term memory activation during score reading.

    PubMed

    Simoens, Veerle L; Tervaniemi, Mari

    2013-01-01

    Performing music on the basis of reading a score requires reading ahead of what is being played in order to anticipate the necessary actions to produce the notes. Score reading thus not only involves the decoding of a visual score and the comparison to the auditory feedback, but also short-term storage of the musical information due to the delay of the auditory feedback during reading ahead. This study investigates the mechanisms of encoding of musical information in short-term memory during such a complicated procedure. There were three parts in this study. First, professional musicians participated in an electroencephalographic (EEG) experiment to study the slow wave potentials during a time interval of short-term memory storage in a situation that requires cross-modal translation and short-term storage of visual material to be compared with delayed auditory material, as it is the case in music score reading. This delayed visual-to-auditory matching task was compared with delayed visual-visual and auditory-auditory matching tasks in terms of EEG topography and voltage amplitudes. Second, an additional behavioural experiment was performed to determine which type of distractor would be the most interfering with the score reading-like task. Third, the self-reported strategies of the participants were also analyzed. All three parts of this study point towards the same conclusion according to which during music score reading, the musician most likely first translates the visual score into an auditory cue, probably starting around 700 or 1300 ms, ready for storage and delayed comparison with the auditory feedback.

  5. Auditory Short-Term Memory Activation during Score Reading

    PubMed Central

    Simoens, Veerle L.; Tervaniemi, Mari

    2013-01-01

    Performing music on the basis of reading a score requires reading ahead of what is being played in order to anticipate the necessary actions to produce the notes. Score reading thus not only involves the decoding of a visual score and the comparison to the auditory feedback, but also short-term storage of the musical information due to the delay of the auditory feedback during reading ahead. This study investigates the mechanisms of encoding of musical information in short-term memory during such a complicated procedure. There were three parts in this study. First, professional musicians participated in an electroencephalographic (EEG) experiment to study the slow wave potentials during a time interval of short-term memory storage in a situation that requires cross-modal translation and short-term storage of visual material to be compared with delayed auditory material, as it is the case in music score reading. This delayed visual-to-auditory matching task was compared with delayed visual-visual and auditory-auditory matching tasks in terms of EEG topography and voltage amplitudes. Second, an additional behavioural experiment was performed to determine which type of distractor would be the most interfering with the score reading-like task. Third, the self-reported strategies of the participants were also analyzed. All three parts of this study point towards the same conclusion according to which during music score reading, the musician most likely first translates the visual score into an auditory cue, probably starting around 700 or 1300 ms, ready for storage and delayed comparison with the auditory feedback. PMID:23326487

  6. Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

    PubMed Central

    Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B.; Chain, Patrick S. G.

    2015-01-01

    A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools. PMID:25765641

  7. Music Memory Following Short-term Practice and Its Relationship with the Sight-reading Abilities of Professional Pianists.

    PubMed

    Aiba, Eriko; Matsui, Toshie

    2016-01-01

    This study investigated the relationship between the ability to sight-read and the ability to memorize a score using a behavioral experiment. By measuring the amount of memorization following short-term practice, we examined whether better sight-readers not only estimate forthcoming notes but also memorize musical structures and phrases with more practice. Eleven pianists performed the music first by sight-reading. After a 20-minute practice, the participants were asked to perform from memory without any advance notice. The number of mistakes was used as an index of performance. There were no correlations in the numbers of mistakes between sight-reading and memory trial performance. Some pianists memorized almost the entire score, while others hardly remembered it despite demonstrating almost completely accurate performance just before memory trial performance. However, judging from the participants' responses to a questionnaire regarding their practice strategies, we found auditory memory was helpful for memorizing music following short-term practice.

  8. Music Memory Following Short-term Practice and Its Relationship with the Sight-reading Abilities of Professional Pianists

    PubMed Central

    Aiba, Eriko; Matsui, Toshie

    2016-01-01

    This study investigated the relationship between the ability to sight-read and the ability to memorize a score using a behavioral experiment. By measuring the amount of memorization following short-term practice, we examined whether better sight-readers not only estimate forthcoming notes but also memorize musical structures and phrases with more practice. Eleven pianists performed the music first by sight-reading. After a 20-minute practice, the participants were asked to perform from memory without any advance notice. The number of mistakes was used as an index of performance. There were no correlations in the numbers of mistakes between sight-reading and memory trial performance. Some pianists memorized almost the entire score, while others hardly remembered it despite demonstrating almost completely accurate performance just before memory trial performance. However, judging from the participants’ responses to a questionnaire regarding their practice strategies, we found auditory memory was helpful for memorizing music following short-term practice. PMID:27242576

  9. Repeat-aware modeling and correction of short read errors.

    PubMed

    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

  10. Indel variant analysis of short-read sequencing data with Scalpel

    PubMed Central

    Fang, Han; Bergmann, Ewa A; Arora, Kanika; Vacic, Vladimir; Zody, Michael C; Iossifov, Ivan; O’Rawe, Jason A; Wu, Yiyang; Barron, Laura T Jimenez; Rosenbaum, Julie; Ronemus, Michael; Lee, Yoon-ha; Wang, Zihua; Dikoglu, Esra; Jobanputra, Vaidehi; Lyon, Gholson J; Wigler, Michael; Schatz, Michael C; Narzisi, Giuseppe

    2017-01-01

    As the second most common type of variation in the human genome, insertions and deletions (indels) have been linked to many diseases, but the discovery of indels of more than a few bases in size from short-read sequencing data remains challenging. Scalpel (http://scalpel.sourceforge.net) is an open-source software for reliable indel detection based on the microassembly technique. It has been successfully used to discover mutations in novel candidate genes for autism, and it is extensively used in other large-scale studies of human diseases. This protocol gives an overview of the algorithm and describes how to use Scalpel to perform highly accurate indel calling from whole-genome and whole-exome sequencing data. We provide detailed instructions for an exemplary family-based de novo study, but we also characterize the other two supported modes of operation: single-sample and somatic analysis. Indel normalization, visualization and annotation of the mutations are also illustrated. Using a standard server, indel discovery and characterization in the exonic regions of the example sequencing data can be completed in ~5 h after read mapping. PMID:27854363

  11. Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data

    PubMed Central

    Ikegami, Tsutomu; Inatsugi, Toyohiro; Kojima, Isao; Umemura, Myco; Hagiwara, Hiroko; Machida, Masayuki; Asai, Kiyoshi

    2015-01-01

    A hybrid de novo assembly pipeline was constructed to utilize both MiSeq and SOLiD short read data in combination in the assembly. The short read data were converted to a standard format of the pipeline, and were supplied to the pipeline components such as ABySS and SOAPdenovo. The assembly pipeline proceeded through several stages, and either MiSeq paired-end data, SOLiD mate-paired data, or both of them could be specified as input data at each stage separately. The pipeline was examined on the filamentous fungus Aspergillus oryzae RIB40, by aligning the assembly results against the reference sequences. Using both the MiSeq and the SOLiD data in the hybrid assembly, the alignment length was improved by a factor of 3 to 8, compared with the assemblies using either one of the data types. The number of the reproduced gene cluster regions encoding secondary metabolite biosyntheses (SMB) was also improved by the hybrid assemblies. These results imply that the MiSeq data with long read length are essential to construct accurate nucleotide sequences, while the SOLiD mate-paired reads with long insertion length enhance long-range arrangements of the sequences. The pipeline was also tested on the actinomycete Streptomyces avermitilis MA-4680, whose gene is known to have high-GC content. Although the quality of the SOLiD reads was too low to perform any meaningful assemblies by themselves, the alignment length to the reference was improved by a factor of 2, compared with the assembly using only the MiSeq data. PMID:25919614

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

    PubMed

    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/.

  13. RAPSearch: a fast protein similarity search tool for short reads

    PubMed Central

    2011-01-01

    Background Next Generation Sequencing (NGS) is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets. Results We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames) we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2%) of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1%) that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST. Conclusions RAPSearch is implemented as open-source software and is accessible at http://omics.informatics.indiana.edu/mg/RAPSearch. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated. PMID:21575167

  14. TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing

    PubMed Central

    Sekizuka, Tsuyoshi; Yamashita, Akifumi; Murase, Yoshiro; Iwamoto, Tomotada; Mitarai, Satoshi; Kato, Seiya; Kuroda, Makoto

    2015-01-01

    Whole-genome sequencing (WGS) with next-generation DNA sequencing (NGS) is an increasingly accessible and affordable method for genotyping hundreds of Mycobacterium tuberculosis (Mtb) isolates, leading to more effective epidemiological studies involving single nucleotide variations (SNVs) in core genomic sequences based on molecular evolution. We developed an all-in-one web-based tool for genotyping Mtb, referred to as the Total Genotyping Solution for TB (TGS-TB), to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenies with core genomic SNVs, IS6110 insertion sites, and 43 customized loci for variable number tandem repeat (VNTR) through a user-friendly, simple click interface. This methodology is implemented with a KvarQ script to predict MTBC lineages/sublineages and potential antimicrobial resistance. Seven Mtb isolates (JP01 to JP07) in this study showing the same VNTR profile were accurately discriminated through median-joining network analysis using SNVs unique to those isolates. An additional IS6110 insertion was detected in one of those isolates as supportive genetic information in addition to core genomic SNVs. The results of in silico analyses using TGS-TB are consistent with those obtained using conventional molecular genotyping methods, suggesting that NGS short reads could provide multiple genotypes to discriminate multiple strains of Mtb, although longer NGS reads (≥300-mer) will be required for full genotyping on the TGS-TB web site. Most available short reads (~100-mer) can be utilized to discriminate the isolates based on the core genome phylogeny. TGS-TB provides a more accurate and discriminative strain typing for clinical and epidemiological investigations; NGS strain typing offers a total genotyping solution for Mtb outbreak and surveillance. TGS-TB web site: https://gph.niid.go.jp/tgs-tb/. PMID:26565975

  15. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads.

    PubMed

    Song, Li; Florea, Liliana

    2015-01-01

    Next-generation sequencing of cellular RNA (RNA-seq) is rapidly becoming the cornerstone of transcriptomic analysis. However, sequencing errors in the already short RNA-seq reads complicate bioinformatics analyses, in particular alignment and assembly. Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing. We developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read correctors, which use a global threshold to determine trusted k-mers, Rcorrector computes a local threshold at every position in a read. Rcorrector has an accuracy higher than or comparable to existing methods, including the only other method (SEECER) designed for RNA-seq reads, and is more time and memory efficient. With a 5 GB memory footprint for 100 million reads, it can be run on virtually any desktop or server. The software is available free of charge under the GNU General Public License from https://github.com/mourisl/Rcorrector/.

  16. ECHO: A reference-free short-read error correction algorithm

    PubMed Central

    Kao, Wei-Chun; Chan, Andrew H.; Song, Yun S.

    2011-01-01

    Developing accurate, scalable algorithms to improve data quality is an important computational challenge associated with recent advances in high-throughput sequencing technology. In this study, a novel error-correction algorithm, called ECHO, is introduced for correcting base-call errors in short-reads, without the need of a reference genome. Unlike most previous methods, ECHO does not require the user to specify parameters of which optimal values are typically unknown a priori. ECHO automatically sets the parameters in the assumed model and estimates error characteristics specific to each sequencing run, while maintaining a running time that is within the range of practical use. ECHO is based on a probabilistic model and is able to assign a quality score to each corrected base. Furthermore, it explicitly models heterozygosity in diploid genomes and provides a reference-free method for detecting bases that originated from heterozygous sites. On both real and simulated data, ECHO is able to improve the accuracy of previous error-correction methods by several folds to an order of magnitude, depending on the sequence coverage depth and the position in the read. The improvement is most pronounced toward the end of the read, where previous methods become noticeably less effective. Using a whole-genome yeast data set, it is demonstrated here that ECHO is capable of coping with nonuniform coverage. Also, it is shown that using ECHO to perform error correction as a preprocessing step considerably facilitates de novo assembly, particularly in the case of low-to-moderate sequence coverage depth. PMID:21482625

  17. Read clouds uncover variation in complex regions of the human genome

    PubMed Central

    Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E.; West, Robert; Sidow, Arend; Batzoglou, Serafim

    2015-01-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies. PMID:26286554

  18. Read clouds uncover variation in complex regions of the human genome.

    PubMed

    Bishara, Alex; Liu, Yuling; Weng, Ziming; Kashef-Haghighi, Dorna; Newburger, Daniel E; West, Robert; Sidow, Arend; Batzoglou, Serafim

    2015-10-01

    Although an increasing amount of human genetic variation is being identified and recorded, determining variants within repeated sequences of the human genome remains a challenge. Most population and genome-wide association studies have therefore been unable to consider variation in these regions. Core to the problem is the lack of a sequencing technology that produces reads with sufficient length and accuracy to enable unique mapping. Here, we present a novel methodology of using read clouds, obtained by accurate short-read sequencing of DNA derived from long fragment libraries, to confidently align short reads within repeat regions and enable accurate variant discovery. Our novel algorithm, Random Field Aligner (RFA), captures the relationships among the short reads governed by the long read process via a Markov Random Field. We utilized a modified version of the Illumina TruSeq synthetic long-read protocol, which yielded shallow-sequenced read clouds. We test RFA through extensive simulations and apply it to discover variants on the NA12878 human sample, for which shallow TruSeq read cloud sequencing data are available, and on an invasive breast carcinoma genome that we sequenced using the same method. We demonstrate that RFA facilitates accurate recovery of variation in 155 Mb of the human genome, including 94% of 67 Mb of segmental duplication sequence and 96% of 11 Mb of transcribed sequence, that are currently hidden from short-read technologies. © 2015 Bishara et al.; Published by Cold Spring Harbor Laboratory Press.

  19. X-MATE: a flexible system for mapping short read data

    PubMed Central

    Pearson, John V.; Cloonan, Nicole; Grimmond, Sean M.

    2011-01-01

    Summary: Accurate and complete mapping of short-read sequencing to a reference genome greatly enhances the discovery of biological results and improves statistical predictions. We recently presented RNA-MATE, a pipeline for the recursive mapping of RNA-Seq datasets. With the rapid increase in genome re-sequencing projects, progression of available mapping software and the evolution of file formats, we now present X-MATE, an updated version of RNA-MATE, capable of mapping both RNA-Seq and DNA datasets and with improved performance, output file formats, configuration files, and flexibility in core mapping software. Availability: Executables, source code, junction libraries, test data and results and the user manual are available from http://grimmond.imb.uq.edu.au/X-MATE/. Contact: n.cloonan@uq.edu.au; s.grimmond@uq.edu.au Supplementary information: Supplementary data are available at Bioinformatics Online. PMID:21216778

  20. ALLPATHS: Assembling Large Genomes with Short Illumina Reads

    ScienceCinema

    Gnerre, Sante

    2018-02-06

    Sante Gnerre from the Broad Institute speaks on the challenge of developing high quality assemblies of large genomes using short reads at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

  1. DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.

    PubMed

    Pandey, Ram Vinay; Schlötterer, Christian

    2013-01-01

    With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chapman, Jarrod A.; Ho, Isaac; Sunkara, Sirisha

    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 inmore » 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.« less

  3. DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

    PubMed Central

    Pandey, Ram Vinay; Schlötterer, Christian

    2013-01-01

    With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/ PMID:24009693

  4. Software for pre-processing Illumina next-generation sequencing short read sequences

    PubMed Central

    2014-01-01

    Background When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specific sequencing artifacts. These characteristics lower the quality of their downstream analyses, e.g. de novo and reference-based assembly, by introducing sequencing artifacts and errors that may contribute to incorrect interpretation of data. Although many tools have been developed for quality control and pre-processing of NGS data, none of them provide flexible and comprehensive trimming options in conjunction with parallel processing to expedite pre-processing of large NGS datasets. Methods We developed ngsShoRT (next-generation sequencing Short Reads Trimmer), a flexible and comprehensive open-source software package written in Perl that provides a set of algorithms commonly used for pre-processing NGS short read sequences. We compared the features and performance of ngsShoRT with existing tools: CutAdapt, NGS QC Toolkit and Trimmomatic. We also compared the effects of using pre-processed short read sequences generated by different algorithms on de novo and reference-based assembly for three different genomes: Caenorhabditis elegans, Saccharomyces cerevisiae S288c, and Escherichia coli O157 H7. Results Several combinations of ngsShoRT algorithms were tested on publicly available Illumina GA II, HiSeq 2000, and MiSeq eukaryotic and bacteria genomic short read sequences with the focus on removing sequencing artifacts and low-quality reads and/or bases. Our results show that across three organisms and three sequencing platforms, trimming improved the mean quality scores of trimmed sequences. Using trimmed sequences for de novo and reference-based assembly improved assembly quality as well as assembler performance. In general, ngsShoRT outperformed comparable trimming tools in terms of trimming speed and improvement of de novo and reference

  5. Do dual-route models accurately predict reading and spelling performance in individuals with acquired alexia and agraphia?

    PubMed

    Rapcsak, Steven Z; Henry, Maya L; Teague, Sommer L; Carnahan, Susan D; Beeson, Pélagie M

    2007-06-18

    Coltheart and co-workers [Castles, A., Bates, T. C., & Coltheart, M. (2006). John Marshall and the developmental dyslexias. Aphasiology, 20, 871-892; Coltheart, M., Rastle, K., Perry, C., Langdon, R., & Ziegler, J. (2001). DRC: A dual route cascaded model of visual word recognition and reading aloud. Psychological Review, 108, 204-256] have demonstrated that an equation derived from dual-route theory accurately predicts reading performance in young normal readers and in children with reading impairment due to developmental dyslexia or stroke. In this paper, we present evidence that the dual-route equation and a related multiple regression model also accurately predict both reading and spelling performance in adult neurological patients with acquired alexia and agraphia. These findings provide empirical support for dual-route theories of written language processing.

  6. Efficient Graph Based Assembly of Short-Read Sequences on Hybrid Core Architecture

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sczyrba, Alex; Pratap, Abhishek; Canon, Shane

    2011-03-22

    Advanced architectures can deliver dramatically increased throughput for genomics and proteomics applications, reducing time-to-completion in some cases from days to minutes. One such architecture, hybrid-core computing, marries a traditional x86 environment with a reconfigurable coprocessor, based on field programmable gate array (FPGA) technology. In addition to higher throughput, increased performance can fundamentally improve research quality by allowing more accurate, previously impractical approaches. We will discuss the approach used by Convey?s de Bruijn graph constructor for short-read, de-novo assembly. Bioinformatics applications that have random access patterns to large memory spaces, such as graph-based algorithms, experience memory performance limitations on cache-based x86more » servers. Convey?s highly parallel memory subsystem allows application-specific logic to simultaneously access 8192 individual words in memory, significantly increasing effective memory bandwidth over cache-based memory systems. Many algorithms, such as Velvet and other de Bruijn graph based, short-read, de-novo assemblers, can greatly benefit from this type of memory architecture. Furthermore, small data type operations (four nucleotides can be represented in two bits) make more efficient use of logic gates than the data types dictated by conventional programming models.JGI is comparing the performance of Convey?s graph constructor and Velvet on both synthetic and real data. We will present preliminary results on memory usage and run time metrics for various data sets with different sizes, from small microbial and fungal genomes to very large cow rumen metagenome. For genomes with references we will also present assembly quality comparisons between the two assemblers.« less

  7. Short-Read Sequencing for Genomic Analysis of the Brown Rot Fungus Fibroporia radiculosa

    Treesearch

    J. D. Tang; A. D. Perkins; T. S. Sonstegard; S. G. Schroeder; S. C. Burgess; S. V. Diehl

    2012-01-01

    The feasibility of short-read sequencing for genomic analysis was demonstrated for Fibroporia radiculosa, a copper-tolerant fungus that causes brown rot decay of wood. The effect of read quality on genomic assembly was assessed by filtering Illumina GAIIx reads from a single run of a paired-end library (75-nucleotide read length and 300-bp fragment...

  8. Working memory, short-term memory and reading proficiency in school-age children with cochlear implants.

    PubMed

    Bharadwaj, Sneha V; Maricle, Denise; Green, Laura; Allman, Tamby

    2015-10-01

    The objective of the study was to examine short-term memory and working memory through both visual and auditory tasks in school-age children with cochlear implants. The relationship between the performance on these cognitive skills and reading as well as language outcomes were examined in these children. Ten children between the ages of 7 and 11 years with early-onset bilateral severe-profound hearing loss participated in the study. Auditory and visual short-term memory, auditory and visual working memory subtests and verbal knowledge measures were assessed using the Woodcock Johnson III Tests of Cognitive Abilities, the Wechsler Intelligence Scale for Children-IV Integrated and the Kaufman Assessment Battery for Children II. Reading outcomes were assessed using the Woodcock Reading Mastery Test III. Performance on visual short-term memory and visual working memory measures in children with cochlear implants was within the average range when compared to the normative mean. However, auditory short-term memory and auditory working memory measures were below average when compared to the normative mean. Performance was also below average on all verbal knowledge measures. Regarding reading outcomes, children with cochlear implants scored below average for listening and passage comprehension tasks and these measures were positively correlated to visual short-term memory, visual working memory and auditory short-term memory. Performance on auditory working memory subtests was not related to reading or language outcomes. The children with cochlear implants in this study demonstrated better performance in visual (spatial) working memory and short-term memory skills than in auditory working memory and auditory short-term memory skills. Significant positive relationships were found between visual working memory and reading outcomes. The results of the study provide support for the idea that WM capacity is modality specific in children with hearing loss. Based on these

  9. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

    DOE PAGES

    Orellana, Luis H.; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

    2016-10-07

    Functional annotation of metagenomic and metatranscriptomic data sets relies on similarity searches based on e-value thresholds resulting in an unknown number of false positive and negative matches. To overcome these limitations, we introduce ROCker, aimed at identifying position-specific, most-discriminant thresholds in sliding windows along the sequence of a target protein, accounting for non-discriminative domains shared by unrelated proteins. ROCker employs the receiver operating characteristic (ROC) curve to minimize false discovery rate (FDR) and calculate the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-curated reference protein sequences and thus, differs from HMM profiles andmore » related methods. We showcase ROCker using ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes, mediating oxidation of ammonia and the reduction of the potent greenhouse gas, N 2O, to inert N 2, respectively. ROCker typically showed 60-fold lower FDR when compared to the common practice of using fixed e-values. Previously uncounted ‘atypical’ nosZ genes were found to be two times more abundant, on average, than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quantified against the highly-related particulate methane monooxygenase (pmoA). Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes.« less

  10. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Orellana, Luis H.; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

    Functional annotation of metagenomic and metatranscriptomic data sets relies on similarity searches based on e-value thresholds resulting in an unknown number of false positive and negative matches. To overcome these limitations, we introduce ROCker, aimed at identifying position-specific, most-discriminant thresholds in sliding windows along the sequence of a target protein, accounting for non-discriminative domains shared by unrelated proteins. ROCker employs the receiver operating characteristic (ROC) curve to minimize false discovery rate (FDR) and calculate the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-curated reference protein sequences and thus, differs from HMM profiles andmore » related methods. We showcase ROCker using ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes, mediating oxidation of ammonia and the reduction of the potent greenhouse gas, N 2O, to inert N 2, respectively. ROCker typically showed 60-fold lower FDR when compared to the common practice of using fixed e-values. Previously uncounted ‘atypical’ nosZ genes were found to be two times more abundant, on average, than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quantified against the highly-related particulate methane monooxygenase (pmoA). Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes.« less

  11. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

    PubMed Central

    2017-01-01

    Abstract Functional annotation of metagenomic and metatranscriptomic data sets relies on similarity searches based on e-value thresholds resulting in an unknown number of false positive and negative matches. To overcome these limitations, we introduce ROCker, aimed at identifying position-specific, most-discriminant thresholds in sliding windows along the sequence of a target protein, accounting for non-discriminative domains shared by unrelated proteins. ROCker employs the receiver operating characteristic (ROC) curve to minimize false discovery rate (FDR) and calculate the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-curated reference protein sequences and thus, differs from HMM profiles and related methods. We showcase ROCker using ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes, mediating oxidation of ammonia and the reduction of the potent greenhouse gas, N2O, to inert N2, respectively. ROCker typically showed 60-fold lower FDR when compared to the common practice of using fixed e-values. Previously uncounted ‘atypical’ nosZ genes were found to be two times more abundant, on average, than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quantified against the highly-related particulate methane monooxygenase (pmoA). Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes. PMID:28180325

  12. The Utility of Maze Accurate Response Rate in Assessing Reading Comprehension in Upper Elementary and Middle School Students

    ERIC Educational Resources Information Center

    McCane-Bowling, Sara J.; Strait, Andrea D.; Guess, Pamela E.; Wiedo, Jennifer R.; Muncie, Eric

    2014-01-01

    This study examined the predictive utility of five formative reading measures: words correct per minute, number of comprehension questions correct, reading comprehension rate, number of maze correct responses, and maze accurate response rate (MARR). Broad Reading cluster scores obtained via the Woodcock-Johnson III (WJ III) Tests of Achievement…

  13. L2 Reading Ability: Further Insight into the Short-Circuit Hypothesis.

    ERIC Educational Resources Information Center

    Taillefer, Gail F.

    1996-01-01

    Discusses the notion of a language proficiency threshold that short circuits the transfer of reading ability from the native language (L1) to a second language (L2). This study, in which cognitive complexity of tasks and students' L2 proficiency levels vary, focuses on university students in France reading preprofessional English texts. (39…

  14. Whole Genome Complete Resequencing of Bacillus subtilis Natto by Combining Long Reads with High-Quality Short Reads

    PubMed Central

    Kamada, Mayumi; Hase, Sumitaka; Sato, Kengo; Toyoda, Atsushi; Fujiyama, Asao; Sakakibara, Yasubumi

    2014-01-01

    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. PMID:25329997

  15. [Developmental changes in reading ability of Japanese elementary school children--analysis of 4 kana reading tasks].

    PubMed

    Kobayashi, Tomoka; Inagaki, Masumi; Gunji, Atsuko; Yatabe, Kiyomi; Kaga, Makiko; Goto, Takaaki; Koike, Toshihide; Wakamiya, Eiji; Koeda, Tatsuya

    2010-01-01

    Five hundred and twenty-eight Japanese elementary school children aged from 6 (Grade 1) to 12 (Grade 6) were tested for their abilities to read Hiragana characters, words, and short sentences. They were typically developing children whom the classroom teachers judged to have no problems with reading and writing in Japanese. Each child was asked to read four tasks which were written in Hiragana script: single mora reading task, four syllable non-word reading task, four syllable word reading task, and short sentence reading task. The total articulation time for reading and performance in terms of accuracy were measured for each task. Developmental changes in these variables were evaluated. The articulation time was significantly longer for the first graders, and it gradually shortened as they moved through to the upper grades in all tasks. The articulation time reached a plateau in the 4th grade for the four syllable word and short sentence reading tasks, while it did so for the single mora and four syllable non-word reading tasks in the 5th grade. The articulation times for the four syllable word and short sentence reading tasks correlated strongly. There were very few clear errors for all tasks, and the number of such errors significantly changed between the school grades only for the single mora and four syllable word reading tasks. It was noted that more than half of the children read the beginning portion of the word or phrase twice or more, in order to read it accurately, and developmental changes were also seen in this pattern of reading. This study revealed that the combination of these reading tasks may function as a screening test for reading disorders such as developmental dyslexia in children below the age of ten or eleven years old.

  16. Optimization of De Novo Short Read Assembly of Seabuckthorn (Hippophae rhamnoides L.) Transcriptome

    PubMed Central

    Ghangal, Rajesh; Chaudhary, Saurabh; Jain, Mukesh; Purty, Ram Singh; Chand Sharma, Prakash

    2013-01-01

    Seabuckthorn ( Hippophae rhamnoides L.) is known for its medicinal, nutritional and environmental importance since ancient times. However, very limited efforts have been made to characterize the genome and transcriptome of this wonder plant. Here, we report the use of next generation massive parallel sequencing technology (Illumina platform) and de novo assembly to gain a comprehensive view of the seabuckthorn transcriptome. We assembled 86,253,874 high quality short reads using six assembly tools. At our hand, assembly of non-redundant short reads following a two-step procedure was found to be the best considering various assembly quality parameters. Initially, ABySS tool was used following an additive k-mer approach. The assembled transcripts were subsequently subjected to TGICL suite. Finally, de novo short read assembly yielded 88,297 transcripts (> 100 bp), representing about 53 Mb of seabuckthorn transcriptome. The average length of transcripts was 610 bp, N50 length 1198 BP and 91% of the short reads uniquely mapped back to seabuckthorn transcriptome. A total of 41,340 (46.8%) transcripts showed significant similarity with sequences present in nr protein databases of NCBI (E-value < 1E-06). We also screened the assembled transcripts for the presence of transcription factors and simple sequence repeats. Our strategy involving the use of short read assembler (ABySS) followed by TGICL will be useful for the researchers working with a non-model organism’s transcriptome in terms of saving time and reducing complexity in data management. The seabuckthorn transcriptome data generated here provide a valuable resource for gene discovery and development of functional molecular markers. PMID:23991119

  17. Insights into Fluency Instruction: Short- and Long-Term Effects of Two Reading Programs

    ERIC Educational Resources Information Center

    Schwanenflugel, Paula J.; Kuhn, Melanie R.; Morris, Robin D.; Morrow, Lesley Mandel; Meisinger, Elizabeth B.; Woo, Deborah Gee; Quirk, Matthew; Sevcik, Rose

    2009-01-01

    The purpose of the study was to examine short- and long-term effects of two instructional approaches designed to improve the reading fluency of second-grade children: Fluency-Oriented Reading Instruction (or FORI; Stahl & Heubach, 2005) and a wide reading approach (Kuhn et al., 2006). By the end of second grade, children in the wide reading…

  18. [Ophthalmologic reading charts : Part 2: Current logarithmically scaled reading charts].

    PubMed

    Radner, W

    2016-12-01

    To analyze currently available reading charts regarding print size, logarithmic print size progression, and the background of test-item standardization. For the present study, the following logarithmically scaled reading charts were investigated using a measuring microscope (iNexis VMA 2520; Nikon, Tokyo): Eschenbach, Zeiss, OCULUS, MNREAD (Minnesota Near Reading Test), Colenbrander, and RADNER. Calculations were made according to EN-ISO 8596 and the International Research Council recommendations. Modern reading charts and cards exhibit a logarithmic progression of print sizes. The RADNER reading charts comprise four different cards with standardized test items (sentence optotypes), a well-defined stop criterion, accurate letter sizes, and a high print quality. Numbers and Landolt rings are also given in the booklet. The OCULUS cards have currently been reissued according to recent standards and also exhibit a high print quality. In addition to letters, numbers, Landolt rings, and examples taken from a timetable and the telephone book, sheet music is also offered. The Colenbrander cards use short sentences of 44 characters, including spaces, and exhibit inaccuracy at smaller letter sizes, as do the MNREAD cards. The MNREAD cards use sentences of 60 characters, including spaces, and have a high print quality. Modern reading charts show that international standards can be achieved with test items similar to optotypes, by using recent technology and developing new concepts of test-item standardization. Accurate print sizes, high print quality, and a logarithmic progression should become the minimum requirements for reading charts and reading cards in ophthalmology.

  19. Unified View of Backward Backtracking in Short Read Mapping

    NASA Astrophysics Data System (ADS)

    Mäkinen, Veli; Välimäki, Niko; Laaksonen, Antti; Katainen, Riku

    Mapping short DNA reads to the reference genome is the core task in the recent high-throughput technologies to study e.g. protein-DNA interactions (ChIP-seq) and alternative splicing (RNA-seq). Several tools for the task (bowtie, bwa, SOAP2, TopHat) have been developed that exploit Burrows-Wheeler transform and the backward backtracking technique on it, to map the reads to their best approximate occurrences in the genome. These tools use different tailored mechanisms for small error-levels to prune the search phase significantly. We propose a new pruning mechanism that can be seen a generalization of the tailored mechanisms used so far. It uses a novel idea of storing all cyclic rotations of fixed length substrings of the reference sequence with a compressed index that is able to exploit the repetitions created to level out the growth of the input set. For RNA-seq we propose a new method that combines dynamic programming with backtracking to map efficiently and correctly all reads that span two exons. Same mechanism can also be used for mapping mate-pair reads.

  20. The Effects of Reading Short Stories in Improving Foreign Language Writing Skills

    ERIC Educational Resources Information Center

    Bartan, Özgür Sen

    2017-01-01

    This study is an inquiry into the effects of reading short stories in improving foreign language writing skills through Read for Writing model, which is the adaptation of the approach called Talk for Writing (Corbett, 2013). It is a quasi-experimental 13-week field study which was implemented in a primary school. The purpose of this study is to…

  1. The contribution of short-term memory capacity to reading ability in adolescents with cochlear implants.

    PubMed

    Edwards, Lindsey; Aitkenhead, Lynne; Langdon, Dawn

    2016-11-01

    This study aimed to establish the relationship between short-term memory capacity and reading skills in adolescents with cochlear implants. A between-groups design compared a group of young people with cochlear implants with a group of hearing peers on measures of reading, and auditory and visual short-term memory capacity. The groups were matched for non-verbal IQ and age. The adolescents with cochlear implants were recruited from the Cochlear Implant Programme at a specialist children's hospital. The hearing participants were recruited from the same schools as those attended by the implanted adolescents. Participants were 18 cochlear implant users and 14 hearing controls, aged between 12 and 18 years. All used English as their main language and had no significant learning disability or neuro-developmental disorder. Short-term memory capacity was assessed in the auditory modality using Forward and Reverse Digit Span from the WISC IV UK, and visually using Forward and Reverse Memory from the Leiter-R. Individual word reading, reading comprehension and pseudoword decoding were assessed using the WIAT II UK. A series of ANOVAs revealed that the adolescents with cochlear implants had significantly poorer auditory short-term memory capacity and reading skills (on all measures) compared with their hearing peers. However, when Forward Digit Span was entered into the analyses as a covariate, none of the differences remained statistically significant. Deficits in immediate auditory memory persist into adolescence in deaf children with cochlear implants. Short-term auditory memory capacity is an important neurocognitive process in the development of reading skills after cochlear implantation in childhood that remains evident in later adolescence. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. A new automatic blood pressure kit auscultates for accurate reading with a smartphone

    PubMed Central

    Wu, Hongjun; Wang, Bingjian; Zhu, Xinpu; Chu, Guang; Zhang, Zhi

    2016-01-01

    Abstract The widely used oscillometric automated blood pressure (BP) monitor was continuously questioned on its accuracy. A novel BP kit named Accutension which adopted Korotkoff auscultation method was then devised. Accutension worked with a miniature microphone, a pressure sensor, and a smartphone. The BP values were automatically displayed on the smartphone screen through the installed App. Data recorded in the phone could be played back and reconfirmed after measurement. They could also be uploaded and saved to the iCloud. The accuracy and consistency of this novel electronic auscultatory sphygmomanometer was preliminarily verified here. Thirty-two subjects were included and 82 qualified readings were obtained. The mean differences ± SD for systolic and diastolic BP readings between Accutension and mercury sphygmomanometer were 0.87 ± 2.86 and −0.94 ± 2.93 mm Hg. Agreements between Accutension and mercury sphygmomanometer were highly significant for systolic (ICC = 0.993, 95% confidence interval (CI): 0.989–0.995) and diastolic (ICC = 0.987, 95% CI: 0.979–0.991). In conclusion, Accutension worked accurately based on our pilot study data. The difference was acceptable. ICC and Bland–Altman plot charts showed good agreements with manual measurements. Systolic readings of Accutension were slightly higher than those of manual measurement, while diastolic readings were slightly lower. One possible reason was that Accutension captured the first and the last korotkoff sound more sensitively than human ear during manual measurement and avoided sound missing, so that it might be more accurate than traditional mercury sphygmomanometer. By documenting and analyzing of variant tendency of BP values, Accutension helps management of hypertension and therefore contributes to the mobile heath service. PMID:27512876

  3. Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses

    PubMed Central

    Pightling, Arthur W.; Petronella, Nicholas; Pagotto, Franco

    2014-01-01

    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 should

  4. Assembling short reads from jumping libraries with large insert sizes.

    PubMed

    Vasilinetc, Irina; Prjibelski, Andrey D; Gurevich, Alexey; Korobeynikov, Anton; Pevzner, Pavel A

    2015-10-15

    Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies. We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads. Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades. ap@bioinf.spbau.ru 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.

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

    PubMed

    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.

  6. Automated Scoring of Short-Answer Reading Items: Implications for Constructs

    ERIC Educational Resources Information Center

    Carr, Nathan T.; Xi, Xiaoming

    2010-01-01

    This article examines how the use of automated scoring procedures for short-answer reading tasks can affect the constructs being assessed. In particular, it highlights ways in which the development of scoring algorithms intended to apply the criteria used by human raters can lead test developers to reexamine and even refine the constructs they…

  7. QSRA: a quality-value guided de novo short read assembler.

    PubMed

    Bryant, Douglas W; Wong, Weng-Keen; Mockler, Todd C

    2009-02-24

    New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers must be designed to account for this error while utilizing all available data. We have designed and implemented an assembler, Quality-value guided Short Read Assembler, created to take advantage of quality-value scores as a further method of dealing with error. Compared to previous published algorithms, our assembler shows significant improvements not only in speed but also in output quality. QSRA generally produced the highest genomic coverage, while being faster than VCAKE. QSRA is extremely competitive in its longest contig and N50/N80 contig lengths, producing results of similar quality to those of EDENA and VELVET. QSRA provides a step closer to the goal of de novo assembly of complex genomes, improving upon the original VCAKE algorithm by not only drastically reducing runtimes but also increasing the viability of the assembly algorithm through further error handling capabilities.

  8. Reading sentences of uniform word length: Evidence for the adaptation of the preferred saccade length during reading.

    PubMed

    Cutter, Michael G; Drieghe, Denis; Liversedge, Simon P

    2017-11-01

    In the current study, the effect of removing word length variability within sentences on spatial aspects of eye movements during reading was investigated. Participants read sentences that were uniform in terms of word length, with each sentence consisting entirely of three-, four-, or five-letter words, or a combination of these word lengths. Several interesting findings emerged. Adaptation of the preferred saccade length occurred for sentences with different uniform word length; participants would be more accurate at making short saccades while reading uniform sentences of three-letter words, while they would be more accurate at making long saccades while reading uniform sentences of five-letter words. Furthermore, word skipping was affected such that three- and four-letter words were more likely, and five-letter words less likely, to be directly fixated in uniform compared to non-uniform sentences. It is argued that saccadic targeting during reading is highly adaptable and flexible toward the characteristics of the text currently being read, as opposed to the idea implemented in most current models of eye movement control during reading that readers develop a preference for making saccades of a certain length across a lifetime of experience with a given language. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  9. CRISPR Detection From Short Reads Using Partial Overlap Graphs.

    PubMed

    Ben-Bassat, Ilan; Chor, Benny

    2016-06-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) are structured regions in bacterial and archaeal genomes, which are part of an adaptive immune system against phages. CRISPRs are important for many microbial studies and are playing an essential role in current gene editing techniques. As such, they attract substantial research interest. The exponential growth in the amount of bacterial sequence data in recent years enables the exploration of CRISPR loci in more and more species. Most of the automated tools that detect CRISPR loci rely on fully assembled genomes. However, many assemblers do not handle repetitive regions successfully. The first tool to work directly on raw sequence data is Crass, which requires reads that are long enough to contain two copies of the same repeat. We present a method to identify CRISPR repeats from raw sequence data of short reads. The algorithm is based on an observation differentiating CRISPR repeats from other types of repeats, and it involves a series of partial constructions of the overlap graph. This enables us to avoid many of the difficulties that assemblers face, as we merely aim to identify the repeats that belong to CRISPR loci. A preliminary implementation of the algorithm shows good results and detects CRISPR repeats in cases where other existing tools fail to do so.

  10. ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

    PubMed Central

    Morgan, Martin; Anders, Simon; Lawrence, Michael; Aboyoun, Patrick; Pagès, Hervé; Gentleman, Robert

    2009-01-01

    Summary: ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready access to additional facilities for advanced statistical analysis, data transformation, visualization and integration with diverse genomic resources. Availability and Implementation: This package is implemented in R and available at the Bioconductor web site; the package contains a ‘vignette’ outlining typical work flows. Contact: mtmorgan@fhcrc.org PMID:19654119

  11. Short Vowels versus Word Familiarity in the Reading Comprehension of Arab Readers: A Revisited Issue

    ERIC Educational Resources Information Center

    Seraye, Abdullah M.

    2016-01-01

    Arab readers, both beginning and advanced, are encouraged to read and accustomed to unvowelized and undiacriticized texts. Previous literature claimed that the presence of short vowels in the text would facilitate the reading comprehension of both beginning and advanced Arab readers. However, with a claimed strict controlling procedure, different…

  12. Parent Assisted Reading Using a Paired Reading Model

    ERIC Educational Resources Information Center

    Howell, Angela

    2006-01-01

    The purpose of this study was to determine the effectiveness of parent-assisted reading on reading comprehension. The study involved the use of the paired-reading model. The teacher made a short video of herself and each child implementing the model. Parents were given the video and a short list of instructions along with a reading log. The study…

  13. Working Memory, Short-Term Memory, and Reading Disabilities: A Selective Meta-Analysis of the Literature

    ERIC Educational Resources Information Center

    Swanson, H. Lee; Zheng, Xinhua; Jerman, Olga

    2009-01-01

    The purpose of the present study was to synthesize research that compares children with and without reading disabilities (RD) on measures of short-term memory (STM) and working memory (WM). Across a broad age, reading, and IQ range, 578 effect sizes (ESs) were computed, yielding a mean ES across studies of -0.89 (SD = 1.03). A total of 257 ESs…

  14. BBMerge – Accurate paired shotgun read merging via overlap

    DOE PAGES

    Bushnell, Brian; Rood, Jonathan; Singer, Esther

    2017-10-26

    Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more important. The accuracy of shotgun read merging is crucial as well, as errors introduced by incorrect merging percolate through to reduce the quality of downstream analysis. Thus, we designed a new tool to maximize accuracy and minimize processing time, allowing the use of read merging on larger datasets, and in analyses highlymore » sensitive to errors. We present BBMerge, a new merging tool for paired-end shotgun sequence data. We benchmark BBMerge by comparison with eight other widely used merging tools, assessing speed, accuracy and scalability. Evaluations of both synthetic and real-world datasets demonstrate that BBMerge produces merged shotgun reads with greater accuracy and at higher speed than any existing merging tool examined. BBMerge also provides the ability to merge non-overlapping shotgun read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy.« less

  15. BBMerge – Accurate paired shotgun read merging via overlap

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bushnell, Brian; Rood, Jonathan; Singer, Esther

    Merging paired-end shotgun reads generated on high-throughput sequencing platforms can substantially improve various subsequent bioinformatics processes, including genome assembly, binning, mapping, annotation, and clustering for taxonomic analysis. With the inexorable growth of sequence data volume and CPU core counts, the speed and scalability of read-processing tools becomes ever-more important. The accuracy of shotgun read merging is crucial as well, as errors introduced by incorrect merging percolate through to reduce the quality of downstream analysis. Thus, we designed a new tool to maximize accuracy and minimize processing time, allowing the use of read merging on larger datasets, and in analyses highlymore » sensitive to errors. We present BBMerge, a new merging tool for paired-end shotgun sequence data. We benchmark BBMerge by comparison with eight other widely used merging tools, assessing speed, accuracy and scalability. Evaluations of both synthetic and real-world datasets demonstrate that BBMerge produces merged shotgun reads with greater accuracy and at higher speed than any existing merging tool examined. BBMerge also provides the ability to merge non-overlapping shotgun read pairs by using k-mer frequency information to assemble the unsequenced gap between reads, achieving a significantly higher merge rate while maintaining or increasing accuracy.« less

  16. Reading without the left ventral occipito-temporal cortex

    PubMed Central

    Seghier, Mohamed L.; Neufeld, Nicholas H.; Zeidman, Peter; Leff, Alex P.; Mechelli, Andrea; Nagendran, Arjuna; Riddoch, Jane M.; Humphreys, Glyn W.; Price, Cathy J.

    2012-01-01

    The left ventral occipito-temporal cortex (LvOT) is thought to be essential for the rapid parallel letter processing that is required for skilled reading. Here we investigate whether rapid written word identification in skilled readers can be supported by neural pathways that do not involve LvOT. Hypotheses were derived from a stroke patient who acquired dyslexia following extensive LvOT damage. The patient followed a reading trajectory typical of that associated with pure alexia, re-gaining the ability to read aloud many words with declining performance as the length of words increased. Using functional MRI and dynamic causal modelling (DCM), we found that, when short (three to five letter) familiar words were read successfully, visual inputs to the patient’s occipital cortex were connected to left motor and premotor regions via activity in a central part of the left superior temporal sulcus (STS). The patient analysis therefore implied a left hemisphere “reading-without-LvOT” pathway that involved STS. We then investigated whether the same reading-without-LvOT pathway could be identified in 29 skilled readers and whether there was inter-subject variability in the degree to which skilled reading engaged LvOT. We found that functional connectivity in the reading-without-LvOT pathway was strongest in individuals who had the weakest functional connectivity in the LvOT pathway. This observation validates the findings of our patient’s case study. Our findings highlight the contribution of a left hemisphere reading pathway that is activated during the rapid identification of short familiar written words, particularly when LvOT is not involved. Preservation and use of this pathway may explain how patients are still able to read short words accurately when LvOT has been damaged. PMID:23017598

  17. Towards accurate localization: long- and short-term correlation filters for tracking

    NASA Astrophysics Data System (ADS)

    Li, Minglangjun; Tian, Chunna

    2018-04-01

    Visual tracking is a challenging problem, especially using a single model. In this paper, we propose a discriminative correlation filter (DCF) based tracking approach that exploits both the long-term and short-term information of the target, named LSTDCF, to improve the tracking performance. In addition to a long-term filter learned through the whole sequence, a short-term filter is trained using only features extracted from most recent frames. The long-term filter tends to capture more semantics of the target as more frames are used for training. However, since the target may undergo large appearance changes, features extracted around the target in non-recent frames prevent the long-term filter from locating the target in the current frame accurately. In contrast, the short-term filter learns more spatial details of the target from recent frames but gets over-fitting easily. Thus the short-term filter is less robust to handle cluttered background and prone to drift. We take the advantage of both filters and fuse their response maps to make the final estimation. We evaluate our approach on a widely-used benchmark with 100 image sequences and achieve state-of-the-art results.

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

    PubMed Central

    Mourier, Tobias; Mollerup, Sarah; Vinner, Lasse; Hansen, Thomas Arn; Kjartansdóttir, Kristín Rós; Guldberg Frøslev, Tobias; Snogdal Boutrup, Torsten; Nielsen, Lars Peter; Willerslev, Eske; Hansen, Anders J.

    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 are derived. First, we showed by simulations that we can robustly infer the level of genetic diversity from short sequence reads. Second, we find that the measures of nucleotide diversity inferred from our retroviral sequences significantly exceed the level observed from Human Immunodeficiency Virus infections, prompting us to conclude that the novel retroviruses are both of endogenous origin. Through further simulations, we rule out the possibility that the observed elevated levels of nucleotide diversity are the result of co-infection with two closely related exogenous retroviruses. PMID:26493184

  19. Reading Recovery--German Style. Short Report.

    ERIC Educational Resources Information Center

    Chambers, Gary N.

    1995-01-01

    This paper describes the Reading Recovery program implemented at a special needs school in Kiel, Germany. The program is intended to offer primary-grade pupils a second chance to obtain reading and writing skills. The highly structured reading program involves isolation of difficulties, work on word structure, learning consonant-vowel combinations…

  20. Reading(s).

    ERIC Educational Resources Information Center

    Summerfield, Geoffrey; Summerfield, Judith

    Developed for college English courses, this book presents selections of poetry, short stories, and commentary intended to invite different ways of reading and interpreting literature. An introduction provides an overview of the book's content, as well as a discussion of how to read. The first section, "Entering a Language," considers the…

  1. How genome complexity can explain the difficulty of aligning reads to genomes.

    PubMed

    Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

    2015-01-01

    Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

  2. Meeting the challenges of non-referenced genome assembly from short-read sequence data

    Treesearch

    M. Parks; A. Liston; R. Cronn

    2010-01-01

    Massively parallel sequencing technologies (MPST) offer unprecedented opportunities for novel sequencing projects. MPST, while offering tremendous sequencing capacity, are typically most effective in resequencing projects (as opposed to the sequencing of novel genomes) due to the fact that sequence is returned in relatively short reads. Nonetheless, there is great...

  3. A new automatic blood pressure kit auscultates for accurate reading with a smartphone: A diagnostic accuracy study.

    PubMed

    Wu, Hongjun; Wang, Bingjian; Zhu, Xinpu; Chu, Guang; Zhang, Zhi

    2016-08-01

    The widely used oscillometric automated blood pressure (BP) monitor was continuously questioned on its accuracy. A novel BP kit named Accutension which adopted Korotkoff auscultation method was then devised. Accutension worked with a miniature microphone, a pressure sensor, and a smartphone. The BP values were automatically displayed on the smartphone screen through the installed App. Data recorded in the phone could be played back and reconfirmed after measurement. They could also be uploaded and saved to the iCloud. The accuracy and consistency of this novel electronic auscultatory sphygmomanometer was preliminarily verified here. Thirty-two subjects were included and 82 qualified readings were obtained. The mean differences ± SD for systolic and diastolic BP readings between Accutension and mercury sphygmomanometer were 0.87 ± 2.86 and -0.94 ± 2.93 mm Hg. Agreements between Accutension and mercury sphygmomanometer were highly significant for systolic (ICC = 0.993, 95% confidence interval (CI): 0.989-0.995) and diastolic (ICC = 0.987, 95% CI: 0.979-0.991). In conclusion, Accutension worked accurately based on our pilot study data. The difference was acceptable. ICC and Bland-Altman plot charts showed good agreements with manual measurements. Systolic readings of Accutension were slightly higher than those of manual measurement, while diastolic readings were slightly lower. One possible reason was that Accutension captured the first and the last korotkoff sound more sensitively than human ear during manual measurement and avoided sound missing, so that it might be more accurate than traditional mercury sphygmomanometer. By documenting and analyzing of variant tendency of BP values, Accutension helps management of hypertension and therefore contributes to the mobile heath service.

  4. Orthographic Structure and Reading Experience Affect the Transfer from Iconic to Short Term Memory

    ERIC Educational Resources Information Center

    Lefton, Lester A.; Spragins, Anne B.

    1974-01-01

    The basic hypothesis of these experiments was that the processing strategy for the transfer of alphabetic material from iconic storage to short-term memory involves a sequential left-to-right factor that develops with increases in experience with reading. (Author)

  5. What Oral Text Reading Fluency Can Reveal about Reading Comprehension

    ERIC Educational Resources Information Center

    Veenendaal, Nathalie J.; Groen, Margriet A.; Verhoeven, Ludo

    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 to reading comprehension outcomes in addition to…

  6. An Investigation of the Effects of Pre-Reading Guides on the Comprehension of Short Stories by Ninth Grade Students.

    ERIC Educational Resources Information Center

    Quick, Charles David

    The purpose of this study was to determine if the use of pre-reading guides would effect better comprehension in the reading of short stories by ninth grade public school students. Four pre-reading guide sheets were prepared and validated for use in this study for each of the following stories: "The Interlopers" by Saki, "The Necklace" by…

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

    PubMed

    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.

  8. The Contribution of Short-Term Memory for Serial Order to Early Reading Acquisition: Evidence from a Longitudinal Study

    ERIC Educational Resources Information Center

    Perez, Trecy Martinez; Majerus, Steve; Poncelet, Martine

    2012-01-01

    Early reading acquisition skills have been linked to verbal short-term memory (STM) capacity. However, the nature of this relationship remains controversial because verbal STM, like reading acquisition, depends on the complexity of underlying phonological processing skills. This longitudinal study addressed the relation between STM and reading…

  9. Speech production in children with Down's syndrome: The effects of reading, naming and imitation.

    PubMed

    Knight, Rachael-Anne; Kurtz, Scilla; Georgiadou, Ioanna

    2015-01-01

    People with DS are known to have difficulties with expressive language, and often have difficulties with intelligibility. They often have stronger visual than verbal short-term memory skills and, therefore, reading has often been suggested as an intervention for speech and language in this population. However, there is as yet no firm evidence that reading can improve speech outcomes. This study aimed to compare reading, picture naming and repetition for the same 10 words, to identify if the speech of eight children with DS (aged 11-14 years) was more accurate, consistent and intelligible when reading. Results show that children were slightly, yet significantly, more accurate and intelligible when they read words compared with when they produced those words in naming or imitation conditions although the reduction in inconsistency was non-significant. The results of this small-scale study provide tentative support for previous claims about the benefits of reading for children with DS. The mechanisms behind a facilitatory effect of reading are considered, and directions are identified for future research.

  10. HCV Genotyping from NGS Short Reads and Its Application in Genotype Detection from HCV Mixed Infected Plasma

    PubMed Central

    Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y. M.; Klappenbach, Joel A.; Marton, Matthew J.

    2015-01-01

    Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection. PMID:25830316

  11. Development and transferability of black and red raspberry microsatellite markers from short-read sequences

    USDA-ARS?s Scientific Manuscript database

    The advent of next-generation sequencing technologies has been a boon to the cost-effective development of molecular markers, particularly in non-model species. Here, we demonstrate the efficiency of microsatellite or simple sequence repeat (SSR) marker development from short-read sequences using th...

  12. Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity

    PubMed Central

    Hurst, Gregory D.D.

    2017-01-01

    High throughput (or ‘next generation’) sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and ‘contaminating’ material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome. Here, we aimed to assess if these ‘contaminations’ provide information with regard to biologically important microorganisms associated with the individual. To achieve this, we examined whether the short read data from Apis retrieved elements of its well established microbiome. To this end, we screened almost 1,000 short read libraries of honey bee (Apis sp.) DNA sequencing project for the presence of microbial sequences, and find sequences from known honey bee microbial associates in at least 11% of them. Further to this, we screened ∼500 Apis RNA sequencing libraries for evidence of viral infections, which were found to be present in about half of them. We then used the data to reconstruct draft genomes of three Apis associated bacteria, as well as several viral strains de novo. We conclude that ‘contamination’ in short read sequencing libraries can provide useful genomic information on microbial taxa known to be associated with the target organisms, and may even lead to the discovery of novel associations. Finally, we demonstrate that RNAseq samples from experiments commonly carry uneven viral loads across libraries. We note variation in viral presence and load may be a confounding feature of differential gene expression analyses, and as such it should be incorporated as a random factor in analyses. PMID:28717593

  13. Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.

    PubMed

    Gerth, Michael; Hurst, Gregory D D

    2017-01-01

    High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome. Here, we aimed to assess if these 'contaminations' provide information with regard to biologically important microorganisms associated with the individual. To achieve this, we examined whether the short read data from Apis retrieved elements of its well established microbiome. To this end, we screened almost 1,000 short read libraries of honey bee ( Apis sp.) DNA sequencing project for the presence of microbial sequences, and find sequences from known honey bee microbial associates in at least 11% of them. Further to this, we screened ∼500 Apis RNA sequencing libraries for evidence of viral infections, which were found to be present in about half of them. We then used the data to reconstruct draft genomes of three Apis associated bacteria, as well as several viral strains de novo . We conclude that 'contamination' in short read sequencing libraries can provide useful genomic information on microbial taxa known to be associated with the target organisms, and may even lead to the discovery of novel associations. Finally, we demonstrate that RNAseq samples from experiments commonly carry uneven viral loads across libraries. We note variation in viral presence and load may be a confounding feature of differential gene expression analyses, and as such it should be incorporated as a random factor in analyses.

  14. Psychomotor Ability and Short-term Memory, and Reading and Mathematics Achievement in Children.

    PubMed

    Murrihy, Cherée; Bailey, Maria; Roodenburg, John

    2017-08-01

    The aim of our study was to examine whether the findings from previous research, indicating the role of short-term memory as a mediator of the relationship between motor coordination and academic achievement in adolescents, is also evident in a younger child population. The study utilized a quantative cross-sectional design involving 133 children aged 8-12. The McCarron Assessment of Neuromuscular Development (MAND) provided four indicators of psychomotor ability (Finger Nose, Walking, Balancing, and Jumping). The Woodcock-Johnson Cognitive battery and the Automated Working Memory Assessment (AWMA) provided two measures of short-term memory (Numbers Reversed and Digit Recall) and the WJIII Achievement battery provided two measures of reading achievement (Letter-word Identification and Passage Comprehension) and two measures of mathematics achievement (Applied Problems and Calculation). Structural equation modeling was used, controlling for age, processing speed, crystallized, and fluid intelligence where appropriate. The results found support for the hypothesis that short-term memory fully mediates the relationship between psychomotor ability and reading and mathematics achievement. These findings indicate the significant affect of psychomotor ability on learning outcomes and consequently the need to assess these in considering learning difficulties, and as such these findings also advance understanding of developmental neural mechanisms underpinning the relationships. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

    PubMed Central

    Wright, Imogen A.; Travers, Simon A.

    2014-01-01

    The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

  16. Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231.

    PubMed

    Baptista, Rodrigo P; Reis-Cunha, Joao Luis; DeBarry, Jeremy D; Chiari, Egler; Kissinger, Jessica C; Bartholomeu, Daniella C; Macedo, Andrea M

    2018-02-14

    Next-generation sequencing (NGS) methods are low-cost high-throughput technologies that produce thousands to millions of sequence reads. Despite the high number of raw sequence reads, their short length, relative to Sanger, PacBio or Nanopore reads, complicates the assembly of genomic repeats. Many genome tools are available, but the assembly of highly repetitive genome sequences using only NGS short reads remains challenging. Genome assembly of organisms responsible for important neglected diseases such as Trypanosoma cruzi, the aetiological agent of Chagas disease, is known to be challenging because of their repetitive nature. Only three of six recognized discrete typing units (DTUs) of the parasite have their draft genomes published and therefore genome evolution analyses in the taxon are limited. In this study, we developed a computational workflow to assemble highly repetitive genomes via a combination of de novo and reference-based assembly strategies to better overcome the intrinsic limitations of each, based on Illumina reads. The highly repetitive genome of the human-infecting parasite T. cruzi 231 strain was used as a test subject. The combined-assembly approach shown in this study benefits from the reference-based assembly ability to resolve highly repetitive sequences and from the de novo capacity to assemble genome-specific regions, improving the quality of the assembly. The acceptable confidence obtained by analyzing our results showed that our combined approach is an attractive option to assemble highly repetitive genomes with NGS short reads. Phylogenomic analysis including the 231 strain, the first representative of DTU III whose genome was sequenced, was also performed and provides new insights into T. cruzi genome evolution.

  17. Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score.

    PubMed

    Lee, Hayan; Schatz, Michael C

    2012-08-15

    Genome resequencing and short read mapping are two of the primary tools of genomics and are used for many important applications. The current state-of-the-art in mapping uses the quality values and mapping quality scores to evaluate the reliability of the mapping. These attributes, however, are assigned to individual reads and do not directly measure the problematic repeats across the genome. Here, we present the Genome Mappability Score (GMS) as a novel measure of the complexity of resequencing a genome. The GMS is a weighted probability that any read could be unambiguously mapped to a given position and thus measures the overall composition of the genome itself. We have developed the Genome Mappability Analyzer to compute the GMS of every position in a genome. It leverages the parallelism of cloud computing to analyze large genomes, and enabled us to identify the 5-14% of the human, mouse, fly and yeast genomes that are difficult to analyze with short reads. We examined the accuracy of the widely used BWA/SAMtools polymorphism discovery pipeline in the context of the GMS, and found discovery errors are dominated by false negatives, especially in regions with poor GMS. These errors are fundamental to the mapping process and cannot be overcome by increasing coverage. As such, the GMS should be considered in every resequencing project to pinpoint the 'dark matter' of the genome, including of known clinically relevant variations in these regions. The source code and profiles of several model organisms are available at http://gma-bio.sourceforge.net

  18. Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.

    PubMed

    Cerdeira, Louise Teixeira; Carneiro, Adriana Ribeiro; Ramos, Rommel Thiago Jucá; de Almeida, Sintia Silva; D'Afonseca, Vivian; Schneider, Maria Paula Cruz; Baumbach, Jan; Tauch, Andreas; McCulloch, John Anthony; Azevedo, Vasco Ariston Carvalho; Silva, Artur

    2011-08-01

    Due to the advent of the so-called Next-Generation Sequencing (NGS) technologies the amount of monetary and temporal resources for whole-genome sequencing has been reduced by several orders of magnitude. Sequence reads can be assembled either by anchoring them directly onto an available reference genome (classical reference assembly), or can be concatenated by overlap (de novo assembly). The latter strategy is preferable because it tends to maintain the architecture of the genome sequence the however, depending on the NGS platform used, the shortness of read lengths cause tremendous problems the in the subsequent genome assembly phase, impeding closing of the entire genome sequence. To address the problem, we developed a multi-pronged hybrid de novo strategy combining De Bruijn graph and Overlap-Layout-Consensus methods, which was used to assemble from short reads the entire genome of Corynebacterium pseudotuberculosis strain I19, a bacterium with immense importance in veterinary medicine that causes Caseous Lymphadenitis in ruminants, principally ovines and caprines. Briefly, contigs were assembled de novo from the short reads and were only oriented using a reference genome by anchoring. Remaining gaps were closed using iterative anchoring of short reads by craning to gap flanks. Finally, we compare the genome sequence assembled using our hybrid strategy to a classical reference assembly using the same data as input and show that with the availability of a reference genome, it pays off to use the hybrid de novo strategy, rather than a classical reference assembly, because more genome sequences are preserved using the former. Copyright © 2011 Elsevier B.V. All rights reserved.

  19. The Relative Predictive Contribution and Causal Role of Phoneme Awareness, Rhyme Awareness, and Verbal Short-Term Memory in Reading Skills: A Review

    ERIC Educational Resources Information Center

    Melby-Lervag, Monica

    2012-01-01

    The acknowledgement that educational achievement is highly dependent on successful reading development has led to extensive research on its underlying factors. A strong argument has been made for a causal relationship between reading and phoneme awareness; similarly, causal relations have been suggested for reading with short-term memory and rhyme…

  20. The Role of Morphology and Short Vowelization in Reading Arabic among Normal and Dyslexic Readers in Grades 3, 6, 9, and 12

    ERIC Educational Resources Information Center

    Abu-Rabia, Salim

    2007-01-01

    This study was an investigation of several Arabic reading measures among dyslexics and normal Arabic readers across different ages (grades 3, 6, 9, and 12): the role of morphology, short vowelization (phonological and syntactic skills), spelling, reading isolated words, and reading comprehension. The results of the one-way ANOVAs indicated clear…

  1. Unpacking Direct and Indirect Relationships of Short-Term Memory to Word Reading: Evidence From Korean-Speaking Children.

    PubMed

    Kim, Young-Suk Grace; Cho, Jeung-Ryeul; Park, Soon-Gil

    2017-08-01

    We examined the relations of short-term memory (STM), metalinguistic awareness (phonological, morphological, and orthographic awareness), and rapid automatized naming (RAN) to word reading in Korean, a language with a relatively transparent orthography. STM, metalinguistic awareness, and RAN have been shown to be important to word reading, but the nature of the relations of STM, metalinguistic awareness, and RAN to word reading has rarely been investigated. Two alternative models were fitted. In the indirect relation model, STM was hypothesized to be indirectly related to word reading via metalinguistic awareness and RAN. In the direct and indirect relations model, STM was hypothesized to be directly and indirectly related to word reading. Results from 207 beginning readers in South Korea showed that STM was directly related to word reading as well as indirectly via metalinguistic awareness and RAN. Although the direct effect of STM was relatively small (.16), the total effect incorporating the indirect effect was substantial (.42). These results suggest that STM is an important, foundational cognitive capacity that underpins metalinguistic awareness and RAN as well as word reading, and further indicate the importance of considering both direct and indirect effects of language and cognitive skills on word reading.

  2. RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.

    PubMed

    Wright, Imogen A; Travers, Simon A

    2014-07-01

    The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. Repeated Reading for Developing Reading Fluency and Reading Comprehension: The Case of EFL Learners in Vietnam

    ERIC Educational Resources Information Center

    Gorsuch, Greta; Taguchi, Etsuo

    2008-01-01

    Reading in a foreign or second language is often a laborious process, often caused by underdeveloped word recognition skills, among other things, of second and foreign language readers. Developing fluency in L2/FL reading has become an important pedagogical issue in L2 settings and one major component of reading fluency is fast and accurate word…

  4. Effects of irrelevant sounds on phonological coding in reading comprehension and short-term memory.

    PubMed

    Boyle, R; Coltheart, V

    1996-05-01

    The effects of irrelevant sounds on reading comprehension and short-term memory were studied in two experiments. In Experiment 1, adults judged the acceptability of written sentences during irrelevant speech, accompanied and unaccompanied singing, instrumental music, and in silence. Sentences varied in syntactic complexity: Simple sentences contained a right-branching relative clause (The applause pleased the woman that gave the speech) and syntactically complex sentences included a centre-embedded relative clause (The hay that the farmer stored fed the hungry animals). Unacceptable sentences either sounded acceptable (The dog chased the cat that eight up all his food) or did not (The man praised the child that sight up his spinach). Decision accuracy was impaired by syntactic complexity but not by irrelevant sounds. Phonological coding was indicated by increased errors on unacceptable sentences that sounded correct. These errors rates were unaffected by irrelevant sounds. Experiment 2 examined effects of irrelevant sounds on ordered recall of phonologically similar and dissimilar word lists. Phonological similarity impaired recall. Irrelevant speech reduced recall but did not interact with phonological similarity. The results of these experiments question assumptions about the relationship between speech input and phonological coding in reading and the short-term store.

  5. GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

    PubMed

    Alser, Mohammed; Hassan, Hasan; Xin, Hongyi; Ergin, Oguz; Mutlu, Onur; Alkan, Can

    2017-11-01

    High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10. https://github.com/BilkentCompGen/GateKeeper. mohammedalser@bilkent.edu.tr or onur.mutlu@inf.ethz.ch or calkan@cs.bilkent.edu.tr. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press

  6. Intermediate addition multifocals provide safe stair ambulation with adequate 'short-term' reading.

    PubMed

    Elliott, David B; Hotchkiss, John; Scally, Andrew J; Foster, Richard; Buckley, John G

    2016-01-01

    A recent randomised controlled trial indicated that providing long-term multifocal wearers with a pair of distance single-vision spectacles for use outside the home reduced falls risk in active older people. However, it also found that participants disliked continually switching between using two pairs of glasses and adherence to the intervention was poor. In this study we determined whether intermediate addition multifocals (which could be worn most of the time inside and outside the home and thus avoid continual switching) could provide similar gait safety on stairs to distance single vision spectacles whilst also providing adequate 'short-term' reading and near vision. Fourteen healthy long-term multifocal wearers completed stair ascent and descent trials over a 3-step staircase wearing intermediate and full addition bifocals and progression-addition lenses (PALs) and single-vision distance spectacles. Gait safety/caution was assessed using foot clearance measurements (toe on ascent, heel on descent) over the step edges and ascent and descent duration. Binocular near visual acuity, critical print size and reading speed were measured using Bailey-Lovie near charts and MNRead charts at 40 cm. Gait safety/caution measures were worse with full addition bifocals and PALs compared to intermediate bifocals and PALs. The intermediate PALs provided similar gait ascent/descent measures to those with distance single-vision spectacles. The intermediate addition PALs also provided good reading ability: Near word acuity and MNRead critical print size were better with the intermediate addition PALs than with the single-vision lenses (p < 0.0001), with a mean near visual acuity of 0.24 ± 0.13 logMAR (~N5.5) which is satisfactory for most near vision tasks when performed for a short period of time. The better ability to 'spot read' with the intermediate addition PALs compared to single-vision spectacles suggests that elderly individuals might better comply with the use of

  7. Scheimpflug image-based changes in anterior segment parameters during accommodation induced by short-term reading.

    PubMed

    Lipecz, Agnes; Tsorbatzoglou, Alexis; Hassan, Ziad; Berta, Andras; Modis, Laszlo; Nemeth, Gabor

    2017-05-11

    To analyze the effect of the accommodation on the anterior segment data (corneal and anterior chamber parameters) induced by short-time reading in a healthy, nonpresbyopic adult patient group. Images of both eyes of nonpresbyopic volunteers were captured with a Scheimpflug device (Pentacam HR) in a nonaccommodative state. Fifteen minutes of reading followed and through fixation of the built-in target of Pentacam HR further accommodation was achieved and new images were captured by the device. Anterior segment parameters were observed and the differences were analyzed. Fifty-two healthy eyes of 26 subjects (range 20.04-28.58 years) were analyzed. No significant differences were observed in the keratometric values before and after the accommodative task (p = 0.35). A statistically significant difference was measured in the 5.0-mm-diameter and the 7.0-mm-diameter corneal volume (p = 0.01 and p = 0.03) between accommodation states. Corneal aberrometric data did not change significantly during short-term accommodation. Significant differences were observed between nonaccommodative and accommodative states of the eyes for all measured anterior chamber parameters. Among the parameters of the cornea, only corneal volume changed during the short-term accommodation process, showing some fine changes with accommodation of the cornea in young, emmetropic patients. The position of the pupil and the anterior chamber parameters were observed to change with accommodation as captured by a Scheimpflug device.

  8. Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.

    PubMed

    Misra, Sanchit; Agrawal, Ankit; Liao, Wei-keng; Choudhary, Alok

    2011-01-15

    Recently, a number of programs have been proposed for mapping short reads to a reference genome. Many of them are heavily optimized for short-read mapping and hence are very efficient for shorter queries, but that makes them inefficient or not applicable for reads longer than 200 bp. However, many sequencers are already generating longer reads and more are expected to follow. For long read sequence mapping, there are limited options; BLAT, SSAHA2, FANGS and BWA-SW are among the popular ones. However, resequencing and personalized medicine need much faster software to map these long sequencing reads to a reference genome to identify SNPs or rare transcripts. We present AGILE (AliGnIng Long rEads), a hash table based high-throughput sequence mapping algorithm for longer 454 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process. In our experiments, we observe that AGILE is more accurate than BLAT, and comparable to BWA-SW and SSAHA2. For practical error rates (< 5%) and read lengths (200-1000 bp), AGILE is significantly faster than BLAT, SSAHA2 and BWA-SW. Even for the other cases, AGILE is comparable to BWA-SW and several times faster than BLAT and SSAHA2. http://www.ece.northwestern.edu/~smi539/agile.html.

  9. Leveraging FPGAs for Accelerating Short Read Alignment.

    PubMed

    Arram, James; Kaplan, Thomas; Luk, Wayne; Jiang, Peiyong

    2017-01-01

    One of the key challenges facing genomics today is how to efficiently analyze the massive amounts of data produced by next-generation sequencing platforms. With general-purpose computing systems struggling to address this challenge, specialized processors such as the Field-Programmable Gate Array (FPGA) are receiving growing interest. The means by which to leverage this technology for accelerating genomic data analysis is however largely unexplored. In this paper, we present a runtime reconfigurable architecture for accelerating short read alignment using FPGAs. This architecture exploits the reconfigurability of FPGAs to allow the development of fast yet flexible alignment designs. We apply this architecture to develop an alignment design which supports exact and approximate alignment with up to two mismatches. Our design is based on the FM-index, with optimizations to improve the alignment performance. In particular, the n-step FM-index, index oversampling, a seed-and-compare stage, and bi-directional backtracking are included. Our design is implemented and evaluated on a 1U Maxeler MPC-X2000 dataflow node with eight Altera Stratix-V FPGAs. Measurements show that our design is 28 times faster than Bowtie2 running with 16 threads on dual Intel Xeon E5-2640 CPUs, and nine times faster than Soap3-dp running on an NVIDIA Tesla C2070 GPU.

  10. Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.

    PubMed

    Malhis, Nawar; Butterfield, Yaron S N; Ester, Martin; Jones, Steven J M

    2009-01-01

    A plethora of alignment tools have been created that are designed to best fit different types of alignment conditions. While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. In this article, we will introduce a new alignment approach (Slider) that reduces the alignment problem space by utilizing each read base's probabilities given in the prb files. Compared with other aligners, Slider has higher alignment accuracy and efficiency. In addition, given that Slider matches bases with probabilities other than the most probable, it significantly reduces the percentage of base mismatches. The result is that its SNP predictions are more accurate than other SNP prediction approaches used today that start from the most probable sequence, including those using base quality.

  11. Are Fluency Measures Accurate Predictors of Reading Achievement?

    ERIC Educational Resources Information Center

    Schilling, Stephen G.; Carlisle, Joanne F.; Scott, Sarah E.; Zeng, Ji

    2007-01-01

    This study focused on the predictive validity of fluency measures that comprise Dynamic Indicators of Basic Early Literacy Skills (DIBELS). Data were gathered from first through third graders attending 44 schools in 9 districts or local educational agencies that made up the first Reading First cohort in Michigan. Students were administered DIBELS…

  12. Survey of gene splicing algorithms based on reads.

    PubMed

    Si, Xiuhua; Wang, Qian; Zhang, Lei; Wu, Ruo; Ma, Jiquan

    2017-11-02

    Gene splicing is the process of assembling a large number of unordered short sequence fragments to the original genome sequence as accurately as possible. Several popular splicing algorithms based on reads are reviewed in this article, including reference genome algorithms and de novo splicing algorithms (Greedy-extension, Overlap-Layout-Consensus graph, De Bruijn graph). We also discuss a new splicing method based on the MapReduce strategy and Hadoop. By comparing these algorithms, some conclusions are drawn and some suggestions on gene splicing research are made.

  13. The Relative Predictive Contribution and Causal Role of Phoneme Awareness, Rhyme Awareness and Verbal Short-Term Memory in Reading Skills: A Review

    ERIC Educational Resources Information Center

    Melby-Lervag, Monica

    2012-01-01

    The acknowledgement that educational achievement is highly dependent on successful reading development, has led to extensive research on its underlying factors. Evidence clearly suggests that the relation between reading skills, phoneme awareness, rhyme awareness, and verbal short-term memory is more than a mere association. A strong argument has…

  14. From Expressive Reading to Rapid Reading: The Rise in Reading Rate During the Efficiency Movement (1910-1925)

    ERIC Educational Resources Information Center

    Taylor, Laura A.

    2015-01-01

    Reading rate, a component of reading not closely attended to by educators and researchers prior to the 20th century, quickly became the subject of considerable research shortly after the turn of the century. This article uses historical content analysis to examine primary source documents from that period (1910-1925) to explore why reading rate…

  15. Using Supplementary Readings (Short Stories) in Increasing the Conceptual Fluency, the Case of Idioms in English

    ERIC Educational Resources Information Center

    Mokhtari, Elahe; Talebinezhad, Mohammed Reza

    2014-01-01

    The aim of this research was to probed whether using supplementary readings (short stories containing idioms) increase conceptual fluency of L2 learners. In line with the goal of the study, first, the researcher selected a sample of 30 female lower-intermediate L2 learners from Sadr Private Language Centre in Isfahan. She selected them based on…

  16. Social Perspectives on Reading: Social Influences and Reading Achievement. Perspectives in Reading No. 17.

    ERIC Educational Resources Information Center

    Macdonald, James B., Ed.

    This collection of short papers examines reading as a social institution. Rolland Callaway begins with the idea that the teaching of reading must be looked at in terms of educational policy or politics. Jack E. Williams follows with a semihistorical orientation which traces social class, ethnic, and racial biases on achievement. James B. Macdonald…

  17. The Short Circuit Hypothesis of ESL Reading--Or when Language Competence Interferes with Reading Performance.

    ERIC Educational Resources Information Center

    Clarke, Mark A.

    1980-01-01

    Examines a sampling of current ESL reading instruction practices, addressing the concern that the lack of a generally accepted theory of L2 reading constitutes a major obstacle to teaching and testing ESL reading skills. Summarizes the results of two studies and discusses their implications for ESL teachers. (MES)

  18. Short-Read Whole-Genome Sequencing for Laboratory-Based Surveillance of Bordetella pertussis.

    PubMed

    Marchand-Austin, Alex; Tsang, Raymond S W; Guthrie, Jennifer L; Ma, Jennifer H; Lim, Gillian H; Crowcroft, Natasha S; Deeks, Shelley L; Farrell, David J; Jamieson, Frances B

    2017-05-01

    Bordetella pertussis is a Gram-negative bacterium that causes respiratory infections in humans. Ongoing molecular surveillance of B. pertussis acellular vaccine (aP) antigens is critical for understanding the interaction between evolutionary pressures, disease pathogenesis, and vaccine effectiveness. Methods currently used to characterize aP components are relatively labor-intensive and low throughput. To address this challenge, we sought to derive aP antigen genotypes from minimally processed short-read whole-genome sequencing data generated from 40 clinical B. pertussis isolates and analyzed using the SRST2 bioinformatic package. SRST2 was able to identify aP antigen genotypes for all antigens with the exception of pertactin, possibly due to low read coverage in GC-rich low-complexity regions of variation. Two main genotypes were observed in addition to a singular third genotype that contained an 84-bp deletion that was identified by SRST2 despite the issues in allele calling. This method has the potential to generate large pools of B. pertussis molecular data that can be linked to clinical and epidemiological information to facilitate research of vaccine effectiveness and disease severity in the context of emerging vaccine antigen-deficient strains. Copyright © 2017 American Society for Microbiology.

  19. Developing Reading Fluency and Comprehension Using Repeated Reading: Evidence from Longitudinal Student Reports

    ERIC Educational Resources Information Center

    Gorsuch, Greta; Taguchi, Etsuo

    2010-01-01

    In recent years, interest in reading fluency development in first language, and second and foreign language (L2/FL) settings has increased. Reading fluency, in which readers decode and comprehend at the same time, is critical to successful reading. Fluent readers are accurate and fast in their ability to recognize words, and in their use of…

  20. Functional and Structural Neuroplasticity Induced by Short-Term Tactile Training Based on Braille Reading.

    PubMed

    Debowska, Weronika; Wolak, Tomasz; Nowicka, Anna; Kozak, Anna; Szwed, Marcin; Kossut, Malgorzata

    2016-01-01

    Neuroplastic changes induced by sensory learning have been recognized within the cortices of specific modalities as well as within higher ordered multimodal areas. The interplay between these areas is not fully understood, particularly in the case of somatosensory learning. Here we examined functional and structural changes induced by short-term tactile training based of Braille reading, a task that requires both significant tactile expertise and mapping of tactile input onto multimodal representations. Subjects with normal vision were trained for 3 weeks to read Braille exclusively by touch and scanned before and after training, while performing a same-different discrimination task on Braille characters and meaningless characters. Functional and diffusion-weighted magnetic resonance imaging sequences were used to assess resulting changes. The strongest training-induced effect was found in the primary somatosensory cortex (SI), where we observed bilateral augmentation in activity accompanied by an increase in fractional anisotropy (FA) within the contralateral SI. Increases of white matter fractional anisotropy were also observed in the secondary somatosensory area (SII) and the thalamus. Outside of somatosensory system, changes in both structure and function were found in i.e., the fusiform gyrus, the medial frontal gyri and the inferior parietal lobule. Our results provide evidence for functional remodeling of the somatosensory pathway and higher ordered multimodal brain areas occurring as a result of short-lasting tactile learning, and add to them a novel picture of extensive white matter plasticity.

  1. Functional and Structural Neuroplasticity Induced by Short-Term Tactile Training Based on Braille Reading

    PubMed Central

    Debowska, Weronika; Wolak, Tomasz; Nowicka, Anna; Kozak, Anna; Szwed, Marcin; Kossut, Malgorzata

    2016-01-01

    Neuroplastic changes induced by sensory learning have been recognized within the cortices of specific modalities as well as within higher ordered multimodal areas. The interplay between these areas is not fully understood, particularly in the case of somatosensory learning. Here we examined functional and structural changes induced by short-term tactile training based of Braille reading, a task that requires both significant tactile expertise and mapping of tactile input onto multimodal representations. Subjects with normal vision were trained for 3 weeks to read Braille exclusively by touch and scanned before and after training, while performing a same-different discrimination task on Braille characters and meaningless characters. Functional and diffusion-weighted magnetic resonance imaging sequences were used to assess resulting changes. The strongest training-induced effect was found in the primary somatosensory cortex (SI), where we observed bilateral augmentation in activity accompanied by an increase in fractional anisotropy (FA) within the contralateral SI. Increases of white matter fractional anisotropy were also observed in the secondary somatosensory area (SII) and the thalamus. Outside of somatosensory system, changes in both structure and function were found in i.e., the fusiform gyrus, the medial frontal gyri and the inferior parietal lobule. Our results provide evidence for functional remodeling of the somatosensory pathway and higher ordered multimodal brain areas occurring as a result of short-lasting tactile learning, and add to them a novel picture of extensive white matter plasticity. PMID:27790087

  2. CNV-TV: a robust method to discover copy number variation from short sequencing reads.

    PubMed

    Duan, Junbo; Zhang, Ji-Gang; Deng, Hong-Wen; Wang, Yu-Ping

    2013-05-02

    Copy number variation (CNV) is an important structural variation (SV) in human genome. Various studies have shown that CNVs are associated with complex diseases. Traditional CNV detection methods such as fluorescence in situ hybridization (FISH) and array comparative genomic hybridization (aCGH) suffer from low resolution. The next generation sequencing (NGS) technique promises a higher resolution detection of CNVs and several methods were recently proposed for realizing such a promise. However, the performances of these methods are not robust under some conditions, e.g., some of them may fail to detect CNVs of short sizes. There has been a strong demand for reliable detection of CNVs from high resolution NGS data. A novel and robust method to detect CNV from short sequencing reads is proposed in this study. The detection of CNV is modeled as a change-point detection from the read depth (RD) signal derived from the NGS, which is fitted with a total variation (TV) penalized least squares model. The performance (e.g., sensitivity and specificity) of the proposed approach are evaluated by comparison with several recently published methods on both simulated and real data from the 1000 Genomes Project. The experimental results showed that both the true positive rate and false positive rate of the proposed detection method do not change significantly for CNVs with different copy numbers and lengthes, when compared with several existing methods. Therefore, our proposed approach results in a more reliable detection of CNVs than the existing methods.

  3. Working memory, short-term memory, and reading disabilities: a selective meta-analysis of the literature.

    PubMed

    Swanson, H Lee; Xinhua Zheng; Jerman, Olga

    2009-01-01

    The purpose of the present study was to synthesize research that compares children with and without reading disabilities (RD) on measures of short-term memory (STM) and working memory (WM). Across a broad age, reading, and IQ range, 578 effect sizes (ESs) were computed, yielding a mean ES across studies of -.89 (SD = 1.03). A total of 257 ESs were in the moderate range for STM measures (M = -.61, 95% confidence range of -.65 to -.58), and 320 ESs were in the moderate range for WM measures (M = -.67, 95% confidence range of -.68 to -.64). The results indicated that children with RD were distinctively disadvantaged compared with average readers on (a) STM measures requiring the recall of phonemes and digit sequences and (b) WM measures requiring the simultaneous processing and storage of digits within sentence sequences and final words from unrelated sentences. No significant moderating effects emerged for age, IQ, or reading level on memory ESs. The findings indicated that domain-specific STM and WM differences between ability groups persisted across age, suggesting that a verbal deficit model that fails to efficiently draw resources from both a phonological and executive system underlies RD.

  4. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

    PubMed Central

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-01-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

  5. Assembled sequence contigs by SOAPdenova and Volvet algorithms from metagenomic short reads of a new bacterial isolate of gut origin

    USDA-ARS?s Scientific Manuscript database

    Assembled sequence contigs by SOAPdenova and Volvet algorithms from metagenomic short reads of a new bacterial isolate of gut origin. This study included 2 submissions with a total of 9.8 million bp of assembled contigs....

  6. GapFiller: a de novo assembly approach to fill the gap within paired reads

    PubMed Central

    2012-01-01

    Background Next Generation Sequencing technologies are able to provide high genome coverages at a relatively low cost. However, due to limited reads' length (from 30 bp up to 200 bp), specific bioinformatics problems have become even more difficult to solve. De novo assembly with short reads, for example, is more complicated at least for two reasons: first, the overall amount of "noisy" data to cope with increased and, second, as the reads' length decreases the number of unsolvable repeats grows. Our work's aim is to go at the root of the problem by providing a pre-processing tool capable to produce (in-silico) longer and highly accurate sequences from a collection of Next Generation Sequencing reads. Results In this paper a seed-and-extend local assembler is presented. The kernel algorithm is a loop that, starting from a read used as seed, keeps extending it using heuristics whose main goal is to produce a collection of error-free and longer sequences. In particular, GapFiller carefully detects reliable overlaps and operates clustering similar reads in order to reconstruct the missing part between the two ends of the same insert. Our tool's output has been validated on 24 experiments using both simulated and real paired reads datasets. The output sequences are declared correct when the seed-mate is found. In the experiments performed, GapFiller was able to extend high percentages of the processed seeds and find their mates, with a false positives rate that turned out to be nearly negligible. Conclusions GapFiller, starting from a sufficiently high short reads coverage, is able to produce high coverages of accurate longer sequences (from 300 bp up to 3500 bp). The procedure to perform safe extensions, together with the mate-found check, turned out to be a powerful criterion to guarantee contigs' correctness. GapFiller has further potential, as it could be applied in a number of different scenarios, including the post-processing validation of insertions

  7. A High Intensity, Short-Term, Tutorial/Enrichment Program in Reading.

    ERIC Educational Resources Information Center

    Martin, Rita J.; And Others.

    1981-01-01

    The Summer Adventure in Learning (SAIL) program was developed to train prospective teachers in tutorial methods intended to improve reading achievement. The program's primary instructional objective was to decrease the pupil reading rate resulting in improved reading comprehension. (JN)

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

    PubMed

    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.

  9. Modern Speed-Reading Apps Do Not Foster Reading Comprehension.

    PubMed

    Acklin, Dina; Papesh, Megan H

    2017-01-01

    New computer apps are gaining popularity by suggesting that reading speeds can be drastically increased when eye movements that normally occur during reading are eliminated. This is done using rapid serial visual presentation (RSVP), where words are presented 1 at a time, thus preventing natural eye movements such as saccades, fixations, and regressions from occurring. Al- though the companies producing these apps suggest that RSVP reading does not yield comprehension deficits, research investigating the role of eye movements in reading documents shows the necessity of natural eye movements for accurate comprehension. The current study explored variables that may affect reading comprehension during RSVP reading, including text difficulty (6th grade and 12th grade), text presentation speed (static, 700 wpm, and 1,000 wpm), and working memory capacity (WMC). Consistent with recent work showing a tenuous relationship between comprehension and WMC, participants' WMC did not predict comprehension scores. Instead, comprehension was most affected by reading speed: Static text was associated with superior performance, relative to either RSVP reading condition. Furthermore, slower RSVP speeds yielded better verbatim comprehension, and faster speeds benefited inferential comprehension.

  10. Functional MRI evidence for the importance of visual short-term memory in logographic reading.

    PubMed

    Koyama, Maki S; Stein, John F; Stoodley, Catherine J; Hansen, Peter C

    2011-02-01

    Logographic symbols are visually complex, and thus children's abilities for visual short-term memory (VSTM) predict their reading competence in logographic systems. In the present study, we investigated the importance of VSTM in logographic reading in adults, both behaviorally and by means of fMRI. Outside the scanner, VSTM predicted logographic Kanji reading in native Japanese adults (n=45), a finding consistent with previous observations in Japanese children. In the scanner, participants (n=15) were asked to perform a visual one-back task. For this fMRI experiment, we took advantage of the unique linguistic characteristic of the Japanese writing system, whereby syllabic Kana and logographic Kanji can share the same sound and meaning, but differ only in the complexity of their visual features. Kanji elicited greater activation than Kana in the cerebellum and two regions associated with VSTM, the lateral occipital complex and the superior intraparietal sulcus, bilaterally. The same regions elicited the highest activation during the control condition (an unfamiliar, unpronounceable script to the participants), presumably due to the increased VSTM demands for processing the control script. In addition, individual differences in VSTM performance (outside the scanner) significantly predicted blood oxygen level-dependent signal changes in the identified VSTM regions, during the Kanji and control conditions, but not during the Kana condition. VSTM appears to play an important role in reading logographic words, even in skilled adults, as evidenced at the behavioral and neural level, most likely due to the increased VSTM/visual attention demands necessary for processing complex visual features inherent in logographic symbols. European Journal of Neuroscience © 2010 Federation of European Neuroscience Societies and Blackwell Publishing Ltd. No claim to original US government works.

  11. 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

    PubMed Central

    Karamitros, Timokratis; 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 <1% to 53% of amino acids in each gene exhibiting at least one substitution within the pool of samples. The UL23 gene had one of the highest genetic variabilities at 35.2% in keeping with its role in development of drug resistance. The assembly of accurate, full-length HHV-1 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. PMID:27309375

  12. 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.

    PubMed

    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 <1% to 53% of amino acids in each gene exhibiting at least one substitution within the pool of samples. The UL23 gene had one of the highest genetic variabilities at 35.2% in keeping with its role in development of drug resistance. The assembly of accurate, full-length HHV-1 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.

  13. Educational Innovation: Reading Meaning and Sense

    ERIC Educational Resources Information Center

    Hortiales, Evelyne Suárez; Nieto, Angelica Ramos; Hurtado, María Elena Zepeda

    2017-01-01

    In recent years concern about Mexican reading habits has increased. Statistics show short reading interest; an average Mexican reads 3.8 books a year [1]. As teachers, reading habits are important and reflect students' skills and academic performances. Many teachers would complain about students reading habits; it is considered to be non-existent.…

  14. Is a "Phoenician" reading style superior to a "Chinese" reading style? Evidence from fourth graders.

    PubMed

    Bowey, Judith A

    2008-07-01

    This study compared normally achieving fourth-grade "Phoenician" readers, who identify nonwords significantly more accurately than they do exception words, with "Chinese" readers, who show the reverse pattern. Phoenician readers scored lower than Chinese readers on word identification, exception word reading, orthographic choice, spelling, reading comprehension, and verbal ability. When compared with normally achieving children who read nonwords and exception words equally well, Chinese readers scored as well as these children on word identification, regular word reading, orthographic choice, spelling, reading comprehension, phonological sensitivity, and verbal ability and scored better on exception word reading. Chinese readers also used rhyme-based analogies to read nonwords derived from high-frequency exception words just as often as did these children. As predicted, Phoenician and Chinese readers adopted somewhat different strategies in reading ambiguous nonwords constructed by analogy to high-frequency exception words. Phoenician readers were more likely than Chinese readers to read ambiguous monosyllabic nonwords via context-free grapheme-phoneme correspondences and were less likely to read disyllabic nonwords by analogy to high-frequency analogues. Although the Chinese reading style was more common than the Phoenician style in normally achieving fourth graders, there were similar numbers of poor readers with phonological dyslexia (identifying nonwords significantly more accurately than exception words) and surface dyslexia (showing the reverse pattern), although surface dyslexia was more common in the severely disabled readers. However, few of the poor readers showed pure patterns of phonological or surface dyslexia.

  15. Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data.

    PubMed

    Nishito, Yukari; Osana, Yasunori; Hachiya, Tsuyoshi; Popendorf, Kris; Toyoda, Atsushi; Fujiyama, Asao; Itaya, Mitsuhiro; Sakakibara, Yasubumi

    2010-04-16

    Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and functions as a starter for the production of the traditional Japanese food "natto" made from soybeans. Although re-sequencing whole genomes of several laboratory domesticated B. subtilis 168 derivatives has already been attempted using short read sequencing data, the assembly of the whole genome sequence of a closely related strain, B. subtilis natto, from very short read data is more challenging, particularly with our aim to assemble one fully connected scaffold from short reads around 35 bp in length. We applied a comparative genome assembly method, which combines de novo assembly and reference guided assembly, to one of the B. subtilis natto strains. We successfully assembled 28 scaffolds and managed to avoid substantial fragmentation. Completion of the assembly through long PCR experiments resulted in one connected scaffold for B. subtilis natto. Based on the assembled genome sequence, our orthologous gene analysis between natto BEST195 and Marburg 168 revealed that 82.4% of 4375 predicted genes in BEST195 are one-to-one orthologous to genes in 168, with two genes in-paralog, 3.2% are deleted in 168, 14.3% are inserted in BEST195, and 5.9% of genes present in 168 are deleted in BEST195. The natto genome contains the same alleles in the promoter region of degQ and the coding region of swrAA as the wild strain, RO-FF-1. These are specific for gamma-PGA production ability, which is related to natto production. Further, the B. subtilis natto strain completely lacked a polyketide synthesis operon, disrupted the plipastatin production operon, and possesses previously unidentified transposases. The determination of the whole genome sequence of Bacillus subtilis natto provided detailed analyses of a set of genes related to natto production, demonstrating the number and locations of insertion sequences that B. subtilis natto harbors but B. subtilis 168 lacks

  16. Improve Reading with Complex Texts

    ERIC Educational Resources Information Center

    Fisher, Douglas; Frey, Nancy

    2015-01-01

    The Common Core State Standards have cast a renewed light on reading instruction, presenting teachers with the new requirements to teach close reading of complex texts. Teachers and administrators should consider a number of essential features of close reading: They are short, complex texts; rich discussions based on worthy questions; revisiting…

  17. Comparison of methods for library construction and short read annotation of shellfish viral metagenomes.

    PubMed

    Wei, Hong-Ying; Huang, Sheng; Wang, Jiang-Yong; Gao, Fang; Jiang, Jing-Zhe

    2018-03-01

    The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI's NR and Uniprot's Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.

  18. Phonological working memory and reading in students with dyslexia

    PubMed Central

    de Carvalho, Carolina A. F.; Kida, Adriana de S. B.; Capellini, Simone A.; de Avila, Clara R. B.

    2014-01-01

    Purpose: To investigate parameters related to fluency, reading comprehension and phonological processing (operational and short-term memory) and identify potential correlation between the variables in Dyslexia and in the absence of reading difficulties. Method: One hundred and fifteen students from the third to eighth grade of elementary school were grouped into a Control Group (CG) and Group with Dyslexia (GDys). Reading of words, pseudowords and text (decoding); listening and reading comprehension; phonological short-term and working memory (repetition of pseudowords and Digit Span) were evaluated. Results: The comparison of the groups showed significant differences in decoding, phonological short-term memory (repetition of pseudowords) and answers to text-connecting questions (TC) on reading comprehension, with the worst performances identified for GDys. In this group there were negative correlations between pseudowords repetition and TC answers and total score, both on listening comprehension. No correlations were found between operational and short-term memory (Digit Span) and parameters of fluency and reading comprehension in dyslexia. For the sample without complaint, there were positive correlations between some parameters of reading fluency and repetition of pseudowords and also between answering literal questions in listening comprehension and repetition of digits on the direct and reverse order. There was no correlation with the parameters of reading comprehension. Conclusion: GDys and CG showed similar performance in listening comprehension and in understanding of explicit information and gap-filling inference on reading comprehension. Students of GDys showed worst performance in reading decoding, phonological short-term memory (pseudowords) and on inferences that depends on textual cohesion understanding in reading. There were negative correlations between pseudowords repetition and TC answers and total score, both in listening comprehension. PMID

  19. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

    PubMed

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-05-05

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. The Short Circuit Model of Reading.

    ERIC Educational Resources Information Center

    Lueers, Nancy M.

    The name "short circuit" has been given to this model because, in many ways, it adequately describes what happens bioelectrically in the brain. The "short-circuiting" factors include linguistic, sociocultural, attitudinal and motivational, neurological, perceptual, and cognitive factors. Research is reviewed on ways in which each one affects any…

  1. Nonword Repetition: The Relative Contributions of Phonological Short-Term Memory and Phonological Representations in Children with Language and Reading Impairment

    ERIC Educational Resources Information Center

    Rispens, Judith; Baker, Anne

    2012-01-01

    Purpose: This study investigates the relative contributions of phonological short-term memory and phonological representations to nonword repetition (NWR). This was evaluated in children with specific language impairment (SLI) and/or reading impairment (RI); it was also studied from a developmental perspective by comparing 2 groups of typically…

  2. Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq.

    PubMed

    Barrick, Jeffrey E; Colburn, Geoffrey; Deatherage, Daniel E; Traverse, Charles C; Strand, Matthew D; Borges, Jordan J; Knoester, David B; Reba, Aaron; Meyer, Austin G

    2014-11-29

    Mutations that alter chromosomal structure play critical roles in evolution and disease, including in the origin of new lifestyles and pathogenic traits in microbes. Large-scale rearrangements in genomes are often mediated by recombination events involving new or existing copies of mobile genetic elements, recently duplicated genes, or other repetitive sequences. Most current software programs for predicting structural variation from short-read DNA resequencing data are intended primarily for use on human genomes. They typically disregard information in reads mapping to repeat sequences, and significant post-processing and manual examination of their output is often required to rule out false-positive predictions and precisely describe mutational events. We have implemented an algorithm for identifying structural variation from DNA resequencing data as part of the breseq computational pipeline for predicting mutations in haploid microbial genomes. Our method evaluates the support for new sequence junctions present in a clonal sample from split-read alignments to a reference genome, including matches to repeat sequences. Then, it uses a statistical model of read coverage evenness to accept or reject these predictions. Finally, breseq combines predictions of new junctions and deleted chromosomal regions to output biologically relevant descriptions of mutations and their effects on genes. We demonstrate the performance of breseq on simulated Escherichia coli genomes with deletions generating unique breakpoint sequences, new insertions of mobile genetic elements, and deletions mediated by mobile elements. Then, we reanalyze data from an E. coli K-12 mutation accumulation evolution experiment in which structural variation was not previously identified. Transposon insertions and large-scale chromosomal changes detected by breseq account for ~25% of spontaneous mutations in this strain. In all cases, we find that breseq is able to reliably predict structural variation

  3. Accuracy of student performance while reading leveled books rated at their instructional level by a reading inventory.

    PubMed

    Burns, Matthew K; Pulles, Sandra M; Maki, Kathrin E; Kanive, Rebecca; Hodgson, Jennifer; Helman, Lori A; McComas, Jennifer J; Preast, June L

    2015-12-01

    Identifying a student's instructional level is necessary to ensure that students are appropriately challenged in reading. Informal reading inventories (IRIs) purport to assess the highest reading level at which a student can accurately decode and comprehend text. However, the use of IRIs in determining a student's instructional level has been questioned because of a lack of research. The current study examined the percentage of words read correctly with 64 second- and third-grade students while reading from texts at their instructional level as determined by an IRI. Students read for 1 min from three leveled texts that corresponded to their instructional level as measured by an IRI, and the percentage of words read correctly was recorded. The percentage read correctly correlated across the three books from r=.47 to r=.68 and instructional level categories correlated from tau=.59 to tau=.65. Percent agreement calculations showed that the categorical scores (frustration, instructional, and independent) for the three readings agreed approximately 67% to 70% of the time, which resulted in a kappa estimate of less than .50. Kappa coefficients of .70 are considered strong indicators of agreement. Moreover, more than half of the students with the lowest reading skills read at a frustration level when attempting to read books rated at their instructional level by an IRI. The current study questions how reliably and accurately IRIs identify students' instructional level for reading. Copyright © 2015 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

  4. Reading in French-Speaking Adults with Dyslexia

    ERIC Educational Resources Information Center

    Martin, Jennifer; Cole, Pascale; Leuwers, Christel; Casalis, Severine; Zorman, Michel; Sprenger-Charolles, Liliane

    2010-01-01

    This study investigated the reading and reading-related skills of 15 French-speaking adults with dyslexia, whose performance was compared with that of chronological-age controls (CA) and reading-level controls (RL). Experiment 1 assessed the efficiency of their phonological reading-related skills (phonemic awareness, phonological short-term…

  5. Grade 12 Diploma Examination, English 33. Part B: Reading (Multiple Choice). Readings Booklet.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton.

    Intended for students taking the Grade 12 Examination in English 33 in Alberta, Canada, this reading test (to be administered along with the questions booklet) contains short reading selections taken from fiction, nonfiction, poetry, and drama, including the following: an excerpt from "Catch-22" (Joseph Heller); "School Thief"…

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

    PubMed

    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.

  7. LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences.

    PubMed

    Disdero, Eric; Filée, Jonathan

    2017-01-01

    Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available. However, existing TE population genomic softwares were not designed to handle long reads and the development of new dedicated tools is needed. LoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against simulated and genuine Drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tool to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences. LoRTE is an efficient and accurate tool to identify structural genomic variants caused by TE insertion or deletion. LoRTE is available for download at http://www.egce.cnrs-gif.fr/?p=6422.

  8. Grade 12 Diploma Examination, English 30. Part B: Reading (Multiple Choice). Readings Booklet.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton.

    Intended for students taking the Grade 12 Examination in English 30 in Alberta, Canada, this reading test (to be administered along with the questions booklet) contains 10 short reading selections taken from fiction, nonfiction, poetry, and drama, including the following: an excerpt from "Where Did You Go?""Out." (Robert Paul…

  9. Learning to Read Music Fluently

    ERIC Educational Resources Information Center

    Stauffer, Donald W.

    2005-01-01

    The ability to read music accurately at sight is an extremely important, if not indispensable, qualification of both professional and amateur musicians. Sight-reading can be defined as the ability to translate musical symbols and terms into a musical performance using strict time limits. The musician must quickly perceive symbols ahead while…

  10. A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).

    PubMed

    Fuselli, S; Baptista, R P; Panziera, A; Magi, A; Guglielmi, S; Tonin, R; Benazzo, A; Bauzer, L G; Mazzoni, C J; Bertorelle, G

    2018-03-24

    The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utilized long-range PCR to generate a 9 Kb fragment of the DRB locus. Amplicons from six different individuals were fragmented, tagged, and simultaneously sequenced with Illumina MiSeq. One of these amplicons was sequenced with the MinION device, which produced long reads covering the entire amplified fragment. A pipeline that combines short and long reads resolved several short tandem repeats and homopolymers and produced a de novo reference, which was then used to map and genotype the short reads from all individuals. The assembled DRB locus showed a high level of polymorphism and the presence of a recombination breakpoint. Our results suggest that an amplicon-based NGS approach coupled with single-molecule MinION nanopore sequencing can efficiently achieve both the assembly and the genotyping of complex genomic regions in multiple individuals in the absence of a reference sequence.

  11. Reading Recovery[R]. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2008

    2008-01-01

    "Reading Recovery"[R] is a short-term tutoring intervention intended to serve the lowest-achieving (bottom 20%) first-grade students. The goals of "Reading Recovery"[R] are to promote literacy skills, reduce the number of first-grade students who are struggling to read, and prevent long-term reading difficulties. "Reading Recovery"[R] supplements…

  12. Tracking Reading: Dual Task Costs of Oral Reading for Young versus Older Adults

    ERIC Educational Resources Information Center

    Kemper, Susan; Bontempo, Daniel; Schmalzried, RaLynn; McKedy, Whitney; Tagliaferri, Bruno; Kieweg, Doug

    2014-01-01

    A digital pursuit rotor was used to monitor oral reading costs by time-locking tracking performance to the auditory wave form produced as young and older adults were reading out short paragraphs. Multilevel modeling was used to determine how paragraph-level predictors of length, grammatical complexity, and readability and person-level predictors…

  13. Grade 12 Diploma Examination, English 30. Part B: Reading (Multiple Choice). Readings Booklet.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton.

    Intended for students taking the Grade 12 Examination in English 30 in Alberta, Canada, this reading test (to be administered along with the questions booklet) contains 10 short reading selections taken from fiction, nonfiction, poetry and drama, including the following: "At the Age at Which Mozart Was Dead Already" (Ellen Goodman);…

  14. Reading Intervention and Special Education Referrals

    ERIC Educational Resources Information Center

    Polcyn, Dawn M.; Levine-Donnerstein, Deborah; Perfect, Michelle M.; Obrzut, John E.

    2014-01-01

    This study examined whether consistently implementing reading fluency interventions prior to referring students for a special education evaluation led to fewer overall special education referrals, as well as more accurate special education referrals. Results indicated that the implementation of a peer-mediated reading fluency intervention…

  15. Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome

    PubMed Central

    Li, Runsheng; Hsieh, Chia-Ling; Young, Amanda; Zhang, Zhihong; Ren, Xiaoliang; Zhao, Zhongying

    2015-01-01

    Most next-generation sequencing platforms permit acquisition of high-throughput DNA sequences, but the relatively short read length limits their use in genome assembly or finishing. Illumina has recently released a technology called Synthetic Long-Read Sequencing that can produce reads of unusual length, i.e., predominately around 10 Kb. However, a systematic assessment of their use in genome finishing and assembly is still lacking. We evaluate the promise and deficiency of the long reads in these aspects using isogenic C. elegans genome with no gap. First, the reads are highly accurate and capable of recovering most types of repetitive sequences. However, the presence of tandem repetitive sequences prevents pre-assembly of long reads in the relevant genomic region. Second, the reads are able to reliably detect missing but not extra sequences in the C. elegans genome. Third, the reads of smaller size are more capable of recovering repetitive sequences than those of bigger size. Fourth, at least 40 Kbp missing genomic sequences are recovered in the C. elegans genome using the long reads. Finally, an N50 contig size of at least 86 Kbp can be achieved with 24×reads but with substantial mis-assembly errors, highlighting a need for novel assembly algorithm for the long reads. PMID:26039588

  16. The Role of Visual Processing Speed in Reading Speed Development

    PubMed Central

    Lobier, Muriel; Dubois, Matthieu; Valdois, Sylviane

    2013-01-01

    A steady increase in reading speed is the hallmark of normal reading acquisition. However, little is known of the influence of visual attention capacity on children's reading speed. The number of distinct visual elements that can be simultaneously processed at a glance (dubbed the visual attention span), predicts single-word reading speed in both normal reading and dyslexic children. However, the exact processes that account for the relationship between the visual attention span and reading speed remain to be specified. We used the Theory of Visual Attention to estimate visual processing speed and visual short-term memory capacity from a multiple letter report task in eight and nine year old children. The visual attention span and text reading speed were also assessed. Results showed that visual processing speed and visual short term memory capacity predicted the visual attention span. Furthermore, visual processing speed predicted reading speed, but visual short term memory capacity did not. Finally, the visual attention span mediated the effect of visual processing speed on reading speed. These results suggest that visual attention capacity could constrain reading speed in elementary school children. PMID:23593117

  17. The role of visual processing speed in reading speed development.

    PubMed

    Lobier, Muriel; Dubois, Matthieu; Valdois, Sylviane

    2013-01-01

    A steady increase in reading speed is the hallmark of normal reading acquisition. However, little is known of the influence of visual attention capacity on children's reading speed. The number of distinct visual elements that can be simultaneously processed at a glance (dubbed the visual attention span), predicts single-word reading speed in both normal reading and dyslexic children. However, the exact processes that account for the relationship between the visual attention span and reading speed remain to be specified. We used the Theory of Visual Attention to estimate visual processing speed and visual short-term memory capacity from a multiple letter report task in eight and nine year old children. The visual attention span and text reading speed were also assessed. Results showed that visual processing speed and visual short term memory capacity predicted the visual attention span. Furthermore, visual processing speed predicted reading speed, but visual short term memory capacity did not. Finally, the visual attention span mediated the effect of visual processing speed on reading speed. These results suggest that visual attention capacity could constrain reading speed in elementary school children.

  18. Haplotype estimation using sequencing reads.

    PubMed

    Delaneau, Olivier; Howie, Bryan; Cox, Anthony J; Zagury, Jean-François; Marchini, Jonathan

    2013-10-03

    High-throughput sequencing technologies produce short sequence reads that can contain phase information if they span two or more heterozygote genotypes. This information is not routinely used by current methods that infer haplotypes from genotype data. We have extended the SHAPEIT2 method to use phase-informative sequencing reads to improve phasing accuracy. Our model incorporates the read information in a probabilistic model through base quality scores within each read. The method is primarily designed for high-coverage sequence data or data sets that already have genotypes called. One important application is phasing of single samples sequenced at high coverage for use in medical sequencing and studies of rare diseases. Our method can also use existing panels of reference haplotypes. We tested the method by using a mother-father-child trio sequenced at high-coverage by Illumina together with the low-coverage sequence data from the 1000 Genomes Project (1000GP). We found that use of phase-informative reads increases the mean distance between switch errors by 22% from 274.4 kb to 328.6 kb. We also used male chromosome X haplotypes from the 1000GP samples to simulate sequencing reads with varying insert size, read length, and base error rate. When using short 100 bp paired-end reads, we found that using mixtures of insert sizes produced the best results. When using longer reads with high error rates (5-20 kb read with 4%-15% error per base), phasing performance was substantially improved. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  19. Dyslexie font does not benefit reading in children with or without dyslexia.

    PubMed

    Kuster, Sanne M; van Weerdenburg, Marjolijn; Gompel, Marjolein; Bosman, Anna M T

    2018-04-01

    In two experiments, the claim was tested that the font "Dyslexie", specifically designed for people with dyslexia, eases reading performance of children with (and without) dyslexia. Three questions were investigated. (1) Does the Dyslexie font lead to faster and/or more accurate reading? (2) Do children have a preference for the Dyslexie font? And, (3) is font preference related to reading performance? In Experiment 1, children with dyslexia (n = 170) did not read text written in Dyslexie font faster or more accurately than in Arial font. The majority preferred reading in Arial and preference was not related to reading performance. In Experiment 2, children with (n = 102) and without dyslexia (n = 45) read word lists in three different font types (Dyslexie, Arial, Times New Roman). Words written in Dyslexie font were not read faster or more accurately. Moreover, participants showed a preference for the fonts Arial and Times New Roman rather than Dyslexie, and again, preference was not related to reading performance. These experiments clearly justify the conclusion that the Dyslexie font neither benefits nor impedes the reading process of children with and without dyslexia.

  20. Design of short Italian sentences to assess near vision performance.

    PubMed

    Calossi, Antonio; Boccardo, Laura; Fossetti, Alessandro; Radner, Wolfgang

    2014-01-01

    To develop and validate 28 short Italian sentences for the construction of the Italian version of the Radner Reading Chart to simultaneously measure near visual acuity and reading speed. 41 sentences were constructed in Italian language, following the procedure defined by Radner, to obtain "sentence optotypes" with comparable structure and with the same lexical and grammatical difficulty. Sentences were statistically selected and used in 211 normal, non-presbyopic, native Italian-speaking persons. The most equally matched sentences in terms of reading speed and number of reading errors were selected. To assess the validity of the reading speed results obtained with the 28 selected short sentences, we compared the reading speed and reading errors with the average obtained by reading two long 4th-grade paragraphs (97 and 90 words) under the same conditions. The overall mean reading speed of the tested persons was 189±26wpm. The 28 sentences more similar in terms of reading times were selected, achieving a coefficient of variation (the relative SD) of 2.2%. The reliability analyses yielded an overall Cronbach's alpha coefficient of 0.98. The correlation between the short sentences and the long paragraph was high (r=0.85, P<0.0001). The 28 short single Italian sentences optotypes were highly comparable in syntactical structure, number, position, and length of words, lexical difficulty, and reading length. The resulting Italian Radner Reading Chart is precise (high consistency) and practical (short sentences) and therefore useful for research and clinical practice to simultaneously measure near reading acuity and reading speed. Copyright © 2013 Spanish General Council of Optometry. Published by Elsevier Espana. All rights reserved.

  1. Reading Recovery[R]. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2009

    2009-01-01

    "Reading Recovery"[R] is a short-term tutoring intervention designed to serve the lowest-achieving (bottom 20%) first-grade students. The goals of "Reading Recovery"[R] include: promoting literacy skills; reducing the number of first-grade students who are struggling to read; and preventing long-term reading difficulties. The…

  2. Accurate measurement of dispersion data through short and narrow tubes used in very high-pressure liquid chromatography.

    PubMed

    Gritti, Fabrice; McDonald, Thomas; Gilar, Martin

    2015-09-04

    An original method is proposed for the accurate and reproducible measurement of the time-based dispersion properties of short L< 50cm and narrow rc< 50μm tubes at mobile phase flow rates typically used in very high-pressure liquid chromatography (vHPLC). Such tubes are used to minimize sample dispersion in vHPLC; however, their dispersion characteristics cannot be accurately measured at such flow rates due to system dispersion contribution of vHPLC injector and detector. It is shown that using longer and wider tubes (>10μL) enables a reliable measurement of the dispersion data. We confirmed that the dimensionless plot of the reduced dispersion coefficient versus the reduced linear velocity (Peclet number) depends on the aspect ratio, L/rc, of the tube, and unexpectedly also on the diffusion coefficient of the analyte. This dimensionless plot could be easily obtained for a large volume tube, which has the same aspect ratio as that of the short and narrow tube, and for the same diffusion coefficient. The dispersion data for the small volume tube are then directly extrapolated from this plot. For instance, it is found that the maximum volume variances of 75μm×30.5cm and 100μm×30.5cm prototype finger-tightened connecting tubes are 0.10 and 0.30μL(2), respectively, with an accuracy of a few percent and a precision smaller than seven percent. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Grade 12 Diploma Examination, English 30. Part B: Reading (Multiple Choice). Readings Booklet. 1986 Edition.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton.

    Intended for students taking the Grade 12 Examination in English 30 in Alberta, Canada, this reading test (to be administered along with the questions booklet) contains 10 short reading selections taken from fiction, nonfiction, poetry, and drama, including the following: "My Magical Metronome" (Lewis Thomas); "Queen Street…

  4. Reading and Reading-Related Skills in Children Using Cochlear Implants: Prospects for the Influence of Cued Speech

    ERIC Educational Resources Information Center

    Bouton, Sophie; Bertoncini, Josiane; Serniclaes, Willy; Cole, Pascale

    2011-01-01

    We assessed the reading and reading-related skills (phonemic awareness and phonological short-term memory) of deaf children fitted with cochlear implants (CI), either exposed to cued speech early (before 2 years old) (CS+) or never (CS-). Their performance was compared to that of 2 hearing control groups, 1 matched for reading level (RL), and 1…

  5. Accurate classical short-range forces for the study of collision cascades in Fe–Ni–Cr

    DOE PAGES

    Béland, Laurent Karim; Tamm, Artur; Mu, Sai; ...

    2017-05-10

    The predictive power of a classical molecular dynamics simulation is largely determined by the physical validity of its underlying empirical potential. In the case of high-energy collision cascades, it was recently shown that correctly modeling interactions at short distances is necessary to accurately predict primary damage production. An ab initio based framework is introduced for modifying an existing embedded-atom method FeNiCr potential to handle these short-range interactions. Density functional theory is used to calculate the energetics of two atoms approaching each other, embedded in the alloy, and to calculate the equation of state of the alloy as it is compressed.more » The pairwise terms and the embedding terms of the potential are modi ed in accordance with the ab initio results. Using this reparametrized potential, collision cascades are performed in Ni 50Fe 50, Ni 80Cr 20 and Ni 33Fe 33Cr 33. The simulations reveal that alloying Ni and NiCr to Fe reduces primary damage production, in agreement with some previous calculations. Alloying Ni and NiFe to Cr does not reduce primary damage production, in contradiction with previous calculations.« less

  6. Is More Screening Better? The Relationship between Frequent Screening, Accurate Decisions, and Reading Proficiency

    ERIC Educational Resources Information Center

    VanDerHeyden, Amanda M.; Burns, Matthew K.; Bonifay, Wesley

    2018-01-01

    Screening is necessary to detect risk and prevent reading failure. Yet the amount of screening that commonly occurs in U.S. schools may undermine its value, creating more error in decision making and lost instructional opportunity. This 2-year longitudinal study examined the decision accuracy associated with collecting concurrent reading screening…

  7. Reading Self-Efficacy Predicts Word Reading But Not Comprehension in Both Girls and Boys.

    PubMed

    Carroll, Julia M; Fox, Amy C

    2016-01-01

    The relationship between cognitive skills and reading has been well-established. However, the role of motivational factors such as self-efficacy in reading progress is less clear. In particular, it is not clear how self-efficacy relates to word level reading versus comprehension, and whether this differs in boys and girls. This study examines the relationship between self-efficacy, word reading and reading comprehension across the range of reading abilities after controlling for reading-related cognitive factors. One hundred and seventy nine children (86 males and 93 females) between 8 and 11 years old completed a self-report measure of reading self-efficacy together with measures of reading comprehension and word reading, working memory, auditory short-term memory, phonological awareness, and vocabulary. Boys and girls showed similar levels of attainment and reading self-efficacy. Reading self-efficacy was associated with word reading, but not with reading comprehension in either boys or girls. It is argued that this may reflect important differences between reading self-efficacy and more general measures of reading motivation and engagement. Reading self-efficacy is an element of reading motivation that is closely associated with a child's perceived attainments in reading and is less susceptible to the gender differences seen in broader measures.

  8. Reading Self-Efficacy Predicts Word Reading But Not Comprehension in Both Girls and Boys

    PubMed Central

    Carroll, Julia M.; Fox, Amy C.

    2017-01-01

    The relationship between cognitive skills and reading has been well-established. However, the role of motivational factors such as self-efficacy in reading progress is less clear. In particular, it is not clear how self-efficacy relates to word level reading versus comprehension, and whether this differs in boys and girls. This study examines the relationship between self-efficacy, word reading and reading comprehension across the range of reading abilities after controlling for reading-related cognitive factors. One hundred and seventy nine children (86 males and 93 females) between 8 and 11 years old completed a self-report measure of reading self-efficacy together with measures of reading comprehension and word reading, working memory, auditory short-term memory, phonological awareness, and vocabulary. Boys and girls showed similar levels of attainment and reading self-efficacy. Reading self-efficacy was associated with word reading, but not with reading comprehension in either boys or girls. It is argued that this may reflect important differences between reading self-efficacy and more general measures of reading motivation and engagement. Reading self-efficacy is an element of reading motivation that is closely associated with a child’s perceived attainments in reading and is less susceptible to the gender differences seen in broader measures. PMID:28144223

  9. The Interdependence of Long- and Short-Term Components in Unmasked Repetition Priming: An Indication of Shared Resources.

    PubMed

    Merema, Matt R; Speelman, Craig P

    2015-01-01

    It has been suggested that unmasked repetition priming is composed of distinct long-and short-term priming components. The current study sought to clarify the relationship between these components by examining the relationship between them. A total of 60 people (45 females, 15 males) participated in a computer-based lexical decision task designed to measure levels of short-term priming across different levels of long-term priming. The results revealed an interdependent relationship between the two components, whereby an increase in long-term priming prompted a decrease in short-term priming. Both long-term and short-term priming were accurately captured by a single power function over seven minutes post repetition, suggesting the two components may draw on the same resources. This interdependence between long- and short-term priming may serve to improve fluency in reading.

  10. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling.

    PubMed

    Li, Shan; Dong, Xia; Su, Zhengchang

    2013-07-30

    Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamically transcribed under different conditions, and a large portion of genes and intergenic regions have antisense RNA (asRNA) and non-coding RNA (ncRNA) transcripts, respectively. Ironically, similar studies have not been conducted in the model bacterium E coli K12, thus it is unknown whether or not the bacterium possesses similar complex transcriptomes. Furthermore, although RNA-seq becomes the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads. To fill these gaps, we have profiled the transcriptomes of E. coli K12 under different culture conditions and growth phases using a highly specific directional RNA-seq technique that can capture various types of transcripts in the bacterial cells, combined with a highly accurate and robust algorithm and tool TruHMM (http://bioinfolab.uncc.edu/TruHmm_package/) for assembling full length transcripts. We found that 46.9 ~ 63.4% of expressed operons were utilized in their putative alternative forms, 72.23 ~ 89.54% genes had putative asRNA transcripts and 51.37 ~ 72.74% intergenic regions had putative ncRNA transcripts under different culture conditions and growth phases. As has been demonstrated in many other prokaryotes, E. coli K12 also has a highly complex and dynamic transcriptomes under different culture conditions and growth phases. Such complex and dynamic transcriptomes might play important roles in the physiology of the bacterium. TruHMM is a highly accurate and robust algorithm for assembling full-length transcripts in prokaryotes using directional RNA-seq short reads.

  11. Validation of a Supplemental Reading Intervention for First-Grade Children

    ERIC Educational Resources Information Center

    Case, Lisa Pericola; Speece, Deborah L.; Silverman, Rebecca; Ritchey, Kristen D.; Schatschneider, Christopher; Cooper, David H.; Montanaro, Elizabeth; Jacobs, Dawn

    2010-01-01

    This experimental study was designed to validate a short-term supplemental reading intervention for at-risk first-grade children. Although substantial research on long-term supplemental reading interventions exists, less is known about short-term interventions. Thirty first-grade children were randomly assigned to intervention or control…

  12. Finished Prokaryotic Genome Assemblies from a Low-cost Combination of Short and Long Reads (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yin, Shuangye

    2012-06-01

    Shuangye Yin on "Finished prokaryotic genome assemblies from a low-cost combination of short and long reads"; at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  13. Electronic Thermometer Readings

    NASA Technical Reports Server (NTRS)

    2001-01-01

    NASA Stennis' adaptive predictive algorithm for electronic thermometers uses sample readings during the initial rise in temperature and applies an algorithm that accurately and rapidly predicts the steady state temperature. The final steady state temperature of an object can be calculated based on the second-order logarithm of the temperature signals acquired by the sensor and predetermined variables from the sensor characteristics. These variables are calculated during tests of the sensor. Once the variables are determined, relatively little data acquisition and data processing time by the algorithm is required to provide a near-accurate approximation of the final temperature. This reduces the delay in the steady state response time of a temperature sensor. This advanced algorithm can be implemented in existing software or hardware with an erasable programmable read-only memory (EPROM). The capability for easy integration eliminates the expense of developing a whole new system that offers the benefits provided by NASA Stennis' technology.

  14. Impact of sequencing depth and read length on single cell RNA sequencing data of T cells.

    PubMed

    Rizzetto, Simone; Eltahla, Auda A; Lin, Peijie; Bull, Rowena; Lloyd, Andrew R; Ho, Joshua W K; Venturi, Vanessa; Luciani, Fabio

    2017-10-06

    Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.g. RNA library capture, cell quality, and sequencing output affect the quality of scRNA-seq data. We studied the effects of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 single cells from 8 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. Successful TCRαβ reconstruction was achieved for 6 datasets (81% - 100%) with at least 0.25 millions (PE) reads of length >50 bp, while it failed for datasets with <30 bp reads. Sufficient read length and sequencing depth can control technical noise to enable accurate identification of TCRαβ and gene expression profiles from scRNA-seq data of T cells.

  15. Italian Children with Dyslexia Are Also Poor in Reading English Words, but Accurate in Reading English Pseudowords

    ERIC Educational Resources Information Center

    Palladino, Paola; Bellagamba, Isabella; Ferrari, Marcella; Cornoldi, Cesare

    2013-01-01

    It has been argued that children with dyslexia (DC) are poor at learning a foreign language (L2) and, in particular, reading foreign words. This assumption is so general that an Italian law (law 170, October, 2010) has established that DC may be completely exempted from foreign language learning and, in any case, should not be engaged in tuition…

  16. The Influence of Working Memory on Reading Growth in Subgroups of Children with Reading Disabilities

    ERIC Educational Resources Information Center

    Swanson, H. Lee; Jerman, Olga

    2007-01-01

    This 3-year longitudinal study determined whether (a) subgroups of children with reading disabilities (RD) (children with RD only, children with both reading and arithmetic deficits, and low verbal IQ readers) and skilled readers varied in working memory (WM) and short-term memory (STM) growth and (b) whether growth in an executive system and/or a…

  17. Reading difficulties in Albanian.

    PubMed

    Avdyli, Rrezarta; Cuetos, Fernando

    2012-10-01

    Albanian is an Indo-European language with a shallow orthography, in which there is an absolute correspondence between graphemes and phonemes. We aimed to know reading strategies used by Albanian disabled children during word and pseudoword reading. A pool of 114 Kosovar reading disabled children matched with 150 normal readers aged 6 to 11 years old were tested. They had to read 120 stimuli varied in lexicality, frequency, and length. The results in terms of reading accuracy as well as in reading times show that both groups were affected by lexicality and length effects. In both groups, length and lexicality effects were significantly modulated by school year being greater in early grades and later diminish in length and just the opposite in lexicality. However, the reading difficulties group was less accurate and slower than the control group across all school grades. Analyses of the error patterns showed that phonological errors, when the letter replacement leading to new nonwords, are the most common error type in both groups, although as grade rises, visual errors and lexicalizations increased more in the control group than the reading difficulties group. These findings suggest that Albanian normal children use both routes (lexical and sublexical) from the beginning of reading despite of the complete regularity of Albanian, while children with reading difficulties start using sublexical reading and the lexical reading takes more time to acquire, but finally both routes are functional.

  18. Passage Independence within Standardized Reading Comprehension Tests

    ERIC Educational Resources Information Center

    Roy-Charland, Annie; Colangelo, Gabrielle; Foglia, Victoria; Reguigui, Leïla

    2017-01-01

    In tests used to measure reading comprehension, validity is important in obtaining accurate results. Unfortunately, studies have shown that people can correctly answer some questions of these tests without reading the related passage. These findings bring forth the need to address whether this phenomenon is observed in multiple-choice only tests…

  19. Direct reading of electrocardiograms and respiration rates

    NASA Technical Reports Server (NTRS)

    Wise, J. P.

    1969-01-01

    Technique for reading heart and respiration rates is more accurate and direct than the previous method. Index of a plastic calibrated card is aligned with a point on the electrocardiogram. Complexes are counted as indicated on the card and heart or respiration rate is read directly from the appropriate scale.

  20. Reading Recovery[R]. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2007

    2007-01-01

    "Reading Recovery"[R] is a short-term tutoring intervention program intended to serve the lowest achieving (bottom 20%) first-grade students. Students are chosen for "Reading Recovery"[R] by school staff, and selection is based on prior reading achievement, diagnostic testing (the Clay Observation Survey of Early Literacy Achievement), and teacher…

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

    PubMed

    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.

  2. Parallel versus Sequential Processing in Print and Braille Reading

    ERIC Educational Resources Information Center

    Veispak, Anneli; Boets, Bart; Ghesquiere, Pol

    2012-01-01

    In the current study we investigated word, pseudoword and story reading in Dutch speaking braille and print readers. To examine developmental patterns, these reading skills were assessed in both children and adults. The results reveal that braille readers read less accurately and fast than print readers. While item length has no impact on word…

  3. What Evidence Says about Reading Recovery.

    ERIC Educational Resources Information Center

    Reading Recovery Council of North America, Columbus, OH.

    Reading Recovery (RR) is a short-term intervention for the lowest-achieving children in first grade. Children meet individually with a specially trained teacher for 30 minutes daily for 12 to 20 weeks. There is substantial scientific evidence to support Reading Recovery's effectiveness with the lowest-performing first-grade students. Reading…

  4. Grade 12 Diploma Examination, English 33. Part B: Reading (Multiple Choice). Readings Booklet. June 1988 Edition.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton.

    Intended for students taking the English 33 Grade 12 Diploma Examinations in Alberta, Canada, this test (to be administered along with a questions booklet) contains the reading selections portion of Part B, the reading component of the June 1988 tests. The following short selections taken from fiction, nonfiction, poetry, drama, and day-to-day…

  5. Assessing Reading Rate in the Primary Grades (1-3)

    ERIC Educational Resources Information Center

    Morris, Darrell; Trathen, Woodrow; Gill, Tom; Schlagal, Robert; Ward, Devery; Frye, Elizabeth M.

    2017-01-01

    In this study we explore students' reading rates in grades 1-3. We begin with a short history of reading rate as an assessment measure in the early grades. Next, we share rate data from a recent study (N = 305) where children's contextual reading was assessed with a traditional passage-reading inventory. A comparison of our average grade-level…

  6. Novice Teachers' Knowledge of Reading-Related Disabilities and Dyslexia

    ERIC Educational Resources Information Center

    Washburn, Erin K.; Mulcahy, Candance A.; Musante, Gail; Joshi, R. Malatesha

    2017-01-01

    Current understandings about the nature of persistent reading problems have been influenced by researchers in numerous fields. Researchers have noted that a current and accurate understanding of reading disabilities, such as dyslexia, can be helpful in assessing, teaching and supporting individuals with persistent reading problems. The purpose of…

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

    ScienceCinema

    Sakakibara, Yasumbumi

    2018-02-13

    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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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.

  9. Parallel and Serial Reading Processes in Children's Word and Nonword Reading

    ERIC Educational Resources Information Center

    van den Boer, Madelon; de Jong, Peter F.

    2015-01-01

    Fluent reading is characterized by rapid and accurate identification of words. It is commonly accepted that such identification relies on the availability of orthographic knowledge. However, whether this orthographic knowledge should be seen as an accumulation of word-specific knowledge in a lexicon acquired through decoding or as a well-developed…

  10. Genome assembly from synthetic long read clouds

    PubMed Central

    Kuleshov, Volodymyr; Snyder, Michael P.; Batzoglou, Serafim

    2016-01-01

    Motivation: Despite rapid progress in sequencing technology, assembling de novo the genomes of new species as well as reconstructing complex metagenomes remains major technological challenges. New synthetic long read (SLR) technologies promise significant advances towards these goals; however, their applicability is limited by high sequencing requirements and the inability of current assembly paradigms to cope with combinations of short and long reads. Results: Here, we introduce Architect, a new de novo scaffolder aimed at SLR technologies. Unlike previous assembly strategies, Architect does not require a costly subassembly step; instead it assembles genomes directly from the SLR’s underlying short reads, which we refer to as read clouds. This enables a 4- to 20-fold reduction in sequencing requirements and a 5-fold increase in assembly contiguity on both genomic and metagenomic datasets relative to state-of-the-art assembly strategies aimed directly at fully subassembled long reads. Availability and Implementation: Our source code is freely available at https://github.com/kuleshov/architect. Contact: kuleshov@stanford.edu PMID:27307620

  11. The Group Reading Inventory in the Social Studies Classroom.

    ERIC Educational Resources Information Center

    Henk, William A.; Helfeldt, John P.

    1985-01-01

    The Group Reading Inventory (GRI) is a reading evaluation tool that can survey an entire class of students at the same time. A testing sequence using GRI that allows teachers to identify the functional reading levels of most students in three short examination sessions is presented. (RM)

  12. In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages.

    PubMed

    Ingle, Danielle J; Valcanis, Mary; Kuzevski, Alex; Tauschek, Marija; Inouye, Michael; Stinear, Tim; Levine, Myron M; Robins-Browne, Roy M; Holt, Kathryn E

    2016-07-01

    The lipopolysaccharide (O) and flagellar (H) surface antigens of Escherichia coli are targets for serotyping that have traditionally been used to identify pathogenic lineages. These surface antigens are important for the survival of E. coli within mammalian hosts. However, traditional serotyping has several limitations, and public health reference laboratories are increasingly moving towards whole genome sequencing (WGS) to characterize bacterial isolates. Here we present a method to rapidly and accurately serotype E. coli isolates from raw, short read WGS data. Our approach bypasses the need for de novo genome assembly by directly screening WGS reads against a curated database of alleles linked to known and novel E. coli O-groups and H-types (the EcOH database) using the software package srst2. We validated the approach by comparing in silico results for 197 enteropathogenic E. coli isolates with those obtained by serological phenotyping in an independent laboratory. We then demonstrated the utility of our method to characterize isolates in public health and clinical settings, and to explore the genetic diversity of >1500 E. coli genomes from multiple sources. Importantly, we showed that transfer of O- and H-antigen loci between E. coli chromosomal backbones is common, with little evidence of constraints by host or pathotype, suggesting that E. coli ' strain space' may be virtually unlimited, even within specific pathotypes. Our findings show that serotyping is most useful when used in combination with strain genotyping to characterize microevolution events within an inferred population structure.

  13. Accurate Filtering of Privacy-Sensitive Information in Raw Genomic Data.

    PubMed

    Decouchant, Jérémie; Fernandes, Maria; Völp, Marcus; Couto, Francisco M; Esteves-Veríssimo, Paulo

    2018-04-13

    Sequencing thousands of human genomes has enabled breakthroughs in many areas, among them precision medicine, the study of rare diseases, and forensics. However, mass collection of such sensitive data entails enormous risks if not protected to the highest standards. In this article, we follow the position and argue that post-alignment privacy is not enough and that data should be automatically protected as early as possible in the genomics workflow, ideally immediately after the data is produced. We show that a previous approach for filtering short reads cannot extend to long reads and present a novel filtering approach that classifies raw genomic data (i.e., whose location and content is not yet determined) into privacy-sensitive (i.e., more affected by a successful privacy attack) and non-privacy-sensitive information. Such a classification allows the fine-grained and automated adjustment of protective measures to mitigate the possible consequences of exposure, in particular when relying on public clouds. We present the first filter that can be indistinctly applied to reads of any length, i.e., making it usable with any recent or future sequencing technologies. The filter is accurate, in the sense that it detects all known sensitive nucleotides except those located in highly variable regions (less than 10 nucleotides remain undetected per genome instead of 100,000 in previous works). It has far less false positives than previously known methods (10% instead of 60%) and can detect sensitive nucleotides despite sequencing errors (86% detected instead of 56% with 2% of mutations). Finally, practical experiments demonstrate high performance, both in terms of throughput and memory consumption. Copyright © 2018. Published by Elsevier Inc.

  14. Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.

    PubMed

    Liu, Xuejun; Shi, Xinxin; Chen, Chunlin; Zhang, Li

    2015-10-16

    The high-throughput sequencing technology, RNA-Seq, has been widely used to quantify gene and isoform expression in the study of transcriptome in recent years. Accurate expression measurement from the millions or billions of short generated reads is obstructed by difficulties. One is ambiguous mapping of reads to reference transcriptome caused by alternative splicing. This increases the uncertainty in estimating isoform expression. The other is non-uniformity of read distribution along the reference transcriptome due to positional, sequencing, mappability and other undiscovered sources of biases. This violates the uniform assumption of read distribution for many expression calculation approaches, such as the direct RPKM calculation and Poisson-based models. Many methods have been proposed to address these difficulties. Some approaches employ latent variable models to discover the underlying pattern of read sequencing. However, most of these methods make bias correction based on surrounding sequence contents and share the bias models by all genes. They therefore cannot estimate gene- and isoform-specific biases as revealed by recent studies. We propose a latent variable model, NLDMseq, to estimate gene and isoform expression. Our method adopts latent variables to model the unknown isoforms, from which reads originate, and the underlying percentage of multiple spliced variants. The isoform- and exon-specific read sequencing biases are modeled to account for the non-uniformity of read distribution, and are identified by utilizing the replicate information of multiple lanes of a single library run. We employ simulation and real data to verify the performance of our method in terms of accuracy in the calculation of gene and isoform expression. Results show that NLDMseq obtains competitive gene and isoform expression compared to popular alternatives. Finally, the proposed method is applied to the detection of differential expression (DE) to show its usefulness in the

  15. Flexible taxonomic assignment of ambiguous sequencing reads

    PubMed Central

    2011-01-01

    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. PMID:21211059

  16. DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.

    PubMed

    Yavaş, Gökhan; Koyutürk, Mehmet; Gould, Meetha P; McMahon, Sarah; LaFramboise, Thomas

    2014-03-05

    With the advent of paired-end high throughput sequencing, it is now possible to identify various types of structural variation on a genome-wide scale. Although many methods have been proposed for structural variation detection, most do not provide precise boundaries for identified variants. In this paper, we propose a new method, Distribution Based detection of Duplication Boundaries (DB2), for accurate detection of tandem duplication breakpoints, an important class of structural variation, with high precision and recall. Our computational experiments on simulated data show that DB2 outperforms state-of-the-art methods in terms of finding breakpoints of tandem duplications, with a higher positive predictive value (precision) in calling the duplications' presence. In particular, DB2's prediction of tandem duplications is correct 99% of the time even for very noisy data, while narrowing down the space of possible breakpoints within a margin of 15 to 20 bps on the average. Most of the existing methods provide boundaries in ranges that extend to hundreds of bases with lower precision values. Our method is also highly robust to varying properties of the sequencing library and to the sizes of the tandem duplications, as shown by its stable precision, recall and mean boundary mismatch performance. We demonstrate our method's efficacy using both simulated paired-end reads, and those generated from a melanoma sample and two ovarian cancer samples. Newly discovered tandem duplications are validated using PCR and Sanger sequencing. Our method, DB2, uses discordantly aligned reads, taking into account the distribution of fragment length to predict tandem duplications along with their breakpoints on a donor genome. The proposed method fine tunes the breakpoint calls by applying a novel probabilistic framework that incorporates the empirical fragment length distribution to score each feasible breakpoint. DB2 is implemented in Java programming language and is freely available

  17. Tracking reading: dual task costs of oral reading for young versus older adults.

    PubMed

    Kemper, Susan; Bontempo, Daniel; Schmalzried, RaLynn; McKedy, Whitney; Tagliaferri, Bruno; Kieweg, Doug

    2014-02-01

    A digital pursuit rotor was used to monitor oral reading costs by time-locking tracking performance to the auditory wave form produced as young and older adults were reading out short paragraphs. Multilevel modeling was used to determine how paragraph-level predictors of length, grammatical complexity, and readability and person-level predictors such as speaker age or working memory capacity predicted reading and tracking performance. In addition, sentence-by-sentence variation in tracking performance was examined during the production of individual sentences and during the pauses before upcoming sentences. The results suggest that dual tasking has a greater impact on older adults' reading comprehension and tracking performance. At the level of individual sentences, young and older adults adopt different strategies to deal with grammatically complex and propositionally dense sentences.

  18. There are multiple contributors to the verbal short-term memory deficit in children with developmental reading disabilities.

    PubMed

    Kibby, Michelle Y

    2009-09-01

    Prior research has put forth at least four possible contributors to the verbal short-term memory (VSTM) deficit in children with developmental reading disabilities (RD): poor phonological awareness that affects phonological coding into VSTM, a less effective phonological store, slow articulation rate, and fewer/poorer quality long-term memory (LTM) representations. This project is among the first to test the four suppositions in one study. Participants included 18 children with RD and 18 controls. VSTM was assessed using Baddeley's model of the phonological loop. Findings suggest all four suppositions are correct, depending upon the type of material utilized. Children with RD performed comparably to controls in VSTM for common words but worse for less frequent words and nonwords. Furthermore, only articulation rate predicted VSTM for common words, whereas Verbal IQ and articulation rate predicted VSTM for less frequent words, and phonological awareness and articulation rate predicted VSTM for nonwords. Overall, findings suggest that the mechanism(s) used to code and store items by their meaning is intact in RD, and the deficit in VSTM for less frequent words may be a result of fewer/poorer quality LTM representations for these words. In contrast, phonological awareness and the phonological store are impaired, affecting VSTM for items that are coded phonetically. Slow articulation rate likely affects VSTM for most material when present. When assessing reading performance, VSTM predicted decoding skill but not word identification after controlling Verbal IQ and phonological awareness. Thus, VSTM likely contributes to reading ability when words are novel and must be decoded.

  19. The draft genome of MD-2 pineapple using hybrid error correction of long reads

    PubMed Central

    Redwan, Raimi M.; Saidin, Akzam; Kumar, S. Vijay

    2016-01-01

    The introduction of the elite pineapple variety, MD-2, has caused a significant market shift in the pineapple industry. Better productivity, overall increased in fruit quality and taste, resilience to chilled storage and resistance to internal browning are among the key advantages of the MD-2 as compared with its previous predecessor, the Smooth Cayenne. Here, we present the genome sequence of the MD-2 pineapple (Ananas comosus (L.) Merr.) by using the hybrid sequencing technology from two highly reputable platforms, i.e. the PacBio long sequencing reads and the accurate Illumina short reads. Our draft genome achieved 99.6% genome coverage with 27,017 predicted protein-coding genes while 45.21% of the genome was identified as repetitive elements. Furthermore, differential expression of ripening RNASeq library of pineapple fruits revealed ethylene-related transcripts, believed to be involved in regulating the process of non-climacteric pineapple fruit ripening. The MD-2 pineapple draft genome serves as an example of how a complex heterozygous genome is amenable to whole genome sequencing by using a hybrid technology that is both economical and accurate. The genome will make genomic applications more feasible as a medium to understand complex biological processes specific to pineapple. PMID:27374615

  20. A survey of the sorghum transcriptome using single-molecule long reads

    DOE PAGES

    Abdel-Ghany, Salah E.; Hamilton, Michael; Jacobi, Jennifer L.; ...

    2016-06-24

    Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novelmore » splice isoforms. Additionally, we uncover APA ofB11,000 expressed genes and more than 2,100 novel genes. Lastly, these results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism.« less

  1. A survey of the sorghum transcriptome using single-molecule long reads

    PubMed Central

    Abdel-Ghany, Salah E.; Hamilton, Michael; Jacobi, Jennifer L.; Ngam, Peter; Devitt, Nicholas; Schilkey, Faye; Ben-Hur, Asa; Reddy, Anireddy S. N.

    2016-01-01

    Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA of ∼11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism. PMID:27339290

  2. Reading Recovery[R]. What Works Clearinghouse Intervention Report. Updated

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2013

    2013-01-01

    Reading Recovery[R]” is a short-term intervention that provides one-on-one tutoring to first-grade students who are struggling in reading and writing. The supplementary program aims to promote literacy skills and foster the development of reading and writing strategies by tailoring individualized lessons to each student. Tutoring is delivered by…

  3. The influence of working memory on reading growth in subgroups of children with reading disabilities.

    PubMed

    Swanson, H Lee; Jerman, Olga

    2007-04-01

    This 3-year longitudinal study determined whether (a) subgroups of children with reading disabilities (RD) (children with RD only, children with both reading and arithmetic deficits, and low verbal IQ readers) and skilled readers varied in working memory (WM) and short-term memory (STM) growth and (b) whether growth in an executive system and/or a phonological storage system mediated growth in reading performance. A battery of memory and reading measures was administered to 84 children (11-17 years of age) across three testing waves spaced 1 year apart. The results showed that skilled readers yielded higher WM growth estimates than did the RD groups. No significant differentiation among subgroups of children with RD on growth measures emerged. Hierarchical linear modeling showed that WM (controlled attention), rather than STM (phonological loop), was related to growth in reading comprehension and reading fluency. The results support the notion that deficient growth in the executive component of WM underlies RD.

  4. A Reader, Inside and Out: Exploring More Ecologically Valid Understandings of Reading Motivation

    ERIC Educational Resources Information Center

    Neugebauer, Sabina Rak

    2011-01-01

    Literacy development is one of the most accurate predictors of academic success with motivation to read being a central component of that development. The documented decrease in reading motivation in adolescence is concerning for educators because of the strong association between reading motivation and reading performance. This motivational…

  5. Long Reads: their Purpose and Place.

    PubMed

    Pollard, Martin O; Gurdasani, Deepti; Mentzer, Alexander J; Porter, Tarryn; Sandhu, Manjinder S

    2018-05-14

    In recent years long read technologies have moved from being a niche and specialist field to a point of relative maturity likely to feature frequently in the genomic landscape. Analogous to next generation sequencing (NGS), the cost of sequencing using long read technologies has materially dropped whilst the instrument throughput continues to increase. Together these changes present the prospect of sequencing large numbers of individuals with the aim of fully characterising genomes at high resolution. In this article, we will endeavour to present an introduction to long read technologies showing: what long reads are; how they are distinct from short reads; why long reads are useful; and how they are being used. We will highlight the recent developments in this field, and the applications and potential of these technologies in medical research, and clinical diagnostics and therapeutics.

  6. Working Memory in Children with Reading Disabilities

    ERIC Educational Resources Information Center

    Gathercole, Susan Elizabeth; Alloway, Tracy Packiam; Willis, Catherine; Adams, Anne-Marie

    2006-01-01

    This study investigated associations between working memory (measured by complex memory tasks) and both reading and mathematics abilities, as well as the possible mediating factors of fluid intelligence, verbal abilities, short-term memory (STM), and phonological awareness, in a sample of 46 6- to 11-year-olds with reading disabilities. As a…

  7. Reading Comprehension: Techniques for Assessment and Optimization.

    ERIC Educational Resources Information Center

    Tyler, Sherman W.; And Others

    Three studies examined the nature of individual differences and the role of advance information in reading comprehension. The subjects, 116 college students, read short passages--in some cases preceded by a given type of advance organizer--recalled the information therein, and finally sorted ideas from the passage into groups of similar ideas.…

  8. Differential cognitive and perceptual correlates of print reading versus braille reading.

    PubMed

    Veispak, Anneli; Boets, Bart; Ghesquière, Pol

    2013-01-01

    The relations between reading, auditory, speech, phonological and tactile spatial processing are investigated in a Dutch speaking sample of blind braille readers as compared to sighted print readers. Performance is assessed in blind and sighted children and adults. Regarding phonological ability, braille readers perform equally well compared to print readers on phonological awareness, better on verbal short-term memory and significantly worse on lexical retrieval. The groups do not differ on speech perception or auditory processing. Braille readers, however, have more sensitive fingers than print readers. Investigation of the relations between these cognitive and perceptual skills and reading performance indicates that in the group of braille readers auditory temporal processing has a longer lasting and stronger impact not only on phonological abilities, which have to satisfy the high processing demands of the strictly serial language input, but also directly on the reading ability itself. Print readers switch between grapho-phonological and lexical reading modes depending on the familiarity of the items. Furthermore, the auditory temporal processing and speech perception, which were substantially interrelated with phonological processing, had no direct associations with print reading measures. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Fast, accurate and easy-to-pipeline methods for amplicon sequence processing

    NASA Astrophysics Data System (ADS)

    Antonielli, Livio; Sessitsch, Angela

    2016-04-01

    Next generation sequencing (NGS) technologies established since years as an essential resource in microbiology. While on the one hand metagenomic studies can benefit from the continuously increasing throughput of the Illumina (Solexa) technology, on the other hand the spreading of third generation sequencing technologies (PacBio, Oxford Nanopore) are getting whole genome sequencing beyond the assembly of fragmented draft genomes, making it now possible to finish bacterial genomes even without short read correction. Besides (meta)genomic analysis next-gen amplicon sequencing is still fundamental for microbial studies. Amplicon sequencing of the 16S rRNA gene and ITS (Internal Transcribed Spacer) remains a well-established widespread method for a multitude of different purposes concerning the identification and comparison of archaeal/bacterial (16S rRNA gene) and fungal (ITS) communities occurring in diverse environments. Numerous different pipelines have been developed in order to process NGS-derived amplicon sequences, among which Mothur, QIIME and USEARCH are the most well-known and cited ones. The entire process from initial raw sequence data through read error correction, paired-end read assembly, primer stripping, quality filtering, clustering, OTU taxonomic classification and BIOM table rarefaction as well as alternative "normalization" methods will be addressed. An effective and accurate strategy will be presented using the state-of-the-art bioinformatic tools and the example of a straightforward one-script pipeline for 16S rRNA gene or ITS MiSeq amplicon sequencing will be provided. Finally, instructions on how to automatically retrieve nucleotide sequences from NCBI and therefore apply the pipeline to targets other than 16S rRNA gene (Greengenes, SILVA) and ITS (UNITE) will be discussed.

  10. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling

    PubMed Central

    2013-01-01

    Background Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamically transcribed under different conditions, and a large portion of genes and intergenic regions have antisense RNA (asRNA) and non-coding RNA (ncRNA) transcripts, respectively. Ironically, similar studies have not been conducted in the model bacterium E coli K12, thus it is unknown whether or not the bacterium possesses similar complex transcriptomes. Furthermore, although RNA-seq becomes the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads. Results To fill these gaps, we have profiled the transcriptomes of E. coli K12 under different culture conditions and growth phases using a highly specific directional RNA-seq technique that can capture various types of transcripts in the bacterial cells, combined with a highly accurate and robust algorithm and tool TruHMM (http://bioinfolab.uncc.edu/TruHmm_package/) for assembling full length transcripts. We found that 46.9 ~ 63.4% of expressed operons were utilized in their putative alternative forms, 72.23 ~ 89.54% genes had putative asRNA transcripts and 51.37 ~ 72.74% intergenic regions had putative ncRNA transcripts under different culture conditions and growth phases. Conclusions As has been demonstrated in many other prokaryotes, E. coli K12 also has a highly complex and dynamic transcriptomes under different culture conditions and growth phases. Such complex and dynamic transcriptomes might play important roles in the physiology of the bacterium. TruHMM is a highly accurate and robust algorithm for assembling full-length transcripts in prokaryotes using directional RNA

  11. Identifying At-Risk Students for Early Reading Intervention: Challenges and Possible Solutions

    ERIC Educational Resources Information Center

    McAlenney, Athena Lentini; Coyne, Michael D.

    2011-01-01

    Accurate identification of at-risk kindergarten and 1st-grade students through early reading screening is an essential element of responsiveness to intervention models of reading instruction. The authors consider predictive validity and classification accuracy of early reading screening assessments with attention to sensitivity and specificity.…

  12. Reading Trajectories of Children with Language Difficulties from Preschool through Fifth Grade

    ERIC Educational Resources Information Center

    Skibbe, Lori E.; Grimm, Kevin J.; Stanton-Chapman, Tina L.; Justice, Laura M.; Pence, Khara L.; Bowles, Ryan P.

    2008-01-01

    Purpose: The current work examined which theory of reading development, the "cumulative reading trajectory or the compensatory trajectory of development," most accurately represents the reading trajectories of children with language difficulties (LD) relative to their peers with typical language (TL) skills. Specifically, initial levels of reading…

  13. Simple scale interpolator facilitates reading of graphs

    NASA Technical Reports Server (NTRS)

    Fetterman, D. E., Jr.

    1965-01-01

    Simple transparent overlay with interpolation scale facilitates accurate, rapid reading of graph coordinate points. This device can be used for enlarging drawings and locating points on perspective drawings.

  14. Semantic interference in picture naming during dual-task performance does not vary with reading ability.

    PubMed

    Piai, Vitória; Roelofs, Ardi; Roete, Ingeborg

    2015-01-01

    Previous dual-task studies examining the locus of semantic interference of distractor words in picture naming have obtained diverging results. In these studies, participants manually responded to tones and named pictures while ignoring distractor words (picture-word interference, PWI) with varying stimulus onset asynchrony (SOA) between tone and PWI stimulus. Whereas some studies observed no semantic interference at short SOAs, other studies observed effects of similar magnitude at short and long SOAs. The absence of semantic interference in some studies may perhaps be due to better reading skill of participants in these than in the other studies. According to such a reading-ability account, participants' reading skill should be predictive of the magnitude of their interference effect at short SOAs. To test this account, we conducted a dual-task study with tone discrimination and PWI tasks and measured participants' reading ability. The semantic interference effect was of similar magnitude at both short and long SOAs. Participants' reading ability was predictive of their naming speed but not of their semantic interference effect, contrary to the reading ability account. We conclude that the magnitude of semantic interference in picture naming during dual-task performance does not depend on reading skill.

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

    PubMed

    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.

  16. Underlying skills of oral and silent reading.

    PubMed

    van den Boer, Madelon; van Bergen, Elsje; de Jong, Peter F

    2014-12-01

    Many studies have examined reading and reading development. The majority of these studies, however, focused on oral reading rather than on the more dominant silent reading mode. Similarly, it is common practice to assess oral reading abilities rather than silent reading abilities in schools and in diagnosis of reading impairments. More important, insights gained through examinations of oral reading tend to be generalized to silent reading. In the current study, we examined whether such generalizations are justified. We directly compared oral and silent reading fluency by examining whether these reading modes relate to the same underlying skills. In total, 132 fourth graders read words, sentences, and text orally, and 123 classmates read the same material silently. As underlying skills, we considered phonological awareness, rapid naming, and visual attention span. All skills correlated significantly with both reading modes. Phonological awareness contributed equally to oral and silent reading. Rapid naming, however, correlated more strongly with oral reading than with silent reading. Visual attention span correlated equally strongly with both reading modes but showed a significant unique contribution only to silent reading. In short, we showed that oral and silent reading indeed are fairly similar reading modes, based on the relations with reading-related cognitive skills. However, we also found differences that warrant caution in generalizing findings across reading modes. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs.

    PubMed

    Chen-Harris, Haiyin; Borucki, Monica K; Torres, Clinton; Slezak, Tom R; Allen, Jonathan E

    2013-02-12

    High throughput sequencing is beginning to make a transformative impact in the area of viral evolution. Deep sequencing has the potential to reveal the mutant spectrum within a viral sample at high resolution, thus enabling the close examination of viral mutational dynamics both within- and between-hosts. The challenge however, is to accurately model the errors in the sequencing data and differentiate real viral mutations, particularly those that exist at low frequencies, from sequencing errors. We demonstrate that overlapping read pairs (ORP) -- generated by combining short fragment sequencing libraries and longer sequencing reads -- significantly reduce sequencing error rates and improve rare variant detection accuracy. Using this sequencing protocol and an error model optimized for variant detection, we are able to capture a large number of genetic mutations present within a viral population at ultra-low frequency levels (<0.05%). Our rare variant detection strategies have important implications beyond viral evolution and can be applied to any basic and clinical research area that requires the identification of rare mutations.

  18. Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.

    PubMed

    Tárraga, Joaquín; Arnau, Vicente; Martínez, Héctor; Moreno, Raul; Cazorla, Diego; Salavert-Torres, José; Blanquer-Espert, Ignacio; Dopazo, Joaquín; Medina, Ignacio

    2014-12-01

    HPG Aligner applies suffix arrays for DNA read mapping. This implementation produces a highly sensitive and extremely fast mapping of DNA reads that scales up almost linearly with read length. The approach presented here is faster (over 20× for long reads) and more sensitive (over 98% in a wide range of read lengths) than the current state-of-the-art mappers. HPG Aligner is not only an optimal alternative for current sequencers but also the only solution available to cope with longer reads and growing throughputs produced by forthcoming sequencing technologies. https://github.com/opencb/hpg-aligner. © The Author 2014. Published by Oxford University Press.

  19. The effect of word length and other sublexical, lexical, and semantic variables on developmental reading deficits.

    PubMed

    De Luca, Maria; Barca, Laura; Burani, Cristina; Zoccolotti, Pierluigi

    2008-12-01

    To examine the effect of word length and several sublexical, and lexico-semantic variables on the reading of Italian children with a developmental reading deficit. Previous studies indicated the role of word length in transparent orthographies. However, several factors that may interact with word length were not controlled for. Seventeen impaired and 34 skilled sixth-grade readers were presented words of different lengths, matched for initial phoneme, bigram frequency, word frequency, age of acquisition, and imageability. Participants were asked to read aloud, as quickly and as accurately as possible. Reaction times at the onset of pronunciation and mispronunciations were recorded. Impaired readers' reaction times indicated a marked effect of word length; in skilled readers, there was no length effect for short words but, rather, a monotonic increase from 6-letter words on. Regression analyses confirmed the role of word length and indicated the influence of word frequency (similar in impaired and skilled readers). No other variables predicted reading latencies. Word length differentially influenced word recognition in impaired versus skilled readers, irrespective of the action of (potentially interfering) sublexical, lexical, and semantic variables. It is proposed that the locus of the length effect is at a perceptual level of analysis. The independent influence of word frequency on the reading performance of both groups of participants indicates the sparing of lexical activation in impaired readers.

  20. Wired for Short Fiction: A Paradigm Shift for the 21st Century.

    ERIC Educational Resources Information Center

    Nellen, Ted

    For one instructor of eleventh and twelfth grade English, teaching the short story offers the best opportunity to teach fiction writing to students. It contains all the elements novels contain, but students can read many short stories in the same time they need to read a novel. Students can also write their own short stories. Above all, literature…

  1. The Short Readings Project: A CALL Reading Activity Utilizing Vocabulary Recycling

    ERIC Educational Resources Information Center

    Johnson, Andrew; Heffernan, Neil

    2006-01-01

    In 2003 multimedia-based English Trailers (www.english-trailers.com) joined the vast array of web sites dedicated to language learning enabling students, either autonomously or in a CALL classroom, to study English via movie commercials. To assist students in comprehending 10 trailers found on the site, the authors created the Short Readings…

  2. Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

    PubMed

    Rando, Halie M; Farré, Marta; Robson, Michael P; Won, Naomi B; Johnson, Jennifer L; Buch, Ronak; Bastounes, Estelle R; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Xiong, Zijun; Kim, Jaebum; Zhang, Guojie; Trut, Lyudmila N; Larkin, Denis M; Kukekova, Anna V

    2018-06-20

    The genome of a red fox ( Vulpes vulpes ) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

  3. Assessing Situated Reading Motivations across Content Areas: A Dynamic Literacy Motivation Instrument

    ERIC Educational Resources Information Center

    Neugebauer, Sabina Rak

    2017-01-01

    While educators and researchers agree on the crucial role of literacy motivation for performance, research on methods for accurately assessing adolescent reading motivation is still uncommon. The most used reading motivation instruments do not attend to the multiple content areas in which adolescents read. The present study examines a new…

  4. Effects of an Informational Text Reading Comprehension Intervention for Fifth-Grade Students

    ERIC Educational Resources Information Center

    Ritchey, Kristen D.; Palombo, Kimberly; Silverman, Rebecca D.; Speece, Deborah L.

    2017-01-01

    Upper elementary school students who have reading problems may have difficulty in one or more areas of reading, each requiring specific types of interventions. This study evaluated a short-term reading intervention for 46 fifth-grade students with poor reading comprehension. Students were randomly assigned to an intervention or no treatment…

  5. The Effect of Key on Vocal Sight-Reading Achievement

    ERIC Educational Resources Information Center

    Henry, Michele L.

    2013-01-01

    At its most basic level, sight-reading can be defined as the production of accurate pitch and rhythm from a previously unseen musical score. For vocalists, sight-reading principally involves the production of pitches by determining their relationship within a tonal framework. The ability to mentally conceive tonal function and convert it into…

  6. Phonological skills and their role in learning to read: a meta-analytic review.

    PubMed

    Melby-Lervåg, Monica; Lyster, Solveig-Alma Halaas; Hulme, Charles

    2012-03-01

    The authors report a systematic meta-analytic review of the relationships among 3 of the most widely studied measures of children's phonological skills (phonemic awareness, rime awareness, and verbal short-term memory) and children's word reading skills. The review included both extreme group studies and correlational studies with unselected samples (235 studies were included, and 995 effect sizes were calculated). Results from extreme group comparisons indicated that children with dyslexia show a large deficit on phonemic awareness in relation to typically developing children of the same age (pooled effect size estimate: -1.37) and children matched on reading level (pooled effect size estimate: -0.57). There were significantly smaller group deficits on both rime awareness and verbal short-term memory (pooled effect size estimates: rime skills in relation to age-matched controls, -0.93, and reading-level controls, -0.37; verbal short-term memory skills in relation to age-matched controls, -0.71, and reading-level controls, -0.09). Analyses of studies of unselected samples showed that phonemic awareness was the strongest correlate of individual differences in word reading ability and that this effect remained reliable after controlling for variations in both verbal short-term memory and rime awareness. These findings support the pivotal role of phonemic awareness as a predictor of individual differences in reading development. We discuss whether such a relationship is a causal one and the implications of research in this area for current approaches to the teaching of reading and interventions for children with reading difficulties.

  7. L2 Working Memory Capacity and L2 Reading Skill.

    ERIC Educational Resources Information Center

    Harrington, Mike; Sawyer, Mark

    1992-01-01

    Examines the sensitivity of second-language (L2) working memory (ability to store and process information simultaneously) to differences in reading skills among advanced L2 learners. Subjects with larger L2 working memory capacities scored higher on measures of L2 reading skills, but no correlation was found between reading and passive short-term…

  8. Working memory and arithmetic calculation in children: the contributory roles of processing speed, short-term memory, and reading.

    PubMed

    Berg, Derek H

    2008-04-01

    The cognitive underpinnings of arithmetic calculation in children are noted to involve working memory; however, cognitive processes related to arithmetic calculation and working memory suggest that this relationship is more complex than stated previously. The purpose of this investigation was to examine the relative contributions of processing speed, short-term memory, working memory, and reading to arithmetic calculation in children. Results suggested four important findings. First, processing speed emerged as a significant contributor of arithmetic calculation only in relation to age-related differences in the general sample. Second, processing speed and short-term memory did not eliminate the contribution of working memory to arithmetic calculation. Third, individual working memory components--verbal working memory and visual-spatial working memory--each contributed unique variance to arithmetic calculation in the presence of all other variables. Fourth, a full model indicated that chronological age remained a significant contributor to arithmetic calculation in the presence of significant contributions from all other variables. Results are discussed in terms of directions for future research on working memory in arithmetic calculation.

  9. Can We 'Read' the Eye-Movement Patterns of Readers? Unraveling the Relationship Between Reading Profiles and Processing Strategies.

    PubMed

    Koornneef, Arnout; Mulders, Iris

    2017-02-01

    In an eye-tracking experiment we examined the risky reading hypothesis, in which long saccades and many regressions are considered to be indicative of a proactive reading style (Rayner et al. in Psychol Aging 21(3):448, 2006; Psychol Aging 24(3):755, 2009). We did so by presenting short texts-that confirmed or disconfirmed verb-based implicit causality expectations-to two types of readers: proactive readers (long saccades, many regressions) and conservative readers (short saccades, few regressions). Whereas proactive readers used implicit causality information to predict upcoming referents, and slowed down immediately when they encountered a pronoun that was inconsistent with these verb-based expectations, the conservative readers slowed down much later in the sentence. These findings were consistent with the predictions of the risky reading hypothesis and as such presented novel evidence for the general idea that the eye-movement profile of readers reveals valuable information about their processing strategy.

  10. Fast and accurate de novo genome assembly from long uncorrected reads

    PubMed Central

    Vaser, Robert; Sović, Ivan; Nagarajan, Niranjan

    2017-01-01

    The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment–based, stand-alone consensus module called Racon. Based on tests with PacBio and Oxford Nanopore data sets, we show that Racon coupled with miniasm enables consensus genomes with similar or better quality than state-of-the-art methods while being an order of magnitude faster. PMID:28100585

  11. Parallel versus sequential processing in print and braille reading.

    PubMed

    Veispak, Anneli; Boets, Bart; Ghesquière, Pol

    2012-01-01

    In the current study we investigated word, pseudoword and story reading in Dutch speaking braille and print readers. To examine developmental patterns, these reading skills were assessed in both children and adults. The results reveal that braille readers read less accurately and fast than print readers. While item length has no impact on word reading accuracy and speed in the group of print readers, it has a significant impact on reading accuracy and speed in the group of braille readers, particularly in the younger sample. This suggests that braille readers rely more strongly on an enduring sequential reading strategy. Comparison of the different reading tasks suggests that the advantage in accuracy and speed of reading in adult as compared to young braille readers is achieved through semantic top-down processing. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Academic Reading Strategies Used by Leeds Metropolitan University Graduates: A Case Study

    ERIC Educational Resources Information Center

    Sohail, Samira

    2015-01-01

    Academic reading is different from other forms of reading because it is complex and discipline-specific. It involves a measured, challenging, and multifaceted process in which students are dynamically engaged with a range of reading strategies. Academic reading improvement is possible, provided students work on it and there are no short cuts or…

  13. Bridging Theory and Practice: Developing Lower-Level Skills in L2 Reading

    ERIC Educational Resources Information Center

    Kato, Shigeo

    2012-01-01

    Studies on L2 reading have provided extensive evidence for the significant contribution of lower-level processing skills in learning to read and the critical impact on the overall development of L2 reading of more accurate and fluent connections between three sub-lexical components: phonology, orthography and semantics. The broad consensus among…

  14. Iconic Memory and Reading Performance in Nine-Year-Old Children

    ERIC Educational Resources Information Center

    Riding, R. J.; Pugh, J. C.

    1977-01-01

    The reading process incorporates three factors: images registered in visual sensory memory, semantic analysis in short-term memory, and long-term memory storage. The focus here is on the contribution of sensory memory to reading performance. (Author/RK)

  15. Fast and accurate read-out of interferometric optical fiber sensors

    NASA Astrophysics Data System (ADS)

    Bartholsen, Ingebrigt; Hjelme, Dag R.

    2016-03-01

    We present results from an evaluation of phase and frequency estimation algorithms for read-out instrumentation of interferometric sensors. Tests on interrogating a micro Fabry-Perot sensor made of semi-spherical stimuli-responsive hydrogel immobilized on a single mode fiber end face, shows that an iterative quadrature demodulation technique (IQDT) implemented on a 32-bit microcontroller unit can achieve an absolute length accuracy of ±50 nm and length change accuracy of ±3 nm using an 80 nm SLED source and a grating spectrometer for interrogation. The mean absolute error for the frequency estimator is a factor 3 larger than the theoretical lower bound for a maximum likelihood estimator. The corresponding factor for the phase estimator is 1.3. The computation time for the IQDT algorithm is reduced by a factor 1000 compared to the full QDT for the same accuracy requirement.

  16. SOPRA: Scaffolding algorithm for paired reads via statistical optimization.

    PubMed

    Dayarian, Adel; Michael, Todd P; Sengupta, Anirvan M

    2010-06-24

    High throughput sequencing (HTS) platforms produce gigabases of short read (<100 bp) data per run. While these short reads are adequate for resequencing applications, de novo assembly of moderate size genomes from such reads remains a significant challenge. These limitations could be partially overcome by utilizing mate pair technology, which provides pairs of short reads separated by a known distance along the genome. We have developed SOPRA, a tool designed to exploit the mate pair/paired-end information for assembly of short reads. The main focus of the algorithm is selecting a sufficiently large subset of simultaneously satisfiable mate pair constraints to achieve a balance between the size and the quality of the output scaffolds. Scaffold assembly is presented as an optimization problem for variables associated with vertices and with edges of the contig connectivity graph. Vertices of this graph are individual contigs with edges drawn between contigs connected by mate pairs. Similar graph problems have been invoked in the context of shotgun sequencing and scaffold building for previous generation of sequencing projects. However, given the error-prone nature of HTS data and the fundamental limitations from the shortness of the reads, the ad hoc greedy algorithms used in the earlier studies are likely to lead to poor quality results in the current context. SOPRA circumvents this problem by treating all the constraints on equal footing for solving the optimization problem, the solution itself indicating the problematic constraints (chimeric/repetitive contigs, etc.) to be removed. The process of solving and removing of constraints is iterated till one reaches a core set of consistent constraints. For SOLiD sequencer data, SOPRA uses a dynamic programming approach to robustly translate the color-space assembly to base-space. For assessing the quality of an assembly, we report the no-match/mismatch error rate as well as the rates of various rearrangement errors

  17. YAHA: fast and flexible long-read alignment with optimal breakpoint detection.

    PubMed

    Faust, Gregory G; Hall, Ira M

    2012-10-01

    With improved short-read assembly algorithms and the recent development of long-read sequencers, split mapping will soon be the preferred method for structural variant (SV) detection. Yet, current alignment tools are not well suited for this. We present YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints. YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from http://faculty.virginia.edu/irahall/YAHA. imh4y@virginia.edu.

  18. A Study of the Effects of Variation of Short-Term Memory Load, Reading Response Length, and Processing Hierarchy on TOEFL Listening Comprehension Item Performance. Report 33.

    ERIC Educational Resources Information Center

    Henning, Grant

    Criticisms of the Test of English as a Foreign Language (TOEFL) have included speculation that the listening test places too much burden on short-term memory as compared with comprehension, that a knowledge of reading is required to respond successfully, and that many items appear to require mere recall and matching rather than higher-order…

  19. Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

    PubMed Central

    2011-01-01

    Background Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes. Results A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads with median read length of 61 bases. The assemblies generated by VELVET, OASES, and SeqMan NGEN differed in the total number of contigs, contig length, the number and quality of gene hits obtained by BLAST searches against various databases, and contig performance in the mt genome comparison. While VELVET produced the highest overall number of contigs, a large fraction of these were of small size (< 200bp), and gave redundant hits in BLAST searches and the mt genome alignment. The best overall contig performance resulted from the NGEN assembly. It produced the second largest number of contigs, which on average were comparable to the OASES contigs but gave the highest number of gene hits in two out of four BLAST searches against different reference databases. A subsequent meta-assembly of the four contig sets resulted in larger contigs, less redundancy and a higher number of BLAST hits. Conclusion Our results document the first de novo transcriptome assembly of a non-model species using Illumina sequencing data. We show that de novo transcriptome assembly using this approach yields results useful for downstream applications, in particular if a meta-assembly of contig sets is used to increase contig

  20. Correlates of Early Reading Comprehension Skills: A Componential Analysis

    ERIC Educational Resources Information Center

    Babayigit, Selma; Stainthorp, Rhona

    2014-01-01

    This study had three main aims. First, we examined to what extent listening comprehension, vocabulary, grammatical skills and verbal short-term memory (VSTM) assessed prior to formal reading instruction explained individual differences in early reading comprehension levels. Second, we examined to what extent the three common component skills,…

  1. Escape from the Twilight Zone: Reading and Writing with "At Risk" Students.

    ERIC Educational Resources Information Center

    Henly, Carolyn Powell

    1992-01-01

    Discusses how science fiction can be used as a part of the reading for students who may not like reading and writing. Details a course for at-risk students involving an independent reading project, an original short story, a group movie project, and a daily journal. (PRA)

  2. The regulatory element READ1 epistatically influences reading and language, with both deleterious and protective alleles

    PubMed Central

    Powers, Natalie R; Eicher, John D; Miller, Laura L; Kong, Yong; Smith, Shelley D; Pennington, Bruce F; Willcutt, Erik G; Olson, Richard K; Ring, Susan M; Gruen, Jeffrey R

    2016-01-01

    Background Reading disability (RD) and language impairment (LI) are heritable learning disabilities that obstruct acquisition and use of written and spoken language, respectively. We previously reported that two risk haplotypes, each in strong linkage disequilibrium (LD) with an allele of READ1, a polymorphic compound short tandem repeat within intron 2 of risk gene DCDC2, are associated with RD and LI. Additionally, we showed a non-additive genetic interaction between READ1 and KIAHap, a previously reported risk haplotype in risk gene KIAA0319, and that READ1 binds the transcriptional regulator ETV6. Objective To examine the hypothesis that READ1 is a transcriptional regulator of KIAA0319. Methods We characterised associations between READ1 alleles and RD and LI in a large European cohort, and also assessed interactions between READ1 and KIAHap and their effect on performance on measures of reading, language and IQ. We also used family-based data to characterise the genetic interaction, and chromatin conformation capture (3C) to investigate the possibility of a physical interaction between READ1 and KIAHap. Results and conclusions READ1 and KIAHap show interdependence—READ1 risk alleles synergise with KIAHap, whereas READ1 protective alleles act epistatically to negate the effects of KIAHap. The family data suggest that these variants interact in trans genetically, while the 3C results show that a region of DCDC2 containing READ1 interacts physically with the region upstream of KIAA0319. These data support a model in which READ1 regulates KIAA0319 expression through KIAHap and in which the additive effects of READ1 and KIAHap alleles are responsible for the trans genetic interaction. PMID:26660103

  3. Reading Speed, Comprehension and Eye Movements While Reading Japanese Novels: Evidence from Untrained Readers and Cases of Speed-Reading Trainees

    PubMed Central

    Miyata, Hiromitsu; Minagawa-Kawai, Yasuyo; Watanabe, Shigeru; Sasaki, Toyofumi; Ueda, Kazuhiro

    2012-01-01

    Background A growing body of evidence suggests that meditative training enhances perception and cognition. In Japan, the Park-Sasaki method of speed-reading involves organized visual training while forming both a relaxed and concentrated state of mind, as in meditation. The present study examined relationships between reading speed, sentence comprehension, and eye movements while reading short Japanese novels. In addition to normal untrained readers, three middle-level trainees and one high-level expert on this method were included for the two case studies. Methodology/Principal Findings In Study 1, three of 17 participants were middle-level trainees on the speed-reading method. Immediately after reading each story once on a computer monitor, participants answered true or false questions regarding the content of the novel. Eye movements while reading were recorded using an eye-tracking system. Results revealed higher reading speed and lower comprehension scores in the trainees than in the untrained participants. Furthermore, eye-tracking data by untrained participants revealed multiple correlations between reading speed, accuracy and eye-movement measures, with faster readers showing shorter fixation durations and larger saccades in X than slower readers. In Study 2, participants included a high-level expert and 14 untrained students. The expert showed higher reading speed and statistically comparable, although numerically lower, comprehension scores compared with the untrained participants. During test sessions this expert moved her eyes along a nearly straight horizontal line as a first pass, without moving her eyes over the whole sentence display as did the untrained students. Conclusions/Significance In addition to revealing correlations between speed, comprehension and eye movements in reading Japanese contemporary novels by untrained readers, we describe cases of speed-reading trainees regarding relationships between these variables. The trainees overall

  4. De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

    PubMed Central

    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

    2010-01-01

    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 ∼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 comparative

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

    PubMed

    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

  6. Benchmarking short sequence mapping tools

    PubMed Central

    2013-01-01

    Background The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools. However, the current proposed tools make different compromises between the accuracy and the speed of mapping. Moreover, many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects. In this work, we introduce a benchmarking suite to extensively analyze sequencing tools with respect to various aspects and provide an objective comparison. Results We applied our benchmarking tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool. The results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests while BWA performed better for longer read lengths. The benchmarking tests are not restricted to the mentioned tools and can be further applied to others. Conclusion The mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results. PMID:23758764

  7. Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies.

    PubMed

    Michael, Todd P; Bryant, Douglas; Gutierrez, Ryan; Borisjuk, Nikolai; Chu, Philomena; Zhang, Hanzhong; Xia, Jing; Zhou, Junfei; Peng, Hai; El Baidouri, Moaine; Ten Hallers, Boudewijn; Hastie, Alex R; Liang, Tiffany; Acosta, Kenneth; Gilbert, Sarah; McEntee, Connor; Jackson, Scott A; Mockler, Todd C; Zhang, Weixiong; Lam, Eric

    2017-02-01

    Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  8. Serial Recall and Nonword Repetition in Reading Disabled Children.

    ERIC Educational Resources Information Center

    Roodenrys, Steven; Stokes, Julie

    2001-01-01

    Examines the performance on verbal short-term memory tasks of specifically reading disabled children relative to reading-age matched and chronological-age matched control groups. Examines memory span for words, highly wordlike nonwords and less wordlike nonwords, speech rates for these items, and nonword repetition. Suggests that there is a…

  9. Short Historical Fiction To Get Children Reading.

    ERIC Educational Resources Information Center

    Sullivan, Kathleen

    1997-01-01

    Provides an annotated bibliography of short historical fiction and picture books for readers in grades K-8. Includes a list of selected Caldecott and Newbery winners with historical themes or backgrounds and a list of activity books featuring Spanish exploration in Mexico, Roman art and fashion, medieval Europe, and cowboys. (PEN)

  10. [Predictive power of working memory task for reading comprehension: an investigation using reading span test].

    PubMed

    Morishita, Masanao; Kondo, Hirohito; Ashida, Kayo; Otsuka, Yuki; Osaka, Naoyuki

    2007-02-01

    This study investigated the crucial factor mediating a correlation between performance of reading span test (RST) and reading comprehension. In the research literature on this issue, one of the remaining controversial points is whether the similarity of sentence processing between RST and comprehension contributes to the correlation. In this study, four RST conditions were created by the combination of two factors: relatedness of stimulus sentences (related or unrelated with each other) and focus of target words (focus or non-focus with respect to sentence meaning). If the correlation is mediated by the similarity of sentence processing, RST performance of related and focus condition, which was most akin to comprehension, would have higher correlation with reading comprehension than other conditions. However, as a result of correlation analysis based on data from ninety-six participants, no such evidence was obtained. On the other hand, RST performance of unrelated conditions that were supposed to strongly require attention control showed significant correlation with reading comprehension. These findings are discussed in terms of the contribution of attention control and short-term memory to performing RST and reading comprehension.

  11. "Sponge" Up that Time for Reading.

    ERIC Educational Resources Information Center

    Clary, Linda Mixon

    1989-01-01

    Presents 50 short reading activities designed to occupy students during transition periods between activities or classes. Lists 35 activities which are quiet and individual, and 15 which can be done in small or large groups. (RS)

  12. The Practicality of Poetry: Using Sonnets to Improve Reading Ability

    ERIC Educational Resources Information Center

    Vallicelli, Arthur E.

    2012-01-01

    This dissertation examines the way in which sonnets improved reading comprehension through a case study. The study was conceptually framed around the ideas of the New Critics, who employed two particular fallacies to ensure the most accurate reading of literature. The purpose of the study was to see the potential benefits that could come from…

  13. Lexical-Semantic Reading in a Shallow Orthography: Evidence from a Girl with Williams Syndrome

    ERIC Educational Resources Information Center

    Barca, Laura; Bello, Arianna; Volterra, Virginia; Burani, Cristina

    2010-01-01

    The reading skills of a girl with Williams Syndrome are assessed by a timed word-naming task. To test the efficiency of lexical and nonlexical reading, we considered four marker effects: Lexicality (better reading of words than nonwords), frequency (better reading of high than low frequency words), length (better reading of short than long words),…

  14. Accurately Predicting Future Reading Difficulty for Bilingual Latino Children at Risk for Language Impairment

    ERIC Educational Resources Information Center

    Petersen, Douglas B.; Gillam, Ronald B.

    2013-01-01

    Sixty-three bilingual Latino children who were at risk for language impairment were administered reading-related measures in English and Spanish (letter identification, phonological awareness, rapid automatized naming, and sentence repetition) and descriptive measures including English language proficiency (ELP), language ability (LA),…

  15. High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.

    PubMed

    Lagarde, Julien; Uszczynska-Ratajczak, Barbara; Carbonell, Silvia; Pérez-Lluch, Sílvia; Abad, Amaya; Davis, Carrie; Gingeras, Thomas R; Frankish, Adam; Harrow, Jennifer; Guigo, Roderic; Johnson, Rory

    2017-12-01

    Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines targeted RNA capture with third-generation long-read sequencing. Here we present an experimental reannotation of the GENCODE intergenic lncRNA populations in matched human and mouse tissues that resulted in novel transcript models for 3,574 and 561 gene loci, respectively. CLS approximately doubled the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enabled us to definitively characterize the genomic features of lncRNAs, including promoter and gene structure, and protein-coding potential. Thus, CLS removes a long-standing bottleneck in transcriptome annotation and generates manual-quality full-length transcript models at high-throughput scales.

  16. Motor-Perceptual Function in Children with Developmental Reading Disorders: Neuropsychophysiological Analysis.

    ERIC Educational Resources Information Center

    Chiarenza, Giuseppe Augusto

    1990-01-01

    Eight reading-disordered and 9 nondisabled males (age 10) performed a skilled motor-perceptual task. The children with reading disorders were slower, less accurate, and achieved a smaller number of target performances. Their brain macropotentials associated with motor programing, processing of sensory information, and evaluation of the results…

  17. The use of music to enhance reading skills of second grade students and students with reading disabilities.

    PubMed

    Register, Dena; Darrow, Alice-Ann; Standley, Jayne; Swedberg, Olivia

    2007-01-01

    The purpose of the present study was to determine the efficacy of using music as a remedial strategy to enhance the reading skills of second-grade students and students who have been identified as having a specific learning disability (SLD) in reading. First, an intensive short-term music curriculum was designed to target reading comprehension and vocabulary skills at the second grade level. The curriculum was then implemented in classrooms at two public schools in the Southeast. Reading skills were evaluated pre and post curriculum intervention via the vocabulary and reading comprehension subtests of the Gates-MacGinitie Reading Test for second grade. Analysis of pre/posttest data revealed that students with a specific disability in reading improved significantly from pre to post on all three subtests: word decoding (p = .04), word knowledge (p = .01), reading comprehension (p = .01), and test total (p = .01). Paired t-tests revealed that for 2nd grade students, both treatment and control classes improved significantly from pre to post on the subtests word decoding, word knowledge, and test total. While both classes made gains from pre to post on the subtest, reading comprehension, neither improved significantly. Analysis of Covariance revealed that the treatment class made greater gains pre to post than the control class on all 3 subtests (Including reading comprehension), and significantly greater gains on the subtest, word knowledge (p = .01).

  18. Efficient Learning for the Poor: New Insights into Literacy Acquisition for Children

    ERIC Educational Resources Information Center

    Abadzi, Helen

    2008-01-01

    Reading depends on the speed of visual recognition and capacity of short-term memory. To understand a sentence, the mind must read it fast enough to capture it within the limits of the short-term memory. This means that children must attain a minimum speed of fairly accurate reading to understand a passage. Learning to read involves "tricking" the…

  19. Perspective Effects during Reading: Evidence from Text Change-Detection

    ERIC Educational Resources Information Center

    Bohan, Jason; Filik, Ruth

    2018-01-01

    We report two text change-detection studies in which we investigate the influence of reading perspective on text memory. In Experiment 1 participants read from the perspective of one of two characters in a series of short stories, and word changes were either semantically close or distant. Participants correctly reported more changes to…

  20. Automatic draft reading based on image processing

    NASA Astrophysics Data System (ADS)

    Tsujii, Takahiro; Yoshida, Hiromi; Iiguni, Youji

    2016-10-01

    In marine transportation, a draft survey is a means to determine the quantity of bulk cargo. Automatic draft reading based on computer image processing has been proposed. However, the conventional draft mark segmentation may fail when the video sequence has many other regions than draft marks and a hull, and the estimated waterline is inherently higher than the true one. To solve these problems, we propose an automatic draft reading method that uses morphological operations to detect draft marks and estimate the waterline for every frame with Canny edge detection and a robust estimation. Moreover, we emulate surveyors' draft reading process for getting the understanding of a shipper and a receiver. In an experiment in a towing tank, the draft reading error of the proposed method was <1 cm, showing the advantage of the proposed method. It is also shown that accurate draft reading has been achieved in a real-world scene.

  1. Prosodic Similarity Effects in Short-Term Memory in Developmental Dyslexia.

    PubMed

    Goswami, Usha; Barnes, Lisa; Mead, Natasha; Power, Alan James; Leong, Victoria

    2016-11-01

    Children with developmental dyslexia are characterized by phonological difficulties across languages. Classically, this 'phonological deficit' in dyslexia has been investigated with tasks using single-syllable words. Recently, however, several studies have demonstrated difficulties in prosodic awareness in dyslexia. Potential prosodic effects in short-term memory have not yet been investigated. Here we create a new instrument based on three-syllable words that vary in stress patterns, to investigate whether prosodic similarity (the same prosodic pattern of stressed and unstressed syllables) exerts systematic effects on short-term memory. We study participants with dyslexia and age-matched and younger reading-level-matched typically developing controls. We find that all participants, including dyslexic participants, show prosodic similarity effects in short-term memory. All participants exhibited better retention of words that differed in prosodic structure, although participants with dyslexia recalled fewer words accurately overall compared to age-matched controls. Individual differences in prosodic memory were predicted by earlier vocabulary abilities, by earlier sensitivity to syllable stress and by earlier phonological awareness. To our knowledge, this is the first demonstration of prosodic similarity effects in short-term memory. The implications of a prosodic similarity effect for theories of lexical representation and of dyslexia are discussed. © 2016 The Authors. Dyslexia published by John Wiley & Sons Ltd. © 2016 The Authors. Dyslexia published by John Wiley & Sons Ltd.

  2. Hidden Language Impairments in Children: Parallels between Poor Reading Comprehension and Specific Language Impairment?

    ERIC Educational Resources Information Center

    Nation, Kate; Clarke, Paula; Marshall, Catherine M.; Durand, Marianne

    2004-01-01

    This study investigates the oral language skills of 8-year-old children with impaired reading comprehension. Despite fluent and accurate reading and normal nonverbal ability, these children are poor at understanding what they have read. Tasks tapping 3 domains of oral language, namely phonology, semantics, and morphosyntax, were administered,…

  3. Toward developing a standardized Arabic continuous text reading chart.

    PubMed

    Alabdulkader, Balsam; Leat, Susan Jennifer

    Near visual acuity is an essential measurement during an oculo-visual assessment. Short duration continuous text reading charts measure reading acuity and other aspects of reading performance. There is no standardized version of such chart in Arabic. The aim of this study is to create sentences of equal readability to use in the development of a standardized Arabic continuous text reading chart. Initially, 109 Arabic pairs of sentences were created for use in constructing a chart with similar layout to the Colenbrander chart. They were created to have the same grade level of difficulty and physical length. Fifty-three adults and sixteen children were recruited to validate the sentences. Reading speed in correct words per minute (CWPM) and standard length words per minute (SLWPM) was measured and errors were counted. Criteria based on reading speed and errors made in each sentence pair were used to exclude sentence pairs with more outlying characteristics, and to select the final group of sentence pairs. Forty-five sentence pairs were selected according to the elimination criteria. For adults, the average reading speed for the final sentences was 166 CWPM and 187 SLWPM and the average number of errors per sentence pair was 0.21. Childrens' average reading speed for the final group of sentences was 61 CWPM and 72 SLWPM. Their average error rate was 1.71. The reliability analysis showed that the final 45 sentence pairs are highly comparable. They will be used in constructing an Arabic short duration continuous text reading chart. Copyright © 2016 Spanish General Council of Optometry. Published by Elsevier España, S.L.U. All rights reserved.

  4. Strategies for Improving Our Concepts and Techniques in Regard to Speed Reading.

    ERIC Educational Resources Information Center

    Howards, Melvin

    The author discounts the effects of currently promoted speed reading programs as resulting in short-term effectiveness and disregarding a consideration of what constitutes good reading at any speed. He claims that the types and levels of transformations and interpretations, verbal and nonverbal, that must go into good reading are not susceptible…

  5. Shortening the incubation time for antimicrobial susceptibility testing by disk diffusion for Enterobacteriaceae: how short can it be and are the results accurate?

    PubMed

    van den Bijllaardt, Wouter; Buiting, Anton G; Mouton, Johan W; Muller, Anouk E

    2017-05-01

    The standard incubation time for antimicrobial susceptibility testing (AST) by disk diffusion is primarily based on laboratory working hours rather than growth and kill characteristics of bacteria. Faster AST results could result in better patient outcomes and reduced costs by initiating earlier appropriate therapy. The earliest possible reading moment for disk diffusion using established disk zone diameter breakpoints for Enterobacteriaceae was determined with a special focus on the accuracy of the results. A total of 88 Enterobacteriaceae challenge isolates, including isolates with specific resistance mechanisms such as extended-spectrum β-lactamase (ESBL), were subjected to disk diffusion with 15 antibiotics. Hourly images were automatically produced by an incubator/camera combination from 1 h to 20 h. Disk zones were plotted over time for all combinations. Essential and categorical agreement rates using the final reading after 20 h of incubation as a reference were calculated for every hour. In total, 1320 antibiotic-micro-organism combinations were tested. Clear growth with readable inhibition zones was visible after 6 h of incubation for the majority (95.8%) of plates and after 7 h for all incubated plates. However, zone sizes changed significantly after those time points for a number of strains. After 10 h of incubation, minor, major and very major error rates were 1.6% (n = 21), 0.2% (n = 1) and 0.7% (n = 4), respectively. The results of this study clearly indicate that early reading of inhibition zones to 10 h after incubation is feasible and accurate and thus may save significantly on turnaround time. Copyright © 2017 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

  6. A new strategy for genome assembly using short sequence reads and reduced representation libraries.

    PubMed

    Young, Andrew L; Abaan, Hatice Ozel; Zerbino, Daniel; Mullikin, James C; Birney, Ewan; Margulies, Elliott H

    2010-02-01

    We have developed a novel approach for using massively parallel short-read sequencing to generate fast and inexpensive de novo genomic assemblies comparable to those generated by capillary-based methods. The ultrashort (<100 base) sequences generated by this technology pose specific biological and computational challenges for de novo assembly of large genomes. To account for this, we devised a method for experimentally partitioning the genome using reduced representation (RR) libraries prior to assembly. We use two restriction enzymes independently to create a series of overlapping fragment libraries, each containing a tractable subset of the genome. Together, these libraries allow us to reassemble the entire genome without the need of a reference sequence. As proof of concept, we applied this approach to sequence and assembled the majority of the 125-Mb Drosophila melanogaster genome. We subsequently demonstrate the accuracy of our assembly method with meaningful comparisons against the current available D. melanogaster reference genome (dm3). The ease of assembly and accuracy for comparative genomics suggest that our approach will scale to future mammalian genome-sequencing efforts, saving both time and money without sacrificing quality.

  7. Influencing the occurrence of mind wandering while reading.

    PubMed

    Kopp, Kristopher; D'Mello, Sidney; Mills, Caitlin

    2015-07-01

    The current concerns hypothesis suggests that directing attention towards unfulfilled plans of the individual prior to a task would result in more off-task thoughts (or mind wandering). In this experiment, participants were asked to read a scientific text and self-report instances of mind wandering by indicating when they were experiencing task-unrelated thoughts (TUTs) or task-related interferences (TRIs). Prior to reading, participants in the individual plans experimental condition were asked to reflect upon their short-term plans by making a "to do" list while participants in a control condition were asked to make a list of the components of an automobile. In support of the current concerns hypothesis, directing attention towards the short-term plans resulted in significantly more TUTs, but not TRIs. Furthermore, participants in the individual plans condition had significantly lower scores on an assessment of reading comprehension, and this relationship was mediated by the frequency of TUTs. Copyright © 2015 Elsevier Inc. All rights reserved.

  8. A Secure Alignment Algorithm for Mapping Short Reads to Human Genome.

    PubMed

    Zhao, Yongan; Wang, Xiaofeng; Tang, Haixu

    2018-05-09

    The elastic and inexpensive computing resources such as clouds have been recognized as a useful solution to analyzing massive human genomic data (e.g., acquired by using next-generation sequencers) in biomedical researches. However, outsourcing human genome computation to public or commercial clouds was hindered due to privacy concerns: even a small number of human genome sequences contain sufficient information for identifying the donor of the genomic data. This issue cannot be directly addressed by existing security and cryptographic techniques (such as homomorphic encryption), because they are too heavyweight to carry out practical genome computation tasks on massive data. In this article, we present a secure algorithm to accomplish the read mapping, one of the most basic tasks in human genomic data analysis based on a hybrid cloud computing model. Comparing with the existing approaches, our algorithm delegates most computation to the public cloud, while only performing encryption and decryption on the private cloud, and thus makes the maximum use of the computing resource of the public cloud. Furthermore, our algorithm reports similar results as the nonsecure read mapping algorithms, including the alignment between reads and the reference genome, which can be directly used in the downstream analysis such as the inference of genomic variations. We implemented the algorithm in C++ and Python on a hybrid cloud system, in which the public cloud uses an Apache Spark system.

  9. Strategic Processing and Predictive Inference Generation in L2 Reading

    ERIC Educational Resources Information Center

    Nahatame, Shingo

    2014-01-01

    Predictive inference is the anticipation of the likely consequences of events described in a text. This study investigated predictive inference generation during second language (L2) reading, with a focus on the effects of strategy instructions. In this experiment, Japanese university students read several short narrative passages designed to…

  10. Adults Who Read Like Children: The Psycholinguistic Bases. Final Report.

    ERIC Educational Resources Information Center

    Read, Charles

    A study examined basic reading skills among men in prison, comparing poor and adequate readers with respect to comprehension, decoding, short-term memory, and speech perception. Subjects, 88 inmates of normal intelligence, normal hearing, and no significant speech abnormalities, at a minimum-security prison, were given reading comprehension tests…

  11. Supporting read-across using biological data.

    PubMed

    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.

  12. Reading Visual Braille with a Retinal Prosthesis

    PubMed Central

    Lauritzen, Thomas Z.; Harris, Jordan; Mohand-Said, Saddek; Sahel, Jose A.; Dorn, Jessy D.; McClure, Kelly; Greenberg, Robert J.

    2012-01-01

    Retinal prostheses, which restore partial vision to patients blinded by outer retinal degeneration, are currently in clinical trial. The Argus II retinal prosthesis system was recently awarded CE approval for commercial use in Europe. While retinal prosthesis users have achieved remarkable visual improvement to the point of reading letters and short sentences, the reading process is still fairly cumbersome. This study investigates the possibility of using an epiretinal prosthesis to stimulate visual braille as a sensory substitution for reading written letters and words. The Argus II retinal prosthesis system, used in this study, includes a 10 × 6 electrode array implanted epiretinally, a tiny video camera mounted on a pair of glasses, and a wearable computer that processes the video and determines the stimulation current of each electrode in real time. In the braille reading system, individual letters are created by a subset of dots from a 3 by 2 array of six dots. For the visual braille experiment, a grid of six electrodes was chosen out of the 10 × 6 Argus II array. Groups of these electrodes were then directly stimulated (bypassing the camera) to create visual percepts of individual braille letters. Experiments were performed in a single subject. Single letters were stimulated in an alternative forced choice (AFC) paradigm, and short 2–4-letter words were stimulated (one letter at a time) in an open-choice reading paradigm. The subject correctly identified 89% of single letters, 80% of 2-letter, 60% of 3-letter, and 70% of 4-letter words. This work suggests that text can successfully be stimulated and read as visual braille in retinal prosthesis patients. PMID:23189036

  13. Reading visual braille with a retinal prosthesis.

    PubMed

    Lauritzen, Thomas Z; Harris, Jordan; Mohand-Said, Saddek; Sahel, Jose A; Dorn, Jessy D; McClure, Kelly; Greenberg, Robert J

    2012-01-01

    Retinal prostheses, which restore partial vision to patients blinded by outer retinal degeneration, are currently in clinical trial. The Argus II retinal prosthesis system was recently awarded CE approval for commercial use in Europe. While retinal prosthesis users have achieved remarkable visual improvement to the point of reading letters and short sentences, the reading process is still fairly cumbersome. This study investigates the possibility of using an epiretinal prosthesis to stimulate visual braille as a sensory substitution for reading written letters and words. The Argus II retinal prosthesis system, used in this study, includes a 10 × 6 electrode array implanted epiretinally, a tiny video camera mounted on a pair of glasses, and a wearable computer that processes the video and determines the stimulation current of each electrode in real time. In the braille reading system, individual letters are created by a subset of dots from a 3 by 2 array of six dots. For the visual braille experiment, a grid of six electrodes was chosen out of the 10 × 6 Argus II array. Groups of these electrodes were then directly stimulated (bypassing the camera) to create visual percepts of individual braille letters. Experiments were performed in a single subject. Single letters were stimulated in an alternative forced choice (AFC) paradigm, and short 2-4-letter words were stimulated (one letter at a time) in an open-choice reading paradigm. The subject correctly identified 89% of single letters, 80% of 2-letter, 60% of 3-letter, and 70% of 4-letter words. This work suggests that text can successfully be stimulated and read as visual braille in retinal prosthesis patients.

  14. Phonological and Non-Phonological Language Skills as Predictors of Early Reading Performance

    ERIC Educational Resources Information Center

    Batson-Magnuson, LuAnn

    2010-01-01

    Accurate prediction of early childhood reading performance could help identify at-risk students, aid in the development of evidence-based intervention strategies, and further our theoretical understanding of reading development. This study assessed the validity of the Developmental Indicator for the Assessment of Learning (DIAL) language-based…

  15. Long Read Alignment with Parallel MapReduce Cloud Platform

    PubMed Central

    Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

    2015-01-01

    Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms. PMID:26839887

  16. Long Read Alignment with Parallel MapReduce Cloud Platform.

    PubMed

    Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

    2015-01-01

    Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms.

  17. Working Memory Influences Processing Speed and Reading Fluency in ADHD

    PubMed Central

    Jacobson, Lisa A.; Ryan, Matthew; Martin, Rebecca B.; Ewen, Joshua; Mostofsky, Stewart H.; Denckla, Martha B.; Mahone, E. Mark

    2012-01-01

    Processing speed deficits affect reading efficiency, even among individuals who recognize and decode words accurately. Children with ADHD who decode words accurately can still have inefficient reading fluency, leading to a bottleneck in other cognitive processes. This “slowing” in ADHD is associated with deficits in fundamental components of executive function underlying processing speed, including response selection. The purpose of the present study was to deconstruct processing speed in order to determine which components of executive control best explain the “processing” speed deficits related to reading fluency in ADHD. Participants (41 ADHD, 21 controls), ages 9-14, screened for language disorders, word reading deficits, and psychiatric disorders, were administered measures of copying speed, processing speed, reading fluency, working memory, reaction time, inhibition, and auditory attention span. Compared to controls, children with ADHD showed reduced oral and silent reading fluency, and reduced processing speed—driven primarily by deficits on WISC-IV Coding. In contrast, groups did not differ on copying speed. After controlling for copying speed, sex, severity of ADHD-related symptomatology, and GAI, slowed “processing” speed (i.e., Coding) was significantly associated with verbal span and measures of working memory, but not with measures of response control/inhibition, lexical retrieval speed, reaction time, or intra-subject variability. Further, “processing” speed (i.e., Coding, residualized for copying speed) and working memory were significant predictors of oral reading fluency. Abnormalities in working memory and response selection (which are frontally-mediated and enter into the output side of processing speed) may play an important role in deficits in reading fluency in ADHD, potentially more than posteriorally-mediated problems with orienting of attention or perceiving the stimulus. PMID:21287422

  18. Working memory influences processing speed and reading fluency in ADHD.

    PubMed

    Jacobson, Lisa A; Ryan, Matthew; Martin, Rebecca B; Ewen, Joshua; Mostofsky, Stewart H; Denckla, Martha B; Mahone, E Mark

    2011-01-01

    Processing-speed deficits affect reading efficiency, even among individuals who recognize and decode words accurately. Children with ADHD who decode words accurately can still have inefficient reading fluency, leading to a bottleneck in other cognitive processes. This "slowing" in ADHD is associated with deficits in fundamental components of executive function underlying processing speed, including response selection. The purpose of the present study was to deconstruct processing speed in order to determine which components of executive control best explain the "processing" speed deficits related to reading fluency in ADHD. Participants (41 ADHD, 21 controls), ages 9-14 years, screened for language disorders, word reading deficits, and psychiatric disorders, were administered measures of copying speed, processing speed, reading fluency, working memory, reaction time, inhibition, and auditory attention span. Compared to controls, children with ADHD showed reduced oral and silent reading fluency and reduced processing speed-driven primarily by deficits on WISC-IV Coding. In contrast, groups did not differ on copying speed. After controlling for copying speed, sex, severity of ADHD-related symptomatology, and GAI, slowed "processing" speed (i.e., Coding) was significantly associated with verbal span and measures of working memory but not with measures of response control/inhibition, lexical retrieval speed, reaction time, or intrasubject variability. Further, "processing" speed (i.e., Coding, residualized for copying speed) and working memory were significant predictors of oral reading fluency. Abnormalities in working memory and response selection (which are frontally mediated and enter into the output side of processing speed) may play an important role in deficits in reading fluency in ADHD, potentially more than posteriorally mediated problems with orienting of attention or perceiving the stimulus.

  19. Grade 12 Diploma Examination, English 30. Part B: Reading (Multiple Choice). Readings Booklet. 1988 Edition.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton.

    Intended for students taking the Grade 12 Examinations in English 30 in Alberta, Canada, this reading test (to be administered along with a questions booklet) includes the following nine short selections taken from fiction, nonfiction, poetry, and drama: "The Biggest Liar in the World" (Harry Mark Petrakis); "Victorian…

  20. Grade 12 Diploma Examination, English 30. Part B: Reading (Multiple Choice). Readings Booklet. 1987 Edition.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton.

    Intended for students taking the Grade 12 Examination in English 30 in Alberta, Canada, this reading test (to be administered along with a questions booklet) includes the following 10 short selections taken from fiction, nonfiction, poetry, and drama: "Parents as People (with Children)" (Ellen Goodman); "Everybody Knows about the…

  1. Language differences in the brain network for reading in naturalistic story reading and lexical decision.

    PubMed

    Wang, Xiaojuan; Yang, Jianfeng; Yang, Jie; Mencl, W Einar; Shu, Hua; Zevin, Jason David

    2015-01-01

    Differences in how writing systems represent language raise important questions about whether there could be a universal functional architecture for reading across languages. In order to study potential language differences in the neural networks that support reading skill, we collected fMRI data from readers of alphabetic (English) and morpho-syllabic (Chinese) writing systems during two reading tasks. In one, participants read short stories under conditions that approximate natural reading, and in the other, participants decided whether individual stimuli were real words or not. Prior work comparing these two writing systems has overwhelmingly used meta-linguistic tasks, generally supporting the conclusion that the reading system is organized differently for skilled readers of Chinese and English. We observed that language differences in the reading network were greatly dependent on task. In lexical decision, a pattern consistent with prior research was observed in which the Middle Frontal Gyrus (MFG) and right Fusiform Gyrus (rFFG) were more active for Chinese than for English, whereas the posterior temporal sulcus was more active for English than for Chinese. We found a very different pattern of language effects in a naturalistic reading paradigm, during which significant differences were only observed in visual regions not typically considered specific to the reading network, and the middle temporal gyrus, which is thought to be important for direct mapping of orthography to semantics. Indeed, in areas that are often discussed as supporting distinct cognitive or linguistic functions between the two languages, we observed interaction. Specifically, language differences were most pronounced in MFG and rFFG during the lexical decision task, whereas no language differences were observed in these areas during silent reading of text for comprehension.

  2. Identifying Children in Middle Childhood Who Are at Risk for Reading Problems.

    PubMed

    Speece, Deborah L; Ritchey, Kristen D; Silverman, Rebecca; Schatschneider, Christopher; Walker, Caroline Y; Andrusik, Katryna N

    2010-06-01

    The purpose of this study was to identify and evaluate a universal screening battery for reading that is appropriate for older elementary students in a response to intervention model. Multiple measures of reading and reading correlates were administered to 230 fourth-grade children. Teachers rated children's reading skills, academic competence, and attention. Children were classified as not-at-risk or at-risk readers based on a three-factor model reflecting reading comprehension, word recognition/decoding, and word fluency. Predictors of reading status included group-administered tests of reading comprehension, silent word reading fluency, and teacher ratings of reading problems. Inclusion of individually administered tests and growth estimates did not add substantial variance. The receiver-operator characteristic curve analysis yielded an area under the curve index of 0.90, suggesting this model may both accurately and efficiently screen older elementary students with reading problems.

  3. Prosodic Encoding in Silent Reading.

    ERIC Educational Resources Information Center

    Wilkenfeld, Deborah

    In silent reading, short-memory tasks, such as semantic and syntactic processing, require a stage of phonetic encoding between visual representation and the actual extraction of meaning, and this encoding includes prosodic as well as segmental features. To test for this suprasegmental coding, an experiment was conducted in which subjects were…

  4. Processing Determinants of Reading Speed.

    ERIC Educational Resources Information Center

    Jackson, Mark D.; McClelland, James L.

    1979-01-01

    Two groups of undergraduates differing in reading ability were tested on a number of reaction-time tasks designed to determine the speed of encoding visual information at several different levels, tests of sensory functions, verbal and quantitative reasoning ability, short-term auditory memory span, and ability to comprehend spoken text.…

  5. Reading Exercises on Mexican Americans.

    ERIC Educational Resources Information Center

    Almaraz, Felix D., Jr.; Almaraz, Maria O.

    Short biographical sketches and drawings of 30 prominent Mexican Americans are presented in this book of reading exercises. Written on a fourth or fifth grade level, the book includes figures representing a variety of occupations and fields of achievement: the arts, sports, business, journalism, education, entertainment, literature, medicine, law,…

  6. Indexed variation graphs for efficient and accurate resistome profiling.

    PubMed

    Rowe, Will P M; Winn, Martyn D

    2018-05-14

    Antimicrobial resistance remains a major threat to global health. Profiling the collective antimicrobial resistance genes within a metagenome (the "resistome") facilitates greater understanding of antimicrobial resistance gene diversity and dynamics. In turn, this can allow for gene surveillance, individualised treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Our method combines a variation graph representation of gene sets with an LSH Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, GROOT, and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 minutes using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). will.rowe@stfc.ac.uk. Supplementary data are available at Bioinformatics online.

  7. Gender-specific contribution of a visual cognition network to reading abilities.

    PubMed

    Huestegge, Lynn; Heim, Stefan; Zettelmeyer, Elena; Lange-Küttner, Christiane

    2012-02-01

    Based on the assumption that boys are more likely to tackle reading based on the visual modality, we assessed reading skills, visual short-term memory (VSTM), visual long-term memory for details (VLTM-D), and general non-verbal cognitive ability in primary school children. Reading was within the normal range in both accuracy and understanding. There was no reading performance gap in favour of girls, on the contrary, in this sample boys read better. An entire array of visual, non-verbal processes was associated directly or indirectly with reading in boys, whereas this pattern was not observed for the girls. ©2011 The British Psychological Society.

  8. Behavioral Attention: A Longitudinal Study of Whether and How It Influences the Development of Word Reading and Reading Comprehension among At-Risk Readers

    PubMed Central

    Miller, Amanda C.; Fuchs, Douglas; Fuchs, Lynn S.; Compton, Donald L.; Kearns, Devin; Zhang, Wenjuan; Yen, Loulee; Patton, Samuel; Kirchner, Danielle

    2014-01-01

    The purpose of this study was to examine the extent to which teacher ratings of behavioral attention predicted responsiveness to word reading instruction in first grade and third-grade reading comprehension performance. Participants were 110 first grade students identified as at-risk for reading difficulties who received 20 weeks of intensive reading intervention in combination with classroom reading instruction. Path analysis indicated that teacher ratings of student attention significantly predicted students’ word reading growth in first grade even when they were competed against other relevant predictors (phonological awareness, nonword reading, sight word efficiency, vocabulary, listening comprehension, hyperactivity, nonverbal reasoning, and short term memory). Also, student attention demonstrated a significant indirect effect on third grade reading comprehension via word reading, but not via listening comprehension. Results suggest that student attention (indexed by teacher ratings) is an important predictor of at-risk readers’ responsiveness to reading instruction in first grade and that first-grade reading growth mediates the relationship between students’ attention and their future level of reading comprehension. The importance of considering ways to manage and improve behavioral attention when implementing reading instruction is discussed. PMID:25110548

  9. Simple scale interpolator facilitates reading of graphs

    NASA Technical Reports Server (NTRS)

    Fazio, A.; Henry, B.; Hood, D.

    1966-01-01

    Set of cards with scale divisions and a scale finder permits accurate reading of the coordinates of points on linear or logarithmic graphs plotted on rectangular grids. The set contains 34 different scales for linear plotting and 28 single cycle scales for log plots.

  10. The effect of speech rate on stuttering frequency, phonated intervals, speech effort, and speech naturalness during chorus reading.

    PubMed

    Davidow, Jason H; Ingham, Roger J

    2013-01-01

    This study examined the effect of speech rate on phonated intervals (PIs), in order to test whether a reduction in the frequency of short PIs is an important part of the fluency-inducing mechanism of chorus reading. The influence of speech rate on stuttering frequency, speaker-judged speech effort, and listener-judged naturalness was also examined. An added purpose was to determine if chorus reading could be further refined so as to provide a perceptual guide for gauging the level of physical effort exerted during speech production. A repeated-measures design was used to compare data obtained during control reading conditions and during several chorus reading conditions produced at different speech rates. Participants included 8 persons who stutter (PWS) between the ages of 16 and 32 years. There were significant reductions in the frequency of short PIs from the habitual reading condition during slower chorus conditions, no change when speech rates were matched between habitual reading and chorus conditions, and an increase in the frequency of short PIs during chorus reading produced at a faster rate than the habitual condition. Speech rate did not have an effect on stuttering frequency during chorus reading. In general, speech effort ratings improved and naturalness ratings worsened as speech rate decreased. These results provide evidence that (a) a reduction in the frequency of short PIs is not necessary for fluency improvement during chorus reading, and (b) speech rate may be altered to provide PWS with a more appropriate reference for how physically effortful normally fluent speech production should be. Future investigations should examine the necessity of changes in the activation of neural regions during chorus reading, the possibility of defining individualized units on a 9-point effort scale, and if there are upper and lower speech rate boundaries for receiving ratings of "highly natural sounding" speech during chorus reading. The reader will be able to: (1

  11. Grade 12 Diploma Examination, English 30. Part B: Reading (Multiple Choice). Readings Booklet. June 1989 Edition.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton.

    Intended for students taking the Grade 12 Examination in English 30 in Alberta, Canada, this reading test (to be administered along with a questions booklet) includes the following eight short selections taken from fiction, nonfiction, poetry, and drama: "Loyalties" (Roo Borson); "Clever Animals" (Lewis Thomas); "Death of…

  12. Calibrating GPS With TWSTFT For Accurate Time Transfer

    DTIC Science & Technology

    2008-12-01

    40th Annual Precise Time and Time Interval (PTTI) Meeting 577 CALIBRATING GPS WITH TWSTFT FOR ACCURATE TIME TRANSFER Z. Jiang1 and...primary time transfer techniques are GPS and TWSTFT (Two-Way Satellite Time and Frequency Transfer, TW for short). 83% of UTC time links are...Calibrating GPS With TWSTFT For Accurate Time Transfer 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT

  13. Information Processing Abilities and Reading.

    ERIC Educational Resources Information Center

    Samuels, S. Jay

    1987-01-01

    A major focus in reading difficulty is lack of automaticity in decoding, which overloads the attentional system, leads to the use of small, meaningless visual processing units such as the individual letter, places heavy demands on short-term memory, and interferes with comprehension. Techniques for diagnosis and remediation are noted. (Author/JW)

  14. What Type of Vocabulary Knowledge Predicts Reading Comprehension: Word Meaning Recall or Word Meaning Recognition?

    ERIC Educational Resources Information Center

    Laufer, Batia; Aviad-Levitzky, Tami

    2017-01-01

    This study examined how well second language (L2) recall and recognition vocabulary tests correlated with a reading test, how well each vocabulary test discriminated between reading proficiency levels, and how accurate each test was in predicting reading proficiency when compared with corpus studies. A total of 116 college-level learners of…

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

    USDA-ARS?s Scientific Manuscript database

    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...

  16. Questioning and reading goals: information-seeking questions asked on scientific texts read under different task conditions.

    PubMed

    Ishiwa, Koto; Sanjosé, Vicente; Otero, José

    2013-09-01

    A number of studies report that few questions are asked in classrooms and that many of them are shallow questions. This study investigates the way in which reading goals determine questioning on scientific texts. Reading goals were manipulated through two different tasks: reading for understanding versus reading to solve a problem. A total of 183 university students. In the first and third questioning experiments, the participants read two short texts. Students in one condition were instructed to understand the texts, whereas in the alternative condition they had to read texts to solve a problem. Students were instructed to write down any questions they might have about the texts. The questions were categorized according to the type of underlying obstacle: associative, explanatory, or predictive. The second experiment used a think-aloud methodology to identify the mental representations generated by the students. The two questioning experiments show that the questions asked depend on the reading goals. Significantly more explanation questions were asked in the understanding condition than in the problem-solving condition. Also, the two conditions were found to have a different influence on the generation of association and explanation questions. Very few prediction questions were asked in either condition. The think-aloud experiment revealed that the mental representations attempted by readers under the two conditions were indeed different. In conclusion, the experiments showed that, given a certain textual input, readers' questions depend on the reading goals associated with tasks. © 2012 The British Psychological Society.

  17. Verbal and visuospatial working memory as predictors of children's reading ability.

    PubMed

    Pham, Andy V; Hasson, Ramzi M

    2014-08-01

    Children with reading difficulties often demonstrate weaknesses in working memory (WM). This research study explored the relation between two WM systems (verbal and visuospatial WM) and reading ability in a sample of school-aged children with a wide range of reading skills. Children (N = 157), ages 9-12, were administered measures of short-term memory, verbal WM, visuospatial WM, and reading measures (e.g., reading fluency and comprehension). Although results indicated that verbal WM was a stronger predictor in reading fluency and comprehension, visuospatial WM also significantly predicted reading skills, but provided more unique variance in reading comprehension than reading fluency. These findings suggest that visuospatial WM may play a significant role in higher level reading processes, particularly in reading comprehension, than previously thought. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Stories to Be Read Aloud (Booksearch).

    ERIC Educational Resources Information Center

    English Journal, 1989

    1989-01-01

    Presents junior and senior high school teachers' suggestions for short stories to read aloud in a single class period, including "The Laughing Man" (J. D. Salinger), "A & P" (John Updike), "Epicac" (Kurt Vonnegut), "The Story of an Hour" (Kate Chopin), and "The Yellow Wallpaper" (Charlotte…

  19. Reading Profiles in Multi-Site Data With Missingness.

    PubMed

    Eckert, Mark A; Vaden, Kenneth I; Gebregziabher, Mulugeta

    2018-01-01

    Children with reading disability exhibit varied deficits in reading and cognitive abilities that contribute to their reading comprehension problems. Some children exhibit primary deficits in phonological processing, while others can exhibit deficits in oral language and executive functions that affect comprehension. This behavioral heterogeneity is problematic when missing data prevent the characterization of different reading profiles, which often occurs in retrospective data sharing initiatives without coordinated data collection. Here we show that reading profiles can be reliably identified based on Random Forest classification of incomplete behavioral datasets, after the missForest method is used to multiply impute missing values. Results from simulation analyses showed that reading profiles could be accurately classified across degrees of missingness (e.g., ∼5% classification error for 30% missingness across the sample). The application of missForest to a real multi-site dataset with missingness ( n = 924) showed that reading disability profiles significantly and consistently differed in reading and cognitive abilities for cases with and without missing data. The results of validation analyses indicated that the reading profiles (cases with and without missing data) exhibited significant differences for an independent set of behavioral variables that were not used to classify reading profiles. Together, the results show how multiple imputation can be applied to the classification of cases with missing data and can increase the integrity of results from multi-site open access datasets.

  20. Neural Correlates of Coherence-Break Detection during Reading of Narratives

    ERIC Educational Resources Information Center

    Helder, Anne; van den Broek, Paul; Karlsson, Josefine; Van Leijenhorst, Linda

    2017-01-01

    This functional magnetic resonance imaging study examined the neural correlates of coherence-break detection during reading in the context of a contradiction paradigm. Young adults (N = 31, ages 19-27) read short narratives (half contained a break in coherence) that were presented sentence by sentence in a self-paced, slow event-related design.…

  1. Grade 12 Diploma Examination, English 33. Part B: Reading. (Multiple Choice). Readings Booklet. 1988 Edition.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton.

    Intended for students taking Grade 12 Diploma Examinations in English 33 in Alberta, Canada, this reading test is designed to be administered with a questions booklet. The following short selections taken from fiction, nonfiction, poetry, drama, and day-to-day functional materials are included: (1) "M is for Mother" (Marjorie Riddle);…

  2. Dyslexie Font Does Not Benefit Reading in Children with or without Dyslexia

    ERIC Educational Resources Information Center

    Kuster, Sanne M.; van Weerdenburg, Marjolijn; Gompel, Marjolein; Bosman, Anna M. T.

    2018-01-01

    In two experiments, the claim was tested that the font "Dyslexie", specifically designed for people with dyslexia, eases reading performance of children with (and without) dyslexia. Three questions were investigated. (1) Does the Dyslexie font lead to faster and/or more accurate reading? (2) Do children have a preference for the Dyslexie…

  3. Shorter lines facilitate reading in those who struggle.

    PubMed

    Schneps, Matthew H; Thomson, Jenny M; Sonnert, Gerhard; Pomplun, Marc; Chen, Chen; Heffner-Wong, Amanda

    2013-01-01

    People with dyslexia, who ordinarily struggle to read, sometimes remark that reading is easier when e-readers are used. Here, we used eye tracking to observe high school students with dyslexia as they read using these devices. Among the factors investigated, we found that reading using a small device resulted in substantial benefits, improving reading speeds by 27%, reducing the number of fixations by 11%, and importantly, reducing the number of regressive saccades by more than a factor of 2, with no cost to comprehension. Given that an expected trade-off between horizontal and vertical regression was not observed when line lengths were altered, we speculate that these effects occur because sluggish attention spreads perception to the left as the gaze shifts during reading. Short lines eliminate crowded text to the left, reducing regression. The effects of attention modulation by the hand, and of increased letter spacing to reduce crowding, were also found to modulate the oculomotor dynamics in reading, but whether these factors resulted in benefits or costs depended on characteristics, such as visual attention span, that varied within our sample.

  4. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

    PubMed Central

    Degner, Jacob F.; Marioni, John C.; Pai, Athma A.; Pickrell, Joseph K.; Nkadori, Everlyne; Gilad, Yoav; Pritchard, Jonathan K.

    2009-01-01

    Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE). Results: We generated 16 million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias toward higher mapping rates of the allele in the reference sequence, compared with the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, ∼5–10% of SNPs still have an inherent bias toward more effective mapping of one allele. Filtering out inherently biased SNPs removes 40% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data. Availability: Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome and analyzing the simulation output are available upon request from JFD. Raw short read data were deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE18156. Contact: jdegner@uchicago.edu; marioni@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19808877

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

    PubMed

    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.

  6. Emergence of representations through repeated training on pronouncing novel letter combinations leads to efficient reading.

    PubMed

    Takashima, Atsuko; Hulzink, Iris; Wagensveld, Barbara; Verhoeven, Ludo

    2016-08-01

    Printed text can be decoded by utilizing different processing routes depending on the familiarity of the script. A predominant use of word-level decoding strategies can be expected in the case of a familiar script, and an almost exclusive use of letter-level decoding strategies for unfamiliar scripts. Behavioural studies have revealed that frequently occurring words are read more efficiently, suggesting that these words are read in a more holistic way at the word-level, than infrequent and unfamiliar words. To test whether repeated exposure to specific letter combinations leads to holistic reading, we monitored both behavioural and neural responses during novel script decoding and examined changes related to repeated exposure. We trained a group of Dutch university students to decode pseudowords written in an unfamiliar script, i.e., Korean Hangul characters. We compared behavioural and neural responses to pronouncing trained versus untrained two-character pseudowords (equivalent to two-syllable pseudowords). We tested once shortly after the initial training and again after a four days' delay that included another training session. We found that trained pseudowords were pronounced faster and more accurately than novel combinations of radicals (equivalent to letters). Imaging data revealed that pronunciation of trained pseudowords engaged the posterior temporo-parietal region, and engagement of this network was predictive of reading efficiency a month later. The results imply that repeated exposure to specific combinations of graphemes can lead to emergence of holistic representations that result in efficient reading. Furthermore, inter-individual differences revealed that good learners retained efficiency more than bad learners one month later. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. A Developmental Examination of Basic Perceptual Processes in Reading. Final Report.

    ERIC Educational Resources Information Center

    Lefton, Lester A.

    This report summarizes four groups of experiments examining the nature of basic perceptual processes in reading. The first group examined the relationship of English orthography to reading, specifically the transfer of information from the icon to short-term memory. The second group of experiments examined the use of peripheral information…

  8. Short and Medium Run Effects of Parents Reading to Pre-School Children in a Disadvantaged Locality.

    ERIC Educational Resources Information Center

    Toomey, Derek

    A study examined the effectiveness of an emergent literacy program designed to encourage low-income parents to read to their children. Pre-school teachers in four low-income areas in Australia read to children in their class regularly. Three books were sent home with each child twice a week and the parents were asked to read to their children. A…

  9. Reading the Writer's Craft: The Hemingway Short Stories

    ERIC Educational Resources Information Center

    Garrigues, Lisa

    2004-01-01

    The high school students who spent five weeks studying the style and craft of Ernest Hemingway experienced the power and plus points of apprenticeships. Several assignments that helped the high school juniors to analyze Hemingway's work on short stories and learn from this master craftsman are presented.

  10. Neurobiological bases of reading comprehension: Insights from neuroimaging studies of word level and text level processing in skilled and impaired readers

    PubMed Central

    Landi, Nicole; Frost, Stephen J.; Menc, W. Einar; Sandak, Rebecca; Pugh, Kenneth R.

    2012-01-01

    For accurate reading comprehension, readers must first learn to map letters to their corresponding speech sounds and meaning and then they must string the meanings of many words together to form a representation of the text. Furthermore, readers must master the complexities involved in parsing the relevant syntactic and pragmatic information necessary for accurate interpretation. Failure in this process can occur at multiple levels and cognitive neuroscience has been helpful in identifying the underlying causes of success and failure in reading single words and in reading comprehension. In general, neurobiological studies of skilled reading comprehension indicate a highly overlapping language circuit for single word reading, reading comprehension and listening comprehension with largely quantitative differences in a number of reading and language related areas. This paper reviews relevant research from studies employing neuroimaging techniques to study reading with a focus on the relationship between reading skill, single word reading, and text comprehension. PMID:23662034

  11. Discourse Memory and Reading Comprehension Skill

    ERIC Educational Resources Information Center

    Perfetti, Charles A.; Goldman, Susan R.

    1976-01-01

    A study is reported in which short-term memory capacity, estimated by a probe digit task, and memory for structured language, measured by a probe discourse task, were investigated in an experiment with third and fifth grade IQ-matched children representing two levels of reading comprehension skill. (Author/RM)

  12. (Con)text-specific effects of visual dysfunction on reading in posterior cortical atrophy.

    PubMed

    Yong, Keir X X; Shakespeare, Timothy J; Cash, Dave; Henley, Susie M D; Warren, Jason D; Crutch, Sebastian J

    2014-08-01

    Reading deficits are a common early feature of the degenerative syndrome posterior cortical atrophy (PCA) but are poorly understood even at the single word level. The current study evaluated the reading accuracy and speed of 26 PCA patients, 17 typical Alzheimer's disease (tAD) patients and 14 healthy controls on a corpus of 192 single words in which the following perceptual properties were manipulated systematically: inter-letter spacing, font size, length, font type, case and confusability. PCA reading was significantly less accurate and slower than tAD patients and controls, with performance significantly adversely affected by increased letter spacing, size, length and font (cursive < non-cursive), and characterised by visual errors (69% of all error responses). By contrast, tAD and control accuracy rates were at or near ceiling, letter spacing was the only perceptual factor to influence reading speed in the same direction as controls, and, in contrast to PCA patients, control reading was faster for larger font sizes. The inverse size effect in PCA (less accurate reading of large than small font size print) was associated with lower grey matter volume in the right superior parietal lobule. Reading accuracy was associated with impairments of early visual (especially crowding), visuoperceptual and visuospatial processes. However, these deficits were not causally related to a universal impairment of reading as some patients showed preserved reading for small, unspaced words despite grave visual deficits. Rather, the impact of specific types of visual dysfunction on reading was found to be (con)text specific, being particularly evident for large, spaced, lengthy words. These findings improve the characterisation of dyslexia in PCA, shed light on the causative and associative factors, and provide clear direction for the development of reading aids and strategies to maximise and sustain reading ability in the early stages of disease. Copyright © 2014. Published by

  13. (Con)text-specific effects of visual dysfunction on reading in posterior cortical atrophy

    PubMed Central

    Yong, Keir X.X.; Shakespeare, Timothy J.; Cash, Dave; Henley, Susie M.D.; Warren, Jason D.; Crutch, Sebastian J.

    2014-01-01

    Reading deficits are a common early feature of the degenerative syndrome posterior cortical atrophy (PCA) but are poorly understood even at the single word level. The current study evaluated the reading accuracy and speed of 26 PCA patients, 17 typical Alzheimer's disease (tAD) patients and 14 healthy controls on a corpus of 192 single words in which the following perceptual properties were manipulated systematically: inter-letter spacing, font size, length, font type, case and confusability. PCA reading was significantly less accurate and slower than tAD patients and controls, with performance significantly adversely affected by increased letter spacing, size, length and font (cursive < non-cursive), and characterised by visual errors (69% of all error responses). By contrast, tAD and control accuracy rates were at or near ceiling, letter spacing was the only perceptual factor to influence reading speed in the same direction as controls, and, in contrast to PCA patients, control reading was faster for larger font sizes. The inverse size effect in PCA (less accurate reading of large than small font size print) was associated with lower grey matter volume in the right superior parietal lobule. Reading accuracy was associated with impairments of early visual (especially crowding), visuoperceptual and visuospatial processes. However, these deficits were not causally related to a universal impairment of reading as some patients showed preserved reading for small, unspaced words despite grave visual deficits. Rather, the impact of specific types of visual dysfunction on reading was found to be (con)text specific, being particularly evident for large, spaced, lengthy words. These findings improve the characterisation of dyslexia in PCA, shed light on the causative and associative factors, and provide clear direction for the development of reading aids and strategies to maximise and sustain reading ability in the early stages of disease. PMID:24841985

  14. The Utility of the Dynamic Indicators of Basic Early Literacy Skills (DIBELS) in Predicting Reading Achievement

    ERIC Educational Resources Information Center

    Echols, Julie M. Young

    2010-01-01

    Reading proficiency is the goal of many local and national reading initiatives. A key component of these initiatives is accurate and reliable reading assessment. In this high-stakes testing arena, the Dynamic Indicators of Basic Early Literacy Skills (DIBELS) has emerged as a preferred measure for identification of students at risk for reading…

  15. Effects of audio-visual aids on foreign language test anxiety, reading and listening comprehension, and retention in EFL learners.

    PubMed

    Lee, Shu-Ping; Lee, Shin-Da; Liao, Yuan-Lin; Wang, An-Chi

    2015-04-01

    This study examined the effects of audio-visual aids on anxiety, comprehension test scores, and retention in reading and listening to short stories in English as a Foreign Language (EFL) classrooms. Reading and listening tests, general and test anxiety, and retention were measured in English-major college students in an experimental group with audio-visual aids (n=83) and a control group without audio-visual aids (n=94) with similar general English proficiency. Lower reading test anxiety, unchanged reading comprehension scores, and better reading short-term and long-term retention after four weeks were evident in the audiovisual group relative to the control group. In addition, lower listening test anxiety, higher listening comprehension scores, and unchanged short-term and long-term retention were found in the audiovisual group relative to the control group after the intervention. Audio-visual aids may help to reduce EFL learners' listening test anxiety and enhance their listening comprehension scores without facilitating retention of such materials. Although audio-visual aids did not increase reading comprehension scores, they helped reduce EFL learners' reading test anxiety and facilitated retention of reading materials.

  16. Accurate T1 mapping of short T2 tissues using a three-dimensional ultrashort echo time cones actual flip angle imaging-variable repetition time (3D UTE-Cones AFI-VTR) method.

    PubMed

    Ma, Ya-Jun; Lu, Xing; Carl, Michael; Zhu, Yanchun; Szeverenyi, Nikolaus M; Bydder, Graeme M; Chang, Eric Y; Du, Jiang

    2018-08-01

    To develop an accurate T 1 measurement method for short T 2 tissues using a combination of a 3-dimensional ultrashort echo time cones actual flip angle imaging technique and a variable repetition time technique (3D UTE-Cones AFI-VTR) on a clinical 3T scanner. First, the longitudinal magnetization mapping function of the excitation pulse was obtained with the 3D UTE-Cones AFI method, which provided information about excitation efficiency and B 1 inhomogeneity. Then, the derived mapping function was substituted into the VTR fitting to generate accurate T 1 maps. Numerical simulation and phantom studies were carried out to compare the AFI-VTR method with a B 1 -uncorrected VTR method, a B 1 -uncorrected variable flip angle (VFA) method, and a B 1 -corrected VFA method. Finally, the 3D UTE-Cones AFI-VTR method was applied to bovine bone samples (N = 6) and healthy volunteers (N = 3) to quantify the T 1 of cortical bone. Numerical simulation and phantom studies showed that the 3D UTE-Cones AFI-VTR technique provides more accurate measurement of the T 1 of short T 2 tissues than the B 1 -uncorrected VTR and VFA methods or the B 1 -corrected VFA method. The proposed 3D UTE-Cones AFI-VTR method showed a mean T 1 of 240 ± 25 ms for bovine cortical bone and 218 ± 10 ms for the tibial midshaft of human volunteers, respectively, at 3 T. The 3D UTE-Cones AFI-VTR method can provide accurate T 1 measurements of short T 2 tissues such as cortical bone. Magn Reson Med 80:598-608, 2018. © 2018 International Society for Magnetic Resonance in Medicine. © 2018 International Society for Magnetic Resonance in Medicine.

  17. Teachable Anthologies of Short Fiction for Developmental Students.

    ERIC Educational Resources Information Center

    Ngovo, Bernard L.

    2002-01-01

    Explains the rationale for including short fiction in the curricula for two college developmental reading classes and describes the features of the anthologies used. Suggests the use of the middle and the advanced levels of "Best Short Stories" published by Jamestown Publishers. Notes that these anthologies contain features that make…

  18. Online inferential and textual processing by adolescents with attention-deficit/hyperactivity disorder during reading comprehension: Evidence from a probing method.

    PubMed

    Yeari, Menahem; Avramovich, Adi; Schiff, Rachel

    2017-06-01

    Previous studies have demonstrated that students with attention-deficit/hyperactivity disorder (ADHD) struggle particularly with grasping the implicit, inferential level of narratives that is crucial for story comprehension. However, these studies used offline tasks (i.e., after story presentation), used indirect measurements (e.g., identifying main ideas), and/or yielded inconclusive results using think-aloud techniques. Moreover, most studies were conducted with preschool or elementary school children with ADHD, using listening or televised story comprehension. In this study, we were interested in examining the spontaneous, immediate activation and/or suppression of forward-predictive inferences, backward-explanatory inferences, and inference-evoking textual information, as they occur online during reading comprehension by adolescents with ADHD. Participants with and without ADHD read short narrative texts, each of which included a predictive sentence, a bridging sentence that referred back to the predictive sentence via actualization of the predicted event, and two intervening sentences positioned between the predictive and bridging sentences that introduced a temporary transition from the main (predictive) episode. Activation and suppression of inferential and/or textual information were assessed using naming times of word probes that were implied by the preceding text, explicitly mentioned in it, or neither when following control texts. In some cases, a true-false inferential or textual question followed the probe. Naming facilitations were observed for the control but not for the ADHD group, in responding to inference probes that followed the predictive and bridging sentences, and to text probes that followed the predictive sentences. Participants with ADHD were accurate, albeit slower, than controls in answering the true-false questions. Adolescents with ADHD have difficulties in generating predictive and explanatory inferences and in retaining relevant

  19. Foundations of reading comprehension in children with intellectual disabilities.

    PubMed

    van Wingerden, Evelien; Segers, Eliane; van Balkom, Hans; Verhoeven, Ludo

    2017-01-01

    Knowledge about predictors for reading comprehension in children with intellectual disabilities (ID) is still fragmented. This study compared reading comprehension, word decoding, listening comprehension, and reading related linguistic and cognitive precursor measures in children with mild ID and typically developing controls. Moreover, it was explored how the precursors related to reading achievement. Children with mild ID and typical controls were assessed on reading comprehension, decoding, language comprehension, and linguistic (early literacy skills, vocabulary, grammar) and cognitive (rapid naming, phonological short-term memory, working memory, temporal processing, nonverbal reasoning) precursor measures. It was tested to what extent variations in reading comprehension could be explained from word decoding, listening comprehension and precursor measures. The ID group scored significantly below typical controls on all measures. Word decoding was at or above first grade level in half the ID group. Reading comprehension in the ID group was related to word decoding, listening comprehension, early literacy skills, and temporal processing. The reading comprehension profile of children with mild ID strongly resembles typical early readers. The simple view of reading pertains to children with mild ID, with additional influence of early literacy skills and temporal processing. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. Stem and Derivational-Suffix Processing during Reading by French Second and Third Graders

    ERIC Educational Resources Information Center

    Cole, Pascale; Bouton, Sophie; Leuwers, Christel; Casalis, Severine; Sprenger-Charolles, Liliane

    2012-01-01

    Morphological processing by French children was investigated in two experiments. The first showed that second and third graders read pseudowords such as "chat-ure" ("cat-ish") composed of an illegally combined real stem and real derivational suffix faster and more accurately than they read matched pseudowords composed of a pseudostem and a real…

  1. Neural activity tied to reading predicts individual differences in extended-text comprehension

    PubMed Central

    Mossbridge, Julia A.; Grabowecky, Marcia; Paller, Ken A.; Suzuki, Satoru

    2013-01-01

    Reading comprehension depends on neural processes supporting the access, understanding, and storage of words over time. Examinations of the neural activity correlated with reading have contributed to our understanding of reading comprehension, especially for the comprehension of sentences and short passages. However, the neural activity associated with comprehending an extended text is not well-understood. Here we describe a current-source-density (CSD) index that predicts individual differences in the comprehension of an extended text. The index is the difference in CSD-transformed event-related potentials (ERPs) to a target word between two conditions: a comprehension condition with words from a story presented in their original order, and a scrambled condition with the same words presented in a randomized order. In both conditions participants responded to the target word, and in the comprehension condition they also tried to follow the story in preparation for a comprehension test. We reasoned that the spatiotemporal pattern of difference-CSDs would reflect comprehension-related processes beyond word-level processing. We used a pattern-classification method to identify the component of the difference-CSDs that accurately (88%) discriminated good from poor comprehenders. The critical CSD index was focused at a frontal-midline scalp site, occurred 400–500 ms after target-word onset, and was strongly correlated with comprehension performance. Behavioral data indicated that group differences in effort or motor preparation could not explain these results. Further, our CSD index appears to be distinct from the well-known P300 and N400 components, and CSD transformation seems to be crucial for distinguishing good from poor comprehenders using our experimental paradigm. Once our CSD index is fully characterized, this neural signature of individual differences in extended-text comprehension may aid the diagnosis and remediation of reading comprehension deficits. PMID

  2. Shorter Lines Facilitate Reading in Those Who Struggle

    PubMed Central

    Schneps, Matthew H.; Thomson, Jenny M.; Sonnert, Gerhard; Pomplun, Marc; Chen, Chen; Heffner-Wong, Amanda

    2013-01-01

    People with dyslexia, who ordinarily struggle to read, sometimes remark that reading is easier when e-readers are used. Here, we used eye tracking to observe high school students with dyslexia as they read using these devices. Among the factors investigated, we found that reading using a small device resulted in substantial benefits, improving reading speeds by 27%, reducing the number of fixations by 11%, and importantly, reducing the number of regressive saccades by more than a factor of 2, with no cost to comprehension. Given that an expected trade-off between horizontal and vertical regression was not observed when line lengths were altered, we speculate that these effects occur because sluggish attention spreads perception to the left as the gaze shifts during reading. Short lines eliminate crowded text to the left, reducing regression. The effects of attention modulation by the hand, and of increased letter spacing to reduce crowding, were also found to modulate the oculomotor dynamics in reading, but whether these factors resulted in benefits or costs depended on characteristics, such as visual attention span, that varied within our sample. PMID:23940709

  3. Using pseudoalignment and base quality to accurately quantify microbial community composition

    PubMed Central

    Novembre, John

    2018-01-01

    Pooled DNA from multiple unknown organisms arises in a variety of contexts, for example microbial samples from ecological or human health research. Determining the composition of pooled samples can be difficult, especially at the scale of modern sequencing data and reference databases. Here we propose a novel method for taxonomic profiling in pooled DNA that combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood framework that uses base quality information to better resolve multiply mapped reads. We apply the method to the problem of classifying 16S rRNA reads using a reference database of known organisms, a common challenge in microbiome research. Using simulations, we show the method is accurate across a variety of read lengths, with different length reference sequences, at different sample depths, and when samples contain reads originating from organisms absent from the reference. We also assess performance in real 16S data, where we reanalyze previous genetic association data to show our method discovers a larger number of quantitative trait associations than other widely used methods. We implement our method in the software Karp, for k-mer based analysis of read pools, to provide a novel combination of speed and accuracy that is uniquely suited for enhancing discoveries in microbial studies. PMID:29659582

  4. Using Subjective and Objective Measures to Predict Level of Reading Fluency at the End of First Grade

    ERIC Educational Resources Information Center

    Morris, Darrell; Pennell, Ashley M.; Perney, Jan; Trathen, Woodrow

    2018-01-01

    This study compared reading rate to reading fluency (as measured by a rating scale). After listening to first graders read short passages, we assigned an overall fluency rating (low, average, or high) to each reading. We then used predictive discriminant analyses to determine which of five measures--accuracy, rate (objective); accuracy, phrasing,…

  5. Using Serial and Discrete Digit Naming to Unravel Word Reading Processes

    PubMed Central

    Altani, Angeliki; Protopapas, Athanassios; Georgiou, George K.

    2018-01-01

    During reading acquisition, word recognition is assumed to undergo a developmental shift from slow serial/sublexical processing of letter strings to fast parallel processing of whole word forms. This shift has been proposed to be detected by examining the size of the relationship between serial- and discrete-trial versions of word reading and rapid naming tasks. Specifically, a strong association between serial naming of symbols and single word reading suggests that words are processed serially, whereas a strong association between discrete naming of symbols and single word reading suggests that words are processed in parallel as wholes. In this study, 429 Grade 1, 3, and 5 English-speaking Canadian children were tested on serial and discrete digit naming and word reading. Across grades, single word reading was more strongly associated with discrete naming than with serial naming of digits, indicating that short high-frequency words are processed as whole units early in the development of reading ability in English. In contrast, serial naming was not a unique predictor of single word reading across grades, suggesting that within-word sequential processing was not required for the successful recognition for this set of words. Factor mixture analysis revealed that our participants could be clustered into two classes, namely beginning and more advanced readers. Serial naming uniquely predicted single word reading only among the first class of readers, indicating that novice readers rely on a serial strategy to decode words. Yet, a considerable proportion of Grade 1 students were assigned to the second class, evidently being able to process short high-frequency words as unitized symbols. We consider these findings together with those from previous studies to challenge the hypothesis of a binary distinction between serial/sublexical and parallel/lexical processing in word reading. We argue instead that sequential processing in word reading operates on a continuum

  6. Using Serial and Discrete Digit Naming to Unravel Word Reading Processes.

    PubMed

    Altani, Angeliki; Protopapas, Athanassios; Georgiou, George K

    2018-01-01

    During reading acquisition, word recognition is assumed to undergo a developmental shift from slow serial/sublexical processing of letter strings to fast parallel processing of whole word forms. This shift has been proposed to be detected by examining the size of the relationship between serial- and discrete-trial versions of word reading and rapid naming tasks. Specifically, a strong association between serial naming of symbols and single word reading suggests that words are processed serially, whereas a strong association between discrete naming of symbols and single word reading suggests that words are processed in parallel as wholes. In this study, 429 Grade 1, 3, and 5 English-speaking Canadian children were tested on serial and discrete digit naming and word reading. Across grades, single word reading was more strongly associated with discrete naming than with serial naming of digits, indicating that short high-frequency words are processed as whole units early in the development of reading ability in English. In contrast, serial naming was not a unique predictor of single word reading across grades, suggesting that within-word sequential processing was not required for the successful recognition for this set of words. Factor mixture analysis revealed that our participants could be clustered into two classes, namely beginning and more advanced readers. Serial naming uniquely predicted single word reading only among the first class of readers, indicating that novice readers rely on a serial strategy to decode words. Yet, a considerable proportion of Grade 1 students were assigned to the second class, evidently being able to process short high-frequency words as unitized symbols. We consider these findings together with those from previous studies to challenge the hypothesis of a binary distinction between serial/sublexical and parallel/lexical processing in word reading. We argue instead that sequential processing in word reading operates on a continuum

  7. Task-Oriented Reading of Multiple Documents: Online Comprehension Processes and Offline Products

    ERIC Educational Resources Information Center

    Anmarkrud, Øistein; McCrudden, Matthew T.; Bråten, Ivar; Strømsø, Helge I.

    2013-01-01

    We explored readers' judgments of text relevance and strategy use while they read about a controversial scientific issue in multiple conflicting documents using a think-aloud methodology and had them write a short essay after reading. Participants were university-level students. There were three main findings. First, readers discriminated…

  8. Musical Experience, Auditory Perception and Reading-Related Skills in Children

    PubMed Central

    Banai, Karen; Ahissar, Merav

    2013-01-01

    Background The relationships between auditory processing and reading-related skills remain poorly understood despite intensive research. Here we focus on the potential role of musical experience as a confounding factor. Specifically we ask whether the pattern of correlations between auditory and reading related skills differ between children with different amounts of musical experience. Methodology/Principal Findings Third grade children with various degrees of musical experience were tested on a battery of auditory processing and reading related tasks. Very poor auditory thresholds and poor memory skills were abundant only among children with no musical education. In this population, indices of auditory processing (frequency and interval discrimination thresholds) were significantly correlated with and accounted for up to 13% of the variance in reading related skills. Among children with more than one year of musical training, auditory processing indices were better, yet reading related skills were not correlated with them. A potential interpretation for the reduction in the correlations might be that auditory and reading-related skills improve at different rates as a function of musical training. Conclusions/Significance Participants’ previous musical training, which is typically ignored in studies assessing the relations between auditory and reading related skills, should be considered. Very poor auditory and memory skills are rare among children with even a short period of musical training, suggesting musical training could have an impact on both. The lack of correlation in the musically trained population suggests that a short period of musical training does not enhance reading related skills of individuals with within-normal auditory processing skills. Further studies are required to determine whether the associations between musical training, auditory processing and memory are indeed causal or whether children with poor auditory and memory skills are less

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

    PubMed Central

    2012-01-01

    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 PMID:22244497

  10. A Federal Arts Agency at the Center of Reading Research: How We Got Here

    ERIC Educational Resources Information Center

    Iyengar, Sunil

    2008-01-01

    In this article, the author offers a short summary of the findings of the National Endowment for the Arts report on the status of reading, "To Read or Not to Read: A Question of National Consequence", and an explanation of the guiding rationale for the study and some future areas of research that seem warranted in light of public responses to the…

  11. ARYANA: Aligning Reads by Yet Another Approach

    PubMed Central

    2014-01-01

    Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. Contribution We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. Availability ARYANA with complete source code can be obtained from http://github.com/aryana-aligner PMID:25252881

  12. ARYANA: Aligning Reads by Yet Another Approach.

    PubMed

    Gholami, Milad; Arbabi, Aryan; Sharifi-Zarchi, Ali; Chitsaz, Hamidreza; Sadeghi, Mehdi

    2014-01-01

    Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $10(6) prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads requires fast overlap-layout-concensus algorithms which depend on fast and accurate alignment. We introduce ARYANA, a fast gapped read aligner, developed on the base of BWA indexing infrastructure with a completely new alignment engine that makes it significantly faster than three other aligners: Bowtie2, BWA and SeqAlto, with comparable generality and accuracy. Instead of the time-consuming backtracking procedures for handling mismatches, ARYANA comes with the seed-and-extend algorithmic framework and a significantly improved efficiency by integrating novel algorithmic techniques including dynamic seed selection, bidirectional seed extension, reset-free hash tables, and gap-filling dynamic programming. As the read length increases ARYANA's superiority in terms of speed and alignment rate becomes more evident. This is in perfect harmony with the read length trend as the sequencing technologies evolve. The algorithmic platform of ARYANA makes it easy to develop mission-specific aligners for other applications using ARYANA engine. ARYANA with complete source code can be obtained from http://github.com/aryana-aligner.

  13. MeCorS: Metagenome-enabled error correction of single cell sequencing reads

    DOE PAGES

    Bremges, Andreas; Singer, Esther; Woyke, Tanja; ...

    2016-03-15

    Here we present a new tool, MeCorS, to correct chimeric reads and sequencing errors in Illumina data generated from single amplified genomes (SAGs). It uses sequence information derived from accompanying metagenome sequencing to accurately correct errors in SAG reads, even from ultra-low coverage regions. In evaluations on real data, we show that MeCorS outperforms BayesHammer, the most widely used state-of-the-art approach. MeCorS performs particularly well in correcting chimeric reads, which greatly improves both accuracy and contiguity of de novo SAG assemblies.

  14. Learning to Read in Arabic: Reading, Syntactic, Orthographic and Working Memory Skills in Normally Achieving and Poor Arabic Readers.

    ERIC Educational Resources Information Center

    Abu-Rabia, Salim

    1995-01-01

    Examines relationships between phonological skills and reading in 143 Arab children in Arab villages of central Israel. Finds that a word recognition test was highly correlated with phonological skills, semantic processing, syntactic knowledge, and short-term memory, and that poor readers significantly lagged in skill development. Discusses…

  15. Reading and writing skills in young adults with spina bifida and hydrocephalus.

    PubMed

    Barnes, Marcia; Dennis, Maureen; Hetherington, Ross

    2004-09-01

    Reading and writing were studied in 31 young adults with spina bifida and hydrocephalus (SBH). Like children with this condition, young adults with SBH had better word decoding than reading comprehension, and, compared to population means, had lower scores on a test of writing fluency. Reading comprehension was predicted by word decoding and listening comprehension. Writing was predicted by fine motor finger function, verbal intelligence, and short-term and working memory. These findings are consistent with cognitive models of reading and writing. Writing, but not reading, was related to highest level of education achieved and writing fluency predicted several aspects of functional independence. Reading comprehension and writing remain deficient in adults with SBH and have consequences for educational attainments and functional independence.

  16. Age Differences in the Effects of Domain Knowledge on Reading Efficiency

    PubMed Central

    Miller, Lisa M. Soederberg

    2009-01-01

    The present study investigated age differences in the effects of knowledge on the efficiency with which information is processed while reading. Individuals between 18 and 85 years of age, with varying levels of cooking knowledge, read and recalled a series of short passages within the domain of cooking. Reading efficiency was operationalized as time spent reading divided by the amount recalled for each passage. Results showed that reading efficiency increased with increasing levels of knowledge among older but not younger adults. Similarly, those with smaller working memory capacities showed increasing efficiency with increasing knowledge. These findings suggest that knowledge promotes a more efficient allocation policy which is particularly helpful in later life, perhaps due to age-related declines in working memory capacity. PMID:19290738

  17. What’s the Story? The Tale of Reading Fluency Told at Speed

    PubMed Central

    Benjamin, Christopher F. A.; Gaab, Nadine

    2012-01-01

    Fluent readers process written text rapidly and accurately, and comprehend what they read. Historically, reading fluency has been modeled as the product of discrete skills such as single word decoding. More recent conceptualizations emphasize that fluent reading is the product of competency in, and the coordination of, multiple cognitive sub-skills (a multi-componential view). In this study, we examined how the pattern of activation in core reading regions changes as the ability to read fluently is manipulated through reading speed. We evaluated 13 right-handed adults with a novel fMRI task assessing fluent sentence reading and lower-order letter reading at each participant’s normal fluent reading speed, as well as constrained (slowed) and accelerated reading speeds. Comparing fluent reading conditions with rest revealed regions including bilateral occipito-fusiform, left middle temporal, and inferior frontal gyral clusters across reading speeds. The selectivity of these regions’ responses to fluent sentence reading was shown by comparison with the letter reading task. Region of interest analyses showed that at constrained and accelerated speeds these regions responded significantly more to fluent sentence reading. Critically, as reading speed increased, activation increased in a single reading-related region: occipital/fusiform cortex (left > right). These results demonstrate that while brain regions engaged in reading respond selectively during fluent reading, these regions respond differently as the ability to read fluently is manipulated. Implications for our understanding of reading fluency, reading development, and reading disorders are discussed. PMID:21954000

  18. How Reading Volume Affects Both Reading Fluency and Reading Achievement

    ERIC Educational Resources Information Center

    Allington, Richard L.

    2014-01-01

    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…

  19. Developing Reading Comprehension with Moving Image Narratives

    ERIC Educational Resources Information Center

    Maine, Fiona; Shields, Robin

    2015-01-01

    This paper reports the findings from a small-scale exploratory study that investigated how moving-image narratives might enable children to develop transferable reading comprehension strategies. Using short, animated, narrative films, 28 primary-aged children engaged in a 10-week programme that included the explicit instruction of comprehension…

  20. Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

    PubMed Central

    Liu, Jiemeng; Wang, Haifeng; Yang, Hongxing; Zhang, Yizhe; Wang, Jinfeng; Zhao, Fangqing; Qi, Ji

    2013-01-01

    Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms’ taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75–100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time. PMID:22941634

  1. GLOSSARY TO READINGS IN HINDI LITERATURE.

    ERIC Educational Resources Information Center

    Wisconsin Univ., Madison. Indian Language and Area Center.

    INCLUDED IN THIS GLOSSARY ARE THE IMPORTANT VOCABULARY ITEMS WHICH APPEAR IN THE VOLUME OF READINGS. THESE ITEMS ARE ARRANGED BY SELECTION AND ARE IN SERIAL ORDER. THE LISTING INCLUDES THE DEVANAGARI FORM, AN ABBREVIATION OF THE FORM CLASS, AND A SHORT ENGLISH GLOSS. WHEN A NUMBER OF TRANSLATIONS ARE POSSIBLE, THE FIRST ONE GIVEN IS APPROPRIATE TO…

  2. The relationship of global form and motion detection to reading fluency.

    PubMed

    Englund, Julia A; Palomares, Melanie

    2012-08-15

    Visual motion processing in typical and atypical readers has suggested aspects of reading and motion processing share a common cortical network rooted in dorsal visual areas. Few studies have examined the relationship between reading performance and visual form processing, which is mediated by ventral cortical areas. We investigated whether reading fluency correlates with coherent motion detection thresholds in typically developing children using random dot kinematograms. As a comparison, we also evaluated the correlation between reading fluency and static form detection thresholds. Results show that both dorsal and ventral visual functions correlated with components of reading fluency, but that they have different developmental characteristics. Motion coherence thresholds correlated with reading rate and accuracy, which both improved with chronological age. Interestingly, when controlling for non-verbal abilities and age, reading accuracy significantly correlated with thresholds for coherent form detection but not coherent motion detection in typically developing children. Dorsal visual functions that mediate motion coherence seem to be related maturation of broad cognitive functions including non-verbal abilities and reading fluency. However, ventral visual functions that mediate form coherence seem to be specifically related to accurate reading in typically developing children. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Explaining the association between music training and reading in adults.

    PubMed

    Swaminathan, Swathi; Schellenberg, E Glenn; Venkatesan, Kirthika

    2018-06-01

    We sought to clarify whether the positive association between music lessons and reading ability is explained better by shared resources for processing pitch and temporal information, or by general cognitive abilities. Participants were native and nonnative speakers of English with varying levels of music training. We measured reading ability (comprehension and speed), music-perception skills (melody and rhythm), general cognitive ability (nonverbal intelligence, short-term memory, and working memory), and socioeconomic status (SES; family income, parents' education). Reading ability was associated positively with music training, English as a native language, and general cognitive ability. The association between reading and music training was significant after SES, native language, and music-perception skills were controlled. After general cognitive abilities were held constant, however, there was no longer an association between reading and music training. These findings suggest that the association between reading ability and music training is a consequence of general cognitive abilities. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  4. Morpheme-based Reading and Spelling in Italian Children with Developmental Dyslexia and Dysorthography.

    PubMed

    Angelelli, Paola; Marinelli, Chiara Valeria; De Salvatore, Marinella; Burani, Cristina

    2017-11-01

    Italian sixth graders, with and without dyslexia, read pseudowords and low-frequency words that include high-frequency morphemes better than stimuli not including any morpheme. The present study assessed whether morphemes affect (1) younger children, with and without dyslexia; (2) spelling as well as reading; and (3) words with low-frequency morphemes. Two groups of third graders (16 children with dyslexia and dysorthography and 16 age-matched typically developing children) read aloud and spelt to dictation pseudowords and words. Pseudowords included (1) root + suffix in not existing combinations (e.g. lampadista, formed by lampad-, 'lamp', and -ista, '-ist') and (2) orthographic sequences not corresponding to any Italian root or suffix (e.g. livonosto). Words had low frequency and included: (1) root + suffix, both of high frequency (e.g. bestiale, 'beastly'); (2) root + suffix, both of low frequency (e.g. asprigno, 'rather sour'); and (3) simple words (e.g. insulso, 'vapid'). Children with dyslexia and dysorthography were less accurate than typically developing children. Root + suffix pseudowords were read and spelt more accurately than non-morphological pseudowords by both groups. Morphologically complex (root + suffix) words were read and spelt better than simple words. However, task interacted with morphology: reading was not facilitated by low-frequency morphemes. We conclude that children acquiring a transparent orthography exploit morpheme-based reading and spelling to face difficulties in processing long unfamiliar stimuli. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  5. Literary Reading Activities of Good and Weak Students: A Think Aloud Study

    ERIC Educational Resources Information Center

    Janssen, Tanja; Braaksma, Martine; Rijlaarsdam, Gert

    2006-01-01

    In this study we examined how good and weak students of literature interact with short literary stories. We focused on differences in the use of cognitive and affective reading activities, and in the extent to which good and weak students adapt their activities to (parts of) the story they are reading. 19 Dutch tenth-grade students from 8 classes…

  6. The Gap between Spanish Speakers' Word Reading and Word Knowledge: A Longitudinal Study

    ERIC Educational Resources Information Center

    Mancilla-Martinez, Jeannette; Lesaux, Nonie K.

    2011-01-01

    This longitudinal study modeled growth rates, from ages 4.5 to 11, in English and Spanish oral language and word reading skills among 173 Spanish-speaking children from low-income households. Individual growth modeling was employed using scores from standardized measures of word reading, expressive vocabulary, and verbal short-term language…

  7. Detection of target phonemes in spontaneous and read speech.

    PubMed

    Mehta, G; Cutler, A

    1988-01-01

    Although spontaneous speech occurs more frequently in most listeners' experience than read speech, laboratory studies of human speech recognition typically use carefully controlled materials read from a script. The phonological and prosodic characteristics of spontaneous and read speech differ considerably, however, which suggests that laboratory results may not generalise to the recognition of spontaneous speech. In the present study listeners were presented with both spontaneous and read speech materials, and their response time to detect word-initial target phonemes was measured. Responses were, overall, equally fast in each speech mode. However, analysis of effects previously reported in phoneme detection studies revealed significant differences between speech modes. In read speech but not in spontaneous speech, later targets were detected more rapidly than targets preceded by short words. In contrast, in spontaneous speech but not in read speech, targets were detected more rapidly in accented than in unaccented words and in strong than in weak syllables. An explanation for this pattern is offered in terms of characteristic prosodic differences between spontaneous and read speech. The results support claims from previous work that listeners pay great attention to prosodic information in the process of recognising speech.

  8. Continuities in Reading Acquisition, Reading Skill, and Reading Disability.

    ERIC Educational Resources Information Center

    Perfetti, Charles A.

    1986-01-01

    Learning to read depends on eventual mastery of coding procedures, and even skilled reading depends on coding processes low in cost to processing resources. Reading disability may be understood as a point on an ability continuum or a wide range of coding ability. Instructional goals of word reading skill, including rapid and fluent word…

  9. Illuminator, a desktop program for mutation detection using short-read clonal sequencing.

    PubMed

    Carr, Ian M; Morgan, Joanne E; Diggle, Christine P; Sheridan, Eamonn; Markham, Alexander F; Logan, Clare V; Inglehearn, Chris F; Taylor, Graham R; Bonthron, David T

    2011-10-01

    Current methods for sequencing clonal populations of DNA molecules yield several gigabases of data per day, typically comprising reads of < 100 nt. Such datasets permit widespread genome resequencing and transcriptome analysis or other quantitative tasks. However, this huge capacity can also be harnessed for the resequencing of smaller (gene-sized) target regions, through the simultaneous parallel analysis of multiple subjects, using sample "tagging" or "indexing". These methods promise to have a huge impact on diagnostic mutation analysis and candidate gene testing. Here we describe a software package developed for such studies, offering the ability to resolve pooled samples carrying barcode tags and to align reads to a reference sequence using a mutation-tolerant process. The program, Illuminator, can identify rare sequence variants, including insertions and deletions, and permits interactive data analysis on standard desktop computers. It facilitates the effective analysis of targeted clonal sequencer data without dedicated computational infrastructure or specialized training. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Differential Effects of Oral Reading to Improve Comprehension with Severe Learning Disabled and Educable Mentally Handicapped Students.

    ERIC Educational Resources Information Center

    Chang, S. Q.; And Others

    1983-01-01

    Evaluated the effectiveness of oral reading for improving reading comprehension of 11 educable mentally handicapped or severe learning disabled adolescents who answered comprehension questions from a short factual article. Oral reading appeared to improve comprehension among the poorer readers but not for readers with moderately high ability. (JAC)

  11. Does E-Reading Enhance Reading Fluency?

    ERIC Educational Resources Information Center

    Akbar, Rahima S.; Taqi, Hanan A.; Dashti, Abdulmohsin A.; Sadeq, Taiba M.

    2015-01-01

    Extensive reading is reading as much as possible, for one's own pleasure, at a difficulty level at which one can read smoothly and quickly. In the domain of reading, this paper investigates the effect of extensive reading from e-books, through utilizing a number of downloadable reading application programs on the students' e-devices, as opposed to…

  12. Shallow and Deep Orthographies in Hebrew: The Role of Vowelization in Reading Development for Unvowelized Scripts

    ERIC Educational Resources Information Center

    Schiff, Rachel

    2012-01-01

    The present study explored the speed, accuracy, and reading comprehension of vowelized versus unvowelized scripts among 126 native Hebrew speaking children in second, fourth, and sixth grades. Findings indicated that second graders read and comprehended vowelized scripts significantly more accurately and more quickly than unvowelized scripts,…

  13. Accurate Prediction of Protein Contact Maps by Coupling Residual Two-Dimensional Bidirectional Long Short-Term Memory with Convolutional Neural Networks.

    PubMed

    Hanson, Jack; Paliwal, Kuldip; Litfin, Thomas; Yang, Yuedong; Zhou, Yaoqi

    2018-06-19

    Accurate prediction of a protein contact map depends greatly on capturing as much contextual information as possible from surrounding residues for a target residue pair. Recently, ultra-deep residual convolutional networks were found to be state-of-the-art in the latest Critical Assessment of Structure Prediction techniques (CASP12, (Schaarschmidt et al., 2018)) for protein contact map prediction by attempting to provide a protein-wide context at each residue pair. Recurrent neural networks have seen great success in recent protein residue classification problems due to their ability to propagate information through long protein sequences, especially Long Short-Term Memory (LSTM) cells. Here we propose a novel protein contact map prediction method by stacking residual convolutional networks with two-dimensional residual bidirectional recurrent LSTM networks, and using both one-dimensional sequence-based and two-dimensional evolutionary coupling-based information. We show that the proposed method achieves a robust performance over validation and independent test sets with the Area Under the receiver operating characteristic Curve (AUC)>0.95 in all tests. When compared to several state-of-the-art methods for independent testing of 228 proteins, the method yields an AUC value of 0.958, whereas the next-best method obtains an AUC of 0.909. More importantly, the improvement is over contacts at all sequence-position separations. Specifically, a 8.95%, 5.65% and 2.84% increase in precision were observed for the top L∕10 predictions over the next best for short, medium and long-range contacts, respectively. This confirms the usefulness of ResNets to congregate the short-range relations and 2D-BRLSTM to propagate the long-range dependencies throughout the entire protein contact map 'image'. SPOT-Contact server url: http://sparks-lab.org/jack/server/SPOT-Contact/. Supplementary data is available at Bioinformatics online.

  14. MAWRID: A Model of Arabic Word Reading in Development.

    PubMed

    Saiegh-Haddad, Elinor

    2017-07-01

    This article offers a model of Arabic word reading according to which three conspicuous features of the Arabic language and orthography shape the development of word reading in this language: (a) vowelization/vocalization, or the use of diacritical marks to represent short vowels and other features of articulation; (b) morphological structure, namely, the predominance and transparency of derivational morphological structure in the linguistic and orthographic representation of the Arabic word; and (c) diglossia, specifically, the lexical and lexico-phonological distance between the spoken and the standard forms of Arabic words. It is argued that the triangulation of these features governs the acquisition and deployment of reading mechanisms across development. Moreover, the difficulties that readers encounter in their journey from beginning to skilled reading may be better understood if evaluated within these language-specific features of Arabic language and orthography.

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

    ERIC Educational Resources Information Center

    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…

  16. Greater Media Consumption Needed to Improve Reading

    ERIC Educational Resources Information Center

    Petress, Ken

    2006-01-01

    In more than 30 years of university teaching; hundreds of elementary, middle, and high school visits; and numerous personal interactions with community young people, the author has repeatedly noticed that few students read newspapers or news magazines. In short, most students seem ignorant of and uncaring about current affairs. This is an alarming…

  17. Predicting Reading Growth with Event-Related Potentials: Thinking Differently about Indexing “Responsiveness”

    PubMed Central

    Lemons, Christopher J.; Key, Alexandra P.F.; Fuchs, Douglas; Yoder, Paul J.; Fuchs, Lynn S.; Compton, Donald L.; Williams, Susan M.; Bouton, Bobette

    2009-01-01

    The purpose of this study was to determine if event-related potential (ERP) data collected during three reading-related tasks (Letter Sound Matching, Nonword Rhyming, and Nonword Reading) could be used to predict short-term reading growth on a curriculum-based measure of word identification fluency over 19 weeks in a sample of 29 first-grade children. Results indicate that ERP responses to the Letter Sound Matching task were predictive of reading change and remained so after controlling for two previously validated behavioral predictors of reading, Rapid Letter Naming and Segmenting. ERP data for the other tasks were not correlated with reading change. The potential for cognitive neuroscience to enhance current methods of indexing responsiveness in a response-to-intervention (RTI) model is discussed. PMID:20514353

  18. Reading in developmental prosopagnosia: Evidence for a dissociation between word and face recognition.

    PubMed

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

    2018-02-01

    Recent models suggest that face and word recognition may rely on overlapping cognitive processes and neural regions. In support of this notion, face recognition deficits have been demonstrated in developmental dyslexia. Here we test whether the opposite association can also be found, that is, impaired reading in developmental prosopagnosia. 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 exposure durations (targeting the word superiority effect), and d) text reading. 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, as the difference in performance with faces and words was significantly greater for participants with developmental prosopagnosia than for controls. Adult developmental prosopagnosics read as quickly and fluently as controls, while they are seemingly unable to learn efficient strategies for recognizing faces. We suggest that this is due to the differing demands that face and word recognition put on the perceptual system. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  19. Description and Validation of a Test to Evaluate Sustained Silent Reading

    PubMed Central

    Ramulu, Pradeep Y.; Swenor, Bonnielin K.; Jefferys, Joan L.; Rubin, Gary S.

    2013-01-01

    Purpose. To construct and validate a test of sustained silent reading. Methods. Standardized 7300 and 7600 word passages were written to evaluate sustained silent reading. Two hundred forty subjects validated whether comprehension questions could discriminate subjects who did and did not read the passage. To evaluate test–retest properties, 49 subjects silently read the standardized passages on separate days. Sixty glaucoma suspect controls and 64 glaucoma subjects had their out loud reading evaluated with the MNRead card and an International Reading Speed Texts (IReST) passage, and their silent reading measured using the 7300 word passage. Sustained silent reading parameters included reading speed and reading speed slope over time. Results. Comprehension questions distinguished individuals who had and had not read passage materials. Bland-Altman analyses of intersession sustained reading speed and reading speed slope demonstrated 95% coefficients of repeatability of 57 words per minute (wpm) and 2.76 wpm/minute. Sustained silent reading speed was less correlated with MNRead (r = 0.59) or IReST passage (r = 0.68) reading speeds than the correlation of these two measures of out loud reading speed with each other (r = 0.72). Sustained silent reading speed was more likely to differ from IReST reading speed by more than 50% in rapid silent readers (odds ratio [OR] = 29, 95% confidence interval [CI] = 10–87), and comparisons of sustained and out loud reading speeds demonstrated proportional error in Bland-Altman analyses. Conclusions. Tests of out loud reading do not accurately reflect silent reading speed in individuals with normal vision or glaucoma. The described test offers a standardized way to evaluate the impact of eye disease and/or visual rehabilitation on sustained silent reading. PMID:23258146

  20. Sub-micron accurate track navigation method ``Navi'' for the analysis of Nuclear Emulsion

    NASA Astrophysics Data System (ADS)

    Yoshioka, T.; Yoshida, J.; Kodama, K.

    2011-03-01

    Sub-micron accurate track navigation in Nuclear Emulsion is realized by using low energy signals detected by automated Nuclear Emulsion read-out systems. Using those much dense ``noise'', about 104 times larger than the real tracks, the accuracy of the track position navigation reaches to be sub micron only by using the information of a microscope field of view, 200 micron times 200 micron. This method is applied to OPERA analysis in Japan, i.e. support of human eye checks of the candidate tracks, confirmation of neutrino interaction vertexes and to embed missing track segments to the track data read-out by automated systems.

  1. Identifying Preschool Children At-Risk of Later Reading Difficulties: Evaluation of two Emergent Literacy Screening Tools

    PubMed Central

    Wilson, Shauna B.; Lonigan, Christopher J.

    2012-01-01

    Emergent literacy skills are predictive of children’s early reading success, and literacy achievement in early schooling declines more rapidly for children who are below-average readers. It is therefore important for teachers to identify accurately children at risk for later reading difficulty so children can be exposed to good emergent literacy interventions. In this study, 176 preschoolers were administered two screening tools, the Revised Get Ready to Read! (GRTR-R) and the Individual Growth and Development Indicators (IGDIs), and a diagnostic measure at two time points. Receiver operating characteristic curve analyses revealed that at optimal cut scores, GRTR-R provided more accurate classification of children’s overall emergent literacy skills than did IGDIs. However, neither measure was particularly good at classifying specific emergent literacy skills. PMID:19822699

  2. Effects of Pre-reading Instructions on the Comprehension of Science Texts

    NASA Astrophysics Data System (ADS)

    Lyons, Yuna H.

    This study examined how three different pre-reading (or relevance) instructions led to different learning outcomes for middle school students reading science texts on the topic of sweetness. The first was a generic instruction to read for understanding. The second prompted students to form a holistic explanation of the topic of sweetness, and the third instruction prompted students to focus on the core scientific principle of the relationship between structure and function. The latter two were specifically designed to align with science disciplinary goals. A comparison of the three treatments found that the generic instruction and the structure-function instruction led to better learning outcomes, measured by recall, short-answer performance questions, and a traditional multiple-choice/short-answer assessment. A qualitative analysis of the data also revealed some small yet notable differences in the recall pattern of students, such as an increased recall of key ideas for the structure-function instruction. This effect was seen predominantly for higher-skilled readers. The results suggest the possibility that relevance instructions targeting core ideas may help to orient students to the key ideas and explanations in scientific text, especially for higher-skilled readers, and indirectly highlights some of the challenges for students with less reading competencies. Overall, this study provides greater insight into how middle-school students read science texts, the effectiveness of instructor-provided relevance instructions in promoting (higher-level) comprehension of science texts, and implications for teachers on how to use texts in science instruction. Keywords: relevance instructions, pre-reading instructions, comprehension, science texts, middle school students, low- versus high-skilled readers.

  3. Evaluation of the i3 Scale-up of Reading Recovery: Year One Report, 2011-12. RR-76

    ERIC Educational Resources Information Center

    May, Henry; Gray, Abigail; Gillespie, Jessica N.; Sirinides, Philip; Sam, Cecile; Goldsworthy, Heather; Armijo, Michael; Tognatta, Namrata

    2013-01-01

    Reading Recovery (RR) is a short-term early intervention designed to help the lowest-achieving readers in first grade reach average levels of classroom performance in literacy. Students identified to receive Reading Recovery meet individually with a specially trained Reading Recovery (RR) teacher every school day for 30-minute lessons over a…

  4. The Preferences of a Selected Group of Older Readers for Five Biographical Short Stories.

    ERIC Educational Resources Information Center

    Drotter, Molly Wilson

    The reading interests of a group of older adults were examined. Subjects were 16 adults between the ages of 50 and 85 who read five stories from "Readers' Digest" short story collections and who responded to a questionnaire about their preferences for the stories, their reading habits and interests, and the appealing elements of the stories. The…

  5. Developmental, Component-Based Model of Reading Fluency: An Investigation of Predictors of Word-Reading Fluency, Text-Reading Fluency, and Reading Comprehension.

    PubMed

    Kim, Young-Suk Grace

    2015-01-01

    The primary goal was to expand our understanding of text reading fluency (efficiency or automaticity)-how its relation to other constructs (e.g., word reading fluency and reading comprehension) changes over time and how it is different from word reading fluency and reading comprehension. We examined (1) developmentally changing relations among word reading fluency, listening comprehension, text reading fluency, and reading comprehension; (2) the relation of reading comprehension to text reading fluency; (3) unique emergent literacy predictors (i.e., phonological awareness, orthographic awareness, morphological awareness, letter name knowledge, vocabulary) of text reading fluency vs. word reading fluency; and (4) unique language and cognitive predictors (e.g., vocabulary, grammatical knowledge, theory of mind) of text reading fluency vs. reading comprehension. These questions were addressed using longitudinal data (two timepoints; Mean age = 5;24 & 6;08) from Korean-speaking children ( N = 143). Results showed that listening comprehension was related to text reading fluency at time 2, but not at time 1. At both times text reading fluency was related to reading comprehension, and reading comprehension was related to text reading fluency over and above word reading fluency and listening comprehension. Orthographic awareness was related to text reading fluency over and above other emergent literacy skills and word reading fluency. Vocabulary and grammatical knowledge were independently related to text reading fluency and reading comprehension whereas theory of mind was related to reading comprehension, but not text reading fluency. These results reveal developmental nature of relations and mechanism of text reading fluency in reading development.

  6. Developmental, Component-Based Model of Reading Fluency: An Investigation of Predictors of Word-Reading Fluency, Text-Reading Fluency, and Reading Comprehension

    PubMed Central

    Kim, Young-Suk Grace

    2015-01-01

    The primary goal was to expand our understanding of text reading fluency (efficiency or automaticity)—how its relation to other constructs (e.g., word reading fluency and reading comprehension) changes over time and how it is different from word reading fluency and reading comprehension. We examined (1) developmentally changing relations among word reading fluency, listening comprehension, text reading fluency, and reading comprehension; (2) the relation of reading comprehension to text reading fluency; (3) unique emergent literacy predictors (i.e., phonological awareness, orthographic awareness, morphological awareness, letter name knowledge, vocabulary) of text reading fluency vs. word reading fluency; and (4) unique language and cognitive predictors (e.g., vocabulary, grammatical knowledge, theory of mind) of text reading fluency vs. reading comprehension. These questions were addressed using longitudinal data (two timepoints; Mean age = 5;24 & 6;08) from Korean-speaking children (N = 143). Results showed that listening comprehension was related to text reading fluency at time 2, but not at time 1. At both times text reading fluency was related to reading comprehension, and reading comprehension was related to text reading fluency over and above word reading fluency and listening comprehension. Orthographic awareness was related to text reading fluency over and above other emergent literacy skills and word reading fluency. Vocabulary and grammatical knowledge were independently related to text reading fluency and reading comprehension whereas theory of mind was related to reading comprehension, but not text reading fluency. These results reveal developmental nature of relations and mechanism of text reading fluency in reading development. PMID:26435550

  7. Prosodic and Phonemic Awareness in Children's Reading of Long and Short Words

    ERIC Educational Resources Information Center

    Wade-Woolley, Lesly

    2016-01-01

    Phonemic and prosodic awareness are both phonological processes that operate at different levels: the former at the level of the individual sound segment and the latter at the suprasegmental level across syllables. Both have been shown to be related to word reading in young readers. In this study we examine how these processes are differentially…

  8. Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.

    PubMed

    Lima, Leandro; Sinaimeri, Blerina; Sacomoto, Gustavo; Lopez-Maestre, Helene; Marchet, Camille; Miele, Vincent; Sagot, Marie-France; Lacroix, Vincent

    2017-01-01

    The main challenge in de novo genome assembly of DNA-seq data is certainly to deal with repeats that are longer than the reads. In de novo transcriptome assembly of RNA-seq reads, on the other hand, this problem has been underestimated so far. Even though we have fewer and shorter repeated sequences in transcriptomics, they do create ambiguities and confuse assemblers if not addressed properly. Most transcriptome assemblers of short reads are based on de Bruijn graphs (DBG) and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them. The results of this work are threefold. First, we introduce a formal model for representing high copy-number and low-divergence repeats in RNA-seq data and exploit its properties to infer a combinatorial characteristic of repeat-associated subgraphs. We show that the problem of identifying such subgraphs in a DBG is NP-complete. Second, we show that in the specific case of local assembly of alternative splicing (AS) events, we can implicitly avoid such subgraphs, and we present an efficient algorithm to enumerate AS events that are not included in repeats. Using simulated data, we show that this strategy is significantly more sensitive and precise than the previous version of KisSplice (Sacomoto et al. in WABI, pp 99-111, 1), Trinity (Grabherr et al. in Nat Biotechnol 29(7):644-652, 2), and Oases (Schulz et al. in Bioinformatics 28(8):1086-1092, 3), for the specific task of calling AS events. Third, we turn our focus to full-length transcriptome assembly, and we show that exploring the topology of DBGs can improve de novo transcriptome evaluation methods. Based on the observation that repeats create complicated regions in a DBG, and when assemblers try to traverse these regions, they can infer erroneous transcripts, we propose a measure to flag transcripts traversing such troublesome regions, thereby giving a confidence level for each transcript. The originality of our work when

  9. Does Extensive Reading Promote Reading Speed?

    ERIC Educational Resources Information Center

    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…

  10. Identifying Preschool Children at Risk of Later Reading Difficulties: Evaluation of Two Emergent Literacy Screening Tools

    ERIC Educational Resources Information Center

    Wilson, Shauna B.; Lonigan, Christopher J.

    2010-01-01

    Emergent literacy skills are predictive of children's early reading success, and literacy achievement in early schooling declines more rapidly for children who are below-average readers. It is therefore important for teachers to identify accurately children at risk for later reading difficulty so children can be exposed to effective emergent…

  11. Perception of patterns of musical beat distribution in phonological developmental dyslexia: significant longitudinal relations with word reading and reading comprehension.

    PubMed

    Goswami, Usha; Huss, Martina; Mead, Natasha; Fosker, Tim; Verney, John P

    2013-05-01

    In a recent study, we reported that the accurate perception of beat structure in music ('perception of musical meter') accounted for over 40% of the variance in single word reading in children with and without dyslexia (Huss et al., 2011). Performance in the musical task was most strongly associated with the auditory processing of rise time, even though beat structure was varied by manipulating the duration of the musical notes. Here we administered the same musical task a year later to 88 children with and without dyslexia, and used new auditory processing measures to provide a more comprehensive picture of the auditory correlates of the beat structure task. We also measured reading comprehension and nonword reading in addition to single word reading. One year later, the children with dyslexia performed more poorly in the musical task than younger children reading at the same level, indicating a severe perceptual deficit for musical beat patterns. They now also had significantly poorer perception of sound rise time than younger children. Longitudinal analyses showed that the musical beat structure task was a significant longitudinal predictor of development in reading, accounting for over half of the variance in reading comprehension along with a linguistic measure of phonological awareness. The non-linguistic musical beat structure task is an important independent longitudinal and concurrent predictor of variance in reading attainment by children. The different longitudinal versus concurrent associations between musical beat perception and auditory processing suggest that individual differences in the perception of rhythmic timing are an important shared neural basis for individual differences in children in linguistic and musical processing. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Test anxiety and a high-stakes standardized reading comprehension test: A behavioral genetics perspective.

    PubMed

    Wood, Sarah G; Hart, Sara A; Little, Callie W; Phillips, Beth M

    2016-07-01

    Past research suggests that reading comprehension test performance does not rely solely on targeted cognitive processes such as word reading, but also on other non-target aspects such as test anxiety. Using a genetically sensitive design, we sought to understand the genetic and environmental etiology of the association between test anxiety and reading comprehension as measured by a high-stakes test. Mirroring the behavioral literature of test anxiety, three different dimensions of test anxiety were examined in relation to reading comprehension, namely intrusive thoughts, autonomic reactions, and off-task behaviors. Participants included 426 sets of twins from the Florida Twin Project on Reading. The results indicated test anxiety was negatively associated with reading comprehension test performance, specifically through common shared environmental influences. The significant contribution of test anxiety to reading comprehension on a high-stakes test supports the notion that non-targeted factors may be interfering with accurately assessing students' reading abilities.

  13. Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA

    PubMed Central

    Jann, Johann-Christoph; Nowak, Daniel; Nolte, Florian; Fey, Stephanie; Nowak, Verena; Obländer, Julia; Pressler, Jovita; Palme, Iris; Xanthopoulos, Christina; Fabarius, Alice; Platzbecker, Uwe; Giagounidis, Aristoteles; Götze, Katharina; Letsch, Anne; Haase, Detlef; Schlenk, Richard; Bug, Gesine; Lübbert, Michael; Ganser, Arnold; Germing, Ulrich; Haferlach, Claudia; Hofmann, Wolf-Karsten; Mossner, Maximilian

    2017-01-01

    Background Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. Methods For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Results Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77–0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. Conclusions In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities. PMID:28600436

  14. Atropos: specific, sensitive, and speedy trimming of sequencing reads.

    PubMed

    Didion, John P; Martin, Marcel; Collins, Francis S

    2017-01-01

    A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos.

  15. Atropos: specific, sensitive, and speedy trimming of sequencing reads

    PubMed Central

    Collins, Francis S.

    2017-01-01

    A key step in the transformation of raw sequencing reads into biological insights is the trimming of adapter sequences and low-quality bases. Read trimming has been shown to increase the quality and reliability while decreasing the computational requirements of downstream analyses. Many read trimming software tools are available; however, no tool simultaneously provides the accuracy, computational efficiency, and feature set required to handle the types and volumes of data generated in modern sequencing-based experiments. Here we introduce Atropos and show that it trims reads with high sensitivity and specificity while maintaining leading-edge speed. Compared to other state-of-the-art read trimming tools, Atropos achieves significant increases in trimming accuracy while remaining competitive in execution times. Furthermore, Atropos maintains high accuracy even when trimming data with elevated rates of sequencing errors. The accuracy, high performance, and broad feature set offered by Atropos makes it an appropriate choice for the pre-processing of Illumina, ABI SOLiD, and other current-generation short-read sequencing datasets. Atropos is open source and free software written in Python (3.3+) and available at https://github.com/jdidion/atropos. PMID:28875074

  16. Identification of human short introns

    PubMed Central

    Abebrese, Emmanuel L.; Arnold, Zachary R.; Armstrong, Katharine; Burns, Lindsay; Day, R. Thomas; Hsu, Daniel G.; Jarrell, Katherine; Luo, Yi; Mugayo, Daphine

    2017-01-01

    Canonical pre-mRNA splicing requires snRNPs and associated splicing factors to excise conserved intronic sequences, with a minimum intron length required for efficient splicing. Non-canonical splicing–intron excision without the spliceosome–has been documented; most notably, some tRNAs and the XBP1 mRNA contain short introns that are not removed by the spliceosome. There have been some efforts to identify additional short introns, but little is known about how many short introns are processed from mRNAs. Here, we report an approach to identify RNA short introns from RNA-Seq data, discriminating against small genomic deletions. We identify hundreds of short introns conserved among multiple human cell lines. These short introns are often alternatively spliced and are found in a variety of RNAs–both mRNAs and lncRNAs. Short intron splicing efficiency is increased by secondary structure, and we detect both canonical and non-canonical short introns. In many cases, splicing of these short introns from mRNAs is predicted to alter the reading frame and change protein output. Our findings imply that standard gene prediction models which often assume a lower limit for intron size fail to predict short introns effectively. We conclude that short introns are abundant in the human transcriptome, and short intron splicing represents an added layer to mRNA regulation. PMID:28520720

  17. Orthographic learning in children with isolated and combined reading and spelling deficits.

    PubMed

    Mehlhase, Heike; Bakos, Sarolta; Landerl, Karin; Schulte-Körne, Gerd; Moll, Kristina

    2018-05-07

    Dissociations between reading and spelling problems are likely to be associated with different underlying cognitive deficits, and with different deficits in orthographic learning. In order to understand these differences, the current study examined orthographic learning using a printed-word learning paradigm. Children (4th grade) with isolated reading, isolated spelling and combined reading and spelling problems were compared to children with age appropriate reading and spelling skills on their performance during learning novel words and symbols (non-verbal control condition), and during immediate and delayed reading and spelling recall tasks. No group differences occurred in the non-verbal control condition. In the verbal condition, initial learning was intact in all groups, but differences occurred during recall tasks. Children with reading fluency deficits showed slower reading times, while children with spelling deficits were less accurate, both in reading and spelling recall. Children with isolated spelling problems showed no difficulties in immediate spelling recall, but had problems in remembering the spellings 2 hours later. The results suggest that different orthographic learning deficits underlie reading fluency and spelling problems: Children with isolated reading fluency deficits have no difficulties in building-up orthographic representations, but access to these representations is slowed down while children with isolated spelling deficits have problems in storing precise orthographic representations in long-term memory.

  18. HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

    PubMed Central

    Li, Pinghao; Jiang, Xiaoqian; Wang, Shuang; Kim, Jihoon; Xiong, Hongkai; Ohno-Machado, Lucila

    2014-01-01

    Background and objective Short-read sequencing is becoming the standard of practice for the study of structural variants associated with disease. However, with the growth of sequence data largely surpassing reasonable storage capability, the biomedical community is challenged with the management, transfer, archiving, and storage of sequence data. Methods We developed Hierarchical mUlti-reference Genome cOmpression (HUGO), a novel compression algorithm for aligned reads in the sorted Sequence Alignment/Map (SAM) format. We first aligned short reads against a reference genome and stored exactly mapped reads for compression. For the inexact mapped or unmapped reads, we realigned them against different reference genomes using an adaptive scheme by gradually shortening the read length. Regarding the base quality value, we offer lossy and lossless compression mechanisms. The lossy compression mechanism for the base quality values uses k-means clustering, where a user can adjust the balance between decompression quality and compression rate. The lossless compression can be produced by setting k (the number of clusters) to the number of different quality values. Results The proposed method produced a compression ratio in the range 0.5–0.65, which corresponds to 35–50% storage savings based on experimental datasets. The proposed approach achieved 15% more storage savings over CRAM and comparable compression ratio with Samcomp (CRAM and Samcomp are two of the state-of-the-art genome compression algorithms). The software is freely available at https://sourceforge.net/projects/hierachicaldnac/with a General Public License (GPL) license. Limitation Our method requires having different reference genomes and prolongs the execution time for additional alignments. Conclusions The proposed multi-reference-based compression algorithm for aligned reads outperforms existing single-reference based algorithms. PMID:24368726

  19. Comprehension of Short Stories: Effects of Task Instructions on Literary Interpretation

    ERIC Educational Resources Information Center

    McCarthy, Kathryn S.; Goldman, Susan R.

    2015-01-01

    An important purpose of reading literature is to move beyond the literal text to construct an interpretation of what the text conveys about the human condition and nature of the world. In two experiments, college students with no prior training in literary analysis read a short story and responded to one of four task instructions (plot, ambiguous,…

  20. The Effects of Extensive Reading and Reading Strategies on Reading Self-Efficacy

    ERIC Educational Resources Information Center

    Burrows, Lance

    2012-01-01

    This study is a quasi-experimental, longitudinal investigation into the role that extensive reading and reading strategies play in the cultivation of reading self-efficacy. Conducted over the course of one academic year, how changes in reading self-efficacy translate into changes in reading comprehension was examined. In addition, the…

  1. State Efforts to Promote Reading and Literary Activities in Communities. NGA Center for Best Practices Issue Brief

    ERIC Educational Resources Information Center

    National Governors Association, 2006

    2006-01-01

    Rates of reading in the United States have been declining for at least two decades, with the steepest decline occurring among young adults. Fewer than half of adults read literature--poetry, plays, short stories or novels--in their leisure time. At the current rate of decline, literary reading will virtually disappear in the next half-century. Few…

  2. An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

    PubMed

    Zimin, Aleksey V; Stevens, Kristian A; Crepeau, Marc W; Puiu, Daniela; Wegrzyn, Jill L; Yorke, James A; Langley, Charles H; Neale, David B; Salzberg, Steven L

    2017-01-01

    The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly. © The Author 2017. Published by Oxford University Press.

  3. Subjective impressions do not mirror online reading effort: concurrent EEG-eyetracking evidence from the reading of books and digital media.

    PubMed

    Kretzschmar, Franziska; Pleimling, Dominique; Hosemann, Jana; Füssel, Stephan; Bornkessel-Schlesewsky, Ina; Schlesewsky, Matthias

    2013-01-01

    In the rapidly changing circumstances of our increasingly digital world, reading is also becoming an increasingly digital experience: electronic books (e-books) are now outselling print books in the United States and the United Kingdom. Nevertheless, many readers still view e-books as less readable than print books. The present study thus used combined EEG and eyetracking measures in order to test whether reading from digital media requires higher cognitive effort than reading conventional books. Young and elderly adults read short texts on three different reading devices: a paper page, an e-reader and a tablet computer and answered comprehension questions about them while their eye movements and EEG were recorded. The results of a debriefing questionnaire replicated previous findings in that participants overwhelmingly chose the paper page over the two electronic devices as their preferred reading medium. Online measures, by contrast, showed shorter mean fixation durations and lower EEG theta band voltage density--known to covary with memory encoding and retrieval--for the older adults when reading from a tablet computer in comparison to the other two devices. Young adults showed comparable fixation durations and theta activity for all three devices. Comprehension accuracy did not differ across the three media for either group. We argue that these results can be explained in terms of the better text discriminability (higher contrast) produced by the backlit display of the tablet computer. Contrast sensitivity decreases with age and degraded contrast conditions lead to longer reading times, thus supporting the conclusion that older readers may benefit particularly from the enhanced contrast of the tablet. Our findings thus indicate that people's subjective evaluation of digital reading media must be dissociated from the cognitive and neural effort expended in online information processing while reading from such devices.

  4. Subjective Impressions Do Not Mirror Online Reading Effort: Concurrent EEG-Eyetracking Evidence from the Reading of Books and Digital Media

    PubMed Central

    Kretzschmar, Franziska; Pleimling, Dominique; Hosemann, Jana; Füssel, Stephan; Bornkessel-Schlesewsky, Ina; Schlesewsky, Matthias

    2013-01-01

    In the rapidly changing circumstances of our increasingly digital world, reading is also becoming an increasingly digital experience: electronic books (e-books) are now outselling print books in the United States and the United Kingdom. Nevertheless, many readers still view e-books as less readable than print books. The present study thus used combined EEG and eyetracking measures in order to test whether reading from digital media requires higher cognitive effort than reading conventional books. Young and elderly adults read short texts on three different reading devices: a paper page, an e-reader and a tablet computer and answered comprehension questions about them while their eye movements and EEG were recorded. The results of a debriefing questionnaire replicated previous findings in that participants overwhelmingly chose the paper page over the two electronic devices as their preferred reading medium. Online measures, by contrast, showed shorter mean fixation durations and lower EEG theta band voltage density – known to covary with memory encoding and retrieval – for the older adults when reading from a tablet computer in comparison to the other two devices. Young adults showed comparable fixation durations and theta activity for all three devices. Comprehension accuracy did not differ across the three media for either group. We argue that these results can be explained in terms of the better text discriminability (higher contrast) produced by the backlit display of the tablet computer. Contrast sensitivity decreases with age and degraded contrast conditions lead to longer reading times, thus supporting the conclusion that older readers may benefit particularly from the enhanced contrast of the tablet. Our findings thus indicate that people's subjective evaluation of digital reading media must be dissociated from the cognitive and neural effort expended in online information processing while reading from such devices. PMID:23405265

  5. Using the Dictionary for Improving Adolescents' Reading Comprehension of Short Scientific Texts (Uso del diccionario para mejorar la comprensión lectora de textos científicos cortos en inglés con adolescentes)

    ERIC Educational Resources Information Center

    Becerra Cortés, Ximena

    2013-01-01

    This paper reports on an innovative and action research project which focused on the use of the dictionary and the prior knowledge of Colombian high school students to improve their reading comprehension of short scientific texts. Data collection instruments included students' work gathered during two workshops, field notes, and a questionnaire.…

  6. Reliability of a standardized test in Swedish for evaluation of reading performance in healthy eyes. Interchart and test-retest analyses.

    PubMed

    Thaung, Jörgen; Olseke, Kjell; Ahl, Johan; Sjöstrand, Johan

    2014-09-01

    The purpose of our study was to establish a practical and quick test for assessing reading performance and to statistically analyse interchart and test-retest reliability of a new standardized Swedish reading chart system consisting of three charts constructed according to the principles available in the literature. Twenty-four subjects with healthy eyes, mean age 65 ± 10 years, were tested binocularly and the reading performance evaluated as reading acuity, critical print size and maximum reading speed. The test charts all consist of 12 short text sentences with a print size ranging from 0.9 to -0.2 logMAR in approximate steps of 0.1 logMAR. Two testing sessions, in two different groups (C1 and C2), were under strict control of luminance and lighting environment. Reading performance tests with chart T1, T2 and T3 were used for evaluation of interchart reliability and test data from a second session 1 month or more apart for the test-retest analysis. The testing of reading performance in adult observers with short sentences of continuous text was quick and practical. The agreement between the tests obtained with the three different test charts was high both within the same test session and at retest. This new Swedish variant of a standardized reading system based on short sentences and logarithmic progression of print size provides reliable measurements of reading performance and preliminary norms in an age group around 65 years. The reading test with three independent reading charts can be useful for clinical studies of reading ability before and after treatment. © 2013 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  7. Sources and types of online information that breast cancer patients read and discuss with their doctors.

    PubMed

    Maloney, Erin K; D'Agostino, Thomas A; Heerdt, Alexandra; Dickler, Maura; Li, Yuelin; Ostroff, Jamie S; Bylund, Carma L

    2015-04-01

    Most research examining the impact of patients seeking online health information treats internet information homogenously, rather than recognizing that there are multiple types and sources of available information. The present research was conducted to differentiate among sources and types of internet information that patients search for, intend to discuss with their doctors, and recall discussing with their doctors, and to determine how accurate and hopeful patients rate this information. We surveyed 70 breast cancer patients recruited from the waiting rooms of breast medical oncology and surgery clinics. The main variables in the study were as follows: (1) the sources and types of online information patients have read, intended to discuss, and actually discussed with their doctors, and (2) how accurately and hopefully they rated this information to be. Patients read information most frequently from the websites of cancer organizations, and most often about side effects. Patients planned to discuss fewer types of information with their doctors than they had read about. They most often intended to discuss information from cancer organization websites or WebMD, and the material was most often about alternative therapies, side effects, and proven or traditional treatments. Some 76.8% of total participants rated the information they had read as very or somewhat accurate, and 61% rated the information they had read as very or somewhat hopeful. Internet information varies widely by source and type. Differentiating among sources and types of information is essential to explore the ways in which online health information impacts patients' experiences.

  8. Accurate and exact CNV identification from targeted high-throughput sequence data.

    PubMed

    Nord, Alex S; Lee, Ming; King, Mary-Claire; Walsh, Tom

    2011-04-12

    Massively parallel sequencing of barcoded DNA samples significantly increases screening efficiency for clinically important genes. Short read aligners are well suited to single nucleotide and indel detection. However, methods for CNV detection from targeted enrichment are lacking. We present a method combining coverage with map information for the identification of deletions and duplications in targeted sequence data. Sequencing data is first scanned for gains and losses using a comparison of normalized coverage data between samples. CNV calls are confirmed by testing for a signature of sequences that span the CNV breakpoint. With our method, CNVs can be identified regardless of whether breakpoints are within regions targeted for sequencing. For CNVs where at least one breakpoint is within targeted sequence, exact CNV breakpoints can be identified. In a test data set of 96 subjects sequenced across ~1 Mb genomic sequence using multiplexing technology, our method detected mutations as small as 31 bp, predicted quantitative copy count, and had a low false-positive rate. Application of this method allows for identification of gains and losses in targeted sequence data, providing comprehensive mutation screening when combined with a short read aligner.

  9. Reading Text While Driving

    PubMed Central

    Horrey, William J.; Hoffman, Joshua D.

    2015-01-01

    Objective In this study, we investigated how drivers adapt secondary-task initiation and time-sharing behavior when faced with fluctuating driving demands. Background Reading text while driving is particularly detrimental; however, in real-world driving, drivers actively decide when to perform the task. Method In a test track experiment, participants were free to decide when to read messages while driving along a straight road consisting of an area with increased driving demands (demand zone) followed by an area with low demands. A message was made available shortly before the vehicle entered the demand zone. We manipulated the type of driving demands (baseline, narrow lane, pace clock, combined), message format (no message, paragraph, parsed), and the distance from the demand zone when the message was available (near, far). Results In all conditions, drivers started reading messages (drivers’ first glance to the display) before entering or before leaving the demand zone but tended to wait longer when faced with increased driving demands. While reading messages, drivers looked more or less off road, depending on types of driving demands. Conclusions For task initiation, drivers avoid transitions from low to high demands; however, they are not discouraged when driving demands are already elevated. Drivers adjust time-sharing behavior according to driving demands while performing secondary tasks. Nonetheless, such adjustment may be less effective when total demands are high. Application This study helps us to understand a driver’s role as an active controller in the context of distracted driving and provides insights for developing distraction interventions. PMID:25850162

  10. Reading as Transaction in EFL: A Thematic Analysis.

    ERIC Educational Resources Information Center

    Chi, Feng-ming

    The purpose of this study is to investigate how ten advanced Taiwanese English as a Foreign Language college students comprehend and interpret two English short stories--"The Discus Thrower" and "A Passage to India." Two types of data were gathered for this study: verbal self-reporting and post-reading responses. Oral…

  11. Fast-SG: an alignment-free algorithm for hybrid assembly.

    PubMed

    Di Genova, Alex; Ruz, Gonzalo A; Sagot, Marie-France; Maass, Alejandro

    2018-05-01

    Long-read sequencing technologies are the ultimate solution for genome repeats, allowing near reference-level reconstructions of large genomes. However, long-read de novo assembly pipelines are computationally intense and require a considerable amount of coverage, thereby hindering their broad application to the assembly of large genomes. Alternatively, hybrid assembly methods that combine short- and long-read sequencing technologies can reduce the time and cost required to produce de novo assemblies of large genomes. Here, we propose a new method, called Fast-SG, that uses a new ultrafast alignment-free algorithm specifically designed for constructing a scaffolding graph using light-weight data structures. Fast-SG can construct the graph from either short or long reads. This allows the reuse of efficient algorithms designed for short-read data and permits the definition of novel modular hybrid assembly pipelines. Using comprehensive standard datasets and benchmarks, we show how Fast-SG outperforms the state-of-the-art short-read aligners when building the scaffoldinggraph and can be used to extract linking information from either raw or error-corrected long reads. We also show how a hybrid assembly approach using Fast-SG with shallow long-read coverage (5X) and moderate computational resources can produce long-range and accurate reconstructions of the genomes of Arabidopsis thaliana (Ler-0) and human (NA12878). Fast-SG opens a door to achieve accurate hybrid long-range reconstructions of large genomes with low effort, high portability, and low cost.

  12. Lip-reading enhancement for law enforcement

    NASA Astrophysics Data System (ADS)

    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.

  13. Lateralization of posterior alpha EEG reflects the distribution of spatial attention during saccadic reading.

    PubMed

    Kornrumpf, Benthe; Dimigen, Olaf; Sommer, Werner

    2017-06-01

    Visuospatial attention is an important mechanism in reading that governs the uptake of information from foveal and parafoveal regions of the visual field. However, the spatiotemporal dynamics of how attention is allocated during eye fixations are not completely understood. The current study explored the use of EEG alpha-band oscillations to investigate the spatial distribution of attention during reading. We reanalyzed two data sets, focusing on the lateralization of alpha activity at posterior scalp sites. In each experiment, participants read short lists of German nouns in two paradigms: either by freely moving their eyes (saccadic reading) or by fixating the screen center while the text moved passively from right to left at the same average speed (RSVP paradigm). In both paradigms, upcoming words were either visible or masked, and foveal processing load was manipulated by varying the words' lexical frequencies. Posterior alpha lateralization revealed a sustained rightward bias of attention during saccadic reading, but not in the RSVP paradigm. Interestingly, alpha lateralization was not influenced by word frequency (foveal load) or preview during the preceding fixation. Hence, alpha did not reflect transient attention shifts within a given fixation. However, in both experiments, we found that in the saccadic reading condition a stronger alpha lateralization shortly before a saccade predicted shorter fixations on the subsequently fixated word. These results indicate that alpha lateralization can serve as a measure of attention deployment and its link to oculomotor behavior in reading. © 2017 Society for Psychophysiological Research.

  14. Predicting Next Year's Resources--Short-Term Enrollment Forecasting for Accurate Budget Planning. AIR Forum Paper 1978.

    ERIC Educational Resources Information Center

    Salley, Charles D.

    Accurate enrollment forecasts are a prerequisite for reliable budget projections. This is because tuition payments make up a significant portion of a university's revenue, and anticipated revenue is the immediate constraint on current operating expenditures. Accurate forecasts are even more critical to revenue projections when a university's…

  15. An information propagation model considering incomplete reading behavior in microblog

    NASA Astrophysics Data System (ADS)

    Su, Qiang; Huang, Jiajia; Zhao, Xiande

    2015-02-01

    Microblog is one of the most popular communication channels on the Internet, and has already become the third largest source of news and public opinions in China. Although researchers have studied the information propagation in microblog using the epidemic models, previous studies have not considered the incomplete reading behavior among microblog users. Therefore, the model cannot fit the real situations well. In this paper, we proposed an improved model entitled Microblog-Susceptible-Infected-Removed (Mb-SIR) for information propagation by explicitly considering the user's incomplete reading behavior. We also tested the effectiveness of the model using real data from Sina Microblog. We demonstrate that the new proposed model is more accurate in describing the information propagation in microblog. In addition, we also investigate the effects of the critical model parameters, e.g., reading rate, spreading rate, and removed rate through numerical simulations. The simulation results show that, compared with other parameters, reading rate plays the most influential role in the information propagation performance in microblog.

  16. Visual processing in reading disorders and attention-deficit/hyperactivity disorder and its contribution to basic reading ability

    PubMed Central

    Kibby, Michelle Y.; Dyer, Sarah M.; Vadnais, Sarah A.; Jagger, Audreyana C.; Casher, Gabriel A.; Stacy, Maria

    2015-01-01

    Whether visual processing deficits are common in reading disorders (RD), and related to reading ability in general, has been debated for decades. The type of visual processing affected also is debated, although visual discrimination and short-term memory (STM) may be more commonly related to reading ability. Reading disorders are frequently comorbid with ADHD, and children with ADHD often have subclinical reading problems. Hence, children with ADHD were used as a comparison group in this study. ADHD and RD may be dissociated in terms of visual processing. Whereas RD may be associated with deficits in visual discrimination and STM for order, ADHD is associated with deficits in visual-spatial processing. Thus, we hypothesized that children with RD would perform worse than controls and children with ADHD only on a measure of visual discrimination and a measure of visual STM that requires memory for order. We expected all groups would perform comparably on the measure of visual STM that does not require sequential processing. We found children with RD or ADHD were commensurate to controls on measures of visual discrimination and visual STM that do not require sequential processing. In contrast, both RD groups (RD, RD/ADHD) performed worse than controls on the measure of visual STM that requires memory for order, and children with comorbid RD/ADHD performed worse than those with ADHD. In addition, of the three visual measures, only sequential visual STM predicted reading ability. Hence, our findings suggest there is a deficit in visual sequential STM that is specific to RD and is related to basic reading ability. The source of this deficit is worthy of further research, but it may include both reduced memory for order and poorer verbal mediation. PMID:26579020

  17. Visual processing in reading disorders and attention-deficit/hyperactivity disorder and its contribution to basic reading ability.

    PubMed

    Kibby, Michelle Y; Dyer, Sarah M; Vadnais, Sarah A; Jagger, Audreyana C; Casher, Gabriel A; Stacy, Maria

    2015-01-01

    Whether visual processing deficits are common in reading disorders (RD), and related to reading ability in general, has been debated for decades. The type of visual processing affected also is debated, although visual discrimination and short-term memory (STM) may be more commonly related to reading ability. Reading disorders are frequently comorbid with ADHD, and children with ADHD often have subclinical reading problems. Hence, children with ADHD were used as a comparison group in this study. ADHD and RD may be dissociated in terms of visual processing. Whereas RD may be associated with deficits in visual discrimination and STM for order, ADHD is associated with deficits in visual-spatial processing. Thus, we hypothesized that children with RD would perform worse than controls and children with ADHD only on a measure of visual discrimination and a measure of visual STM that requires memory for order. We expected all groups would perform comparably on the measure of visual STM that does not require sequential processing. We found children with RD or ADHD were commensurate to controls on measures of visual discrimination and visual STM that do not require sequential processing. In contrast, both RD groups (RD, RD/ADHD) performed worse than controls on the measure of visual STM that requires memory for order, and children with comorbid RD/ADHD performed worse than those with ADHD. In addition, of the three visual measures, only sequential visual STM predicted reading ability. Hence, our findings suggest there is a deficit in visual sequential STM that is specific to RD and is related to basic reading ability. The source of this deficit is worthy of further research, but it may include both reduced memory for order and poorer verbal mediation.

  18. Simple Assessment of Nitrogen Nutrition Index in Summer Maize by Using Chlorophyll Meter Readings.

    PubMed

    Zhao, Ben; Ata-Ul-Karim, Syed Tahir; Liu, Zhandong; Zhang, Jiyang; Xiao, Junfu; Liu, Zugui; Qin, Anzhen; Ning, Dongfeng; Yang, Qiuxia; Zhang, Yonghui; Duan, Aiwang

    2018-01-01

    Rapid and non-destructive diagnostic tools to accurately assess crop nitrogen nutrition index (NNI) are imperative for improving crop nitrogen (N) diagnosis and sustaining crop production. This study was aimed to develop the relationships among NNI, leaf N gradient, chlorophyll meter (CM) readings gradient, and positional differences chlorophyll meter index [PDCMI, the ratio of CM readings between different leaf layers (LLs) of crop canopy] and to validate the accuracy and stability of these relationships across the different LLs, years, sites, and cultivars. Six multi-N rates (0-320 kg ha -1 ) field experiments were conducted with four summer maize cultivars (Zhengdan958, Denghai605, Xundan20, and Denghai661) at two different sites located in China. Six summer maize plants per plot were harvested at each sampling stage to assess NNI, leaf N concentration and CM readings of different LLs during the vegetative growth period. The results showed that the leaf N gradient, CM readings gradient and PDCMI of different LLs decreased, while the NNI values increased with increasing N supply. The leaf N gradient and CM readings gradient increased gradually from top to bottom of the canopy and CM readings of the bottom LL were more sensitive to changes in plant N concentration. The significantly positive relationship between NNI and CM readings of different LLs ( LL 1 to LL 3) was observed, yet these relationships varied across the years. In contrast, the relationships between NNI and PDCMI of different LLs ( LL 1 to LL 3) were significantly negative. The strongest relationship between PDCMI and NNI which was stable across the cultivars and years was observed for PDCMI1-3 (NNI = -5.74 × PDCMI1-3+1.5, R 2 = 0.76 ** ). Additionally, the models developed in this study were validated with the data acquired from two independent experiments to assess their accuracy of prediction. The root mean square error value of 0.1 indicated that the most accurate and robust relationship was

  19. Motivating Reading Comprehension: Concept-Oriented Reading Instruction

    ERIC Educational Resources Information Center

    Guthrie, John T., Ed.; Wigfield, Allan, Ed.; Perencevich, Kathleen C., Ed.

    2004-01-01

    Concept Oriented Reading Instruction (CORI) is a unique, classroom-tested model of reading instruction that breaks new ground by explicitly showing how content knowledge, reading strategies, and motivational support all merge in successful reading instruction. A theoretical perspective (engagement in reading) frames the book and provides a…

  20. An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments.

    PubMed

    Bansal, Vikas

    2018-01-01

    The short read lengths of current high-throughput sequencing technologies limit the ability to recover long-range haplotype information. Dilution pool methods for preparing DNA sequencing libraries from high molecular weight DNA fragments enable the recovery of long DNA fragments from short sequence reads. These approaches require computational methods for identifying the DNA fragments using aligned sequence reads and assembling the fragments into long haplotypes. Although a number of computational methods have been developed for haplotype assembly, the problem of identifying DNA fragments from dilution pool sequence data has not received much attention. We formulate the problem of detecting DNA fragments from dilution pool sequencing experiments as a genome segmentation problem and develop an algorithm that uses dynamic programming to optimize a likelihood function derived from a generative model for the sequence reads. This algorithm uses an iterative approach to automatically infer the mean background read depth and the number of fragments in each pool. Using simulated data, we demonstrate that our method, FragmentCut, has 25-30% greater sensitivity compared with an HMM based method for fragment detection and can also detect overlapping fragments. On a whole-genome human fosmid pool dataset, the haplotypes assembled using the fragments identified by FragmentCut had greater N50 length, 16.2% lower switch error rate and 35.8% lower mismatch error rate compared with two existing methods. We further demonstrate the greater accuracy of our method using two additional dilution pool datasets. FragmentCut is available from https://bansal-lab.github.io/software/FragmentCut. vibansal@ucsd.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  1. Concurrent Correlates and Predictors of Reading and Spelling Achievement in Deaf and Hearing School Children

    ERIC Educational Resources Information Center

    Kyle, Fiona E.; Harris, Margaret

    2006-01-01

    Seven-and eight-year-old deaf children and hearing children of equivalent reading age were presented with a number of tasks designed to assess reading, spelling, productive vocabulary, speechreading, phonological awareness, short-term memory, and nonverbal intelligence. The two groups were compared for similarities and differences in the levels of…

  2. Does early reading failure decrease children's reading motivation?

    PubMed

    Morgan, Paul L; Fuchs, Douglas; Compton, Donald L; Cordray, David S; Fuchs, Lynn S

    2008-01-01

    The authors used a pretest-posttest control group design with random assignment to evaluate whether early reading failure decreases children's motivation to practice reading. First, they investigated whether 60 first-grade children would report substantially different levels of interest in reading as a function of their relative success or failure in learning to read. Second, they evaluated whether increasing the word reading ability of 15 at-risk children would lead to gains in their motivation to read. Multivariate analyses of variance suggest marked differences in both motivation and reading practice between skilled and unskilled readers. However, bolstering at-risk children's word reading ability did not yield evidence of a causal relationship between early reading failure and decreased motivation to engage in reading activities. Instead, hierarchical regression analyses indicate a covarying relationship among early reading failure, poor motivation, and avoidance of reading.

  3. Beyond Cognition: Reading Motivation and Reading Comprehension

    PubMed Central

    Wigfield, Allan; Gladstone, Jessica; Turci, Lara

    2016-01-01

    The authors review research on children’s reading motivation and its relation to their reading comprehension. They begin by discussing work on the development of school motivation in general and reading motivation in particular, reviewing work showing that many children’s reading motivation declines over the school years. Girls tend to have more positive motivation for reading than do boys, and there are ethnic differences in children’s reading motivation. Over the last 15 years researchers have identified in both laboratory and classroom-based research instructional practices that positively impact students’ reading motivation and ultimately their reading comprehension. There is a strong need for researchers to build on this work and develop and study in different age groups of children effective classroom-based reading motivation instructional programs for a variety of narrative and informational materials. PMID:27617030

  4. Dual Task Costs of Oral Reading for Young versus Older Adults

    PubMed Central

    Kemper, Susan; Bontempo, Daniel; Schmalzried, RaLynn; McKedy, Whitney; Tagliaferri, Bruno; Kieweg, Doug

    2013-01-01

    A digital pursuit rotor was used to monitor oral reading costs by time-locking tracking performance to the auditory wave form produced as young and older adults were reading out short paragraphs. Multilevel modeling was used to determine how paragraph-level predictors of length, grammatical complexity, and readability and person-level predictors such as speaker age or working memory capacity predicted reading and tracking performance. In addition, sentence-by-sentence variation in tracking performance was examined during the production of individual sentences and during the pauses before upcoming sentences. The results suggest that dual tasking has a greater impact on older adults’ reading comprehension and tracking performance. At the level of individual sentences, young and older adults adopt different strategies to deal with grammatically complex and propositionally dense sentences. PMID:23463405

  5. Increases in Perspective Embedding Increase Reading Time Even with Typical Text Presentation: Implications for the Reading of Literature

    PubMed Central

    Whalen, D. H.; Zunshine, Lisa; Holquist, Michael

    2015-01-01

    Reading fiction is a major component of intellectual life, yet it has proven difficult to study experimentally. One aspect of literature that has recently come to light is perspective embedding (“she thought I left” embedding her perspective on “I left”), which seems to be a defining feature of fiction. Previous work (Whalen et al., 2012) has shown that increasing levels of embedment affects the time that it takes readers to read and understand short vignettes in a moving window paradigm. With increasing levels of embedment from 1 to 5, reading times in a moving window paradigm rose almost linearly. However, level 0 was as slow as 3–4. Accuracy on probe questions was relatively constant until dropping at the fifth level. Here, we assessed this effect in a more ecologically valid (“typical”) reading paradigm, in which the entire vignette was visible at once, either for as long as desired (Experiment 1) or a fixed time (Experiment 2). In Experiment 1, reading times followed a pattern similar to that of the previous experiment, with some differences in absolute speed. Accuracy matched previous results: fairly consistent accuracy until a decline at level 5, indicating that both presentation methods allowed understanding. In Experiment 2, accuracy was somewhat reduced, perhaps because participants were less successful at allocating their attention than they were during the earlier experiment; however, the pattern was the same. It seems that literature does not, on average, use easiest reading level but rather uses a middle ground that challenges the reader, but not too much. PMID:26635684

  6. Of a Village Bomoh and the Lottery: Content Schemata Influence on Second Language Reading

    ERIC Educational Resources Information Center

    Radzi, Amizura Hanadi Mohd.; Aziz, Noor Hashima Abd.

    2013-01-01

    This paper discusses a study on the aspects of content schemata in second language reading, focusing on two contemporary short stories, i.e. "A Quid of Sirih, A Bowl of Water" and "The Lottery." The study explores the cognitive processes of one UiTM Perlis degree level student, reflecting on his L2 reading processes. The…

  7. Effects of Differentiated Reading on Elementary Students' Reading Comprehension and Attitudes toward Reading

    ERIC Educational Resources Information Center

    Shaunessy-Dedrick, Elizabeth; Evans, Linda; Ferron, John; Lindo, Myriam

    2015-01-01

    In this investigation, we examined the effects of a differentiated reading approach on fourth grade students' reading comprehension and attitudes toward reading. Eight Title I schools within one urban district were randomly assigned to treatment (Schoolwide Enrichment Model-Reading [SEM-R]) or control (district reading curriculum) conditions.…

  8. Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing.

    PubMed

    Liu, Chang; Xiao, Fangzhou; Hoisington-Lopez, Jessica; Lang, Kathrin; Quenzel, Philipp; Duffy, Brian; Mitra, Robi David

    2018-04-03

    Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunologic compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. We developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) identifies candidate alleles with the highest read coverage at different resolution levels that are represented as branching nodes and leaves of a tree structure, iii) generates consensus sequences by remapping the reads to the candidate alleles, and iv) calls the final diploid genotype by blasting consensus sequences against the reference database. Using two independent data sets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the two-field resolution. Copyright © 2018 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  9. Oral Reading Fluency in Second Language Reading

    ERIC Educational Resources Information Center

    Jeon, Eun Hee

    2012-01-01

    This study investigated the role of oral reading fluency in second language reading. Two hundred and fifty-five high school students in South Korea were assessed on three oral reading fluency (ORF) variables and six other reading predictors. The relationship between ORF and other reading predictors was examined through an exploratory factor…

  10. Teaching Reading

    ERIC Educational Resources Information Center

    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…

  11. Slow Reading: Reading along "Lectio" Lines

    ERIC Educational Resources Information Center

    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…

  12. Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA.

    PubMed

    Jann, Johann-Christoph; Nowak, Daniel; Nolte, Florian; Fey, Stephanie; Nowak, Verena; Obländer, Julia; Pressler, Jovita; Palme, Iris; Xanthopoulos, Christina; Fabarius, Alice; Platzbecker, Uwe; Giagounidis, Aristoteles; Götze, Katharina; Letsch, Anne; Haase, Detlef; Schlenk, Richard; Bug, Gesine; Lübbert, Michael; Ganser, Arnold; Germing, Ulrich; Haferlach, Claudia; Hofmann, Wolf-Karsten; Mossner, Maximilian

    2017-09-01

    Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77-0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  13. Measurement of hyperpolarized gas diffusion at very short time scales

    PubMed Central

    Carl, Michael; Wilson Miller, G.; Mugler, John P.; Rohrbaugh, Scott; Tobias, William A.; Cates, Gordon D.

    2007-01-01

    We present a new pulse sequence for measuring very-short-time-scale restricted diffusion of hyperpolarized noble gases. The pulse sequence is based on concatenating a large number of bipolar diffusion-sensitizing gradients to increase the diffusion attenuation of the MR signal while maintaining a fundamentally short diffusion time. However, it differs in several respects from existing methods that use oscillating diffusion gradients for this purpose. First, a wait time is inserted between neighboring pairs of gradient pulses; second, consecutive pulse pairs may be applied along orthogonal axes; and finally, the diffusion-attenuated signal is not simply read out at the end of the gradient train but is periodically sampled during the wait times between neighboring pulse pairs. The first two features minimize systematic differences between the measured (apparent) diffusion coefficient and the actual time-dependent diffusivity, while the third feature optimizes the use of the available MR signal to improve the precision of the diffusivity measurement in the face of noise. The benefits of this technique are demonstrated using theoretical calculations, Monte-Carlo simulations of gas diffusion in simple geometries, and experimental phantom measurements in a glass sphere containing hyperpolarized 3He gas. The advantages over the conventional single-bipolar approach were found to increase with decreasing diffusion time, and thus represent a significant step toward making accurate surface-to-volume measurements in the lung airspaces. PMID:17936048

  14. Revisiting the Relations between the WJ-IV Measures of Cattell-Horn-Carroll (CHC) Cognitive Abilities and Reading Achievement during the School-Age Years

    ERIC Educational Resources Information Center

    Cormier, Damien C.; McGrew, Kevin S.; Bulut, Okan; Funamoto, Allyson

    2017-01-01

    This study examined associations between broad cognitive abilities (Fluid Reasoning [Gf], Short-Term Working Memory [Gwm], Long-Term Storage and Retrieval [Glr], Processing Speed [Gs], Comprehension-Knowledge [Gc], Visual Processing [Gv], and Auditory Processing [Ga]) and reading achievement (Basic Reading Skills, Reading Rate, Reading Fluency,…

  15. Improving reading in the primary grades.

    PubMed

    Duke, Nell K; Block, Meghan K

    2012-01-01

    Almost fifteen years have passed since the publication of the National Research Council's seminal report Preventing Reading Difficulties in Young Children, which provided research-based recommendations on what could be done to better position students in prekindergarten through third grade for success in grade four and above. This article by Nell Duke and Meghan Block first examines whether specific key recommendations from the report have been implemented in U.S. classrooms. They find that recommendations regarding increased access to kindergarten and greater attention to and improvement of students' word-reading skills have been widely adopted. Others have not. Vocabulary and comprehension, long neglected in the primary grades, still appear to be neglected. Contrary to the report's recommendations, attention to building conceptual and content knowledge in science and social studies has actually decreased in the past fifteen years. In other words, the easier-to-master skills are being attended to, but the broader domains of accomplishment that constitute preparation for comprehension and learning in the later grades--vocabulary knowledge, comprehension strategy use, and conceptual and content knowledge--are being neglected. Near stagnation in fourth-grade students' comprehension achievement is thus unsurprising. The authors then turn to research and reviews of research on improving primary-grade reading published since 1998, when Preventing Reading Difficulties was issued. They discuss several instructional approaches identified as effective in improving word-reading skill, vocabulary and conceptual knowledge, comprehension strategies, and reading outside of school; they discuss advances in interventions for struggling readers, and in whole-school literacy reform. Duke and Block then identify three key obstacles that have prevented widespread adoption of these best practices in teaching reading. The first obstacle is a short-term orientation toward instruction and

  16. Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing.

    PubMed

    Zuo, Chunman; Blow, Matthew; Sreedasyam, Avinash; Kuo, Rita C; Ramamoorthy, Govindarajan Kunde; Torres-Jerez, Ivone; Li, Guifen; Wang, Mei; Dilworth, David; Barry, Kerrie; Udvardi, Michael; Schmutz, Jeremy; Tang, Yuhong; Xu, Ying

    2018-01-01

    Switchgrass ( Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. We present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.

  17. Fact vs fiction--how paratextual information shapes our reading processes.

    PubMed

    Altmann, Ulrike; Bohrn, Isabel C; Lubrich, Oliver; Menninghaus, Winfried; Jacobs, Arthur M

    2014-01-01

    Our life is full of stories: some of them depict real-life events and were reported, e.g. in the daily news or in autobiographies, whereas other stories, as often presented to us in movies and novels, are fictional. However, we have only little insights in the neurocognitive processes underlying the reading of factual as compared to fictional contents. We investigated the neurocognitive effects of reading short narratives, labeled to be either factual or fictional. Reading in a factual mode engaged an activation pattern suggesting an action-based reconstruction of the events depicted in a story. This process seems to be past-oriented and leads to shorter reaction times at the behavioral level. In contrast, the brain activation patterns corresponding to reading fiction seem to reflect a constructive simulation of what might have happened. This is in line with studies on imagination of possible past or future events.

  18. Fact vs fiction—how paratextual information shapes our reading processes

    PubMed Central

    Altmann, Ulrike; Bohrn, Isabel C.; Lubrich, Oliver; Menninghaus, Winfried; Jacobs, Arthur M.

    2014-01-01

    Our life is full of stories: some of them depict real-life events and were reported, e.g. in the daily news or in autobiographies, whereas other stories, as often presented to us in movies and novels, are fictional. However, we have only little insights in the neurocognitive processes underlying the reading of factual as compared to fictional contents. We investigated the neurocognitive effects of reading short narratives, labeled to be either factual or fictional. Reading in a factual mode engaged an activation pattern suggesting an action-based reconstruction of the events depicted in a story. This process seems to be past-oriented and leads to shorter reaction times at the behavioral level. In contrast, the brain activation patterns corresponding to reading fiction seem to reflect a constructive simulation of what might have happened. This is in line with studies on imagination of possible past or future events. PMID:22956671

  19. Effects of Wh-Question Graphic Organizers on Reading Comprehension Skills of Students with Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Bethune, Keri S.; Wood,Charles L.

    2013-01-01

    Students with autism spectrum disorders often have difficulty with reading comprehension. This study used a delayed multiple baseline across participants design to evaluate the effects of graphic organizers on the accuracy of wh-questions answered following short passage reading. Participants were three elementary-age students with autism spectrum…

  20. The influence of contextual diversity on eye movements in reading.

    PubMed

    Plummer, Patrick; Perea, Manuel; Rayner, Keith

    2014-01-01

    Recent research has shown contextual diversity (i.e., the number of passages in which a given word appears) to be a reliable predictor of word processing difficulty. It has also been demonstrated that word-frequency has little or no effect on word recognition speed when accounting for contextual diversity in isolated word processing tasks. An eye-movement experiment was conducted wherein the effects of word-frequency and contextual diversity were directly contrasted in a normal sentence reading scenario. Subjects read sentences with embedded target words that varied in word-frequency and contextual diversity. All 1st-pass and later reading times were significantly longer for words with lower contextual diversity compared to words with higher contextual diversity when controlling for word-frequency and other important lexical properties. Furthermore, there was no difference in reading times for higher frequency and lower frequency words when controlling for contextual diversity. The results confirm prior findings regarding contextual diversity and word-frequency effects and demonstrate that contextual diversity is a more accurate predictor of word processing speed than word-frequency within a normal reading task. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  1. Reading Function and Content Words in Subtitled Videos

    ERIC Educational Resources Information Center

    Krejtz, Izabela; Szarkowska, Agnieszka; Loginska, Maria

    2016-01-01

    In this study, we examined how function and content words are read in intra- and interlingual subtitles. We monitored eye movements of a group of 39 deaf, 27 hard of hearing, and 56 hearing Polish participants while they viewed English and Polish videos with Polish subtitles. We found that function words and short content words received less…

  2. Individual Differences in Accurately Judging Personality From Text.

    PubMed

    Hall, Judith A; Goh, Jin X; Mast, Marianne Schmid; Hagedorn, Christian

    2016-08-01

    This research examines correlates of accuracy in judging Big Five traits from first-person text excerpts. Participants in six studies were recruited from psychology courses or online. In each study, participants performed a task of judging personality from text and performed other ability tasks and/or filled out questionnaires. Participants who were more accurate in judging personality from text were more likely to be female; had personalities that were more agreeable, conscientious, and feminine, and less neurotic and dominant (all controlling for participant gender); scored higher on empathic concern; self-reported more interest in, and attentiveness to, people's personalities in their daily lives; and reported reading more for pleasure, especially fiction. Accuracy was not associated with SAT scores but had a significant relation to vocabulary knowledge. Accuracy did not correlate with tests of judging personality and emotion based on audiovisual cues. This research is the first to address individual differences in accurate judgment of personality from text, thus adding to the literature on correlates of the good judge of personality. © 2015 Wiley Periodicals, Inc.

  3. Reading comprehension and reading related abilities in adolescents with reading disabilities and attention-deficit/hyperactivity disorder.

    PubMed

    Ghelani, Karen; Sidhu, Robindra; Jain, Umesh; Tannock, Rosemary

    2004-11-01

    Reading comprehension is a very complex task that requires different cognitive processes and reading abilities over the life span. There are fewer studies of reading comprehension relative to investigations of word reading abilities. Reading comprehension difficulties, however, have been identified in two common and frequently overlapping childhood disorders: reading disability (RD) and attention-deficit/hyperactivity disorder (ADHD). The nature of reading comprehension difficulties in these groups remains unclear. The performance of four groups of adolescents (RD, ADHD, comorbid ADHD and RD, and normal controls) was compared on reading comprehension tasks as well as on reading rate and accuracy tasks. Adolescents with RD showed difficulties across most reading tasks, although their comprehension scores were average. Adolescents with ADHD exhibited adequate single word reading abilities. Subtle difficulties were observed, however, on measures of text reading rate and accuracy as well as on silent reading comprehension, but scores remained in the average range. The comorbid group demonstrated similar difficulties to the RD group on word reading accuracy and on reading rate but experienced problems on only silent reading comprehension. Implications for reading interventions are outlined, as well as the clinical relevance for diagnosis.

  4. Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation.

    PubMed

    Szatkiewicz, Jin P; Wang, WeiBo; Sullivan, Patrick F; Wang, Wei; Sun, Wei

    2013-02-01

    Structural variation is an important class of genetic variation in mammals. High-throughput sequencing (HTS) technologies promise to revolutionize copy-number variation (CNV) detection but present substantial analytic challenges. Converging evidence suggests that multiple types of CNV-informative data (e.g. read-depth, read-pair, split-read) need be considered, and that sophisticated methods are needed for more accurate CNV detection. We observed that various sources of experimental biases in HTS confound read-depth estimation, and note that bias correction has not been adequately addressed by existing methods. We present a novel read-depth-based method, GENSENG, which uses a hidden Markov model and negative binomial regression framework to identify regions of discrete copy-number changes while simultaneously accounting for the effects of multiple confounders. Based on extensive calibration using multiple HTS data sets, we conclude that our method outperforms existing read-depth-based CNV detection algorithms. The concept of simultaneous bias correction and CNV detection can serve as a basis for combining read-depth with other types of information such as read-pair or split-read in a single analysis. A user-friendly and computationally efficient implementation of our method is freely available.

  5. Shallow and deep orthographies in Hebrew: the role of vowelization in reading development for unvowelized scripts.

    PubMed

    Schiff, Rachel

    2012-12-01

    The present study explored the speed, accuracy, and reading comprehension of vowelized versus unvowelized scripts among 126 native Hebrew speaking children in second, fourth, and sixth grades. Findings indicated that second graders read and comprehended vowelized scripts significantly more accurately and more quickly than unvowelized scripts, whereas among fourth and sixth graders reading of unvowelized scripts developed to a greater degree than the reading of vowelized scripts. An analysis of the mediation effect for children's mastery of vowelized reading speed and accuracy on their mastery of unvowelized reading speed and comprehension revealed that in second grade, reading accuracy of vowelized words mediated the reading speed and comprehension of unvowelized scripts. In the fourth grade, accuracy in reading both vowelized and unvowelized words mediated the reading speed and comprehension of unvowelized scripts. By sixth grade, accuracy in reading vowelized words offered no mediating effect, either on reading speed or comprehension of unvowelized scripts. The current outcomes thus suggest that young Hebrew readers undergo a scaffolding process, where vowelization serves as the foundation for building initial reading abilities and is essential for successful and meaningful decoding of unvowelized scripts.

  6. Tackling the ‘dyslexia paradox’: reading brain and behavior for early markers of developmental dyslexia

    PubMed Central

    Ozernov-Palchik, Ola; Gaab, Nadine

    2016-01-01

    Developmental dyslexia is an unexplained inability to acquire accurate or fluent reading that affects approximately 5–17% of children. Dyslexia is associated with structural and functional alterations in various brain regions that support reading. Neuroimaging studies in infants and pre-reading children suggest that these alterations predate reading instruction and reading failure, supporting the hypothesis that variant function in dyslexia susceptibility genes lead to atypical neural migration and/or axonal growth during early, most likely in utero, brain development. Yet, dyslexia is typically not diagnosed until a child has failed to learn to read as expected (usually in second grade or later). There is emerging evidence that neuroimaging measures, when combined with key behavioral measures, can enhance the accuracy of identification of dyslexia risk in prereading children but its sensitivity, specificity, and cost-efficiency is still unclear. Early identification of dyslexia risk carries important implications for dyslexia remediation and the amelioration of the psychosocial consequences commonly associated with reading failure. PMID:26836227

  7. The Relationships between Korean University Students' Reading Attitude, Reading Strategy Use, and Reading Proficiency

    ERIC Educational Resources Information Center

    Kim, Hyangil

    2016-01-01

    This present study investigated the relationships among L2 readers' reading attitude, reading strategy use, and reading proficiency in order to identify patterns caused by individuals' differences. For this study, 153 Korean university students replied to a reading attitude and reading strategy questionnaire. An ANOVA and frequency analysis were…

  8. Readings in American History (In Their Own Words), Book III. New Directions for the United States and Teacher's Guide.

    ERIC Educational Resources Information Center

    Abramowitz, Jack

    This skills-text is the third of four books in the series "Readings in American History." The materials allow opportunities to improve reading and comprehension skills in a subject matter context by using certain primary sources related to the topic. Book 3 covers the period from the Civil War to 1900. Each lesson includes short readings with…

  9. Using Diacritics in the Arabic Script of Malay to Scaffold Arab Postgraduate Students in Reading Malay Words

    ERIC Educational Resources Information Center

    Salehuddin, Khazriyati; Winskel, Heather

    2015-01-01

    Purpose: This study aims to investigate the use of diacritics in the Arabic script of Malay to facilitate Arab postgraduate students of UKM to read the Malay words accurately. It is hypothesised that the Arabic script could facilitate the reading of Malay words among the Arab students because of their earlier exposure to the Arabic script in…

  10. Forecasting Reading Anxiety for Promoting English-Language Reading Performance Based on Reading Annotation Behavior

    ERIC Educational Resources Information Center

    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…

  11. Reading Together: A Successful Reading Fluency Intervention

    ERIC Educational Resources Information Center

    Young, Chase; Mohr, Kathleen A. J.; Rasinski, Timothy

    2015-01-01

    The article describes a reading fluency intervention called Reading Together that combines the method of repeated readings (Samuels, 1979) and the Neurological Impress Method (Heckelman, 1969). Sixteen volunteers from various backgrounds were recruited and trained to deliver the Reading Together intervention to struggling readers in third through…

  12. The unique role of executive function skills in predicting Hong Kong kindergarteners' reading comprehension.

    PubMed

    Liu, Yingyi; Sun, Huilin; Lin, Dan; Li, Hong; Yeung, Susanna Siu-Sze; Wong, Terry Tin-Yau

    2018-01-15

    Word reading and linguistic comprehension skills are two crucial components in reading comprehension, according to the Simple View of Reading (SVR). Some researchers have posited that a third component should be involved in reading and understanding texts, namely executive function (EF) skills. This study was novel in two ways. Not only did we tested EF skills as a predictor of reading comprehension in a non-alphabetic language (i.e., Chinese) to extend the theoretical model of SVR, we also examined reading comprehension further in kindergarten children (age 5) in Hong Kong, in the attempt to reveal possible early precursors of reading comprehension. A group of 170 K3 kindergarteners was recruited in Hong Kong. Children's word reading was assessed. Their linguistic comprehension was assessed with phonological awareness, verbal short-term memory, and vocabulary knowledge. Using a structured observation task, Head-Toes-Knees-Shoulders (HTKS), we measured their composite scores for EF skills. Head-Toes-Knees-Shoulders performance predicted unique variance in children's Chinese reading comprehension concurrently beyond word reading and a set of linguistic comprehension skills. The results highlight the important role of EF skills in beginning readers' reading comprehension. © 2018 The British Psychological Society.

  13. Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing.

    PubMed

    Zimin, Aleksey V; Stevens, Kristian A; Crepeau, Marc W; Puiu, Daniela; Wegrzyn, Jill L; Yorke, James A; Langley, Charles H; Neale, David B; Salzberg, Steven L

    2017-10-01

    The 22-gigabase genome of loblolly pine (Pinus taeda) is one of the largest ever sequenced. The draft assembly published in 2014 was built entirely from short Illumina reads, with lengths ranging from 100 to 250 base pairs (bp). The assembly was quite fragmented, containing over 11 million contigs whose weighted average (N50) size was 8206 bp. To improve this result, we generated approximately 12-fold coverage in long reads using the Single Molecule Real Time sequencing technology developed at Pacific Biosciences. We assembled the long and short reads together using the MaSuRCA mega-reads assembly algorithm, which produced a substantially better assembly, P. taeda version 2.0. The new assembly has an N50 contig size of 25 361, more than three times as large as achieved in the original assembly, and an N50 scaffold size of 107 821, 61% larger than the previous assembly. © The Authors 2017. Published by Oxford University Press.

  14. Developmental Relations between Reading Comprehension and Reading Strategies

    ERIC Educational Resources Information Center

    Muijselaar, Marloes M. L.; Swart, Nicole M.; Steenbeek-Planting, Esther G.; Droop, Mienke; Verhoeven, Ludo; de Jong, Peter 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, and working memory were administered. A structural…

  15. Exploring Content Schemata Influence on L2 Reading: "The Hunted Fox" and "Twelve and Not Stupid"

    ERIC Educational Resources Information Center

    Radzi, Amizura Hanadi Mohd; Aziz, Noor Hashima Abd

    2014-01-01

    This paper will discuss the aspects of content schemata in second language reading among diploma level students who were taking a reading course in Universiti Teknologi MARA Perlis. In this qualitative case study, the researcher had selected two short stories that are categorized as content-familiar texts, i.e. "The Hunted Fox" and…

  16. Longitudinal models of reading achievement of students with learning disabilities and without disabilities.

    PubMed

    Sullivan, Amanda L; Kohli, Nidhi; Farnsworth, Elyse M; Sadeh, Shanna; Jones, Leila

    2017-09-01

    Accurate estimation of developmental trajectories can inform instruction and intervention. We compared the fit of linear, quadratic, and piecewise mixed-effects models of reading development among students with learning disabilities relative to their typically developing peers. We drew an analytic sample of 1,990 students from the nationally representative Early Childhood Longitudinal Study-Kindergarten Cohort of 1998, using reading achievement scores from kindergarten through eighth grade to estimate three models of students' reading growth. The piecewise mixed-effects models provided the best functional form of the students' reading trajectories as indicated by model fit indices. Results showed slightly different trajectories between students with learning disabilities and without disabilities, with varying but divergent rates of growth throughout elementary grades, as well as an increasing gap over time. These results highlight the need for additional research on appropriate methods for modeling reading trajectories and the implications for students' response to instruction. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  17. Math Word Problems: Reading Math Situations from the Start

    ERIC Educational Resources Information Center

    Sherman, Khristine; Gabriel, Rachael

    2017-01-01

    Reading and creating stories is a longstanding pedagogical approach to literacy learning in elementary school classrooms because stories offer personal and human experiences to which students can relate and respond. Stories, including digital forms such as short films, offer accounts of what it is to belong to a community and its worldviews and…

  18. Survey of What Secondary Teachers Read Aloud to Students.

    ERIC Educational Resources Information Center

    Carneal, Ann; Bohning, Gerry

    Prompted by the fact that short and interesting materials suitable for reading aloud to secondary school students are difficult to find, a survey was conducted to compile a list of such materials for dissemination. The 260 respondents included secondary school teachers in all curriculum areas. Results indicated that half the respondents read…

  19. The Years Alone: A Reading Comprehension Unit (7-9).

    ERIC Educational Resources Information Center

    Blair-Broeker, Lynn

    Based on Bloom's Taxonomy of thought, this thematic reading comprehension unit on "loneliness" is intended for teachers of grades 7-9. The thinking process is broken into six categories: (1) recall; (2) inference; (3) application; (4) analysis; (5) synthesis; and (6) evaluation. A short description is given for each of these processes.…

  20. Reading and visual search: a developmental study in normal children.

    PubMed

    Seassau, Magali; Bucci, Maria-Pia

    2013-01-01

    Studies dealing with developmental aspects of binocular eye movement behaviour during reading are scarce. In this study we have explored binocular strategies during reading and during visual search tasks in a large population of normal young readers. Binocular eye movements were recorded using an infrared video-oculography system in sixty-nine children (aged 6 to 15) and in a group of 10 adults (aged 24 to 39). The main findings are (i) in both tasks the number of progressive saccades (to the right) and regressive saccades (to the left) decreases with age; (ii) the amplitude of progressive saccades increases with age in the reading task only; (iii) in both tasks, the duration of fixations as well as the total duration of the task decreases with age; (iv) in both tasks, the amplitude of disconjugacy recorded during and after the saccades decreases with age; (v) children are significantly more accurate in reading than in visual search after 10 years of age. Data reported here confirms and expands previous studies on children's reading. The new finding is that younger children show poorer coordination than adults, both while reading and while performing a visual search task. Both reading skills and binocular saccades coordination improve with age and children reach a similar level to adults after the age of 10. This finding is most likely related to the fact that learning mechanisms responsible for saccade yoking develop during childhood until adolescence.

  1. Coval: Improving Alignment Quality and Variant Calling Accuracy for Next-Generation Sequencing Data

    PubMed Central

    Kosugi, Shunichi; Natsume, Satoshi; Yoshida, Kentaro; MacLean, Daniel; Cano, Liliana; Kamoun, Sophien; Terauchi, Ryohei

    2013-01-01

    Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because of a high rate of sequencing error and incorrect mapping of reads to reference genomes. Currently available short read aligners and DNA variant callers suffer from these problems. We developed the Coval software to improve the quality of short read alignments. Coval is designed to minimize the incidence of spurious alignment of short reads, by filtering mismatched reads that remained in alignments after local realignment and error correction of mismatched reads. The error correction is executed based on the base quality and allele frequency at the non-reference positions for an individual or pooled sample. We demonstrated the utility of Coval by applying it to simulated genomes and experimentally obtained short-read data of rice, nematode, and mouse. Moreover, we found an unexpectedly large number of incorrectly mapped reads in ‘targeted’ alignments, where the whole genome sequencing reads had been aligned to a local genomic segment, and showed that Coval effectively eliminated such spurious alignments. We conclude that Coval significantly improves the quality of short-read sequence alignments, thereby increasing the calling accuracy of currently available tools for SNP and indel identification. Coval is available at http://sourceforge.net/projects/coval105/. PMID:24116042

  2. Second Language Reading: Reading, Language, and Metacognition.

    ERIC Educational Resources Information Center

    Carrell, Patricia L.

    A study investigated the role of metacognitive skills and the conception of reading in the reading comprehension of adult native speakers of Spanish and English. The study differed from others in its examination of reading conceptions and comprehension in both the first and second languages. Results suggest that both first language reading ability…

  3. Binocular Coordination during Reading and Non-Reading Tasks

    ERIC Educational Resources Information Center

    Kirkby, Julie A.; Webster, Lisa A. D.; Blythe, Hazel I.; Liversedge, Simon P.

    2008-01-01

    The goal of this review is to evaluate the literature on binocular coordination during reading and non-reading tasks in adult, child, and dyslexic populations. The review begins with a description of the basic characteristics of eye movements during reading. Then, reading and non-reading studies investigating binocular coordination are evaluated.…

  4. Developmental, Component-Based Model of Reading Fluency: An Investigation of Predictors of Word-Reading Fluency, Text-Reading Fluency, and Reading Comprehension

    ERIC Educational Resources Information Center

    Kim, Young-Suk Grace

    2015-01-01

    The primary goal was to expand our understanding of text-reading fluency (efficiency or automaticity): how its relation to other constructs (e.g., word reading fluency, reading comprehension) changes over time and how it is different from word-reading fluency and reading comprehension. The study examined (a) developmentally changing relations…

  5. Developmental, Component-Based Model of Reading Fluency: An Investigation of Predictors of Word-Reading Fluency, Text-Reading Fluency, and Reading Comprehension

    ERIC Educational Resources Information Center

    Kim, Young-Suk Grace

    2015-01-01

    The primary goal was to expand our understanding of text-reading fluency (efficiency or automaticity): how its relation to other constructs (e.g., word-reading fluency, reading comprehension) changes over time and how it is different from word-reading fluency and reading comprehension. The study examined (a) developmentally changing relations…

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

    PubMed

    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 .

  7. Contexts of Digital Reading: How Genres Affect Reading Practices

    ERIC Educational Resources Information Center

    Morris, Janine

    2016-01-01

    "Contexts of Digital Reading: How Genres Affect Reading Practices" is a study of the different ways university students use digital devices to read. Many mainstream representations of digital reading fail to distinguish between different contexts or genres of reading, making digital reading appear transparent rather than mediated by…

  8. Orthographic Transparency Enhances Morphological Segmentation in Children Reading Hebrew Words.

    PubMed

    Haddad, Laurice; Weiss, Yael; Katzir, Tami; Bitan, Tali

    2017-01-01

    Morphological processing of derived words develops simultaneously with reading acquisition. However, the reader's engagement in morphological segmentation may depend on the language morphological richness and orthographic transparency, and the readers' reading skills. The current study tested the common idea that morphological segmentation is enhanced in non-transparent orthographies to compensate for the absence of phonological information. Hebrew's rich morphology and the dual version of the Hebrew script (with and without diacritic marks) provides an opportunity to study the interaction of orthographic transparency and morphological segmentation on the development of reading skills in a within-language design. Hebrew speaking 2nd ( N = 27) and 5th ( N = 29) grade children read aloud 96 noun words. Half of the words were simple mono-morphemic words and half were bi-morphemic derivations composed of a productive root and a morphemic pattern. In each list half of the words were presented in the transparent version of the script (with diacritic marks), and half in the non-transparent version (without diacritic marks). Our results show that in both groups, derived bi-morphemic words were identified more accurately than mono-morphemic words, but only for the transparent, pointed, script. For the un-pointed script the reverse was found, namely, that bi-morphemic words were read less accurately than mono-morphemic words, especially in second grade. Second grade children also read mono-morphemic words faster than bi-morphemic words. Finally, correlations with a standardized measure of morphological awareness were found only for second grade children, and only in bi-morphemic words. These results, showing greater morphological effects in second grade compared to fifth grade children suggest that for children raised in a language with a rich morphology, common and easily segmented morphemic units may be more beneficial for younger compared to older readers. Moreover, in

  9. Orthographic Transparency Enhances Morphological Segmentation in Children Reading Hebrew Words

    PubMed Central

    Haddad, Laurice; Weiss, Yael; Katzir, Tami; Bitan, Tali

    2018-01-01

    Morphological processing of derived words develops simultaneously with reading acquisition. However, the reader’s engagement in morphological segmentation may depend on the language morphological richness and orthographic transparency, and the readers’ reading skills. The current study tested the common idea that morphological segmentation is enhanced in non-transparent orthographies to compensate for the absence of phonological information. Hebrew’s rich morphology and the dual version of the Hebrew script (with and without diacritic marks) provides an opportunity to study the interaction of orthographic transparency and morphological segmentation on the development of reading skills in a within-language design. Hebrew speaking 2nd (N = 27) and 5th (N = 29) grade children read aloud 96 noun words. Half of the words were simple mono-morphemic words and half were bi-morphemic derivations composed of a productive root and a morphemic pattern. In each list half of the words were presented in the transparent version of the script (with diacritic marks), and half in the non-transparent version (without diacritic marks). Our results show that in both groups, derived bi-morphemic words were identified more accurately than mono-morphemic words, but only for the transparent, pointed, script. For the un-pointed script the reverse was found, namely, that bi-morphemic words were read less accurately than mono-morphemic words, especially in second grade. Second grade children also read mono-morphemic words faster than bi-morphemic words. Finally, correlations with a standardized measure of morphological awareness were found only for second grade children, and only in bi-morphemic words. These results, showing greater morphological effects in second grade compared to fifth grade children suggest that for children raised in a language with a rich morphology, common and easily segmented morphemic units may be more beneficial for younger compared to older readers. Moreover

  10. Extensive Graded Reading in the Liberal Arts and Sciences

    ERIC Educational Resources Information Center

    Poulshock, Joseph

    2010-01-01

    For this research, learners did extensive graded reading (EGR) with traditional graded readers, and they also interacted with short graded stories in the liberal arts and sciences (LAS). This study describes the purpose and format of the LAS stories used by hundreds of university students and adult learners in Japan. It summarizes the results of…

  11. Resisting Focalisation, Gaining Empathy: Swedish Teenagers Read Irish Fiction

    ERIC Educational Resources Information Center

    Fjällström, Eva; Kokkola, Lydia

    2015-01-01

    Resisting the will to empathise with a focalised character is assumed to be difficult for young readers, yet empirical evidence on how they actually respond is limited. This paper combines recent insights gleaned from cognitive literary studies with a small-scale empirical study of thirty-five Swedish adolescents reading an Irish short story in…

  12. Reading Ability and Reading Engagement in Older Adults With Glaucoma

    PubMed Central

    Nguyen, Angeline M.; van Landingham, Suzanne W.; Massof, Robert W.; Rubin, Gary S.; Ramulu, Pradeep Y.

    2014-01-01

    Purpose. We evaluated the impact of glaucoma-related vision loss on reading ability and reading engagement in 10 reading activities. Methods. A total of 63 glaucoma patients and 59 glaucoma suspect controls self-rated their level of reading difficulty for 10 reading items, and responses were analyzed using Rasch analysis to determine reading ability. Reading engagement was assessed by asking subjects to report the number of days per week they engaged in each reading activity. Reading restriction was determined as a decrement in engagement. Results. Glaucoma subjects more often described greater reading difficulty than controls for all tasks except puzzles (P < 0.05). The most difficult reading tasks involved puzzles, books, and finances, while the least difficult reading tasks involved notes, bills, and mail. In multivariable weighted least squares regression models of Rasch-estimated person measures of reading ability, less reading ability was found for glaucoma patients compared to controls (β = −1.60 logits, P < 0.001). Among glaucoma patients, less reading ability was associated with more severe visual field (VF) loss (β = −0.68 logits per 5-dB decrement in better-eye VF mean deviation [MD], P < 0.001) and contrast sensitivity (β = −0.76 logits per 0.1-unit lower log CS, P < 0.001). Each 5-dB decrement in the better-eye VF MD was associated with book reading on 18% fewer days (P = 0.003) and newspaper reading on 10% fewer days (P = 0.008). No statistically significant reading restriction was observed for other reading activities (P > 0.05). Conclusions. Glaucoma patients have less reading ability and engage less in a variety of different reading activities, particularly those requiring sustained reading. Future work should evaluate the mechanisms underlying reading disability in glaucoma to determine how patients can maintain reading ability and engagement. PMID:25052992

  13. Verbal Rehearsal and Short-Term Memory in Reading-disabled Children

    ERIC Educational Resources Information Center

    Torgesen, Joseph; Goldman, Tina

    1977-01-01

    To determine whether the frequently found short-term memory deficits in poor readers reflect a lack of ability or inclination to use efficient task strategies, the performances of second-grade good and poor readers were compared on a task which allowed direct observation of the use of verbal rehearsal as a mnemonic strategy. (Author/JMB)

  14. The Correlation of Reading Motivation & Reading Engagement with Reading Comprehension Skills in 8th Graders

    ERIC Educational Resources Information Center

    Karahan, Berna Ürün

    2017-01-01

    One of the four main skills of language, reading is a concept encountered by individuals both in the process of education and social life. Individuals reading and having positive motivation towards reading constitute successful societies. The purpose of this study is to determine the correlation of reading motivation & reading engagement with…

  15. Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files.

    PubMed

    Finney, Richard P; Chen, Qing-Rong; Nguyen, Cu V; Hsu, Chih Hao; Yan, Chunhua; Hu, Ying; Abawi, Massih; Bian, Xiaopeng; Meerzaman, Daoud M

    2015-01-01

    The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview.

  16. Promoting Reading Motivation by Reading Together

    ERIC Educational Resources Information Center

    Monteiro, Vera

    2013-01-01

    In the present project we tested the hypothesis that tutorial situations with peers would benefit children's reading motivation. Participants were from elementary school--80 fourth-graders and 80 second-graders. We used a questionnaire to assess reading motivation. In the tutorial sessions we developed a Paired Reading Program. The children who…

  17. Genome Sequencing and Assembly by Long Reads in Plants

    PubMed Central

    Li, Changsheng; Lin, Feng; An, Dong; Huang, Ruidong

    2017-01-01

    Plant genomes generated by Sanger and Next Generation Sequencing (NGS) have provided insight into species diversity and evolution. However, Sanger sequencing is limited in its applications due to high cost, labor intensity, and low throughput, while NGS reads are too short to resolve abundant repeats and polyploidy, leading to incomplete or ambiguous assemblies. The advent and improvement of long-read sequencing by Third Generation Sequencing (TGS) methods such as PacBio and Nanopore have shown promise in producing high-quality assemblies for complex genomes. Here, we review the development of sequencing, introducing the application as well as considerations of experimental design in TGS of plant genomes. We also introduce recent revolutionary scaffolding technologies including BioNano, Hi-C, and 10× Genomics. We expect that the informative guidance for genome sequencing and assembly by long reads will benefit the initiation of scientists’ projects. PMID:29283420

  18. Separating the influences of prereading skills on early word and nonword reading.

    PubMed

    Shapiro, Laura R; Carroll, Julia M; Solity, Jonathan E

    2013-10-01

    The essential first step for a beginning reader is to learn to match printed forms to phonological representations. For a new word, this is an effortful process where each grapheme must be translated individually (serial decoding). The role of phonological awareness in developing a decoding strategy is well known. We examined whether beginning readers recruit different skills depending on the nature of the words being read (familiar words vs. nonwords). Print knowledge, phoneme and rhyme awareness, rapid automatized naming (RAN), phonological short-term memory (STM), nonverbal reasoning, vocabulary, auditory skills, and visual attention were measured in 392 prereaders 4 and 5 years of age. Word and nonword reading were measured 9 months later. We used structural equation modeling to examine the skills-reading relationship and modeled correlations between our two reading outcomes and among all prereading skills. We found that a broad range of skills were associated with reading outcomes: early print knowledge, phonological STM, phoneme awareness and RAN. Whereas all of these skills were directly predictive of nonword reading, early print knowledge was the only direct predictor of word reading. Our findings suggest that beginning readers draw most heavily on their existing print knowledge to read familiar words. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Short interval expansion of Rényi entropy on torus

    NASA Astrophysics Data System (ADS)

    Chen, Bin; Wu, Jun-Bao; Zhang, Jia-ju

    2016-08-01

    We investigate the short interval expansion of the Rényi entropy for two-dimensional conformal field theory (CFT) on a torus. We require the length of the interval ℓ to be small with respect to the spatial and temporal sizes of the torus. The operator product expansion of the twist operators allows us to compute the short interval expansion of the Rényi entropy at any temperature. In particular, we pay special attention to the large c CFTs dual to the AdS3 gravity and its cousins. At both low and high temperature limits, we read the Rényi entropies to order ℓ6, and find good agreements with holographic results. Moreover, the expansion allows us to read 1 /c contribution, which is hard to get by expanding the thermal density matrix. We generalize the study to the case with the chemical potential as well.

  20. Cognition and Literacy in English Language Learners at Risk for Reading Disabilities: A Latent Transition Analysis

    ERIC Educational Resources Information Center

    Swanson, H. Lee; Kudo, Milagros; Guzman-Orth, Danielle

    2016-01-01

    This study investigated the prevalence and stability of latent classes at risk for reading disabilities (RD) in elementary-aged children whose first language is Spanish. To this end, children (N = 489) in Grades 1, 2, and 3 at Wave 1 were administered a battery of reading, vocabulary, and cognitive measures (short-term memory [STM], working memory…

  1. Influence of automatic word reading on motor control.

    PubMed

    Gentilucci, M; Gangitano, M

    1998-02-01

    We investigated the possible influence of automatic word reading on processes of visuo-motor transformation. Six subjects were required to reach and grasp a rod on whose visible face the word 'long' or 'short' was printed. Word reading was not explicitly required. In order to induce subjects to visually analyse the object trial by trial, object position and size were randomly varied during the experimental session. The kinematics of the reaching component was affected by word presentation. Peak acceleration, peak velocity, and peak deceleration of arm were higher for the word 'long' with respect to the word 'short'. That is, during the initial movement phase subjects automatically associated the meaning of the word with the distance to be covered and activated a motor program for a farther and/or nearer object position. During the final movement phase, subjects modified the braking forces (deceleration) in order to correct the initial error. No effect of the words on the grasp component was observed. These results suggest a possible influence of cognitive functions on motor control and seem to contrast with the notion that the analyses executed in the ventral and dorsal cortical visual streams are different and independent.

  2. Specificity control for read alignments using an artificial reference genome-guided false discovery rate.

    PubMed

    Giese, Sven H; Zickmann, Franziska; Renard, Bernhard Y

    2014-01-01

    Accurate estimation, comparison and evaluation of read mapping error rates is a crucial step in the processing of next-generation sequencing data, as further analysis steps and interpretation assume the correctness of the mapping results. Current approaches are either focused on sensitivity estimation and thereby disregard specificity or are based on read simulations. Although continuously improving, read simulations are still prone to introduce a bias into the mapping error quantitation and cannot capture all characteristics of an individual dataset. We introduce ARDEN (artificial reference driven estimation of false positives in next-generation sequencing data), a novel benchmark method that estimates error rates of read mappers based on real experimental reads, using an additionally generated artificial reference genome. It allows a dataset-specific computation of error rates and the construction of a receiver operating characteristic curve. Thereby, it can be used for optimization of parameters for read mappers, selection of read mappers for a specific problem or for filtering alignments based on quality estimation. The use of ARDEN is demonstrated in a general read mapper comparison, a parameter optimization for one read mapper and an application example in single-nucleotide polymorphism discovery with a significant reduction in the number of false positive identifications. The ARDEN source code is freely available at http://sourceforge.net/projects/arden/.

  3. Modeling and control parameters for GMAW, short-circuiting transfer

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cook, G.E.; DeLapp, D.R.; Barnett, R.J.

    1996-12-31

    Digital signal processing was used to analyze the electrical arc signals of the gas metal arc welding process with short-circuiting transfer. Among the features extracted were arc voltage and current (both average and peak values), short-circuiting frequency, arc period, shorting period, and the ratio of the arcing to shorting period. Additionally , a Joule heating model was derived which accurately predicted the melt-back distance during each short. The short-circuiting frequency, the ratio of the arc period to short periods, and the melt-back distance were found to be good indicators for monitoring and control of stable arc conditions.

  4. Why should I read? - A cross-cultural investigation into adolescents' reading socialisation and reading attitude

    NASA Astrophysics Data System (ADS)

    Broeder, Peter; Stokmans, Mia

    2013-06-01

    While reading behaviour of adolescents is a frequent object of research, most studies in this field are restricted to a single country. This study investigates reading as a leisure-time activity across social groups from three regions differing in reading tradition as well as in the facilities available for reading. The authors analyse the reading behaviour of a total of 2,173 adolescents in the Netherlands, in Beijing (China), and in Cape Town (South Africa). Taking Icek Ajzen's Theory of Planned Behaviour as a starting point, the authors adjusted it to model the three most important determinants of reading behaviour, namely (1) reading attitude; (2) subjective norms (implicit and explicit social pressure to read); and (3) perceived behavioural control, which includes reading proficiency and appropriateness of the available books (book supply). While they found the adjusted model to fit the Dutch and Beijing situation quite well, it appeared to be inappropriate for the Cape Town situation. Despite considerable cultural and situational differences between the Netherlands and Beijing, the results show a similar pattern for these two environments. The most important determinants turn out to be: the hedonic reading attitude, the implicit norm of family and friends, the attractiveness of the available choice of books, and the perceived reading proficiency.

  5. Reading Development in European Portuguese: Relationships between Oral Reading Fluency, Vocabulary and Reading Comprehension

    ERIC Educational Resources Information Center

    Fernandes, Sandra; Querido, Luís; Verhaeghe, Arlette; Marques, Catarina; Araújo, Luísa

    2017-01-01

    This study investigated direct and indirect effects between oral reading fluency, vocabulary and reading comprehension across reading development in European Portuguese. Participants were 329 children attending basic education, from grade 1 to grade 6. The results of path analyses showed that text reading fluency is much more dependent on the…

  6. Short-term memory load and pronunciation rate

    NASA Technical Reports Server (NTRS)

    Schweickert, Richard; Hayt, Cathrin

    1988-01-01

    In a test of short-term memory recall, two subjects attempted to recall various lists. For unpracticed subjects, the time it took to read the list is a better predictor of immediate recall than the number of items on the list. For practiced subjects, the two predictors do about equally well. If the items that must be recalled are unfamiliar, it is advantageous to keep the items short to pronounce. On the other hand, if the same items will be encountered over and over again, it is advantageous to make them distinctive, even at the cost of adding to the number of syllables.

  7. Reading Function and Content Words in Subtitled Videos

    PubMed Central

    Szarkowska, Agnieszka; Łogińska, Maria

    2016-01-01

    In this study, we examined how function and content words are read in intra- and interlingual subtitles. We monitored eye movements of a group of 39 deaf, 27 hard of hearing, and 56 hearing Polish participants while they viewed English and Polish videos with Polish subtitles. We found that function words and short content words received less visual attention than longer content words, which was reflected in shorter dwell time, lower number of fixations, shorter first fixation duration, and lower subject hit count. Deaf participants dwelled significantly longer on function words than other participants, which may be an indication of their difficulty in processing this type of words. The findings are discussed in the context of classical reading research and applied research on subtitling. PMID:26681268

  8. Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population.

    PubMed

    Hirata, Satoshi; Kojima, Kaname; Misawa, Kazuharu; Gervais, Olivier; Kawai, Yosuke; Nagasaki, Masao

    2018-05-01

    Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

  9. Reading Faster

    ERIC Educational Resources Information Center

    Nation, Paul

    2009-01-01

    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…

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

    PubMed

    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.

  11. The Effect of Guided Reading Instruction on Reading Achievement

    ERIC Educational Resources Information Center

    Underwood, Vanda Lea

    2010-01-01

    Although reading achievement correlates highly with a student's ability to do well in school, not all children achieve in reading. The purpose of this mixed-method study was to investigate whether reading instruction provided in small groups at the child's own reading level, known as "guided reading instruction," would result in…

  12. Improving EFL Learners' Reading Levels through Extensive Reading

    ERIC Educational Resources Information Center

    Mermelstein, Aaron David

    2014-01-01

    Today there is an increasing amount of research promoting the effectiveness of extensive reading (ER) towards increasing learners' vocabulary, comprehension, reading speed, and motivation towards reading. However, little has been done to measure the effects of ER on learners' reading levels. This quantitative study examined the effects of ER on…

  13. Reading Motivation and Reading Engagement: Clarifying Commingled Conceptions

    ERIC Educational Resources Information Center

    Unrau, Norman J.; Quirk, Matthew

    2014-01-01

    The constructs of motivation for reading and reading engagement have frequently become blurred and ambiguous in both research and discussions of practice. To address this commingling of constructs, the authors provide a concise review of the literature on motivation for reading and reading engagement and illustrate the blurring of those concepts…

  14. The Binding Problem for Syntax, Semantics, and Prosody: H.M.'s Selective Sentence-Reading Deficits under the Theoretical-Syndrome Approach.

    ERIC Educational Resources Information Center

    MacKay, Donald G.; James, Lori E.

    2001-01-01

    A "hippocampal amnesiac" (H.M.) and memory-normal controls of similar age, background, intelligence, and education read novel sentences aloud in tasks where fast and accurate reading was or was not the primary goal. H.M produced more misreadings than normal and cerebellar controls, usually without self-correction. Results support a theoretical…

  15. Reading Comprehension in Boys with ADHD: The Mediating Roles of Working Memory and Orthographic Conversion.

    PubMed

    Friedman, Lauren M; Rapport, Mark D; Raiker, Joseph S; Orban, Sarah A; Eckrich, Samuel J

    2017-02-01

    Reading comprehension difficulties in children with ADHD are well established; however, limited information exists concerning the cognitive mechanisms that contribute to these difficulties and the extent to which they interact with one another. The current study examines two broad cognitive processes known to be involved in children's reading comprehension abilities-(a) working memory (i.e., central executive processes [CE], phonological short-term memory [PH STM], and visuospatial short-term memory [VS STM]) and (b) orthographic conversion (i.e., conversion of visually presented text to a phonological code)-to elucidate their unique and interactive contribution to ADHD-related reading comprehension differences. Thirty-one boys with ADHD-combined type and 30 typically developing (TD) boys aged 8 to 12 years (M = 9.64, SD = 1.22) were administered multiple counterbalanced tasks assessing WM and orthographic conversion processes. Relative to TD boys, boys with ADHD exhibited significant deficits in PH STM (d = -0.70), VS STM (d = -0.92), CE (d = -1.58), and orthographic conversion (d = -0.93). Bias-corrected, bootstrapped mediation analyses revealed that CE and orthographic conversion processes modeled separately mediated ADHD-related reading comprehension differences partially, whereas PH STM and VS STM did not. CE and orthographic conversion modeled jointly mediated ADHD-related reading comprehension differences fully wherein orthographic conversion's large magnitude influence on reading comprehension occurred indirectly through CE's impact on the orthographic system. The findings suggest that adaptive cognitive interventions designed to improve reading-related outcomes in children with ADHD may benefit by including modules that train CE and orthographic conversion processes independently and interactively.

  16. G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods.

    PubMed

    Manconi, Andrea; Manca, Emanuele; Moscatelli, Marco; Gnocchi, Matteo; Orro, Alessandro; Armano, Giuliano; Milanesi, Luciano

    2015-01-01

    Copy number variations (CNVs) are the most prevalent types of structural variations (SVs) in the human genome and are involved in a wide range of common human diseases. Different computational methods have been devised to detect this type of SVs and to study how they are implicated in human diseases. Recently, computational methods based on high-throughput sequencing (HTS) are increasingly used. The majority of these methods focus on mapping short-read sequences generated from a donor against a reference genome to detect signatures distinctive of CNVs. In particular, read-depth based methods detect CNVs by analyzing genomic regions with significantly different read-depth from the other ones. The pipeline analysis of these methods consists of four main stages: (i) data preparation, (ii) data normalization, (iii) CNV regions identification, and (iv) copy number estimation. However, available tools do not support most of the operations required at the first two stages of this pipeline. Typically, they start the analysis by building the read-depth signal from pre-processed alignments. Therefore, third-party tools must be used to perform most of the preliminary operations required to build the read-depth signal. These data-intensive operations can be efficiently parallelized on graphics processing units (GPUs). In this article, we present G-CNV, a GPU-based tool devised to perform the common operations required at the first two stages of the analysis pipeline. G-CNV is able to filter low-quality read sequences, to mask low-quality nucleotides, to remove adapter sequences, to remove duplicated read sequences, to map the short-reads, to resolve multiple mapping ambiguities, to build the read-depth signal, and to normalize it. G-CNV can be efficiently used as a third-party tool able to prepare data for the subsequent read-depth signal generation and analysis. Moreover, it can also be integrated in CNV detection tools to generate read-depth signals.

  17. Read Hard, Play Later: Putting Summer Reading into Action.

    ERIC Educational Resources Information Center

    Wemett, Lisa C.; Bolan, Kimberly

    1998-01-01

    Provides an overview of "Read on the Wild Side," a summer reading program for young adults established by the Webster (New York) Public Library, and "Read Hard, Play Later," a young adult summer reading program of the Pioneer Library System (New York). Highlights include reading logs, T-shirts, publicity, program evaluation,…

  18. When Reading Gets Ruff: Canine-Assisted Reading Programs

    ERIC Educational Resources Information Center

    Lane, Holly B.; Zavada, Shannon D. W.

    2013-01-01

    Canine-assisted reading programs show promise as an innovative method for engaging reluctant readers and motivating them to practice. In such programs, specially trained dogs visit classrooms and libraries, and children read to them. Children who struggle with reading may be motivated to read more because they find dogs to be calming and…

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

    PubMed Central

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

    2014-01-01

    Background 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. Materials and methods 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). Results The mean reading speed for UiTM-Mrw Reading Chart, MNread Acuity Chart and Colenbrander Reading Chart was 200 ± 30 wpm, 196 ± 28 wpm and 194 ± 31 wpm, 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. Conclusion UiTM-Mrw Reading Chart in Malay language is highly comparable with standardized charts and can be used for evaluating reading speed. PMID:25323642

  20. Differential effects of oral reading to improve comprehension with severe learning disabled and educable mentally handicapped students.

    PubMed

    Chang, S Q; Williams, R L; McLaughlin, T F

    1983-01-01

    The purpose of this study was to evaluate the effectiveness of oral reading as a teaching technique for improving reading comprehension of 11 Educable Mentally Handicapped or Severe Learning Disabled adolescents. Students were tested on their ability to answer comprehension questions from a short factual article. Comprehension improved following the oral reading for students with a reading grade equivalent of less than 5.5 (measured from the Wide Range Achievement Test) but not for those students having a grade equivalent of greater than 5.5. This association was statistically significant (p = less than .01). Oral reading appeared to improve comprehension among the poorer readers but not for readers with moderately high ability.

  1. An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads

    PubMed Central

    2013-01-01

    Background Next generation sequencing technologies have greatly advanced many research areas of the biomedical sciences through their capability to generate massive amounts of genetic information at unprecedented rates. The advent of next generation sequencing has led to the development of numerous computational tools to analyze and assemble the millions to billions of short sequencing reads produced by these technologies. While these tools filled an important gap, current approaches for storing, processing, and analyzing short read datasets generally have remained simple and lack the complexity needed to efficiently model the produced reads and assemble them correctly. Results Previously, we presented an overlap graph coarsening scheme for modeling read overlap relationships on multiple levels. Most current read assembly and analysis approaches use a single graph or set of clusters to represent the relationships among a read dataset. Instead, we use a series of graphs to represent the reads and their overlap relationships across a spectrum of information granularity. At each information level our algorithm is capable of generating clusters of reads from the reduced graph, forming an integrated graph modeling and clustering approach for read analysis and assembly. Previously we applied our algorithm to simulated and real 454 datasets to assess its ability to efficiently model and cluster next generation sequencing data. In this paper we extend our algorithm to large simulated and real Illumina datasets to demonstrate that our algorithm is practical for both sequencing technologies. Conclusions Our overlap graph theoretic algorithm is able to model next generation sequencing reads at various levels of granularity through the process of graph coarsening. Additionally, our model allows for efficient representation of the read overlap relationships, is scalable for large datasets, and is practical for both Illumina and 454 sequencing technologies. PMID:24564333

  2. Developmental Changes in the Visual Span for Reading

    PubMed Central

    Kwon, MiYoung; Legge, Gordon E.; Dubbels, Brock R.

    2007-01-01

    The visual span for reading refers to the range of letters, formatted as in text, that can be recognized reliably without moving the eyes. It is likely that the size of the visual span is determined primarily by characteristics of early visual processing. It has been hypothesized that the size of the visual span imposes a fundamental limit on reading speed (Legge, Mansfield, & Chung, 2001). The goal of the present study was to investigate developmental changes in the size of the visual span in school-age children, and the potential impact of these changes on children’s reading speed. The study design included groups of 10 children in 3rd, 5th, and 7th grade, and 10 adults. Visual span profiles were measured by asking participants to recognize letters in trigrams (random strings of three letters) flashed for 100 ms at varying letter positions left and right of the fixation point. Two print sizes (0.25° and 1.0°) were used. Over a block of trials, a profile was built up showing letter recognition accuracy (% correct) versus letter position. The area under this profile was defined to be the size of the visual span. Reading speed was measured in two ways: with Rapid Serial Visual Presentation (RSVP) and with short blocks of text (termed Flashcard presentation). Consistent with our prediction, we found that the size of the visual span increased linearly with grade level and it was significantly correlated with reading speed for both presentation methods. Regression analysis using the size of the visual span as a predictor indicated that 34% to 52% of variability in reading speeds can be accounted for by the size of the visual span. These findings are consistent with a significant role of early visual processing in the development of reading skills. PMID:17845810

  3. A highly accurate analytical solution for the surface fields of a short vertical wire antenna lying on a multilayer ground

    NASA Astrophysics Data System (ADS)

    Parise, M.

    2018-01-01

    A highly accurate analytical solution is derived to the electromagnetic problem of a short vertical wire antenna located on a stratified ground. The derivation consists of three steps. First, the integration path of the integrals describing the fields of the dipole is deformed and wrapped around the pole singularities and the two vertical branch cuts of the integrands located in the upper half of the complex plane. This allows to decompose the radiated field into its three contributions, namely the above-surface ground wave, the lateral wave, and the trapped surface waves. Next, the square root terms responsible for the branch cuts are extracted from the integrands of the branch-cut integrals. Finally, the extracted square roots are replaced with their rational representations according to Newton's square root algorithm, and residue theorem is applied to give explicit expressions, in series form, for the fields. The rigorous integration procedure and the convergence of square root algorithm ensure that the obtained formulas converge to the exact solution. Numerical simulations are performed to show the validity and robustness of the developed formulation, as well as its advantages in terms of time cost over standard numerical integration procedures.

  4. Reading Comprehension and Phonics Research: Review of Correlational Analyses with Deaf and Hard-of-Hearing Students.

    PubMed

    Luft, Pamela

    2018-04-01

    This manuscript reviews 28 studies of reading research on deaf and hard-of-hearing (DHH) students published since 2000 that used correlational analyses. The examination focused on assessment issues affecting measurement and analysis of relationships between early phonological or orthographic skills and reading comprehension. Mixed outcomes complicate efforts to determine evidence-based practices, and to develop an accurate model of reading. Across the 28 studies, DHH participants represented a wide age range with potential floor and ceiling effects that reduce score variability for valid correlations. Many studies assessed readers beyond the optimal ages during which early skills develop and are most useful for reading. Reading skills also were assessed using a diverse array of measures and skill definitions. Particularly for reading comprehension, word-level and text-level abilities appear to be different constructs. Suggestions include more consistent skill definitions and differential timing for early- versus later-developing skill assessments to ensure more robust correlational relationships.

  5. Word skipping: effects of word length, predictability, spelling and reading skill.

    PubMed

    Slattery, Timothy J; Yates, Mark

    2017-08-31

    Readers eyes often skip over words as they read. Skipping rates are largely determined by word length; short words are skipped more than long words. However, the predictability of a word in context also impacts skipping rates. Rayner, Slattery, Drieghe and Liversedge (2011) reported an effect of predictability on word skipping for even long words (10-13 characters) that extend beyond the word identification span. Recent research suggests that better readers and spellers have an enhanced perceptual span (Veldre & Andrews, 2014). We explored whether reading and spelling skill interact with word length and predictability to impact word skipping rates in a large sample (N=92) of average and poor adult readers. Participants read the items from Rayner et al. (2011) while their eye movements were recorded. Spelling skill (zSpell) was assessed using the dictation and recognition tasks developed by Sally Andrews and colleagues. Reading skill (zRead) was assessed from reading speed (words per minute) and accuracy of three 120 word passages each with 10 comprehension questions. We fit linear mixed models to the target gaze duration data and generalized linear mixed models to the target word skipping data. Target word gaze durations were significantly predicted by zRead while, the skipping likelihoods were significantly predicted by zSpell. Additionally, for gaze durations, zRead significantly interacted with word predictability as better readers relied less on context to support word processing. These effects are discussed in relation to the lexical quality hypothesis and eye movement models of reading.

  6. Language, reading, and math learning profiles in an epidemiological sample of school age children.

    PubMed

    Archibald, Lisa M D; Oram Cardy, Janis; Joanisse, Marc F; Ansari, Daniel

    2013-01-01

    Dyscalculia, dyslexia, and specific language impairment (SLI) are relatively specific developmental learning disabilities in math, reading, and oral language, respectively, that occur in the context of average intellectual capacity and adequate environmental opportunities. Past research has been dominated by studies focused on single impairments despite the widespread recognition that overlapping and comorbid deficits are common. The present study took an epidemiological approach to study the learning profiles of a large school age sample in language, reading, and math. Both general learning profiles reflecting good or poor performance across measures and specific learning profiles involving either weak language, weak reading, weak math, or weak math and reading were observed. These latter four profiles characterized 70% of children with some evidence of a learning disability. Low scores in phonological short-term memory characterized clusters with a language-based weakness whereas low or variable phonological awareness was associated with the reading (but not language-based) weaknesses. The low math only group did not show these phonological deficits. These findings may suggest different etiologies for language-based deficits in language, reading, and math, reading-related impairments in reading and math, and isolated math disabilities.

  7. Language, Reading, and Math Learning Profiles in an Epidemiological Sample of School Age Children

    PubMed Central

    Archibald, Lisa M. D.; Oram Cardy, Janis; Joanisse, Marc F.; Ansari, Daniel

    2013-01-01

    Dyscalculia, dyslexia, and specific language impairment (SLI) are relatively specific developmental learning disabilities in math, reading, and oral language, respectively, that occur in the context of average intellectual capacity and adequate environmental opportunities. Past research has been dominated by studies focused on single impairments despite the widespread recognition that overlapping and comorbid deficits are common. The present study took an epidemiological approach to study the learning profiles of a large school age sample in language, reading, and math. Both general learning profiles reflecting good or poor performance across measures and specific learning profiles involving either weak language, weak reading, weak math, or weak math and reading were observed. These latter four profiles characterized 70% of children with some evidence of a learning disability. Low scores in phonological short-term memory characterized clusters with a language-based weakness whereas low or variable phonological awareness was associated with the reading (but not language-based) weaknesses. The low math only group did not show these phonological deficits. These findings may suggest different etiologies for language-based deficits in language, reading, and math, reading-related impairments in reading and math, and isolated math disabilities. PMID:24155959

  8. The Effects of Extensive Reading on Reading Comprehension, Reading Rate, and Vocabulary Acquisition

    ERIC Educational Resources Information Center

    Suk, Namhee

    2017-01-01

    Several empirical studies and syntheses of extensive reading have concluded that extensive reading has positive impacts on language learning in second- and foreign-language settings. However, many of the studies contained methodological or curricular limitations, raising questions about the asserted positive effects of extensive reading. The…

  9. Treatment for Alexia With Agraphia Following Left Ventral Occipito-Temporal Damage: Strengthening Orthographic Representations Common to Reading and Spelling

    PubMed Central

    Rising, Kindle; Rapcsak, Steven Z.; Beeson, Pélagie M.

    2015-01-01

    Purpose Damage to left ventral occipito-temporal cortex can give rise to written language impairment characterized by pure alexia/letter-by-letter (LBL) reading, as well as surface alexia and agraphia. The purpose of this study was to examine the therapeutic effects of a combined treatment approach to address concurrent LBL reading with surface alexia/agraphia. Method Simultaneous treatment to address slow reading and errorful spelling was administered to 3 individuals with reading and spelling impairments after left ventral occipito-temporal damage due to posterior cerebral artery stroke. Single-word reading/spelling accuracy, reading latencies, and text reading were monitored as outcome measures for the combined effects of multiple oral re-reading treatment and interactive spelling treatment. Results After treatment, participants demonstrated faster and more accurate single-word reading and improved text-reading rates. Spelling accuracy also improved, particularly for untrained irregular words, demonstrating generalization of the trained interactive spelling strategy. Conclusion This case series characterizes concomitant LBL with surface alexia/agraphia and demonstrates a successful treatment approach to address both the reading and spelling impairment. PMID:26110814

  10. Treatment for Alexia With Agraphia Following Left Ventral Occipito-Temporal Damage: Strengthening Orthographic Representations Common to Reading and Spelling.

    PubMed

    Kim, Esther S; Rising, Kindle; Rapcsak, Steven Z; Beeson, Pélagie M

    2015-10-01

    Damage to left ventral occipito-temporal cortex can give rise to written language impairment characterized by pure alexia/letter-by-letter (LBL) reading, as well as surface alexia and agraphia. The purpose of this study was to examine the therapeutic effects of a combined treatment approach to address concurrent LBL reading with surface alexia/agraphia. Simultaneous treatment to address slow reading and errorful spelling was administered to 3 individuals with reading and spelling impairments after left ventral occipito-temporal damage due to posterior cerebral artery stroke. Single-word reading/spelling accuracy, reading latencies, and text reading were monitored as outcome measures for the combined effects of multiple oral re-reading treatment and interactive spelling treatment. After treatment, participants demonstrated faster and more accurate single-word reading and improved text-reading rates. Spelling accuracy also improved, particularly for untrained irregular words, demonstrating generalization of the trained interactive spelling strategy. This case series characterizes concomitant LBL with surface alexia/agraphia and demonstrates a successful treatment approach to address both the reading and spelling impairment.

  11. Teaching Reading Comprehension through Collaborative Strategic Reading.

    ERIC Educational Resources Information Center

    Vaughn, Sharon; Klingner, Janette Kettman

    1999-01-01

    Provides an overview of collaborative strategic reading (CSR) as an approach to enhancing the reading-comprehension skills of students with learning disabilities. Procedures for implementing CSR with collaborative groups and techniques for teaching reading-comprehension skills are provided. The role of the teacher is described and sample teaching…

  12. The Relationship between Reading Self-Efficacy Beliefs, Reading Strategy Use and Reading Comprehension Level of Iranian EFL Learners

    ERIC Educational Resources Information Center

    Naseri, Mahdieh; Zaferanieh, Elaheh

    2012-01-01

    This co-relational study explored the relationship between reading self-efficacy beliefs, reading strategies use and reading comprehension level of Iranian EFL learners. In this study, Michigan reading comprehension test, a self-reported Reading Strategy Use Questionnaire, and a Reading Self-efficacy Questionnaire were administered to eighty…

  13. The Gap Between Spanish-speakers' Word Reading and Word Knowledge: A Longitudinal Study

    PubMed Central

    Mancilla-Martinez, Jeannette; Lesaux, Nonie K.

    2011-01-01

    This longitudinal study modeled growth rates, from age 4.5 to 11, in English and Spanish oral language and word reading skills among 173 Spanish-speaking children from low-income households. Individual growth modeling was employed using scores from standardized measures of word reading, expressive vocabulary, and verbal short-term language memory. The trajectories demonstrate that students' rates of growth and overall ability in word reading were on par with national norms. In contrast, students' oral language skills started out below national norms and their rates of growth, although surpassing the national rates, were not sufficient to reach age-appropriate levels. The results underscore the need for increased and sustained attention to promoting this population's language development. PMID:21848955

  14. Validity Evidence for the Test of Silent Reading Efficiency and Comprehension (TOSREC)

    ERIC Educational Resources Information Center

    Johnson, Evelyn S.; Pool, Juli L.; Carter, Deborah R.

    2011-01-01

    An essential component of a response to intervention (RTI) framework is a screening process that is both accurate and efficient. The purpose of this study was to analyze the validity evidence for the "Test of Silent Reading Efficiency and Comprehension" (TOSREC) to determine its potential for use within a screening process. Participants included…

  15. What determines whether mammalian ribosomes resume scanning after translation of a short upstream open reading frame?

    PubMed Central

    Pöyry, Tuija A.A.; Kaminski, Ann; Jackson, Richard J.

    2004-01-01

    If the 5′-proximal AUG triplet in a mammalian mRNA is followed by a short open reading frame (sORF), a significant fraction of ribosomes resume scanning after termination of sORF translation, and reinitiate at a downstream AUG. To examine the underlying mechanism, we examined reinitiation in vitro using a series of mRNAs that differed only in the 5′-untranslated region (UTR). Efficient reinitiation was found to occur only if the eIF4F complex, or at a minimum the central one-third fragment of eIF4G, participated in the primary initiation event at the sORF initiation codon. It did not occur, however, when sORF translation was driven by the classical swine fever virus or cricket paralysis virus internal ribosome entry sites (IRESs), which do not use eIF4A, 4B, 4E, or 4G. A critical test was provided by an mRNA with an unstructured 5′-UTR, which is translated by scanning but does not absolutely need eIF4G and eIF4A: There was efficient reinitiation in a standard reticulocyte lysate, when initiation would be largely driven by eIF4F, but no reinitiation in an eIF4G-depleted lysate. These results suggest that resumption of scanning may depend on the interaction between eIF4F (or the eIF4G central domain) and the ribosome being maintained while the ribosome translates the sORF. PMID:14701882

  16. Reading Recovery.

    ERIC Educational Resources Information Center

    Jones, Joanna R., Ed.

    1992-01-01

    This issue of the Arizona Reading Journal focuses on the theme "reading recovery" and includes the following articles: "Why Is an Inservice Programme for Reading Recovery Teachers Necessary?" (Marie M. Clay); "What Is Reading Recovery?" (Gay Su Pinnell); "Teaching a Hard To Teach Child" (Constance A.…

  17. The Short- and Long-Term Effectiveness of Reading Recovery in a Rural School Setting

    ERIC Educational Resources Information Center

    Choi, Hee-sook; Bieber, Gregg

    2011-01-01

    Five years of emergent literacy and literacy data from 2002 to 2007 were reviewed for first through third graders in a small, rural school in the Midwest. Forty first graders had received Reading Recovery services over that time span. Their scores on DIBELS were compared to 41 low average to average students. Subsequent placement in special…

  18. Why Should I Read?--A Cross-Cultural Investigation into Adolescents' Reading Socialisation and Reading Attitude

    ERIC Educational Resources Information Center

    Broeder, Peter; Stokmans, Mia

    2013-01-01

    While reading behaviour of adolescents is a frequent object of research, most studies in this field are restricted to a single country. This study investigates reading as a leisure-time activity across social groups from three regions differing in reading tradition as well as in the facilities available for reading. The authors analyse the reading…

  19. Principals Make a Difference: The Role They Play in Quality Reading Programs. OSSC Bulletin, Vol. 22, No. 10.

    ERIC Educational Resources Information Center

    Scofield, Sandra

    Practical ways principals can modify and monitor their school's reading programs are suggested in this report that also presents reading theory and research results. The bulk of the report focuses on the elementary school and is divided into a short section on theory and a longer section on practice. Suggestions are given about establishing…

  20. Fluency and reading comprehension in students with reading difficulties.

    PubMed

    Nascimento, Tânia Augusto; Carvalho, Carolina Alves Ferreira de; Kida, Adriana de Souza Batista; Avila, Clara Regina Brandão de

    2011-12-01

    To characterize the performance of students with reading difficulties in decoding and reading comprehension tasks as well as to investigate the possible correlations between them. Sixty students (29 girls) from 3rd to 5th grades of public Elementary Schools were evaluated. Thirty students (Research Group - RG), ten from each grade, were nominated by their teachers as presenting evidences of learning disabilities. The other thirty students were indicated as good readers, and were matched by gender, age and grade to the RG, composing the Comparison Group (CG). All subjects were assessed regarding the parameters of reading fluency (rate and accuracy in words, pseudowords and text reading) and reading comprehension (reading level, number and type of ideas identified, and correct responses on multiple choice questions). The RG presented significantly lower scores than the CG in fluency and reading comprehension. Different patterns of positive and negative correlations, from weak to excellent, among the decoding and comprehension parameters were found in both groups. In the RG, low values of reading rate and accuracy were observed, which were correlated to low scores in comprehension and improvement in decoding, but not in comprehension, with grade increase. In CG, correlation was found between different fluency parameters, but none of them was correlated to the reading comprehension variables. Students with reading and writing difficulties show lower values of reading fluency and comprehension than good readers. Fluency and comprehension are correlated in the group with difficulties, showing that deficits in decoding influence reading comprehension, which does not improve with age increase.