Sample records for accurate long-read alignment

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  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. 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

  10. 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.

  11. 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.

  12. 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

  13. Minimap2: pairwise alignment for nucleotide sequences.

    PubMed

    Li, Heng

    2018-05-10

    Recent advances in sequencing technologies promise ultra-long reads of ∼100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥ 100bp in length, ≥1kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads, and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions (INDELs) and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. https://github.com/lh3/minimap2. hengli@broadinstitute.org.

  14. Clustering of reads with alignment-free measures and quality values.

    PubMed

    Comin, Matteo; Leoni, Andrea; Schimd, Michele

    2015-01-01

    The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an important aspect is the reduction of data complexity by collapsing redundant reads in a single cluster to improve the run time, memory requirements, and quality of post-processing steps like assembly and error correction. Several alignment-free measures, based on k-mers counts, have been used to cluster reads. Quality scores produced by NGS platforms are fundamental for various analysis of NGS data like reads mapping and error detection. Moreover future-generation sequencing platforms will produce long reads but with a large number of erroneous bases (up to 15 %). In this scenario it will be fundamental to exploit quality value information within the alignment-free framework. To the best of our knowledge this is the first study that incorporates quality value information and k-mers counts, in the context of alignment-free measures, for the comparison of reads data. Based on this principles, in this paper we present a family of alignment-free measures called D (q) -type. A set of experiments on simulated and real reads data confirms that the new measures are superior to other classical alignment-free statistics, especially when erroneous reads are considered. Also results on de novo assembly and metagenomic reads classification show that the introduction of quality values improves over standard alignment-free measures. These statistics are implemented in a software called QCluster (http://www.dei.unipd.it/~ciompin/main/qcluster.html).

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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).

  20. 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

  1. Introducing difference recurrence relations for faster semi-global alignment of long sequences.

    PubMed

    Suzuki, Hajime; Kasahara, Masahiro

    2018-02-19

    The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) operations to accelerate calculation of dynamic programming (DP) matrices in the Smith-Waterman-Gotoh (SWG) algorithm with a fixed alignment start position at the origin. Nonetheless, 16-bit or 32-bit integers are necessary for storing the values in a DP matrix when sequences to be aligned are long; this situation hampers the use of the full SIMD width of modern processors. We proposed a faster semi-global alignment algorithm, "difference recurrence relations," that runs more rapidly than the state-of-the-art algorithm by a factor of 2.1. Instead of calculating and storing all the values in a DP matrix directly, our algorithm computes and stores mainly the differences between the values of adjacent cells in the matrix. Although the SWG algorithm and our algorithm can output exactly the same result, our algorithm mainly involves 8-bit integer operations, enabling us to exploit the full width of SIMD operations (e.g., 32) on modern processors. We also developed a library, libgaba, so that developers can easily integrate our algorithm into alignment programs. Our novel algorithm and optimized library implementation will facilitate accelerating nucleotide long-read analysis algorithms that use pairwise alignment stages. The library is implemented in the C programming language and available at https://github.com/ocxtal/libgaba .

  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. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. DR-TAMAS: Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures

    PubMed Central

    Irfanoglu, M. Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B.; Sadeghi, Neda; Thomas, Cibu P.; Pierpaoli, Carlo

    2016-01-01

    In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. PMID:26931817

  11. 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.

  12. 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.

  13. Does Instructional Alignment Matter?: Effects on Struggling Second Graders' Reading Achievement

    ERIC Educational Resources Information Center

    Wonder-McDowell, Carla; Reutzel, D. Ray; Smith, John A.

    2011-01-01

    The purpose of this study was to explore the effects of aligning classroom core reading instruction with the supplementary reading instruction provided to 133 struggling grade 2 readers. A 2-group, pre-posttest true experimental design was employed in this study. In 11 elementary schools, 12 teachers taught both the aligned and unaligned core and…

  14. HSA: a heuristic splice alignment tool.

    PubMed

    Bu, Jingde; Chi, Xuebin; Jin, Zhong

    2013-01-01

    RNA-Seq methodology is a revolutionary transcriptomics sequencing technology, which is the representative of Next generation Sequencing (NGS). With the high throughput sequencing of RNA-Seq, we can acquire much more information like differential expression and novel splice variants from deep sequence analysis and data mining. But the short read length brings a great challenge to alignment, especially when the reads span two or more exons. A two steps heuristic splice alignment tool is generated in this investigation. First, map raw reads to reference with unspliced aligner--BWA; second, split initial unmapped reads into three equal short reads (seeds), align each seed to the reference, filter hits, search possible split position of read and extend hits to a complete match. Compare with other splice alignment tools like SOAPsplice and Tophat2, HSA has a better performance in call rate and efficiency, but its results do not as accurate as the other software to some extent. HSA is an effective spliced aligner of RNA-Seq reads mapping, which is available at https://github.com/vlcc/HSA.

  15. A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.

    PubMed

    Jain, Chirag; Dilthey, Alexander; Koren, Sergey; Aluru, Srinivas; Phillippy, Adam M

    2018-04-30

    Emerging single-molecule sequencing technologies from Pacific Biosciences and Oxford Nanopore have revived interest in long-read mapping algorithms. Alignment-based seed-and-extend methods demonstrate good accuracy, but face limited scalability, while faster alignment-free methods typically trade decreased precision for efficiency. In this article, we combine a fast approximate read mapping algorithm based on minimizers with a novel MinHash identity estimation technique to achieve both scalability and precision. In contrast to prior methods, we develop a mathematical framework that defines the types of mapping targets we uncover, establish probabilistic estimates of p-value and sensitivity, and demonstrate tolerance for alignment error rates up to 20%. With this framework, our algorithm automatically adapts to different minimum length and identity requirements and provides both positional and identity estimates for each mapping reported. For mapping human PacBio reads to the hg38 reference, our method is 290 × faster than Burrows-Wheeler Aligner-MEM with a lower memory footprint and recall rate of 96%. We further demonstrate the scalability of our method by mapping noisy PacBio reads (each ≥5 kbp in length) to the complete NCBI RefSeq database containing 838 Gbp of sequence and >60,000 genomes.

  16. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space

    PubMed Central

    Budavari, Tamas; Langmead, Ben; Wheelan, Sarah J.; Salzberg, Steven L.; Szalay, Alexander S.

    2015-01-01

    When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU) hardware.We followed this approach in implementing a read aligner called Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. We then carried out a read-by-read comparison of Arioc’s reported alignments with the alignments found by several leading read aligners. With simulated reads, Arioc has comparable or better accuracy than the other read aligners we tested. With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings. The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license. PMID:25780763

  17. 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

  18. Is multiple-sequence alignment required for accurate inference of phylogeny?

    PubMed

    Höhl, Michael; Ragan, Mark A

    2007-04-01

    The process of inferring phylogenetic trees from molecular sequences almost always starts with a multiple alignment of these sequences but can also be based on methods that do not involve multiple sequence alignment. Very little is known about the accuracy with which such alignment-free methods recover the correct phylogeny or about the potential for increasing their accuracy. We conducted a large-scale comparison of ten alignment-free methods, among them one new approach that does not calculate distances and a faster variant of our pattern-based approach; all distance-based alignment-free methods are freely available from http://www.bioinformatics.org.au (as Python package decaf+py). We show that most methods exhibit a higher overall reconstruction accuracy in the presence of high among-site rate variation. Under all conditions that we considered, variants of the pattern-based approach were significantly better than the other alignment-free methods. The new pattern-based variant achieved a speed-up of an order of magnitude in the distance calculation step, accompanied by a small loss of tree reconstruction accuracy. A method of Bayesian inference from k-mers did not improve on classical alignment-free (and distance-based) methods but may still offer other advantages due to its Bayesian nature. We found the optimal word length k of word-based methods to be stable across various data sets, and we provide parameter ranges for two different alphabets. The influence of these alphabets was analyzed to reveal a trade-off in reconstruction accuracy between long and short branches. We have mapped the phylogenetic accuracy for many alignment-free methods, among them several recently introduced ones, and increased our understanding of their behavior in response to biologically important parameters. In all experiments, the pattern-based approach emerged as superior, at the expense of higher resource consumption. Nonetheless, no alignment-free method that we examined recovers

  19. 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/.

  20. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

    PubMed

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan; Brent, Michael R

    2009-07-01

    The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary determinant of alignment accuracy, while heuristics that prevent consideration of certain alignments are a primary determinant of runtime and memory usage. Both accuracy and speed are important considerations in choosing an alignment algorithm, but scoring systems have received much less attention than heuristics. We present Pairagon, a pair hidden Markov model based cDNA-to-genome alignment program, as the most accurate aligner for sequences with high- and low-identity levels. We conducted a series of experiments testing alignment accuracy with varying sequence identity. We first created 'perfect' simulated cDNA sequences by splicing the sequences of exons in the reference genome sequences of fly and human. The complete reference genome sequences were then mutated to various degrees using a realistic mutation simulator and the perfect cDNAs were aligned to them using Pairagon and 12 other aligners. To validate these results with natural sequences, we performed cross-species alignment using orthologous transcripts from human, mouse and rat. We found that aligner accuracy is heavily dependent on sequence identity. For sequences with 100% identity, Pairagon achieved accuracy levels of >99.6%, with one quarter of the errors of any other aligner. Furthermore, for human/mouse alignments, which are only 85% identical, Pairagon achieved 87% accuracy, higher than any other aligner. Pairagon source and executables are freely available at http://mblab.wustl.edu/software/pairagon/

  1. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

    PubMed

    Liu, Kevin; Warnow, Tandy J; Holder, Mark T; Nelesen, Serita M; Yu, Jiaye; Stamatakis, Alexandros P; Linder, C Randal

    2012-01-01

    Highly accurate estimation of phylogenetic trees for large data sets is difficult, in part because multiple sequence alignments must be accurate for phylogeny estimation methods to be accurate. Coestimation of alignments and trees has been attempted but currently only SATé estimates reasonably accurate trees and alignments for large data sets in practical time frames (Liu K., Raghavan S., Nelesen S., Linder C.R., Warnow T. 2009b. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science. 324:1561-1564). Here, we present a modification to the original SATé algorithm that improves upon SATé (which we now call SATé-I) in terms of speed and of phylogenetic and alignment accuracy. SATé-II uses a different divide-and-conquer strategy than SATé-I and so produces smaller more closely related subsets than SATé-I; as a result, SATé-II produces more accurate alignments and trees, can analyze larger data sets, and runs more efficiently than SATé-I. Generally, SATé is a metamethod that takes an existing multiple sequence alignment method as an input parameter and boosts the quality of that alignment method. SATé-II-boosted alignment methods are significantly more accurate than their unboosted versions, and trees based upon these improved alignments are more accurate than trees based upon the original alignments. Because SATé-I used maximum likelihood (ML) methods that treat gaps as missing data to estimate trees and because we found a correlation between the quality of tree/alignment pairs and ML scores, we explored the degree to which SATé's performance depends on using ML with gaps treated as missing data to determine the best tree/alignment pair. We present two lines of evidence that using ML with gaps treated as missing data to optimize the alignment and tree produces very poor results. First, we show that the optimization problem where a set of unaligned DNA sequences is given and the output is the tree and alignment of

  2. 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.

  3. Fast and accurate reference-free alignment of subtomograms.

    PubMed

    Chen, Yuxiang; Pfeffer, Stefan; Hrabe, Thomas; Schuller, Jan Michael; Förster, Friedrich

    2013-06-01

    In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. 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

  5. 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

  6. Evaluation of microRNA alignment techniques

    PubMed Central

    Kaspi, Antony; El-Osta, Assam

    2016-01-01

    Genomic alignment of small RNA (smRNA) sequences such as microRNAs poses considerable challenges due to their short length (∼21 nucleotides [nt]) as well as the large size and complexity of plant and animal genomes. While several tools have been developed for high-throughput mapping of longer mRNA-seq reads (>30 nt), there are few that are specifically designed for mapping of smRNA reads including microRNAs. The accuracy of these mappers has not been systematically determined in the case of smRNA-seq. In addition, it is unknown whether these aligners accurately map smRNA reads containing sequence errors and polymorphisms. By using simulated read sets, we determine the alignment sensitivity and accuracy of 16 short-read mappers and quantify their robustness to mismatches, indels, and nontemplated nucleotide additions. These were explored in the context of a plant genome (Oryza sativa, ∼500 Mbp) and a mammalian genome (Homo sapiens, ∼3.1 Gbp). Analysis of simulated and real smRNA-seq data demonstrates that mapper selection impacts differential expression results and interpretation. These results will inform on best practice for smRNA mapping and enable more accurate smRNA detection and quantification of expression and RNA editing. PMID:27284164

  7. A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy

    NASA Astrophysics Data System (ADS)

    Popic, Victoria; Batzoglou, Serafim

    2017-05-01

    Low-cost clouds can alleviate the compute and storage burden of the genome sequencing data explosion. However, moving personal genome data analysis to the cloud can raise serious privacy concerns. Here, we devise a method named Balaur, a privacy preserving read mapper for hybrid clouds based on locality sensitive hashing and kmer voting. Balaur can securely outsource a substantial fraction of the computation to the public cloud, while being highly competitive in accuracy and speed with non-private state-of-the-art read aligners on short read data. We also show that the method is significantly faster than the state of the art in long read mapping. Therefore, Balaur can enable institutions handling massive genomic data sets to shift part of their analysis to the cloud without sacrificing accuracy or exposing sensitive information to an untrusted third party.

  8. A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy

    PubMed Central

    Popic, Victoria; Batzoglou, Serafim

    2017-01-01

    Low-cost clouds can alleviate the compute and storage burden of the genome sequencing data explosion. However, moving personal genome data analysis to the cloud can raise serious privacy concerns. Here, we devise a method named Balaur, a privacy preserving read mapper for hybrid clouds based on locality sensitive hashing and kmer voting. Balaur can securely outsource a substantial fraction of the computation to the public cloud, while being highly competitive in accuracy and speed with non-private state-of-the-art read aligners on short read data. We also show that the method is significantly faster than the state of the art in long read mapping. Therefore, Balaur can enable institutions handling massive genomic data sets to shift part of their analysis to the cloud without sacrificing accuracy or exposing sensitive information to an untrusted third party. PMID:28508884

  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. Accurate and robust brain image alignment using boundary-based registration.

    PubMed

    Greve, Douglas N; Fischl, Bruce

    2009-10-15

    The fine spatial scales of the structures in the human brain represent an enormous challenge to the successful integration of information from different images for both within- and between-subject analysis. While many algorithms to register image pairs from the same subject exist, visual inspection shows that their accuracy and robustness to be suspect, particularly when there are strong intensity gradients and/or only part of the brain is imaged. This paper introduces a new algorithm called Boundary-Based Registration, or BBR. The novelty of BBR is that it treats the two images very differently. The reference image must be of sufficient resolution and quality to extract surfaces that separate tissue types. The input image is then aligned to the reference by maximizing the intensity gradient across tissue boundaries. Several lower quality images can be aligned through their alignment with the reference. Visual inspection and fMRI results show that BBR is more accurate than correlation ratio or normalized mutual information and is considerably more robust to even strong intensity inhomogeneities. BBR also excels at aligning partial-brain images to whole-brain images, a domain in which existing registration algorithms frequently fail. Even in the limit of registering a single slice, we show the BBR results to be robust and accurate.

  11. AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

    PubMed

    Zheng, Qi; Grice, Elizabeth A

    2016-10-01

    Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

  12. AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

    PubMed Central

    Zheng, Qi; Grice, Elizabeth A.

    2016-01-01

    Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

  13. 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

  14. 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

  15. rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.

    PubMed

    Hahn, Lars; Leimeister, Chris-André; Ounit, Rachid; Lonardi, Stefano; Morgenstern, Burkhard

    2016-10-01

    Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/.

  16. DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.

    PubMed

    Irfanoglu, M Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B; Sadeghi, Neda; Thomas, Cibu P; Pierpaoli, Carlo

    2016-05-15

    In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. 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

  18. 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.

  19. Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?

    PubMed

    Tso, Kai-Yuen; Lee, Sau Dan; Lo, Kwok-Wai; Yip, Kevin Y

    2014-12-23

    Patient-derived tumor xenografts in mice are widely used in cancer research and have become important in developing personalized therapies. When these xenografts are subject to DNA sequencing, the samples could contain various amounts of mouse DNA. It has been unclear how the mouse reads would affect data analyses. We conducted comprehensive simulations to compare three alignment strategies at different mutation rates, read lengths, sequencing error rates, human-mouse mixing ratios and sequenced regions. We also sequenced a nasopharyngeal carcinoma xenograft and a cell line to test how the strategies work on real data. We found the "filtering" and "combined reference" strategies performed better than aligning reads directly to human reference in terms of alignment and variant calling accuracies. The combined reference strategy was particularly good at reducing false negative variants calls without significantly increasing the false positive rate. In some scenarios the performance gain of these two special handling strategies was too small for special handling to be cost-effective, but it was found crucial when false non-synonymous SNVs should be minimized, especially in exome sequencing. Our study systematically analyzes the effects of mouse contamination in the sequencing data of human-in-mouse xenografts. Our findings provide information for designing data analysis pipelines for these data.

  20. 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

  1. 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/.

  2. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

    PubMed Central

    2014-01-01

    Background The recent introduction of the Pacific Biosciences RS single molecule sequencing technology has opened new doors to scaffolding genome assemblies in a cost-effective manner. The long read sequence information is promised to enhance the quality of incomplete and inaccurate draft assemblies constructed from Next Generation Sequencing (NGS) data. Results Here we propose a novel hybrid assembly methodology that aims to scaffold pre-assembled contigs in an iterative manner using PacBio RS long read information as a backbone. On a test set comprising six bacterial draft genomes, assembled using either a single Illumina MiSeq or Roche 454 library, we show that even a 50× coverage of uncorrected PacBio RS long reads is sufficient to drastically reduce the number of contigs. Comparisons to the AHA scaffolder indicate our strategy is better capable of producing (nearly) complete bacterial genomes. Conclusions The current work describes our SSPACE-LongRead software which is designed to upgrade incomplete draft genomes using single molecule sequences. We conclude that the recent advances of the PacBio sequencing technology and chemistry, in combination with the limited computational resources required to run our program, allow to scaffold genomes in a fast and reliable manner. PMID:24950923

  3. ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

    PubMed

    Coombe, Lauren; Zhang, Jessica; Vandervalk, Benjamin P; Chu, Justin; Jackman, Shaun D; Birol, Inanc; Warren, René L

    2018-06-20

    The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assemblies. We introduce ARKS, an alignment-free linked read genome scaffolding methodology that uses linked reads to organize genome assemblies further into contiguous drafts. Our approach departs from other read alignment-dependent linked read scaffolders, including our own (ARCS), and uses a kmer-based mapping approach. The kmer mapping strategy has several advantages over read alignment methods, including better usability and faster processing, as it precludes the need for input sequence formatting and draft sequence assembly indexing. The reliance on kmers instead of read alignments for pairing sequences relaxes the workflow requirements, and drastically reduces the run time. Here, we show how linked reads, when used in conjunction with Hi-C data for scaffolding, improve a draft human genome assembly of PacBio long-read data five-fold (baseline vs. ARKS NG50 = 4.6 vs. 23.1 Mbp, respectively). We also demonstrate how the method provides further improvements of a megabase-scale Supernova human genome assembly (NG50 = 14.74 Mbp vs. 25.94 Mbp before and after ARKS), which itself exclusively uses linked read data for assembly, with an execution speed six to nine times faster than competitive linked read scaffolders (~ 10.5 h compared to 75.7 h, on average). Following ARKS scaffolding of a human genome 10xG Supernova assembly (of cell line NA12878), fewer than 9 scaffolds cover each chromosome, except the largest (chromosome 1, n = 13). ARKS uses a kmer mapping strategy instead of linked read alignments to record and associate the barcode information needed to order and orient draft assembly sequences. The simplified workflow, when compared to that of our initial implementation, ARCS, markedly improves run time performances on experimental human genome

  4. 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.

  5. The identification of complete domains within protein sequences using accurate E-values for semi-global alignment

    PubMed Central

    Kann, Maricel G.; Sheetlin, Sergey L.; Park, Yonil; Bryant, Stephen H.; Spouge, John L.

    2007-01-01

    The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the corresponding protein sequence. Ideally, complete domains are aligned to protein subsequences, in a ‘semi-global alignment’. Local alignment, which aligns pieces of domains to subsequences, is common in high-throughput annotation applications, however. It is a mature technique, with the heuristics and accurate E-values required for screening large databases and evaluating the screening results. Hidden Markov models (HMMs) provide an alternative theoretical framework for semi-global alignment, but their use is limited because they lack heuristic acceleration and accurate E-values. Our new tool, GLOBAL, overcomes some limitations of previous semi-global HMMs: it has accurate E-values and the possibility of the heuristic acceleration required for high-throughput applications. Moreover, according to a standard of truth based on protein structure, two semi-global HMM alignment tools (GLOBAL and HMMer) had comparable performance in identifying complete domains, but distinctly outperformed two tools based on local alignment. When searching for complete protein domains, therefore, GLOBAL avoids disadvantages commonly associated with HMMs, yet maintains their superior retrieval performance. PMID:17596268

  6. CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping.

    PubMed

    Nguyen, Tung; Shi, Weisong; Ruden, Douglas

    2011-06-06

    Research in genetics has developed rapidly recently due to the aid of next generation sequencing (NGS). However, massively-parallel NGS produces enormous amounts of data, which leads to storage, compatibility, scalability, and performance issues. The Cloud Computing and MapReduce framework, which utilizes hundreds or thousands of shared computers to map sequencing reads quickly and efficiently to reference genome sequences, appears to be a very promising solution for these issues. Consequently, it has been adopted by many organizations recently, and the initial results are very promising. However, since these are only initial steps toward this trend, the developed software does not provide adequate primary functions like bisulfite, pair-end mapping, etc., in on-site software such as RMAP or BS Seeker. In addition, existing MapReduce-based applications were not designed to process the long reads produced by the most recent second-generation and third-generation NGS instruments and, therefore, are inefficient. Last, it is difficult for a majority of biologists untrained in programming skills to use these tools because most were developed on Linux with a command line interface. To urge the trend of using Cloud technologies in genomics and prepare for advances in second- and third-generation DNA sequencing, we have built a Hadoop MapReduce-based application, CloudAligner, which achieves higher performance, covers most primary features, is more accurate, and has a user-friendly interface. It was also designed to be able to deal with long sequences. The performance gain of CloudAligner over Cloud-based counterparts (35 to 80%) mainly comes from the omission of the reduce phase. In comparison to local-based approaches, the performance gain of CloudAligner is from the partition and parallel processing of the huge reference genome as well as the reads. The source code of CloudAligner is available at http://cloudaligner.sourceforge.net/ and its web version is at http

  7. 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.

  8. 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

  9. 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.

  10. Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS.

    PubMed

    Warris, Sven; Yalcin, Feyruz; Jackson, Katherine J L; Nap, Jan Peter

    2015-01-01

    To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on graphics hardware do not report the alignment details necessary for further analysis. With the Parallel SW Alignment Software (PaSWAS) it is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed sequence alignments, and (b) retrieve relevant information such as score, number of gaps and mismatches. The software reports multiple hits per alignment. The added value of the new SW implementation is demonstrated with two test cases: (1) tag recovery in next generation sequence data and (2) isotype assignment within an immunoglobulin 454 sequence data set. Both cases show the usability and versatility of the new parallel Smith-Waterman implementation.

  11. 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

  12. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

    PubMed

    Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

    2013-07-01

    The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

  13. Intraoperative panoramic image using alignment grid, is it accurate?

    PubMed

    Apivatthakakul, T; Duanghakrung, M; Luevitoonvechkit, S; Patumasutra, S

    2013-07-01

    Minimally invasive orthopedic trauma surgery relies heavily on intraoperative fluoroscopic images to evaluate the quality of fracture reduction and fixation. However, fluoroscopic images have a narrow field of view and often cannot visualize the entire long bone axis. To compare the coronal femoral alignment between conventional X-rays to that achieved with a new method of acquiring a panoramic intraoperative image. Twenty-four cadaveric femurs with simple diaphyseal fractures were fixed with an angulated broad DCP to create coronal plane malalignment. An intraoperative alignment grid was used to help stitch different fluoroscopic images together to produce a panoramic image. A conventional X-ray of the entire femur was then performed. The coronal plane angulation in the panoramic images was then compared to the conventional X-rays using a Wilcoxon signed rank test. The mean angle measured from the panoramic view was 173.9° (range 169.3°-178.0°) with median of 173.2°. The mean angle measured from the conventional X-ray was 173.4° (range 167.7°-178.7°) with a median angle of 173.5°. There was no significant difference between both methods of measurement (P = 0.48). Panoramic images produced by stitching fluoroscopic images together with help of an alignment grid demonstrated the same accuracy at evaluating the coronal plane alignment of femur fractures as conventional X-rays.

  14. A practical strategy for the accurate measurement of residual dipolar couplings in strongly aligned small molecules

    NASA Astrophysics Data System (ADS)

    Liu, Yizhou; Cohen, Ryan D.; Martin, Gary E.; Williamson, R. Thomas

    2018-06-01

    Accurate measurement of residual dipolar couplings (RDCs) requires an appropriate degree of alignment in order to optimize data quality. An overly weak alignment yields very small anisotropic data that are susceptible to measurement errors, whereas an overly strong alignment introduces extensive anisotropic effects that severely degrade spectral quality. The ideal alignment amplitude also depends on the specific pulse sequence used for the coupling measurement. In this work, we introduce a practical strategy for the accurate measurement of one-bond 13C-1H RDCs up to a range of ca. -300 to +300 Hz, corresponding to an alignment that is an order of magnitude stronger than typically employed for small molecule structural elucidation. This strong alignment was generated in the mesophase of the commercially available poly-γ-(benzyl-L-glutamate) polymer. The total coupling was measured by the simple and well-studied heteronuclear two-dimensional J-resolved experiment, which performs well in the presence of strong anisotropic effects. In order to unequivocally determine the sign of the total coupling and resolve ambiguities in assigning total couplings in the CH2 group, coupling measurements were conducted at an isotropic condition plus two anisotropic conditions of different alignment amplitudes. Most RDCs could be readily extracted from these measurements whereas more complicated spectral effects resulting from strong homonuclear coupling could be interpreted either theoretically or by simulation. Importantly, measurement of these very large RDCs actually offers significantly improved data quality and utility for the structure determination of small organic molecules.

  15. The Alignment of State Standards and Assessments in Elementary Reading. CIERA Report.

    ERIC Educational Resources Information Center

    Wixson, Karen K.; Fisk, Maria Chesley; Dutro, Elizabeth; McDaniel, Julie

    A study examined the alignment between state standards and assessments in elementary reading. The impetus for the study was a request by the National Research Council's Committee on Title I Testing and Assessment for information on the extent to which students' performance on state assessments could be assumed to provide evidence of their level of…

  16. HIA: a genome mapper using hybrid index-based sequence alignment.

    PubMed

    Choi, Jongpill; Park, Kiejung; Cho, Seong Beom; Chung, Myungguen

    2015-01-01

    A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapidly. Recent studies based on NGS technology have routinely produced exome or whole-genome sequences from several hundreds or thousands of samples. To accommodate the increasing need of analyzing very large NGS data sets, it is necessary to develop faster, more sensitive and accurate mapping tools. HIA uses two indices, a hash table index and a suffix array index. The hash table performs direct lookup of a q-gram, and the suffix array performs very fast lookup of variable-length strings by exploiting binary search. We observed that combining hash table and suffix array (hybrid index) is much faster than the suffix array method for finding a substring in the reference sequence. Here, we defined the matching region (MR) is a longest common substring between a reference and a read. And, we also defined the candidate alignment regions (CARs) as a list of MRs that is close to each other. The hybrid index is used to find candidate alignment regions (CARs) between a reference and a read. We found that aligning only the unmatched regions in the CAR is much faster than aligning the whole CAR. In benchmark analysis, HIA outperformed in mapping speed compared with the other aligners, without significant loss of mapping accuracy. Our experiments show that the hybrid of hash table and suffix array is useful in terms of speed for mapping NGS sequencing reads to the human reference genome sequence. In conclusion, our tool is appropriate for aligning massive data sets generated by NGS sequencing.

  17. Alignment of 1000 Genomes Project reads to reference assembly GRCh38.

    PubMed

    Zheng-Bradley, Xiangqun; Streeter, Ian; Fairley, Susan; Richardson, David; Clarke, Laura; Flicek, Paul

    2017-07-01

    The 1000 Genomes Project produced more than 100 trillion basepairs of short read sequence from more than 2600 samples in 26 populations over a period of five years. In its final phase, the project released over 85 million genotyped and phased variants on human reference genome assembly GRCh37. An updated reference assembly, GRCh38, was released in late 2013, but there was insufficient time for the final phase of the project analysis to change to the new assembly. Although it is possible to lift the coordinates of the 1000 Genomes Project variants to the new assembly, this is a potentially error-prone process as coordinate remapping is most appropriate only for non-repetitive regions of the genome and those that did not see significant change between the two assemblies. It will also miss variants in any region that was newly added to GRCh38. Thus, to produce the highest quality variants and genotypes on GRCh38, the best strategy is to realign the reads and recall the variants based on the new alignment. As the first step of variant calling for the 1000 Genomes Project data, we have finished remapping all of the 1000 Genomes sequence reads to GRCh38 with alternative scaffold-aware BWA-MEM. The resulting alignments are available as CRAM, a reference-based sequence compression format. The data have been released on our FTP site and are also available from European Nucleotide Archive to facilitate researchers discovering variants on the primary sequences and alternative contigs of GRCh38. © The Authors 2017. Published by Oxford University Press.

  18. An Accurate Scalable Template-based Alignment Algorithm

    PubMed Central

    Gardner, David P.; Xu, Weijia; Miranker, Daniel P.; Ozer, Stuart; Cannone, Jamie J.; Gutell, Robin R.

    2013-01-01

    The rapid determination of nucleic acid sequences is increasing the number of sequences that are available. Inherent in a template or seed alignment is the culmination of structural and functional constraints that are selecting those mutations that are viable during the evolution of the RNA. While we might not understand these structural and functional, template-based alignment programs utilize the patterns of sequence conservation to encapsulate the characteristics of viable RNA sequences that are aligned properly. We have developed a program that utilizes the different dimensions of information in rCAD, a large RNA informatics resource, to establish a profile for each position in an alignment. The most significant include sequence identity and column composition in different phylogenetic taxa. We have compared our methods with a maximum of eight alternative alignment methods on different sets of 16S and 23S rRNA sequences with sequence percent identities ranging from 50% to 100%. The results showed that CRWAlign outperformed the other alignment methods in both speed and accuracy. A web-based alignment server is available at http://www.rna.ccbb.utexas.edu/SAE/2F/CRWAlign. PMID:24772376

  19. 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.

  20. 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

  1. Long-read sequencing data analysis for yeasts.

    PubMed

    Yue, Jia-Xing; Liti, Gianni

    2018-06-01

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

  2. Long-Term Outcomes of Early Reading Intervention

    ERIC Educational Resources Information Center

    Hurry, Jane; Sylva, Kathy

    2007-01-01

    This study explores the long-term effectiveness of two differing models of early intervention for children with reading difficulties: Reading Recovery and a specific phonological training. Approximately 400 children were pre-tested, 95 were assigned to Reading Recovery, 97 to Phonological Training and the remainder acted as controls. In the short…

  3. Virtual plate pre-bending for the long bone fracture based on axis pre-alignment.

    PubMed

    Liu, Bin; Luo, Xinjian; Huang, Rui; Wan, Chao; Zhang, Bingbing; Hu, Weihua; Yue, Zongge

    2014-06-01

    In this paper, a modeling and visualizing system for assisting surgeons in correctly registering for the closed fracture reduction surgery is presented. By using this system, the geometric parameters of the target fixation plate before the long bone fracture operation can be obtained. The main processing scheme consists of following steps: firstly (image data process), utilize the Curvelet transform to denoise the CT images of fracture part and then reconstruct the 3D models of the broken bones. Secondly (pre-alignment), extract the axial lines of the broken bones and spatially align them. Then drive the broken bone models to be pre-aligned. Thirdly (mesh segmentation), a method based on vertex normal feature is utilized to obtain the broken bone cross-sections mesh models. Fourthly (fine registration), the ICP (Iterative Closest Point) algorithm is used to register the cross-sections and the broken bone models are driven to achieve the fine registration posture. Lastly (plate fitting), an accurate NURBS surface fitting method is used to construct the virtual plate. The experiment proved that the obtained models of the pre-bended plates were closely bonded to the surface of the registered long bone models. Finally, the lengths, angles and other interested geometric parameters can be measured on the plate models. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.

    PubMed

    Liao, Weinan; Ren, Jie; Wang, Kun; Wang, Shun; Zeng, Feng; Wang, Ying; Sun, Fengzhu

    2016-11-23

    The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC). Under a fixed high order of MC, the parameters might not be accurately estimated owing to the limitation of sequencing depth. In our study, we investigate an alternative to FOMC to model background sequences with the data-driven Variable Length Markov Chain (VLMC) in metatranscriptomic data. The VLMC originally designed for long sequences was extended to apply to high-throughput sequencing reads and the strategies to estimate the corresponding parameters were developed. The flexible number of parameters in VLMC avoids estimating the vast number of parameters of high-order MC under limited sequencing depth. Different from the manual selection in FOMC, VLMC determines the MC order adaptively. Several beta diversity measures based on VLMC were applied to compare the bacterial RNA-Seq and metatranscriptomic datasets. Experiments show that VLMC outperforms FOMC to model the background sequences in transcriptomic and metatranscriptomic samples. A software pipeline is available at https://d2vlmc.codeplex.com.

  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. Scaffolding of long read assemblies using long range contact information

    USDA-ARS?s Scientific Manuscript database

    Long read technologies have made a revolution in de novo genome assembly by generating long contigs. Although the assembly contiguity has increased, it may not span a chromosome, resulting in an unfinished chromosome level assembly. To address this problem, we develop a scaffolding method that can b...

  7. ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data

    PubMed Central

    Li, You; Heavican, Tayla B.; Vellichirammal, Neetha N.; Iqbal, Javeed

    2017-01-01

    Abstract The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The ‘fusion’ or ‘chimeric’ transcripts have improved the diagnosis and prognosis of several tumors, and have led to the development of novel therapeutic regimen. The fusion transcript detection is currently accomplished by several software packages, primarily relying on sequence alignment algorithms. The alignment of sequencing reads from fusion transcript loci in cancer genomes can be highly challenging due to the incorrect mapping induced by genomic alterations, thereby limiting the performance of alignment-based fusion transcript detection methods. Here, we developed a novel alignment-free method, ChimeRScope that accurately predicts fusion transcripts based on the gene fingerprint (as k-mers) profiles of the RNA-Seq paired-end reads. Results on published datasets and in-house cancer cell line datasets followed by experimental validations demonstrate that ChimeRScope consistently outperforms other popular methods irrespective of the read lengths and sequencing depth. More importantly, results on our in-house datasets show that ChimeRScope is a better tool that is capable of identifying novel fusion transcripts with potential oncogenic functions. ChimeRScope is accessible as a standalone software at (https://github.com/ChimeRScope/ChimeRScope/wiki) or via the Galaxy web-interface at (https://galaxy.unmc.edu/). PMID:28472320

  8. HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.

    PubMed

    Hashemifar, Somaye; Xu, Jinbo

    2014-09-01

    High-throughput experimental techniques have produced a large amount of protein-protein interaction (PPI) data. The study of PPI networks, such as comparative analysis, shall benefit the understanding of life process and diseases at the molecular level. One way of comparative analysis is to align PPI networks to identify conserved or species-specific subnetwork motifs. A few methods have been developed for global PPI network alignment, but it still remains challenging in terms of both accuracy and efficiency. This paper presents a novel global network alignment algorithm, denoted as HubAlign, that makes use of both network topology and sequence homology information, based upon the observation that topologically important proteins in a PPI network usually are much more conserved and thus, more likely to be aligned. HubAlign uses a minimum-degree heuristic algorithm to estimate the topological and functional importance of a protein from the global network topology information. Then HubAlign aligns topologically important proteins first and gradually extends the alignment to the whole network. Extensive tests indicate that HubAlign greatly outperforms several popular methods in terms of both accuracy and efficiency, especially in detecting functionally similar proteins. HubAlign is available freely for non-commercial purposes at http://ttic.uchicago.edu/∼hashemifar/software/HubAlign.zip. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  9. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

    PubMed

    Hu, Jialu; Kehr, Birte; Reinert, Knut

    2014-02-15

    Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing. We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments. The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.

  10. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

    PubMed

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-05-01

    Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. ivan.borozan@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  11. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

    PubMed Central

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-01-01

    Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

  12. Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.

    PubMed

    Neuwald, Andrew F

    2009-08-01

    The patterns of sequence similarity and divergence present within functionally diverse, evolutionarily related proteins contain implicit information about corresponding biochemical similarities and differences. A first step toward accessing such information is to statistically analyze these patterns, which, in turn, requires that one first identify and accurately align a very large set of protein sequences. Ideally, the set should include many distantly related, functionally divergent subgroups. Because it is extremely difficult, if not impossible for fully automated methods to align such sequences correctly, researchers often resort to manual curation based on detailed structural and biochemical information. However, multiply-aligning vast numbers of sequences in this way is clearly impractical. This problem is addressed using Multiply-Aligned Profiles for Global Alignment of Protein Sequences (MAPGAPS). The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences. It relies on Karlin-Altschul statistics for sensitivity and on PSI-BLAST (and other) heuristics for speed. Using as input a carefully curated multiple-profile alignment for P-loop GTPases, MAPGAPS correctly aligned weakly conserved sequence motifs within 33 distantly related GTPases of known structure. By comparison, the sequence- and structurally based alignment methods hmmalign and PROMALS3D misaligned at least 11 and 23 of these regions, respectively. When applied to a dataset of 65 million protein sequences, MAPGAPS identified, classified and aligned (with comparable accuracy) nearly half a million putative P-loop GTPase sequences. A C++ implementation of MAPGAPS is available at http://mapgaps.igs.umaryland.edu. Supplementary data are available at Bioinformatics online.

  13. 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…

  14. Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic.

    PubMed

    Brown, Peter; Pullan, Wayne; Yang, Yuedong; Zhou, Yaoqi

    2016-02-01

    The three dimensional tertiary structure of a protein at near atomic level resolution provides insight alluding to its function and evolution. As protein structure decides its functionality, similarity in structure usually implies similarity in function. As such, structure alignment techniques are often useful in the classifications of protein function. Given the rapidly growing rate of new, experimentally determined structures being made available from repositories such as the Protein Data Bank, fast and accurate computational structure comparison tools are required. This paper presents SPalignNS, a non-sequential protein structure alignment tool using a novel asymmetrical greedy search technique. The performance of SPalignNS was evaluated against existing sequential and non-sequential structure alignment methods by performing trials with commonly used datasets. These benchmark datasets used to gauge alignment accuracy include (i) 9538 pairwise alignments implied by the HOMSTRAD database of homologous proteins; (ii) a subset of 64 difficult alignments from set (i) that have low structure similarity; (iii) 199 pairwise alignments of proteins with similar structure but different topology; and (iv) a subset of 20 pairwise alignments from the RIPC set. SPalignNS is shown to achieve greater alignment accuracy (lower or comparable root-mean squared distance with increased structure overlap coverage) for all datasets, and the highest agreement with reference alignments from the challenging dataset (iv) above, when compared with both sequentially constrained alignments and other non-sequential alignments. SPalignNS was implemented in C++. The source code, binary executable, and a web server version is freely available at: http://sparks-lab.org yaoqi.zhou@griffith.edu.au. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Application of fast Fourier transform cross-correlation and mass spectrometry data for accurate alignment of chromatograms.

    PubMed

    Zheng, Yi-Bao; Zhang, Zhi-Min; Liang, Yi-Zeng; Zhan, De-Jian; Huang, Jian-Hua; Yun, Yong-Huan; Xie, Hua-Lin

    2013-04-19

    Chromatography has been established as one of the most important analytical methods in the modern analytical laboratory. However, preprocessing of the chromatograms, especially peak alignment, is usually a time-consuming task prior to extracting useful information from the datasets because of the small unavoidable differences in the experimental conditions caused by minor changes and drift. Most of the alignment algorithms are performed on reduced datasets using only the detected peaks in the chromatograms, which means a loss of data and introduces the problem of extraction of peak data from the chromatographic profiles. These disadvantages can be overcome by using the full chromatographic information that is generated from hyphenated chromatographic instruments. A new alignment algorithm called CAMS (Chromatogram Alignment via Mass Spectra) is present here to correct the retention time shifts among chromatograms accurately and rapidly. In this report, peaks of each chromatogram were detected based on Continuous Wavelet Transform (CWT) with Haar wavelet and were aligned against the reference chromatogram via the correlation of mass spectra. The aligning procedure was accelerated by Fast Fourier Transform cross correlation (FFT cross correlation). This approach has been compared with several well-known alignment methods on real chromatographic datasets, which demonstrates that CAMS can preserve the shape of peaks and achieve a high quality alignment result. Furthermore, the CAMS method was implemented in the Matlab language and available as an open source package at http://www.github.com/matchcoder/CAMS. Copyright © 2013. Published by Elsevier B.V.

  16. An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

    An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

  17. Kraken: ultrafast metagenomic sequence classification using exact alignments

    PubMed Central

    2014-01-01

    Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/. PMID:24580807

  18. Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads

    PubMed Central

    Schröder, Jan; Hsu, Arthur; Boyle, Samantha E.; Macintyre, Geoff; Cmero, Marek; Tothill, Richard W.; Johnstone, Ricky W.; Shackleton, Mark; Papenfuss, Anthony T.

    2014-01-01

    Motivation: Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital in cancer genomics. Available algorithms use one or more sources of evidence, such as read depth, paired-end reads or split reads to predict structural variants. However, the problem remains challenging due to the significant computational burden and high false-positive or false-negative rates. Results: In this article, we present Socrates (SOft Clip re-alignment To idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours that uses only split-read data. Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. We demonstrate using simulated and real data that Socrates performs well compared with a number of existing structural variant detection tools. Availability and implementation: Socrates is released as open source and available from http://bioinf.wehi.edu.au/socrates. Contact: papenfuss@wehi.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24389656

  19. Monitoring Children with Reading Disabilities' Response to Phonics Intervention: Are There Differences between Intervention Aligned and General Skill Progress Monitoring Assessments?

    ERIC Educational Resources Information Center

    Olinghouse, Natalie G.; Lambert, Warren; Compton, Donald L.

    2006-01-01

    This study investigated whether 2 different progress monitoring assessments differentially predicted growth in reading skills associated with systematic phonics instruction. Oral reading fluency (ORE) was compared with an intervention aligned word list (IAWL) as predictors of growth in untimed and timed decoding and word identification and text…

  20. MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins.

    PubMed

    Jones, David T; Singh, Tanya; Kosciolek, Tomasz; Tetchner, Stuart

    2015-04-01

    Recent developments of statistical techniques to infer direct evolutionary couplings between residue pairs have rendered covariation-based contact prediction a viable means for accurate 3D modelling of proteins, with no information other than the sequence required. To extend the usefulness of contact prediction, we have designed a new meta-predictor (MetaPSICOV) which combines three distinct approaches for inferring covariation signals from multiple sequence alignments, considers a broad range of other sequence-derived features and, uniquely, a range of metrics which describe both the local and global quality of the input multiple sequence alignment. Finally, we use a two-stage predictor, where the second stage filters the output of the first stage. This two-stage predictor is additionally evaluated on its ability to accurately predict the long range network of hydrogen bonds, including correctly assigning the donor and acceptor residues. Using the original PSICOV benchmark set of 150 protein families, MetaPSICOV achieves a mean precision of 0.54 for top-L predicted long range contacts-around 60% higher than PSICOV, and around 40% better than CCMpred. In de novo protein structure prediction using FRAGFOLD, MetaPSICOV is able to improve the TM-scores of models by a median of 0.05 compared with PSICOV. Lastly, for predicting long range hydrogen bonding, MetaPSICOV-HB achieves a precision of 0.69 for the top-L/10 hydrogen bonds compared with just 0.26 for the baseline MetaPSICOV. MetaPSICOV is available as a freely available web server at http://bioinf.cs.ucl.ac.uk/MetaPSICOV. Raw data (predicted contact lists and 3D models) and source code can be downloaded from http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  1. CLAST: CUDA implemented large-scale alignment search tool.

    PubMed

    Yano, Masahiro; Mori, Hiroshi; Akiyama, Yutaka; Yamada, Takuji; Kurokawa, Ken

    2014-12-11

    Metagenomics is a powerful methodology to study microbial communities, but it is highly dependent on nucleotide sequence similarity searching against sequence databases. Metagenomic analyses with next-generation sequencing technologies produce enormous numbers of reads from microbial communities, and many reads are derived from microbes whose genomes have not yet been sequenced, limiting the usefulness of existing sequence similarity search tools. Therefore, there is a clear need for a sequence similarity search tool that can rapidly detect weak similarity in large datasets. We developed a tool, which we named CLAST (CUDA implemented large-scale alignment search tool), that enables analyses of millions of reads and thousands of reference genome sequences, and runs on NVIDIA Fermi architecture graphics processing units. CLAST has four main advantages over existing alignment tools. First, CLAST was capable of identifying sequence similarities ~80.8 times faster than BLAST and 9.6 times faster than BLAT. Second, CLAST executes global alignment as the default (local alignment is also an option), enabling CLAST to assign reads to taxonomic and functional groups based on evolutionarily distant nucleotide sequences with high accuracy. Third, CLAST does not need a preprocessed sequence database like Burrows-Wheeler Transform-based tools, and this enables CLAST to incorporate large, frequently updated sequence databases. Fourth, CLAST requires <2 GB of main memory, making it possible to run CLAST on a standard desktop computer or server node. CLAST achieved very high speed (similar to the Burrows-Wheeler Transform-based Bowtie 2 for long reads) and sensitivity (equal to BLAST, BLAT, and FR-HIT) without the need for extensive database preprocessing or a specialized computing platform. Our results demonstrate that CLAST has the potential to be one of the most powerful and realistic approaches to analyze the massive amount of sequence data from next-generation sequencing

  2. 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.

  3. 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

  4. 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

  5. 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

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

    PubMed

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

    2016-06-15

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

  7. Angle and Base of Gait Long Leg Axial and Intraoperative Simulated Weightbearing Long Leg Axial Imaging to Capture True Frontal Plane Tibia to Calcaneus Alignment in Valgus and Varus Deformities of the Rearfoot and Ankle.

    PubMed

    Boffeli, Troy J; Waverly, Brett J

    2016-01-01

    The long leg axial view is primarily used to evaluate the frontal plane alignment of the calcaneus in relation to the long axis of the tibia when standing. This view allows both angular measurement and assessment for the apex of varus and valgus deformity of the rearfoot and ankle with clinical utility in the preoperative, intraoperative, and postoperative settings. The frontal plane alignment of the calcaneus to the long axis of the tibia is rarely fixed in the varus or valgus position because of the inherent flexibility of the foot and ankle, which makes patient positioning critical to obtain accurate and reproducible images. Inconsistent patient positioning and imaging techniques are commonly encountered with the long leg axial view for a variety of reasons, including the lack of a standardized or validated protocol. This angle and base of gait imaging protocol involves positioning the patient to align the tibia with the long axis of the foot, which is represented by the second metatarsal. Non-weightbearing long leg axial imaging is commonly performed intraoperatively, which requires a modified patient positioning technique to capture simulated weightbearing long leg axial images. A case series is presented to demonstrate our angle and base of gait long leg axial and intraoperative simulated weightbearing long leg axial imaging protocols that can be applied throughout all phases of patient care for various foot and ankle conditions. Copyright © 2015 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

  8. The Parable of the Sower and the Long-Term Effects of Early Reading

    ERIC Educational Resources Information Center

    Suggate, Sebastian P.

    2015-01-01

    Previous work on the long-term effects of early reading focuses on whether children can read early (i.e. capability) not on whether this is beneficial (i.e. optimality). The Luke Effect is introduced to predict long-term reading development as a function of when children learn to read. A review of correlational, intervention, and comparative…

  9. Dry contact transfer printing of aligned carbon nanotube patterns and characterization of their optical properties for diameter distribution and alignment.

    PubMed

    Pint, Cary L; Xu, Ya-Qiong; Moghazy, Sharief; Cherukuri, Tonya; Alvarez, Noe T; Haroz, Erik H; Mahzooni, Salma; Doorn, Stephen K; Kono, Junichiro; Pasquali, Matteo; Hauge, Robert H

    2010-02-23

    A scalable and facile approach is demonstrated where as-grown patterns of well-aligned structures composed of single-walled carbon nanotubes (SWNT) synthesized via water-assisted chemical vapor deposition (CVD) can be transferred, or printed, to any host surface in a single dry, room-temperature step using the growth substrate as a stamp. We demonstrate compatibility of this process with multiple transfers for large-scale device and specifically tailored pattern fabrication. Utilizing this transfer approach, anisotropic optical properties of the SWNT films are probed via polarized absorption, Raman, and photoluminescence spectroscopies. Using a simple model to describe optical transitions in the large SWNT species present in the aligned samples, polarized absorption data are demonstrated as an effective tool for accurate assignment of the diameter distribution from broad absorption features located in the infrared. This can be performed on either well-aligned samples or unaligned doped samples, allowing simple and rapid feedback of the SWNT diameter distribution that can be challenging and time-consuming to obtain in other optical methods. Furthermore, we discuss challenges in accurately characterizing alignment in structures of long versus short carbon nanotubes through optical techniques, where SWNT length makes a difference in the information obtained in such measurements. This work provides new insight to the efficient transfer and optical properties of an emerging class of long, large diameter SWNT species typically produced in the CVD process.

  10. 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

  11. SCRAM: a pipeline for fast index-free small RNA read alignment and visualization.

    PubMed

    Fletcher, Stephen J; Boden, Mikael; Mitter, Neena; Carroll, Bernard J

    2018-03-15

    Small RNAs play key roles in gene regulation, defense against viral pathogens and maintenance of genome stability, though many aspects of their biogenesis and function remain to be elucidated. SCRAM (Small Complementary RNA Mapper) is a novel, simple-to-use short read aligner and visualization suite that enhances exploration of small RNA datasets. The SCRAM pipeline is implemented in Go and Python, and is freely available under MIT license. Source code, multiplatform binaries and a Docker image can be accessed via https://sfletc.github.io/scram/. s.fletcher@uq.edu.au. Supplementary data are available at Bioinformatics online.

  12. A new principle for the standardization of long paragraphs for reading speed analysis.

    PubMed

    Radner, Wolfgang; Radner, Stephan; Diendorfer, Gabriela

    2016-01-01

    To investigate the reliability, validity, and statistical comparability of long paragraphs that were developed to be equivalent in construction and difficulty. Seven long paragraphs were developed that were equal in syntax, morphology, and number and position of words (111), with the same number of syllables (179) and number of characters (660). For validity analyses, the paragraphs were compared with the mean reading speed of a set of seven sentence optotypes of the RADNER Reading Charts (mean of 7 × 14 = 98 words read). Reliability analyses were performed by calculating the Cronbach's alpha value and the corrected total item correlation. Sixty participants (aged 20-77 years) read the paragraphs and the sentences (distance 40 cm; font: Times New Roman 12 pt). Test items were presented randomly; reading length was measured with a stopwatch. Reliability analysis yielded a Cronbach's alpha value of 0.988. When the long paragraphs were compared in pairwise fashion, significant differences were found in 13 of the 21 pairs (p < 0.05). In two sequences of three paragraphs each and in eight pairs of paragraphs, the paragraphs did not differ significantly, and these paragraph combinations are therefore suitable for comparative research studies. The mean reading speed was 173.34 ± 24.01 words per minute (wpm) for the long paragraphs and 198.26 ± 28.60 wpm for the sentence optotypes. The maximum difference in reading speed was 5.55 % for the long paragraphs and 2.95 % for the short sentence optotypes. The correlation between long paragraphs and sentence optotypes was high (r = 0.9243). Despite good reliability and equivalence in construction and degree of difficulty, a statistically significant difference in reading speed can occur between long paragraphs. Since statistical significance should be dependent only on the persons tested, either standardizing long paragraphs for statistical equality of reading speed measurements or increasing the number

  13. Response to Intervention as a Predictor of Long-Term Reading Outcomes in Children with Dyslexia.

    PubMed

    van der Kleij, Sanne W; Segers, Eliane; Groen, Margriet A; Verhoeven, Ludo

    2017-08-01

    The goal of this study was to investigate how growth during a phonics-based intervention, as well as reading levels at baseline testing, predicted long-term reading outcomes of children with dyslexia. Eighty Dutch children with dyslexia who had completed a 50-week phonics-based intervention in grade 4 were tested in grade 5 on both word and pseudoword (following regular Dutch orthographic patterns) reading efficiency and compared to 93 typical readers. In grade 5 the children with dyslexia were still significantly slower in word and pseudoword reading than their typically developing peers. Results showed that long-term pseudoword reading in the group with dyslexia was predicted by pseudoword reading at pretest and growth in pseudoword reading during the intervention, which was itself predicted by pseudoword reading at pretest. This was not the case for word reading. We found that long-term word reading was directly predicted from pretest word reading, and indirectly via pretest pseudoword reading, via growth in pseudoword and word reading. It can be concluded that pseudoword reading is not only a good indicator of severity of reading difficulties in children with dyslexia, it is also an indicator of who will profit from intervention in the long-term. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  14. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

    PubMed

    Koren, Sergey; Phillippy, Adam M

    2015-02-01

    Like a jigsaw puzzle with large pieces, a genome sequenced with long reads is easier to assemble. However, recent sequencing technologies have favored lowering per-base cost at the expense of read length. This has dramatically reduced sequencing cost, but resulted in fragmented assemblies, which negatively affect downstream analyses and hinder the creation of finished (gapless, high-quality) genomes. In contrast, emerging long-read sequencing technologies can now produce reads tens of kilobases in length, enabling the automated finishing of microbial genomes for under $1000. This promises to improve the quality of reference databases and facilitate new studies of chromosomal structure and variation. We present an overview of these new technologies and the methods used to assemble long reads into complete genomes. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. 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

  16. 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

  17. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

    PubMed

    Bauer, Markus; Klau, Gunnar W; Reinert, Knut

    2007-07-27

    The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

  18. Propagation and stability characteristics of a 500-m-long laser-based fiducial line for high-precision alignment of long-distance linear accelerators.

    PubMed

    Suwada, Tsuyoshi; Satoh, Masanori; Telada, Souichi; Minoshima, Kaoru

    2013-09-01

    A laser-based alignment system with a He-Ne laser has been newly developed in order to precisely align accelerator units at the KEKB injector linac. The laser beam was first implemented as a 500-m-long fiducial straight line for alignment measurements. We experimentally investigated the propagation and stability characteristics of the laser beam passing through laser pipes in vacuum. The pointing stability at the last fiducial point was successfully obtained with the transverse displacements of ±40 μm level in one standard deviation by applying a feedback control. This pointing stability corresponds to an angle of ±0.08 μrad. This report contains a detailed description of the experimental investigation for the propagation and stability characteristics of the laser beam in the laser-based alignment system for long-distance linear accelerators.

  19. Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches.

    PubMed

    Lin, Hsin-Hung; Liao, Yu-Chieh

    2015-01-01

    Despite the ever-increasing output of next-generation sequencing data along with developing assemblers, dozens to hundreds of gaps still exist in de novo microbial assemblies due to uneven coverage and large genomic repeats. Third-generation single-molecule, real-time (SMRT) sequencing technology avoids amplification artifacts and generates kilobase-long reads with the potential to complete microbial genome assembly. However, due to the low accuracy (~85%) of third-generation sequences, a considerable amount of long reads (>50X) are required for self-correction and for subsequent de novo assembly. Recently-developed hybrid approaches, using next-generation sequencing data and as few as 5X long reads, have been proposed to improve the completeness of microbial assembly. In this study we have evaluated the contemporary hybrid approaches and demonstrated that assembling corrected long reads (by runCA) produced the best assembly compared to long-read scaffolding (e.g., AHA, Cerulean and SSPACE-LongRead) and gap-filling (SPAdes). For generating corrected long reads, we further examined long-read correction tools, such as ECTools, LSC, LoRDEC, PBcR pipeline and proovread. We have demonstrated that three microbial genomes including Escherichia coli K12 MG1655, Meiothermus ruber DSM1279 and Pdeobacter heparinus DSM2366 were successfully hybrid assembled by runCA into near-perfect assemblies using ECTools-corrected long reads. In addition, we developed a tool, Patch, which implements corrected long reads and pre-assembled contigs as inputs, to enhance microbial genome assemblies. With the additional 20X long reads, short reads of S. cerevisiae W303 were hybrid assembled into 115 contigs using the verified strategy, ECTools + runCA. Patch was subsequently applied to upgrade the assembly to a 35-contig draft genome. Our evaluation of the hybrid approaches shows that assembling the ECTools-corrected long reads via runCA generates near complete microbial genomes, suggesting

  20. 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

  1. Optimizing Mechanical Alignment With Modular Stems in Revision TKA.

    PubMed

    Fleischman, Andrew N; Azboy, Ibrahim; Restrepo, Camilo; Maltenfort, Mitchell G; Parvizi, Javad

    2017-09-01

    Although mechanical alignment is critical for optimal function and long-term implant durability, the role of modular stems in achieving ideal alignment is unclear. We identified 319 revision total knee arthroplasty from 2003-2013, for which stem length, stem diameter, and stem fixation method were recorded prospectively. Three-dimensional canal-filling ratio, the product of canal-filling ratio at the stem tip in both the anteroposterior and lateral planes, and alignment were measured radiographically. Ideal alignment of the femur was considered to be 95° in the anteroposterior (AP) plane and from 1° of extension to 4° of flexion in the lateral plane, and ideal tibial alignment was considered to be 90° in the AP plane. Even after accounting for difference in stem size and canal-fill, ideal AP alignment was more reliably achieved with press-fit stems. Furthermore, increased engagement of the diaphysis and its anatomical axis with canal-filling stems facilitates accurate alignment. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. 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

  3. Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement

    NASA Astrophysics Data System (ADS)

    Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.

    2016-03-01

    Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

  4. Propagation and stability characteristics of a 500-m-long laser-based fiducial line for high-precision alignment of long-distance linear accelerators

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

    Suwada, Tsuyoshi; Satoh, Masanori; Telada, Souichi

    2013-09-15

    A laser-based alignment system with a He-Ne laser has been newly developed in order to precisely align accelerator units at the KEKB injector linac. The laser beam was first implemented as a 500-m-long fiducial straight line for alignment measurements. We experimentally investigated the propagation and stability characteristics of the laser beam passing through laser pipes in vacuum. The pointing stability at the last fiducial point was successfully obtained with the transverse displacements of ±40 μm level in one standard deviation by applying a feedback control. This pointing stability corresponds to an angle of ±0.08 μrad. This report contains a detailedmore » description of the experimental investigation for the propagation and stability characteristics of the laser beam in the laser-based alignment system for long-distance linear accelerators.« less

  5. 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.

  6. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

    PubMed

    Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver

    2012-07-15

    In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.

  7. 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

  8. 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...

  9. 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.

  10. Desktop aligner for fabrication of multilayer microfluidic devices.

    PubMed

    Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

    2015-07-01

    Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm(-1). To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices.

  11. Desktop aligner for fabrication of multilayer microfluidic devices

    PubMed Central

    Li, Xiang; Yu, Zeta Tak For; Geraldo, Dalton; Weng, Shinuo; Alve, Nitesh; Dun, Wu; Kini, Akshay; Patel, Karan; Shu, Roberto; Zhang, Feng; Li, Gang; Jin, Qinghui; Fu, Jianping

    2015-01-01

    Multilayer assembly is a commonly used technique to construct multilayer polydimethylsiloxane (PDMS)-based microfluidic devices with complex 3D architecture and connectivity for large-scale microfluidic integration. Accurate alignment of structure features on different PDMS layers before their permanent bonding is critical in determining the yield and quality of assembled multilayer microfluidic devices. Herein, we report a custom-built desktop aligner capable of both local and global alignments of PDMS layers covering a broad size range. Two digital microscopes were incorporated into the aligner design to allow accurate global alignment of PDMS structures up to 4 in. in diameter. Both local and global alignment accuracies of the desktop aligner were determined to be about 20 μm cm−1. To demonstrate its utility for fabrication of integrated multilayer PDMS microfluidic devices, we applied the desktop aligner to achieve accurate alignment of different functional PDMS layers in multilayer microfluidics including an organs-on-chips device as well as a microfluidic device integrated with vertical passages connecting channels located in different PDMS layers. Owing to its convenient operation, high accuracy, low cost, light weight, and portability, the desktop aligner is useful for microfluidic researchers to achieve rapid and accurate alignment for generating multilayer PDMS microfluidic devices. PMID:26233409

  12. 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).

  13. 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.

  14. Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

    PubMed Central

    Burger, Lukas; van Nimwegen, Erik

    2008-01-01

    Accurate and large-scale prediction of protein–protein interactions directly from amino-acid sequences is one of the great challenges in computational biology. Here we present a new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains, without tunable parameters, and without the need for any training examples. We first apply the method to bacterial two-component systems and comprehensively reconstruct two-component signaling networks across all sequenced bacteria. Comparisons of our predictions with known interactions show that our method infers interaction partners genome-wide with high accuracy. To demonstrate the general applicability of our method we show that it also accurately predicts interaction partners in a recent dataset of polyketide synthases. Analysis of the predicted genome-wide two-component signaling networks shows that cognates (interacting kinase/regulator pairs, which lie adjacent on the genome) and orphans (which lie isolated) form two relatively independent components of the signaling network in each genome. In addition, while most genes are predicted to have only a small number of interaction partners, we find that 10% of orphans form a separate class of ‘hub' nodes that distribute and integrate signals to and from up to tens of different interaction partners. PMID:18277381

  15. Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.

    PubMed

    Liu, Ruolin; Dickerson, Julie

    2017-11-01

    We propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and independent of gene annotation. Strawberry consists of two modules: assembly and quantification. The novelty of Strawberry is that the two modules use different optimization frameworks but utilize the same data graph structure, which allows a highly efficient, expandable and accurate algorithm for dealing large data. The assembly module parses aligned reads into splicing graphs, and uses network flow algorithms to select the most likely transcripts. The quantification module uses a latent class model to assign read counts from the nodes of splicing graphs to transcripts. Strawberry simultaneously estimates the transcript abundances and corrects for sequencing bias through an EM algorithm. Based on simulations, Strawberry outperforms Cufflinks and StringTie in terms of both assembly and quantification accuracies. Under the evaluation of a real data set, the estimated transcript expression by Strawberry has the highest correlation with Nanostring probe counts, an independent experiment measure for transcript expression. Strawberry is written in C++14, and is available as open source software at https://github.com/ruolin/strawberry under the MIT license.

  16. 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

  17. 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

  18. extendFromReads

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

    Williams, Kelly P.

    2013-10-03

    This package assists in genome assembly. extendFromReads takes as input a set of Illumina (eg, MiSeq) DNA sequencing reads, a query seed sequence and a direction to extend the seed. The algorithm collects all seed-- ]matching reads (flipping reverse-- ]orientation hits), trims off the seed and additional sequence in the other direction, sorts the remaining sequences alphabetically, and prints them aligned without gaps from the point of seed trimming. This produces a visual display distinguishing the flanks of multi- ]copy seeds. A companion script hitMates.pl collects the mates of seed-- ]hi]ng reads, whose alignment reveals longer extensions from the seed.more » The collect/trim/sort strategy was made iterative and scaled up in the script denovo.pl, for de novo contig assembly. An index is pre-- ]built using indexReads.pl that for each unique 21-- ]mer found in all the reads, records its gfate h of extension (whether extendable, blocked by low coverage, or blocked by branching after a duplicated sequence) and other characteristics. Importantly, denovo.pl records all branchings that follow a branching contig endpoint, providing contig- ]extension information« less

  19. A statistically harmonized alignment-classification in image space enables accurate and robust alignment of noisy images in single particle analysis.

    PubMed

    Kawata, Masaaki; Sato, Chikara

    2007-06-01

    In determining the three-dimensional (3D) structure of macromolecular assemblies in single particle analysis, a large representative dataset of two-dimensional (2D) average images from huge number of raw images is a key for high resolution. Because alignments prior to averaging are computationally intensive, currently available multireference alignment (MRA) software does not survey every possible alignment. This leads to misaligned images, creating blurred averages and reducing the quality of the final 3D reconstruction. We present a new method, in which multireference alignment is harmonized with classification (multireference multiple alignment: MRMA). This method enables a statistical comparison of multiple alignment peaks, reflecting the similarities between each raw image and a set of reference images. Among the selected alignment candidates for each raw image, misaligned images are statistically excluded, based on the principle that aligned raw images of similar projections have a dense distribution around the correctly aligned coordinates in image space. This newly developed method was examined for accuracy and speed using model image sets with various signal-to-noise ratios, and with electron microscope images of the Transient Receptor Potential C3 and the sodium channel. In every data set, the newly developed method outperformed conventional methods in robustness against noise and in speed, creating 2D average images of higher quality. This statistically harmonized alignment-classification combination should greatly improve the quality of single particle analysis.

  20. 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…

  1. 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.

  2. 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…

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

    PubMed

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

    2017-03-15

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

  4. Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

    DOE PAGES

    Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; ...

    2017-02-21

    The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. Here, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by constructionmore » captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. This approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.« less

  5. Energy level alignment at molecule-metal interfaces from an optimally tuned range-separated hybrid functional

    NASA Astrophysics Data System (ADS)

    Liu, Zhen-Fei; Egger, David A.; Refaely-Abramson, Sivan; Kronik, Leeor; Neaton, Jeffrey B.

    2017-03-01

    The alignment of the frontier orbital energies of an adsorbed molecule with the substrate Fermi level at metal-organic interfaces is a fundamental observable of significant practical importance in nanoscience and beyond. Typical density functional theory calculations, especially those using local and semi-local functionals, often underestimate level alignment leading to inaccurate electronic structure and charge transport properties. In this work, we develop a new fully self-consistent predictive scheme to accurately compute level alignment at certain classes of complex heterogeneous molecule-metal interfaces based on optimally tuned range-separated hybrid functionals. Starting from a highly accurate description of the gas-phase electronic structure, our method by construction captures important nonlocal surface polarization effects via tuning of the long-range screened exchange in a range-separated hybrid in a non-empirical and system-specific manner. We implement this functional in a plane-wave code and apply it to several physisorbed and chemisorbed molecule-metal interface systems. Our results are in quantitative agreement with experiments, the both the level alignment and work function changes. Our approach constitutes a new practical scheme for accurate and efficient calculations of the electronic structure of molecule-metal interfaces.

  6. Using structure to explore the sequence alignment space of remote homologs.

    PubMed

    Kuziemko, Andrew; Honig, Barry; Petrey, Donald

    2011-10-01

    Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

  7. ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly.

    PubMed

    Yang, Rendong; Nelson, Andrew C; Henzler, Christine; Thyagarajan, Bharat; Silverstein, Kevin A T

    2015-12-07

    Comprehensive identification of insertions/deletions (indels) across the full size spectrum from second generation sequencing is challenging due to the relatively short read length inherent in the technology. Different indel calling methods exist but are limited in detection to specific sizes with varying accuracy and resolution. We present ScanIndel, an integrated framework for detecting indels with multiple heuristics including gapped alignment, split reads and de novo assembly. Using simulation data, we demonstrate ScanIndel's superior sensitivity and specificity relative to several state-of-the-art indel callers across various coverage levels and indel sizes. ScanIndel yields higher predictive accuracy with lower computational cost compared with existing tools for both targeted resequencing data from tumor specimens and high coverage whole-genome sequencing data from the human NIST standard NA12878. Thus, we anticipate ScanIndel will improve indel analysis in both clinical and research settings. ScanIndel is implemented in Python, and is freely available for academic use at https://github.com/cauyrd/ScanIndel.

  8. RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

    PubMed Central

    Munger, Steven C.; Raghupathy, Narayanan; Choi, Kwangbom; Simons, Allen K.; Gatti, Daniel M.; Hinerfeld, Douglas A.; Svenson, Karen L.; Keller, Mark P.; Attie, Alan D.; Hibbs, Matthew A.; Graber, Joel H.; Chesler, Elissa J.; Churchill, Gary A.

    2014-01-01

    Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of short sequence reads to a common reference genome or transcriptome. Genetic variants that distinguish individual genomes from the reference sequence can cause reads to be misaligned, resulting in biased estimates of transcript abundance. Fine-tuning of read alignment algorithms does not correct this problem. We have developed Seqnature software to construct individualized diploid genomes and transcriptomes for multiparent populations and have implemented a complete analysis pipeline that incorporates other existing software tools. We demonstrate in simulated and real data sets that alignment to individualized transcriptomes increases read mapping accuracy, improves estimation of transcript abundance, and enables the direct estimation of allele-specific expression. Moreover, when applied to expression QTL mapping we find that our individualized alignment strategy corrects false-positive linkage signals and unmasks hidden associations. We recommend the use of individualized diploid genomes over reference sequence alignment for all applications of high-throughput sequencing technology in genetically diverse populations. PMID:25236449

  9. Can a semi-automated surface matching and principal axis-based algorithm accurately quantify femoral shaft fracture alignment in six degrees of freedom?

    PubMed

    Crookshank, Meghan C; Beek, Maarten; Singh, Devin; Schemitsch, Emil H; Whyne, Cari M

    2013-07-01

    Accurate alignment of femoral shaft fractures treated with intramedullary nailing remains a challenge for orthopaedic surgeons. The aim of this study is to develop and validate a cone-beam CT-based, semi-automated algorithm to quantify the malalignment in six degrees of freedom (6DOF) using a surface matching and principal axes-based approach. Complex comminuted diaphyseal fractures were created in nine cadaveric femora and cone-beam CT images were acquired (27 cases total). Scans were cropped and segmented using intensity-based thresholding, producing superior, inferior and comminution volumes. Cylinders were fit to estimate the long axes of the superior and inferior fragments. The angle and distance between the two cylindrical axes were calculated to determine flexion/extension and varus/valgus angulation and medial/lateral and anterior/posterior translations, respectively. Both surfaces were unwrapped about the cylindrical axes. Three methods of matching the unwrapped surface for determination of periaxial rotation were compared based on minimizing the distance between features. The calculated corrections were compared to the input malalignment conditions. All 6DOF were calculated to within current clinical tolerances for all but two cases. This algorithm yielded accurate quantification of malalignment of femoral shaft fractures for fracture gaps up to 60 mm, based on a single CBCT image of the fractured limb. Copyright © 2012 IPEM. Published by Elsevier Ltd. All rights reserved.

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

    PubMed

    Schwessinger, Benjamin; Rathjen, John P

    2017-01-01

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

  11. Relationship between reading and long-term storage and retrieval (Glr) in college students.

    PubMed

    Avitia, Maria Jesus; Kaufman, Alan S; Bray, Melissa; Kaufman, James C

    2017-09-21

    The purpose of this study was to (a) identify the relationship between specific types of reading ability, different forms of learning, and long-term memory and retrieval (Glr); and then (b) to determine the degree to which self-assessed reading ability and a Glr measure could predict objective reading ability. College students were administered three different reading assessments from the Kaufman Test of Educational Achievement, Second Edition (KTEA-II): word reading, reading comprehension, and nonsense word decoding. They were also given two pairs of Glr subtests that consisted of immediate and delayed versions from the Kaufman Assessment Battery for Children, Second Edition (KABC-II). One set was embedded within context, whereas the other was not. Results showed that although overall reading ability and reading comprehension correlated the highest with Glr measures that were embedded in context, word reading, and nonsense word decoding were correlated the highest with delayed measures of Glr. Second, the self-assessment accounted for 23% of the variability in overall reading ability. Not only do these results show the strength of the relationship between Glr and reading, but also the ability to use these measures along with self-assessment to screen for reading disabilities.

  12. 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.

  13. 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…

  14. Alignment and qualification of the Gaia telescope using a Shack-Hartmann sensor

    NASA Astrophysics Data System (ADS)

    Dovillaire, G.; Pierot, D.

    2017-09-01

    Since almost 20 years, Imagine Optic develops, manufactures and offers to its worldwide customers reliable and accurate wavefront sensors and adaptive optics solutions. Long term collaboration between Imagine Optic and Airbus Defence and Space has been initiated on the Herschel program. More recently, a similar technology has been used to align and qualify the GAIA telescope.

  15. Multispectral optical telescope alignment testing for a cryogenic space environment

    NASA Astrophysics Data System (ADS)

    Newswander, Trent; Hooser, Preston; Champagne, James

    2016-09-01

    Multispectral space telescopes with visible to long wave infrared spectral bands provide difficult alignment challenges. The visible channels require precision in alignment and stability to provide good image quality in short wavelengths. This is most often accomplished by choosing materials with near zero thermal expansion glass or ceramic mirrors metered with carbon fiber reinforced polymer (CFRP) that are designed to have a matching thermal expansion. The IR channels are less sensitive to alignment but they often require cryogenic cooling for improved sensitivity with the reduced radiometric background. Finding efficient solutions to this difficult problem of maintaining good visible image quality at cryogenic temperatures has been explored with the building and testing of a telescope simulator. The telescope simulator is an onaxis ZERODUR® mirror, CFRP metered set of optics. Testing has been completed to accurately measure telescope optical element alignment and mirror figure changes in a cryogenic space simulated environment. Measured alignment error and mirror figure error test results are reported with a discussion of their impact on system optical performance.

  16. Long-Term Experience with Chinese Language Shapes the Fusiform Asymmetry of English Reading

    PubMed Central

    Mei, Leilei; Xue, Gui; Lu, Zhong-Lin; Chen, Chuansheng; Wei, Miao; He, Qinghua; Dong, Qi

    2015-01-01

    Previous studies have suggested differential engagement of the bilateral fusiform gyrus in the processing of Chinese and English. The present study tested the possibility that long-term experience with Chinese language affects the fusiform laterality of English reading by comparing three samples: Chinese speakers, English speakers with Chinese experience, and English speakers without Chinese experience. We found that, when reading words in their respective native language, Chinese and English speakers without Chinese experience differed in functional laterality of the posterior fusiform region (right laterality for Chinese speakers, but left laterality for English speakers). More importantly, compared with English speakers without Chinese experience, English speakers with Chinese experience showed more recruitment of the right posterior fusiform cortex for English words and pseudowords, which is similar to how Chinese speakers processed Chinese. These results suggest that long-term experience with Chinese shapes the fusiform laterality of English reading and have important implications for our understanding of the cross-language influences in terms of neural organization and of the functions of different fusiform subregions in reading. PMID:25598049

  17. Aligning Plasma-Arc Welding Oscillations

    NASA Technical Reports Server (NTRS)

    Norris, Jeff; Fairley, Mike

    1989-01-01

    Tool aids in alignment of oscillator probe on variable-polarity plasma-arc welding torch. Probe magnetically pulls arc from side to side as it moves along joint. Tensile strength of joint depends on alignment of weld bead and on alignment of probe. Operator installs new tool on front of torch body, levels it with built-in bubble glass, inserts probe in slot on tool, and locks probe in place. Procedure faster and easier and resulting alignment more accurate and repeatable.

  18. Long-lasting improvement following tDCS treatment combined with a training for reading in children and adolescents with dyslexia.

    PubMed

    Costanzo, Floriana; Rossi, Serena; Varuzza, Cristiana; Varvara, Pamela; Vicari, Stefano; Menghini, Deny

    2018-03-14

    Noninvasive brain stimulation transiently modulates reading ability in individuals with dyslexia by facilitating the underactive neural pathways in them. However, its long-term effects have not been determined. This study confirmed the ameliorative effects of multiple sessions of transcranial direct current stimulation (tDCS) combined with a training for reading on the reading abilities of children and adolescents with dyslexia and examined whether they are long-lasting. Twenty-six children and adolescents with dyslexia received 3 20-min sessions per week for 6 weeks (18 sessions) of left anodal/right cathodal tDCS, set to 1 mA, over the parieto-temporal regions, combined with training for reading. The participants were randomly assigned to receive active or sham treatment. Reading measures (text, high- and low-frequency words, non-words) were recorded before and immediately after the treatment and 1 and 6 months later. The long-term tolerability to tDCS was also evaluated. The active group received long-lasting benefits in reading. Specifically, the non-word reading efficiency index improved at every time point, as did the low-frequency word reading efficiency index at 1 and 6 months after the end of the treatment. No differences emerged in the sham group. No long-term adverse effects were documented. This study provides evidence of persistent improvements in reading in children and adolescents with dyslexia, constituting a new rehabilitative approach for the remediation of dyslexia. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. Radiologic analysis of hindfoot alignment: Comparison of Méary, long axial, and hindfoot alignment views.

    PubMed

    Neri, T; Barthelemy, R; Tourné, Y

    2017-12-01

    Among radiographic views available for assessing hindfoot alignment, the antero-posterior weight-bearing view with metal cerclage of the hindfoot (Méary view) is the most widely used in France. Internationally, the long axial view (LAV) and hindfoot alignment view (HAV) are used also. The objective of this study was to compare the reliability of these three views. The Méary view with cerclage of the hindfoot is as reliable as the LAV and HAV for assessing hindfoot alignment. All three views were obtained in each of 22 prospectively included patients. Intra-observer and inter-observer reliabilities were assessed by having two observers collect the radiographic measurements then computing the intra-class correlation coefficients (ICCs). The intra-observer and inter-observer ICCs were 0.956 and 0.988 with the Méary view, 0.990 and 0.765 with the HAV, and 0.997 and 0.991 with the LAV, respectively. Correlations were far stronger between the LAV and HAV than between each of these and the Méary view. Compared to the LAV and HAV, the Méary view indicated a greater degree of hindfoot valgus. Intra-observer reliability was excellent with both the LAV and HAV, whereas inter-observer reliability was better with the LAV. Excellent reliability was also obtained with the Méary view. Combining the Méary view to obtain a radiographic image of the clinical deformity with the LAV to measure the angular deviation of the hindfoot axis may be useful when assessing hindfoot malalignment. A comparison of the three views in a larger population is needed before clinical recommendations can be made. II, prospective study. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  20. GOSSIP: a method for fast and accurate global alignment of protein structures.

    PubMed

    Kifer, I; Nussinov, R; Wolfson, H J

    2011-04-01

    The database of known protein structures (PDB) is increasing rapidly. This results in a growing need for methods that can cope with the vast amount of structural data. To analyze the accumulating data, it is important to have a fast tool for identifying similar structures and clustering them by structural resemblance. Several excellent tools have been developed for the comparison of protein structures. These usually address the task of local structure alignment, an important yet computationally intensive problem due to its complexity. It is difficult to use such tools for comparing a large number of structures to each other at a reasonable time. Here we present GOSSIP, a novel method for a global all-against-all alignment of any set of protein structures. The method detects similarities between structures down to a certain cutoff (a parameter of the program), hence allowing it to detect similar structures at a much higher speed than local structure alignment methods. GOSSIP compares many structures in times which are several orders of magnitude faster than well-known available structure alignment servers, and it is also faster than a database scanning method. We evaluate GOSSIP both on a dataset of short structural fragments and on two large sequence-diverse structural benchmarks. Our conclusions are that for a threshold of 0.6 and above, the speed of GOSSIP is obtained with no compromise of the accuracy of the alignments or of the number of detected global similarities. A server, as well as an executable for download, are available at http://bioinfo3d.cs.tau.ac.il/gossip/.

  1. Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

    PubMed

    Robinson, Kelly M; Hawkins, Aziah S; Santana-Cruz, Ivette; Adkins, Ricky S; Shetty, Amol C; Nagaraj, Sushma; Sadzewicz, Lisa; Tallon, Luke J; Rasko, David A; Fraser, Claire M; Mahurkar, Anup; Silva, Joana C; Dunning Hotopp, Julie C

    2017-09-01

    As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i.e. Plasmodium falciparum or Brugia malayi ) and one minority member (i.e. human or the Wolbachia endosymbiont w Bm) of the sequence data. Increasing bwa-mem seed length from the default value reduced the number of read pairs from the majority sequence member that incorrectly aligned to the reference genome of the minority sequence member. Combining both source genomes into a single reference genome increased the specificity of mapping, while also reducing the central processing unit (CPU) time. In Plasmodium , at a seed length of 18 nt, 24.1 % of reads mapped to the human genome using 1.7±0.1 CPU hours, while 83.6 % of reads mapped to the Plasmodium genome using 0.2±0.0 CPU hours (total: 107.7 % reads mapping; in 1.9±0.1 CPU hours). In contrast, 97.1 % of the reads mapped to a combined Plasmodium- human reference in only 0.7±0.0 CPU hours. Overall, the results suggest that combining all references into a single reference database and using a 23 nt seed length reduces the computational time, while maximizing specificity. Similar results were found for simulated sequence reads from a mock metagenomic data set. We found similar improvements to computation time in a publicly available human-only data set.

  2. Assessing Lower Limb Alignment: Comparison of Standard Knee Xray vs Long Leg View.

    PubMed

    Zampogna, Biagio; Vasta, Sebastiano; Amendola, Annunziato; Uribe-Echevarria Marbach, Bastian; Gao, Yubo; Papalia, Rocco; Denaro, Vincenzo

    2015-01-01

    High tibial osteotomy (HTO) is a well-established and commonly utilized technique in medial knee osteoarthritis secondary to varus malalignment. Accurate measurement of the preoperative limb alignment, and the amount of correction required are essential when planning limb realignment surgery. The hip-knee-ankle angle (HKA) measured on a full length weightbearing (FLWB) X-ray in the standing position is considered the gold standard, since it allows for reliable and accurate measurement of the mechanical axis of the whole lower extremity. In general practice, alignment is often evaluated on standard anteroposterior weightbearing (APWB) X-rays, as the angle between the femur and tibial anatomic axis (TFa). It is, therefore, of value to establish if measuring the anatomical axis from limited APWB is an effective measure of knee alignment especially in patients undergoing osteotomy about the knee. Three independent observers measured preoperative and postoperative FTa with standard method (FTa1) and with circles method (FTa2) on APWB X-ray and the HKA on FLWB X-ray at three different time-points separated by a two-week period. Intra-observer and inter-observer reliabilities and the comparison and relationship between anatomical and mechanical alignment were calculated. Intra- and interclass coefficients for all the three methods indicated excellent reliability, having all the values above 0.80. Using the mean of paired t-student test, the comparison of HKA versus TFa1 and TFa2 showed a statistically significant difference (p<.0001) both for the pre-operative and post-operative sets of values. The correlation between the HKA and FTal was found poor for the preoperative set (R=0.26) and fair for the postoperative one (R=0.53), while the new circles method showed a higher correlation in both the preoperative (R=0.71) and postoperative sets (R=0.79). Intra-observer reliability was high for HKA, FTal and FTa2 on APWB x-rays in the pre- and post-operative setting. Inter

  3. Assessing Lower Limb Alignment: Comparison of Standard Knee Xray vs Long Leg View

    PubMed Central

    Zampogna, Biagio; Vasta, Sebastiano; Amendola, Annunziato; Uribe-Echevarria Marbach, Bastian; Gao, Yubo; Papalia, Rocco; Denaro, Vincenzo

    2015-01-01

    Background High tibial osteotomy (HTO) is a well-established and commonly utilized technique in medial knee osteoarthritis secondary to varus malalignment. Accurate measurement of the preoperative limb alignment, and the amount of correction required are essential when planning limb realignment surgery. The hip-knee-ankle angle (HKA) measured on a full length weightbearing (FLWB) X-ray in the standing position is considered the gold standard, since it allows for reliable and accurate measurement of the mechanical axis of the whole lower extremity. In general practice, alignment is often evaluated on standard anteroposterior weightbearing (APWB) X-rays, as the angle between the femur and tibial anatomic axis (TFa). It is, therefore, of value to establish if measuring the anatomical axis from limited APWB is an effective measure of knee alignment especially in patients undergoing osteotomy about the knee. Methods Three independent observers measured preoperative and postoperative FTa with standard method (FTa1) and with circles method (FTa2) on APWB X-ray and the HKA on FLWB X-ray at three different time-points separated by a two-week period. Intra-observer and inter-observer reliabilities and the comparison and relationship between anatomical and mechanical alignment were calculated. Results Intra- and interclass coefficients for all the three methods indicated excellent reliability, having all the values above 0.80. Using the mean of paired t-student test, the comparison of HKA versus TFa1 and TFa2 showed a statistically significant difference (p<.0001) both for the pre-operative and post-operative sets of values. The correlation between the HKA and FTal was found poor for the preoperative set (R=0.26) and fair for the postoperative one (R=0.53), while the new circles method showed a higher correlation in both the preoperative (R=0.71) and postoperative sets (R=0.79). Conclusions Intra-observer reliability was high for HKA, FTal and FTa2 on APWB x-rays in the pre

  4. 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.

  5. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

    PubMed

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong; Warnow, Tandy

    2015-05-01

    We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

  6. 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

  7. EST Reading Curriculum & Instruction: An Alignment Analysis

    ERIC Educational Resources Information Center

    Mohammed, Lubna Ali; Sidek, H. M.

    2015-01-01

    In order for a curriculum to achieve its goals, it is imperative that the curriculum is coherent at all levels. In order to determine the coherency of a curriculum, the alignment of its theoretical underpinning and the label of a curriculum is one of the aspects that can be examined. The purpose of the current study was to examine if the…

  8. 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…

  9. Empirical Validation of Reading Proficiency Guidelines

    ERIC Educational Resources Information Center

    Clifford, Ray; Cox, Troy L.

    2013-01-01

    The validation of ability scales describing multidimensional skills is always challenging, but not impossible. This study applies a multistage, criterion-referenced approach that uses a framework of aligned texts and reading tasks to explore the validity of the ACTFL and related reading proficiency guidelines. Rasch measurement and statistical…

  10. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    PubMed

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-08

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. 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.

  12. Fast single-pass alignment and variant calling using sequencing data

    USDA-ARS?s Scientific Manuscript database

    Sequencing research requires efficient computation. Few programs use already known information about DNA variants when aligning sequence data to the reference map. New program findmap.f90 reads the previous variant list before aligning sequence, calling variant alleles, and summing the allele counts...

  13. The Impact of Alignment Coaching on Christian Teachers' Worthy Performance

    ERIC Educational Resources Information Center

    Hines, Linda M.

    2010-01-01

    "The Impact of Alignment Coaching on Christian Teachers' Worthy Performance" uses Human Performance Technology and "teleonomics" (Gilbert 2007) to document several intersecting vantage points as one performance improvement system of alignment coaching (AC). Coaching relationships and accomplishments of consistently (daily) reading the Bible,…

  14. Swine transcriptome characterization by combined Iso-Seq and RNA-seq for annotating the emerging long read-based reference genome

    USDA-ARS?s Scientific Manuscript database

    PacBio long-read sequencing technology is increasingly popular in genome sequence assembly and transcriptome cataloguing. Recently, a new-generation pig reference genome was assembled based on long reads from this technology. To finely annotate this genome assembly, transcriptomes of nine tissues fr...

  15. Boiler: lossy compression of RNA-seq alignments using coverage vectors

    PubMed Central

    Pritt, Jacob; Langmead, Ben

    2016-01-01

    We describe Boiler, a new software tool for compressing and querying large collections of RNA-seq alignments. Boiler discards most per-read data, keeping only a genomic coverage vector plus a few empirical distributions summarizing the alignments. Since most per-read data is discarded, storage footprint is often much smaller than that achieved by other compression tools. Despite this, the most relevant per-read data can be recovered; we show that Boiler compression has only a slight negative impact on results given by downstream tools for isoform assembly and quantification. Boiler also allows the user to pose fast and useful queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler. PMID:27298258

  16. 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

  17. B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC.

    PubMed

    Cui, Yingbo; Liao, Xiangke; Zhu, Xiaoqian; Wang, Bingqiang; Peng, Shaoliang

    2016-03-01

    Sequence alignment is the central process for sequence analysis, where mapping raw sequencing data to reference genome. The large amount of data generated by NGS is far beyond the process capabilities of existing alignment tools. Consequently, sequence alignment becomes the bottleneck of sequence analysis. Intensive computing power is required to address this challenge. Intel recently announced the MIC coprocessor, which can provide massive computing power. The Tianhe-2 is the world's fastest supercomputer now equipped with three MIC coprocessors each compute node. A key feature of sequence alignment is that different reads are independent. Considering this property, we proposed a MIC-oriented three-level parallelization strategy to speed up BWA, a widely used sequence alignment tool, and developed our ultrafast parallel sequence aligner: B-MIC. B-MIC contains three levels of parallelization: firstly, parallelization of data IO and reads alignment by a three-stage parallel pipeline; secondly, parallelization enabled by MIC coprocessor technology; thirdly, inter-node parallelization implemented by MPI. In this paper, we demonstrate that B-MIC outperforms BWA by a combination of those techniques using Inspur NF5280M server and the Tianhe-2 supercomputer. To the best of our knowledge, B-MIC is the first sequence alignment tool to run on Intel MIC and it can achieve more than fivefold speedup over the original BWA while maintaining the alignment precision.

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

    PubMed

    Jayakumar, Vasanthan; Sakakibara, Yasubumi

    2017-11-03

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

  19. Developmental long trace profiler using optimally aligned mirror based pentaprism

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

    Barber, Samuel K; Morrison, Gregory Y.; Yashchuk, Valeriy V.

    2010-07-21

    A low-budget surface slope measuring instrument, the Developmental Long Trace Profiler (DLTP), was recently brought into operation at the Advanced Light Source Optical Metrology Laboratory [Nucl. Instr. and Meth. A 616, 212-223 (2010)]. The instrument is based on a precisely calibrated autocollimator and a movable pentaprism. The capability of the DLTP to achieve sub-microradian surface slope metrology has been verified via cross-comparison measurements with other high-performance slope measuring instruments when measuring the same high-quality test optics. In the present work, a further improvement of the DLTP is achieved by replacing the existing bulk pentaprism with a specially designed mirror basedmore » pentaprism. A mirror based pentaprism offers the possibility to eliminate systematic errors introduced by inhomogeneity of the optical material and fabrication imperfections of a bulk pentaprism. We provide the details of the mirror based pentaprism design and describe an original experimental procedure for precision mutual alignment of the mirrors. The algorithm of the alignment procedure and its efficiency are verified with rigorous ray tracing simulations. Results of measurements of a spherically curved test mirror and a flat test mirror using the original bulk pentaprism are compared with measurements using the new mirror based pentaprism, demonstrating the improved performance.« less

  20. Matching Interventions to Reading Needs: A Case for Differentiation

    ERIC Educational Resources Information Center

    Jones, Jill S.; Conradi, Kristin; Amendum, Steven J.

    2016-01-01

    The purpose of this article is to highlight the importance of providing reading interventions that are differentiated and aligned with an individual student's most foundational reading skill need. The authors present profiles of different readers and suggest three principal areas for support: decoding words, reading at an appropriate rate, and…

  1. Odyssey Reading. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2012

    2012-01-01

    "Odyssey Reading," published by CompassLearning[R], is a web-based K-12 reading/language arts program designed to allow for instructional differentiation and data-driven decision making. The online program includes electronic curricula and materials for individual or small-group work, assessments aligned with state curriculum standards,…

  2. 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…

  3. Simulation-based comprehensive benchmarking of RNA-seq aligners

    PubMed Central

    Baruzzo, Giacomo; Hayer, Katharina E; Kim, Eun Ji; Di Camillo, Barbara; FitzGerald, Garret A; Grant, Gregory R

    2018-01-01

    Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated. The most widely cited tool underperforms for most metrics, particularly when using default settings. PMID:27941783

  4. Boiler: lossy compression of RNA-seq alignments using coverage vectors.

    PubMed

    Pritt, Jacob; Langmead, Ben

    2016-09-19

    We describe Boiler, a new software tool for compressing and querying large collections of RNA-seq alignments. Boiler discards most per-read data, keeping only a genomic coverage vector plus a few empirical distributions summarizing the alignments. Since most per-read data is discarded, storage footprint is often much smaller than that achieved by other compression tools. Despite this, the most relevant per-read data can be recovered; we show that Boiler compression has only a slight negative impact on results given by downstream tools for isoform assembly and quantification. Boiler also allows the user to pose fast and useful queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Alpha Kappa Alpha Sorority's Reading Improvement Program for Minorities.

    ERIC Educational Resources Information Center

    Marable, June Morehead

    This document discusses the founding and establishment of Alpha Kappa Alpha Sorority's reading experience pilot project. The efforts of this project were aligned with those of Right to Read and Reading Is Fundamental (RIF). Because of the response from parents and children, plans are being made to increase present operations within the next…

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

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

    White, Richard Allen; Bottos, Eric M.; Roy Chowdhury, Taniya

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

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

    PubMed Central

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

    2016-01-01

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

  8. Alignment method for solar collector arrays

    DOEpatents

    Driver, Jr., Richard B

    2012-10-23

    The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

  9. GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

    PubMed

    Kim, Jeremie S; Senol Cali, Damla; Xin, Hongyi; Lee, Donghyuk; Ghose, Saugata; Alser, Mohammed; Hassan, Hasan; Ergin, Oguz; Alkan, Can; Mutlu, Onur

    2018-05-09

    Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read mappers 1) quickly generate possible mapping locations for seeds (i.e., smaller segments) within each read, 2) extract reference sequences at each of the mapping locations, and 3) check similarity between each read and its associated reference sequences with a computationally-expensive algorithm (i.e., sequence alignment) to determine the origin of the read. A seed location filter comes into play before alignment, discarding seed locations that alignment would deem a poor match. The ideal seed location filter would discard all poor match locations prior to alignment such that there is no wasted computation on unnecessary alignments. We propose a novel seed location filtering algorithm, GRIM-Filter, optimized to exploit 3D-stacked memory systems that integrate computation within a logic layer stacked under memory layers, to perform processing-in-memory (PIM). GRIM-Filter quickly filters seed locations by 1) introducing a new representation of coarse-grained segments of the reference genome, and 2) using massively-parallel in-memory operations to identify read presence within each coarse-grained segment. Our evaluations show that for a sequence alignment error tolerance of 0.05, GRIM-Filter 1) reduces the false negative rate of filtering by 5.59x-6.41x, and 2) provides an end-to-end read mapper speedup of 1.81x-3.65x, compared to a state-of-the-art read mapper employing the best previous seed location filtering algorithm. GRIM-Filter exploits 3D-stacked memory, which enables the efficient use of processing-in-memory, to overcome the memory bandwidth bottleneck in seed location filtering. We show that GRIM-Filter significantly improves the performance of a state-of-the-art read mapper. GRIM-Filter is a universal seed location filter that can be

  10. Node fingerprinting: an efficient heuristic for aligning biological networks.

    PubMed

    Radu, Alex; Charleston, Michael

    2014-10-01

    With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

  11. Cellular self-organization by autocatalytic alignment feedback

    PubMed Central

    Junkin, Michael; Leung, Siu Ling; Whitman, Samantha; Gregorio, Carol C.; Wong, Pak Kin

    2011-01-01

    Myoblasts aggregate, differentiate and fuse to form skeletal muscle during both embryogenesis and tissue regeneration. For proper muscle function, long-range self-organization of myoblasts is required to create organized muscle architecture globally aligned to neighboring tissue. However, how the cells process geometric information over distances considerably longer than individual cells to self-organize into well-ordered, aligned and multinucleated myofibers remains a central question in developmental biology and regenerative medicine. Using plasma lithography micropatterning to create spatial cues for cell guidance, we show a physical mechanism by which orientation information can propagate for a long distance from a geometric boundary to guide development of muscle tissue. This long-range alignment occurs only in differentiating myoblasts, but not in non-fusing myoblasts perturbed by microfluidic disturbances or other non-fusing cell types. Computational cellular automata analysis of the spatiotemporal evolution of the self-organization process reveals that myogenic fusion in conjunction with rotational inertia functions in a self-reinforcing manner to enhance long-range propagation of alignment information. With this autocatalytic alignment feedback, well-ordered alignment of muscle could reinforce existing orientations and help promote proper arrangement with neighboring tissue and overall organization. Such physical self-enhancement might represent a fundamental mechanism for long-range pattern formation during tissue morphogenesis. PMID:22193956

  12. Automatic joint alignment measurements in pre- and post-operative long leg standing radiographs.

    PubMed

    Goossen, A; Weber, G M; Dries, S P M

    2012-01-01

    For diagnosis or treatment assessment of knee joint osteoarthritis it is required to measure bone morphometry from radiographic images. We propose a method for automatic measurement of joint alignment from pre-operative as well as post-operative radiographs. In a two step approach we first detect and segment any implants or other artificial objects within the image. We exploit physical characteristics and avoid prior shape information to cope with the vast amount of implant types. Subsequently, we exploit the implant delineations to adapt the initialization and adaptation phase of a dedicated bone segmentation scheme using deformable template models. Implant and bone contours are fused to derive the final joint segmentation and thus the alignment measurements. We evaluated our method on clinical long leg radiographs and compared both the initialization rate, corresponding to the number of images successfully processed by the proposed algorithm, and the accuracy of the alignment measurement. Ground truth has been generated by an experienced orthopedic surgeon. For comparison a second reader reevaluated the measurements. Experiments on two sets of 70 and 120 digital radiographs show that 92% of the joints could be processed automatically and the derived measurements of the automatic method are comparable to a human reader for pre-operative as well as post-operative images with a typical error of 0.7° and correlations of r = 0.82 to r = 0.99 with the ground truth. The proposed method allows deriving objective measures of joint alignment from clinical radiographs. Its accuracy and precision are on par with a human reader for all evaluated measurements.

  13. PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

    PubMed Central

    Mirarab, Siavash; Nguyen, Nam; Guo, Sheng; Wang, Li-San; Kim, Junhyong

    2015-01-01

    Abstract We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate—slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory. PMID:25549288

  14. What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual

    USDA-ARS?s Scientific Manuscript database

    BACKGROUND: Next-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain u...

  15. Identification of genomic indels and structural variations using split reads

    PubMed Central

    2011-01-01

    Background Recent studies have demonstrated the genetic significance of insertions, deletions, and other more complex structural variants (SVs) in the human population. With the development of the next-generation sequencing technologies, high-throughput surveys of SVs on the whole-genome level have become possible. Here we present split-read identification, calibrated (SRiC), a sequence-based method for SV detection. Results We start by mapping each read to the reference genome in standard fashion using gapped alignment. Then to identify SVs, we score each of the many initial mappings with an assessment strategy designed to take into account both sequencing and alignment errors (e.g. scoring more highly events gapped in the center of a read). All current SV calling methods have multilevel biases in their identifications due to both experimental and computational limitations (e.g. calling more deletions than insertions). A key aspect of our approach is that we calibrate all our calls against synthetic data sets generated from simulations of high-throughput sequencing (with realistic error models). This allows us to calculate sensitivity and the positive predictive value under different parameter-value scenarios and for different classes of events (e.g. long deletions vs. short insertions). We run our calculations on representative data from the 1000 Genomes Project. Coupling the observed numbers of events on chromosome 1 with the calibrations gleaned from the simulations (for different length events) allows us to construct a relatively unbiased estimate for the total number of SVs in the human genome across a wide range of length scales. We estimate in particular that an individual genome contains ~670,000 indels/SVs. Conclusions Compared with the existing read-depth and read-pair approaches for SV identification, our method can pinpoint the exact breakpoints of SV events, reveal the actual sequence content of insertions, and cover the whole size spectrum for

  16. An improved image alignment procedure for high-resolution transmission electron microscopy.

    PubMed

    Lin, Fang; Liu, Yan; Zhong, Xiaoyan; Chen, Jianghua

    2010-06-01

    Image alignment is essential for image processing methods such as through-focus exit-wavefunction reconstruction and image averaging in high-resolution transmission electron microscopy. Relative image displacements exist in any experimentally recorded image series due to the specimen drifts and image shifts, hence image alignment for correcting the image displacements has to be done prior to any further image processing. The image displacement between two successive images is determined by the correlation function of the two relatively shifted images. Here it is shown that more accurate image alignment can be achieved by using an appropriate aperture to filter the high-frequency components of the images being aligned, especially for a crystalline specimen with little non-periodic information. For the image series of crystalline specimens with little amorphous, the radius of the filter aperture should be as small as possible, so long as it covers the innermost lattice reflections. Testing with an experimental through-focus series of Si[110] images, the accuracies of image alignment with different correlation functions are compared with respect to the error functions in through-focus exit-wavefunction reconstruction based on the maximum-likelihood method. Testing with image averaging over noisy experimental images from graphene and carbon-nanotube samples, clear and sharp crystal lattice fringes are recovered after applying optimal image alignment. Copyright 2010 Elsevier Ltd. All rights reserved.

  17. Efficient alignment-free DNA barcode analytics.

    PubMed

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-11-10

    In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding.

  18. Efficient alignment-free DNA barcode analytics

    PubMed Central

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-01-01

    Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. Results New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Conclusion Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding. PMID:19900305

  19. 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.

  20. A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

    PubMed

    Rajan, Vaibhav

    2013-03-01

    Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

  1. Can CT-based patient-matched instrumentation achieve consistent rotational alignment in knee arthroplasty?

    PubMed

    Tibesku, C O; Innocenti, B; Wong, P; Salehi, A; Labey, L

    2012-02-01

    Long-term success of contemporary total knee replacements relies to a large extent on proper implant alignment. This study was undertaken to test whether specimen-matched cutting blocks based on computed axial tomography (CT) scans could provide accurate rotational alignment of the femoral component. CT scans of five fresh frozen full leg cadaver specimens, equipped with infrared reflective markers, were used to produce a specimen-matched femoral cutting block. Using those blocks, the bone cuts were made to implant a bi-compartmental femoral component. Rotational alignment of the components in the horizontal plane was determined using an optical measurement system and compared with all relevant rotational reference axes identified on the CT scans. Average rotational alignment for the bi-compartmental component in the horizontal plane was 1.9° (range 0°-6.3°; standard deviation 2.6°). One specimen that showed the highest deviation from the planned alignment also featured a completely degraded medial articular surface. The CT-based specimen-matched cutting blocks achieved good rotational alignment accuracy except for one specimen with badly damaged cartilage. In such cases, imaging techniques that visualize the cartilage layer might be more suitable to design cutting blocks, as they will provide a better fit and increased surface support.

  2. 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…

  3. [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.

  4. Application of probabilistic modelling for the uncertainty evaluation of alignment measurements of large accelerator magnets assemblies

    NASA Astrophysics Data System (ADS)

    Doytchinov, I.; Tonnellier, X.; Shore, P.; Nicquevert, B.; Modena, M.; Mainaud Durand, H.

    2018-05-01

    Micrometric assembly and alignment requirements for future particle accelerators, and especially large assemblies, create the need for accurate uncertainty budgeting of alignment measurements. Measurements and uncertainties have to be accurately stated and traceable, to international standards, for metre-long sized assemblies, in the range of tens of µm. Indeed, these hundreds of assemblies will be produced and measured by several suppliers around the world, and will have to be integrated into a single machine. As part of the PACMAN project at CERN, we proposed and studied a practical application of probabilistic modelling of task-specific alignment uncertainty by applying a simulation by constraints calibration method. Using this method, we calibrated our measurement model using available data from ISO standardised tests (10360 series) for the metrology equipment. We combined this model with reference measurements and analysis of the measured data to quantify the actual specific uncertainty of each alignment measurement procedure. Our methodology was successfully validated against a calibrated and traceable 3D artefact as part of an international inter-laboratory study. The validated models were used to study the expected alignment uncertainty and important sensitivity factors in measuring the shortest and longest of the compact linear collider study assemblies, 0.54 m and 2.1 m respectively. In both cases, the laboratory alignment uncertainty was within the targeted uncertainty budget of 12 µm (68% confidence level). It was found that the remaining uncertainty budget for any additional alignment error compensations, such as the thermal drift error due to variation in machine operation heat load conditions, must be within 8.9 µm and 9.8 µm (68% confidence level) respectively.

  5. Aligning for Innovation - Alignment Strategy to Drive Innovation

    NASA Technical Reports Server (NTRS)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James

    2010-01-01

    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  6. A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law.

    PubMed

    Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

    2015-11-01

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. A fast cross-validation method for alignment of electron tomography images based on Beer-Lambert law

    PubMed Central

    Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

    2015-01-01

    In electron tomography, accurate alignment of tilt series is an essential step in attaining high-resolution 3D reconstructions. Nevertheless, quantitative assessment of alignment quality has remained a challenging issue, even though many alignment methods have been reported. Here, we report a fast and accurate method, tomoAlignEval, based on the Beer-Lambert law, for the evaluation of alignment quality. Our method is able to globally estimate the alignment accuracy by measuring the goodness of log-linear relationship of the beam intensity attenuations at different tilt angles. Extensive tests with experimental data demonstrated its robust performance with stained and cryo samples. Our method is not only significantly faster but also more sensitive than measurements of tomogram resolution using Fourier shell correlation method (FSCe/o). From these tests, we also conclude that while current alignment methods are sufficiently accurate for stained samples, inaccurate alignments remain a major limitation for high resolution cryo-electron tomography. PMID:26455556

  8. Long-Read Single Molecule Sequencing to Resolve Tandem Gene Copies: The Mst77Y Region on the Drosophila melanogaster Y Chromosome

    PubMed Central

    Krsticevic, Flavia J.; Schrago, Carlos G.; Carvalho, A. Bernardo

    2015-01-01

    The autosomal gene Mst77F of Drosophila melanogaster is essential for male fertility. In 2010, Krsticevic et al. (Genetics 184: 295−307) found 18 Y-linked copies of Mst77F (“Mst77Y”), which collectively account for 20% of the functional Mst77F-like mRNA. The Mst77Y genes were severely misassembled in the then-available genome assembly and were identified by cloning and sequencing polymerase chain reaction products. The genomic structure of the Mst77Y region and the possible existence of additional copies remained unknown. The recent publication of two long-read assemblies of D. melanogaster prompted us to reinvestigate this challenging region of the Y chromosome. We found that the Illumina Synthetic Long Reads assembly failed in the Mst77Y region, most likely because of its tandem duplication structure. The PacBio MHAP assembly of the Mst77Y region seems to be very accurate, as revealed by comparisons with the previously found Mst77Y genes, a bacterial artificial chromosome sequence, and Illumina reads of the same strain. We found that the Mst77Y region spans 96 kb and originated from a 3.4-kb transposition from chromosome 3L to the Y chromosome, followed by tandem duplications inside the Y chromosome and invasion of transposable elements, which account for 48% of its length. Twelve of the 18 Mst77Y genes found in 2010 were confirmed in the PacBio assembly, the remaining six being polymerase chain reaction−induced artifacts. There are several identical copies of some Mst77Y genes, coincidentally bringing the total copy number to 18. Besides providing a detailed picture of the Mst77Y region, our results highlight the utility of PacBio technology in assembling difficult genomic regions such as tandemly repeated genes. PMID:25858959

  9. 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.

  10. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

    PubMed

    Tan, Yen Hock; Huang, He; Kihara, Daisuke

    2006-08-15

    Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.

  11. Middle School Reading Assessment: Measuring What Matters under a RTI Framework

    ERIC Educational Resources Information Center

    O'reilly, Tenaha; Sabatini, John; Bruce, Kelly; Pillarisetti, Srinivasa; McCormick, Carina

    2012-01-01

    This article presents a prototype reading assessment designed to measure and support component and integrated reading skills. The work is motivated by the need to create a new generation of assessments that are better aligned with the research in cognitive science, reading and learning. An assessment that synthesizes advances in these areas may…

  12. Simple chained guide trees give high-quality protein multiple sequence alignments

    PubMed Central

    Boyce, Kieran; Sievers, Fabian; Higgins, Desmond G.

    2014-01-01

    Guide trees are used to decide the order of sequence alignment in the progressive multiple sequence alignment heuristic. These guide trees are often the limiting factor in making large alignments, and considerable effort has been expended over the years in making these quickly or accurately. In this article we show that, at least for protein families with large numbers of sequences that can be benchmarked with known structures, simple chained guide trees give the most accurate alignments. These also happen to be the fastest and simplest guide trees to construct, computationally. Such guide trees have a striking effect on the accuracy of alignments produced by some of the most widely used alignment packages. There is a marked increase in accuracy and a marked decrease in computational time, once the number of sequences goes much above a few hundred. This is true, even if the order of sequences in the guide tree is random. PMID:25002495

  13. A novel specimen-specific methodology to optimise the alignment of long bones for experimental testing.

    PubMed

    Cheong, Vee San; Bull, Anthony M J

    2015-12-16

    The choice of coordinate system and alignment of bone will affect the quantification of mechanical properties obtained during in-vitro biomechanical testing. Where these are used in predictive models, such as finite element analysis, the fidelic description of these properties is paramount. Currently in bending and torsional tests, bones are aligned on a pre-defined fixed span based on the reference system marked out. However, large inter-specimen differences have been reported. This suggests a need for the development of a specimen-specific alignment system for use in experimental work. Eleven ovine tibiae were used in this study and three-dimensional surface meshes were constructed from micro-Computed Tomography scan images. A novel, semi-automated algorithm was developed and applied to the surface meshes to align the whole bone based on its calculated principal directions. Thereafter, the code isolates the optimised location and length of each bone for experimental testing. This resulted in a lowering of the second moment of area about the chosen bending axis in the central region. More importantly, the optimisation method decreases the irregularity of the shape of the cross-sectional slices as the unbiased estimate of the population coefficient of variation of the second moment of area decreased from a range of (0.210-0.435) to (0.145-0.317) in the longitudinal direction, indicating a minimisation of the product moment, which causes eccentric loading. Thus, this methodology serves as an important pre-step to align the bone for mechanical tests or simulation work, is optimised for each specimen, ensures repeatability, and is general enough to be applied to any long bone. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Tidal alignment of galaxies

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

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used "nonlinear alignment model," finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the "GI" term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

  15. Tidal alignment of galaxies

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

    Blazek, Jonathan; Vlah, Zvonimir; Seljak, Uroš, E-mail: blazek@berkeley.edu, E-mail: zvlah@stanford.edu, E-mail: useljak@berkeley.edu

    We develop an analytic model for galaxy intrinsic alignments (IA) based on the theory of tidal alignment. We calculate all relevant nonlinear corrections at one-loop order, including effects from nonlinear density evolution, galaxy biasing, and source density weighting. Contributions from density weighting are found to be particularly important and lead to bias dependence of the IA amplitude, even on large scales. This effect may be responsible for much of the luminosity dependence in IA observations. The increase in IA amplitude for more highly biased galaxies reflects their locations in regions with large tidal fields. We also consider the impact ofmore » smoothing the tidal field on halo scales. We compare the performance of this consistent nonlinear model in describing the observed alignment of luminous red galaxies with the linear model as well as the frequently used 'nonlinear alignment model,' finding a significant improvement on small and intermediate scales. We also show that the cross-correlation between density and IA (the 'GI' term) can be effectively separated into source alignment and source clustering, and we accurately model the observed alignment down to the one-halo regime using the tidal field from the fully nonlinear halo-matter cross correlation. Inside the one-halo regime, the average alignment of galaxies with density tracers no longer follows the tidal alignment prediction, likely reflecting nonlinear processes that must be considered when modeling IA on these scales. Finally, we discuss tidal alignment in the context of cosmic shear measurements.« less

  16. 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.

  17. Predicting reading outcomes with progress monitoring slopes among middle grade students

    PubMed Central

    Tolar, Tammy D.; Barth, Amy E.; Fletcher, Jack M.; Francis, David J.; Vaughn, Sharon

    2013-01-01

    Effective implementation of response-to-intervention (RTI) frameworks depends on efficient tools for monitoring progress. Evaluations of growth (i.e., slope) may be less efficient than evaluations of status at a single time point, especially if slopes do not add to predictions of outcomes over status. We examined progress monitoring slope validity for predicting reading outcomes among middle school students by evaluating latent growth models for different progress monitoring measure-outcome combinations. We used multi-group modeling to evaluate the effects of reading ability, reading intervention, and progress monitoring administration condition on slope validity. Slope validity was greatest when progress monitoring was aligned with the outcome (i.e., word reading fluency slope was used to predict fluency outcomes in contrast to comprehension outcomes), but effects varied across administration conditions (viz., repeated reading of familiar vs. novel passages). Unless the progress monitoring measure is highly aligned with outcome, slope may be an inefficient method for evaluating progress in an RTI context. PMID:24659899

  18. 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.

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

    PubMed

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

    2016-05-26

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

  20. Fast and accurate phylogeny reconstruction using filtered spaced-word matches

    PubMed Central

    Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

    2017-01-01

    Abstract Motivation: Word-based or ‘alignment-free’ algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. Results: We propose Filtered Spaced Word Matches (FSWM), a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don’t-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don’t-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don’t-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. Availability and Implementation: The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/ Contact: chris.leimeister@stud.uni-goettingen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28073754

  1. Fast and accurate phylogeny reconstruction using filtered spaced-word matches.

    PubMed

    Leimeister, Chris-André; Sohrabi-Jahromi, Salma; Morgenstern, Burkhard

    2017-04-01

    Word-based or 'alignment-free' algorithms are increasingly used for phylogeny reconstruction and genome comparison, since they are much faster than traditional approaches that are based on full sequence alignments. Existing alignment-free programs, however, are less accurate than alignment-based methods. We propose Filtered Spaced Word Matches (FSWM) , a fast alignment-free approach to estimate phylogenetic distances between large genomic sequences. For a pre-defined binary pattern of match and don't-care positions, FSWM rapidly identifies spaced word-matches between input sequences, i.e. gap-free local alignments with matching nucleotides at the match positions and with mismatches allowed at the don't-care positions. We then estimate the number of nucleotide substitutions per site by considering the nucleotides aligned at the don't-care positions of the identified spaced-word matches. To reduce the noise from spurious random matches, we use a filtering procedure where we discard all spaced-word matches for which the overall similarity between the aligned segments is below a threshold. We show that our approach can accurately estimate substitution frequencies even for distantly related sequences that cannot be analyzed with existing alignment-free methods; phylogenetic trees constructed with FSWM distances are of high quality. A program run on a pair of eukaryotic genomes of a few hundred Mb each takes a few minutes. The program source code for FSWM including a documentation, as well as the software that we used to generate artificial genome sequences are freely available at http://fswm.gobics.de/. chris.leimeister@stud.uni-goettingen.de. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

  2. 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.

  3. Solving the shrinkage-induced PDMS alignment registration issue in multilayer soft lithography

    NASA Astrophysics Data System (ADS)

    Moraes, Christopher; Sun, Yu; Simmons, Craig A.

    2009-06-01

    Shrinkage of polydimethylsiloxane (PDMS) complicates alignment registration between layers during multilayer soft lithography fabrication. This often hinders the development of large-scale microfabricated arrayed devices. Here we report a rapid method to construct large-area, multilayered devices with stringent alignment requirements. This technique, which exploits a previously unrecognized aspect of sandwich mold fabrication, improves device yield, enables highly accurate alignment over large areas of multilayered devices and does not require strict regulation of fabrication conditions or extensive calibration processes. To demonstrate this technique, a microfabricated Braille display was developed and characterized. High device yield and accurate alignment within 15 µm were achieved over three layers for an array of 108 Braille units spread over a 6.5 cm2 area, demonstrating the fabrication of well-aligned devices with greater ease and efficiency than previously possible.

  4. A novel approach to multiple sequence alignment using hadoop data grids.

    PubMed

    Sudha Sadasivam, G; Baktavatchalam, G

    2010-01-01

    Multiple alignment of protein sequences helps to determine evolutionary linkage and to predict molecular structures. The factors to be considered while aligning multiple sequences are speed and accuracy of alignment. Although dynamic programming algorithms produce accurate alignments, they are computation intensive. In this paper we propose a time efficient approach to sequence alignment that also produces quality alignment. The dynamic nature of the algorithm coupled with data and computational parallelism of hadoop data grids improves the accuracy and speed of sequence alignment. The principle of block splitting in hadoop coupled with its scalability facilitates alignment of very large sequences.

  5. A survey and evaluations of histogram-based statistics in alignment-free sequence comparison.

    PubMed

    Luczak, Brian B; James, Benjamin T; Girgis, Hani Z

    2017-12-06

    Since the dawn of the bioinformatics field, sequence alignment scores have been the main method for comparing sequences. However, alignment algorithms are quadratic, requiring long execution time. As alternatives, scientists have developed tens of alignment-free statistics for measuring the similarity between two sequences. We surveyed tens of alignment-free k-mer statistics. Additionally, we evaluated 33 statistics and multiplicative combinations between the statistics and/or their squares. These statistics are calculated on two k-mer histograms representing two sequences. Our evaluations using global alignment scores revealed that the majority of the statistics are sensitive and capable of finding similar sequences to a query sequence. Therefore, any of these statistics can filter out dissimilar sequences quickly. Further, we observed that multiplicative combinations of the statistics are highly correlated with the identity score. Furthermore, combinations involving sequence length difference or Earth Mover's distance, which takes the length difference into account, are always among the highest correlated paired statistics with identity scores. Similarly, paired statistics including length difference or Earth Mover's distance are among the best performers in finding the K-closest sequences. Interestingly, similar performance can be obtained using histograms of shorter words, resulting in reducing the memory requirement and increasing the speed remarkably. Moreover, we found that simple single statistics are sufficient for processing next-generation sequencing reads and for applications relying on local alignment. Finally, we measured the time requirement of each statistic. The survey and the evaluations will help scientists with identifying efficient alternatives to the costly alignment algorithm, saving thousands of computational hours. The source code of the benchmarking tool is available as Supplementary Materials. © The Author 2017. Published by Oxford

  6. Boresight alignment method for mobile laser scanning systems

    NASA Astrophysics Data System (ADS)

    Rieger, P.; Studnicka, N.; Pfennigbauer, M.; Zach, G.

    2010-06-01

    Mobile laser scanning (MLS) is the latest approach towards fast and cost-efficient acquisition of 3-dimensional spatial data. Accurately evaluating the boresight alignment in MLS systems is an obvious necessity. However, recent systems available on the market may lack of suitable and efficient practical workflows on how to perform this calibration. This paper discusses an innovative method for accurately determining the boresight alignment of MLS systems by employing 3D laser scanners. Scanning objects using a 3D laser scanner operating in a 2D line-scan mode from various different runs and scan directions provides valuable scan data for determining the angular alignment between inertial measurement unit and laser scanner. Field data is presented demonstrating the final accuracy of the calibration and the high quality of the point cloud acquired during an MLS campaign.

  7. CAFE: aCcelerated Alignment-FrEe sequence analysis.

    PubMed

    Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu

    2017-07-03

    Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

    PubMed

    Tong, Jing; Pei, Jimin; Grishin, Nick V

    2015-09-03

    Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

  9. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.

    PubMed

    Sela, Itamar; Ashkenazy, Haim; Katoh, Kazutaka; Pupko, Tal

    2015-07-01

    Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Implementing a Year-Long Reading While Listening Program for Japanese University EFL Students

    ERIC Educational Resources Information Center

    Gobel, Peter; Kano, Makimi

    2014-01-01

    This paper describes the implementation and evaluation of a year-long reading while listening (RWL) program run for university first-year students at a private university in Japan. The program was developed to give students practice in listening to a large volume of spoken English--a practice that the majority of Japanese students lack. The…

  11. 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.

  12. mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

    PubMed

    Dong, Runze; Pan, Shuo; Peng, Zhenling; Zhang, Yang; Yang, Jianyi

    2018-05-21

    With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop algorithms for efficient protein structure comparisons. In this article, we present the mTM-align server, which consists of two closely related modules: one for structure database search and the other for multiple structure alignment. The database search is speeded up based on a heuristic algorithm and a hierarchical organization of the structures in the database. The multiple structure alignment is performed using the recently developed algorithm mTM-align. Benchmark tests demonstrate that our algorithms outperform other peering methods for both modules, in terms of speed and accuracy. One of the unique features for the server is the interplay between database search and multiple structure alignment. The server provides service not only for performing fast database search, but also for making accurate multiple structure alignment with the structures found by the search. For the database search, it takes about 2-5 min for a structure of a medium size (∼300 residues). For the multiple structure alignment, it takes a few seconds for ∼10 structures of medium sizes. The server is freely available at: http://yanglab.nankai.edu.cn/mTM-align/.

  13. Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome

    PubMed Central

    Fu, Xinhua; Li, Jingjing; Tian, Yu; Quan, Weipeng; Zhang, Shu; Liu, Qian; Liang, Fan; Zhu, Xinlei; Zhang, Liangsheng

    2017-01-01

    Abstract Background Fireflies are a family of insects within the beetle order Coleoptera, or winged beetles, and they are one of the most well-known and loved insect species because of their bioluminescence. However, the firefly is in danger of extinction because of the massive destruction of its living environment. In order to improve the understanding of fireflies and protect them effectively, we sequenced the whole genome of the terrestrial firefly Pyrocoelia pectoralis. Findings Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883; Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8 Gb of long reads were generated and assembled into a 760.4-Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect Benchmarking Universal Single-Copy Orthologs. The k-mer analysis showed that this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3.04 Mb and the longest contig length of 13.69 Mb. Furthermore, 135 589 SSRs and 341 Mb of repeat sequences were detected. A total of 23 092 genes were predicted; 88.44% of genes were annotated with one or more related functions. Conclusions We assembled a high-quality firefly genome, which will not only provide insights into the conservation and biodiversity of fireflies, but also provide a wealth of information to study the mechanisms of their sexual communication, bio-luminescence, and evolution. PMID:29186486

  14. A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

    PubMed Central

    Eddy, Sean R.

    2008-01-01

    Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (λ) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty (“Forward” scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores (“Viterbi” scores) are Gumbel-distributed with constant λ = log 2, and the high scoring tail of Forward scores is exponential with the same constant λ. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments. PMID:18516236

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

    PubMed

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

    2018-03-14

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

  16. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (>11 kb), single molecule, real-time sequencing

    PubMed Central

    Vembar, Shruthi Sridhar; Seetin, Matthew; Lambert, Christine; Nattestad, Maria; Schatz, Michael C.; Baybayan, Primo; Scherf, Artur; Smith, Melissa Laird

    2016-01-01

    The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging due to the skewed AT-richness [∼80.6% (A + T)] of its genome and the lack of technology to assemble highly polymorphic subtelomeric regions that contain clonally variant, multigene virulence families (Ex: var and rifin). To address this, we performed amplification-free, single molecule, real-time sequencing of P. falciparum genomic DNA and generated reads of average length 12 kb, with 50% of the reads between 15.5 and 50 kb in length. Next, using the Hierarchical Genome Assembly Process, we assembled the P. falciparum genome de novo and successfully compiled all 14 nuclear chromosomes telomere-to-telomere. We also accurately resolved centromeres [∼90–99% (A + T)] and subtelomeric regions and identified large insertions and duplications that add extra var and rifin genes to the genome, along with smaller structural variants such as homopolymer tract expansions. Overall, we show that amplification-free, long-read sequencing combined with de novo assembly overcomes major challenges inherent to studying the P. falciparum genome. Indeed, this technology may not only identify the polymorphic and repetitive subtelomeric sequences of parasite populations from endemic areas but may also evaluate structural variation linked to virulence, drug resistance and disease transmission. PMID:27345719

  17. The Importance of Metacognitive Reading Strategy Awareness in Reading Comprehension

    ERIC Educational Resources Information Center

    Ahmadi, Mohammad Reza; Ismail, Hairul Nizam; Abdullah, Muhammad Kamarul Kabilan

    2013-01-01

    Metacognitive reading strategy awareness plays a significant role in reading comprehension and educational process. In spite of its importance, metacognitive strategy has long been the ignored skill in English language teaching, research, learning, and assessment. This lack of good metacognitive reading strategy skill is exacerbated by the central…

  18. LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening.

    PubMed

    Hu, Jun; Liu, Zi; Yu, Dong-Jun; Zhang, Yang

    2018-02-15

    Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening. We propose a novel ligand comparison algorithm, LS-align, to generate fast and accurate atom-level structural alignments of ligand molecules, through an iterative heuristic search of the target function that combines inter-atom distance with mass and chemical bond comparisons. LS-align contains two modules of Rigid-LS-align and Flexi-LS-align, designed for rigid-body and flexible alignments, respectively, where a ligand-size independent, statistics-based scoring function is developed to evaluate the similarity of ligand molecules relative to random ligand pairs. Large-scale benchmark tests are performed on prioritizing chemical ligands of 102 protein targets involving 1,415,871 candidate compounds from the DUD-E (Database of Useful Decoys: Enhanced) database, where LS-align achieves an average enrichment factor (EF) of 22.0 at the 1% cutoff and the AUC score of 0.75, which are significantly higher than other state-of-the-art methods. Detailed data analyses show that the advanced performance is mainly attributed to the design of the target function that combines structural and chemical information to enhance the sensitivity of recognizing subtle difference of ligand molecules and the introduces of structural flexibility that help capture the conformational changes induced by the ligand-receptor binding interactions. These data demonstrate a new avenue to improve the virtual screening efficiency through the development of sensitive ligand structural alignments. http://zhanglab.ccmb.med.umich.edu/LS-align

  19. Initial Alignment for SINS Based on Pseudo-Earth Frame in Polar Regions.

    PubMed

    Gao, Yanbin; Liu, Meng; Li, Guangchun; Guang, Xingxing

    2017-06-16

    An accurate initial alignment must be required for inertial navigation system (INS). The performance of initial alignment directly affects the following navigation accuracy. However, the rapid convergence of meridians and the small horizontalcomponent of rotation of Earth make the traditional alignment methods ineffective in polar regions. In this paper, from the perspective of global inertial navigation, a novel alignment algorithm based on pseudo-Earth frame and backward process is proposed to implement the initial alignment in polar regions. Considering that an accurate coarse alignment of azimuth is difficult to obtain in polar regions, the dynamic error modeling with large azimuth misalignment angle is designed. At the end of alignment phase, the strapdown attitude matrix relative to local geographic frame is obtained without influence of position errors and cumbersome computation. As a result, it would be more convenient to access the following polar navigation system. Then, it is also expected to unify the polar alignment algorithm as much as possible, thereby further unifying the form of external reference information. Finally, semi-physical static simulation and in-motion tests with large azimuth misalignment angle assisted by unscented Kalman filter (UKF) validate the effectiveness of the proposed method.

  20. Surface tension-driven self-alignment.

    PubMed

    Mastrangeli, Massimo; Zhou, Quan; Sariola, Veikko; Lambert, Pierre

    2017-01-04

    Surface tension-driven self-alignment is a passive and highly-accurate positioning mechanism that can significantly simplify and enhance the construction of advanced microsystems. After years of research, demonstrations and developments, the surface engineering and manufacturing technology enabling capillary self-alignment has achieved a degree of maturity conducive to a successful transfer to industrial practice. In view of this transition, a broad and accessible review of the physics, material science and applications of capillary self-alignment is presented. Statics and dynamics of the self-aligning action of deformed liquid bridges are explained through simple models and experiments, and all fundamental aspects of surface patterning and conditioning, of choice, deposition and confinement of liquids, and of component feeding and interconnection to substrates are illustrated through relevant applications in micro- and nanotechnology. A final outline addresses remaining challenges and additional extensions envisioned to further spread the use and fully exploit the potential of the technique.

  1. Computer Vision Syndrome for Non-Native Speaking Students: What Are the Problems with Online Reading?

    ERIC Educational Resources Information Center

    Tseng, Min-chen

    2014-01-01

    This study investigated the online reading performances and the level of visual fatigue from the perspectives of non-native speaking students (NNSs). Reading on a computer screen is more visually more demanding than reading printed text. Online reading requires frequent saccadic eye movements and imposes continuous focusing and alignment demand.…

  2. 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.

  3. Selecting Texts and Tasks for Content Area Reading and Learning

    ERIC Educational Resources Information Center

    Fisher, Douglas; Frey, Nancy

    2015-01-01

    For students to learn science, social studies, and technical subjects, their teachers have to engage them in meaningful lessons. As part of those lessons, students read informational texts. The selection of those texts is critical. Teachers can select texts worthy of attention and then align instruction and the post-reading tasks such that…

  4. Statistical Significance of Optical Map Alignments

    PubMed Central

    Sarkar, Deepayan; Goldstein, Steve; Schwartz, David C.

    2012-01-01

    Abstract The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities. PMID:22506568

  5. 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.

  6. Iterative refinement of structure-based sequence alignments by Seed Extension

    PubMed Central

    Kim, Changhoon; Tai, Chin-Hsien; Lee, Byungkook

    2009-01-01

    Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available, but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. Results RSE uses SE (Seed Extension) in its core, which is an algorithm that we reported recently for obtaining a sequence alignment from two superimposed structures. The RSE procedure was evaluated by comparing the correctly aligned fractions of residues before and after the refinement of the structure-based sequence alignments produced by popular programs. CE, DaliLite, FAST, LOCK2, MATRAS, MATT, TM-align, SHEBA and VAST were included in this analysis and the NCBI's CDD root node set was used as the reference alignments. RSE improved the average accuracy of sequence alignments for all programs tested when no shift error was allowed. The amount of improvement varied depending on the program. The average improvements were small for DaliLite and MATRAS but about 5% for CE and VAST. More substantial improvements have been seen in many individual cases. The additional computation times required for the refinements were negligible compared to the times taken by the structure alignment programs. Conclusion RSE is a computationally inexpensive way of improving the accuracy of a structure-based sequence alignment. It can be used as a standalone procedure following a regular structure-based sequence alignment or to replace the traditional

  7. Effects of a Year Long Supplemental Reading Intervention for Students with Reading Difficulties in Fourth Grade

    ERIC Educational Resources Information Center

    Wanzek, Jeanne; Petscher, Yaacov; Al Otaiba, Stephanie; Rivas, Brenna; Jones, Francesca; Kent, Shawn; Schatschneider, Christopher; Mehta, Paras

    2017-01-01

    Research examining effective reading interventions for students with reading difficulties in the upper elementary grades is limited relative to the information available for the early elementary grades. In the current study, we examined the effects of a multicomponent reading intervention for students with reading comprehension difficulties. We…

  8. Anisotropic piezoresistivity characteristics of aligned carbon nanotube-polymer nanocomposites

    NASA Astrophysics Data System (ADS)

    Sengezer, Engin C.; Seidel, Gary D.; Bodnar, Robert J.

    2017-09-01

    Dielectrophoresis under the application of AC electric fields is one of the primary fabrication techniques for obtaining aligned carbon nanotube (CNT)-polymer nanocomposites, and is used here to generate long range alignment of CNTs at the structural level. The degree of alignment of CNTs within this long range architecture is observed via polarized Raman spectroscopy so that its influence on the electrical conductivity and piezoresistive response in both the alignment and transverse to alignment directions can be assessed. Nanocomposite samples consisting of randomly oriented, well dispersed single-wall carbon nanotubes (SWCNTs) and of long range electric field aligned SWCNTs in a photopolymerizable monomer blend (urethane dimethacrylate and 1,6-hexanediol dimethacrylate) are quantitatively and qualitatively evaluated. Piezoresistive sensitivities in form of gauge factors were measured for randomly oriented, well dispersed specimens with 0.03, 0.1 and 0.5 wt% SWCNTs and compared with gauge factors in both the axial and transverse to SWCNT alignment directions for electric field aligned 0.03 wt% specimens under both quasi-static monotonic and cyclic tensile loading. Gauge factors in the axial direction were observed to be on the order of 2, while gauge factors in the transverse direction demonstrated a 5 fold increase with values on the order of 10 for aligned specimens. Based on Raman analysis, it is believed the higher sensitivity of the transverse direction is related to architectural evolution of misaligned bridging structures which connect alignment structures under load due to Poisson’s contraction.

  9. 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.

  10. Fiber optics welder having movable aligning mirror

    DOEpatents

    Higgins, Robert W.; Robichaud, Roger E.

    1981-01-01

    A system for welding fiber optic waveguides together. The ends of the two fibers to be joined together are accurately, collinearly aligned in a vertical orientation and subjected to a controlled, diffuse arc to effect welding and thermal conditioning. A front-surfaced mirror mounted at a 45.degree. angle to the optical axis of a stereomicroscope mounted for viewing the junction of the ends provides two orthogonal views of the interface during the alignment operation.

  11. SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly

    PubMed Central

    Wala, Jeremiah; Beroukhim, Rameen

    2017-01-01

    Abstract We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. Availability and Implementation: SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. Contact: jwala@broadinstitue.org; rameen@broadinstitute.org PMID:28011768

  12. Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

    PubMed Central

    Cheng, Bing; Furtado, Agnelo

    2017-01-01

    Abstract Polyploidization contributes to the complexity of gene expression, resulting in numerous related but different transcripts. This study explored the transcriptome diversity and complexity of the tetraploid Arabica coffee (Coffea arabica) bean. Long-read sequencing (LRS) by Pacbio Isoform sequencing (Iso-seq) was used to obtain full-length transcripts without the difficulty and uncertainty of assembly required for reads from short-read technologies. The tetraploid transcriptome was annotated and compared with data from the sub-genome progenitors. Caffeine and sucrose genes were targeted for case analysis. An isoform-level tetraploid coffee bean reference transcriptome with 95 995 distinct transcripts (average 3236 bp) was obtained. A total of 88 715 sequences (92.42%) were annotated with BLASTx against NCBI non-redundant plant proteins, including 34 719 high-quality annotations. Further BLASTn analysis against NCBI non-redundant nucleotide sequences, Coffea canephora coding sequences with UTR, C. arabica ESTs, and Rfam resulted in 1213 sequences without hits, were potential novel genes in coffee. Longer UTRs were captured, especially in the 5΄UTRs, facilitating the identification of upstream open reading frames. The LRS also revealed more and longer transcript variants in key caffeine and sucrose metabolism genes from this polyploid genome. Long sequences (>10 kilo base) were poorly annotated. LRS technology shows the limitation of previous studies. It provides an important tool to produce a reference transcriptome including more of the diversity of full-length transcripts to help understand the biology and support the genetic improvement of polyploid species such as coffee. PMID:29048540

  13. 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.

  14. Thematic Roles, Markedness Alignment and Processing Complexity

    ERIC Educational Resources Information Center

    Lee, Yoonhyoung; Kwon, Youan; Gordon, Peter C.

    2015-01-01

    Two experiments used eye-tracking during reading to investigate the role of the consistency of the relative markedness alignment of noun phrases (NPs) in the processing of complex sentences in Korean. To do so, the animacy of the first NP was varied in both experiments to manipulate the relative markedness of NPs. In addition, case markings of the…

  15. 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.

  16. Notes and Talk: An Examination of a Long-Term English Learner Reading-to-Learn in a High School Biology Classroom

    ERIC Educational Resources Information Center

    Brooks, Maneka Deanna

    2016-01-01

    Long-term English learners (LTELs) are frequently characterized as struggling with academic reading in English. This paper moves beyond broad generalizations about this population's English-reading practices to a situated analysis of one "LTEL"--Lizbeth Sanchez's--making meaning in her sophomore biology classroom. This analysis of…

  17. Computer assisted alignment of opening wedge high tibial osteotomy provides limited improvement of radiographic outcomes compared to flouroscopic alignment.

    PubMed

    Stanley, Jeremy C; Robinson, Kerian G; Devitt, Brian M; Richmond, Anneka K; Webster, Kate E; Whitehead, Timothy S; Feller, Julian A

    2016-03-01

    There are numerous methods available to assist surgeons in the accurate correction of varus alignment during medial opening wedge high tibial osteotomy (MOWHTO). Preoperative planning performed with radiographs or more recently intraoperative computer navigation software has been used. The aim of the study was to compare the accuracy of computer navigated versus non-navigated techniques to correct varus alignment of the knee. The preoperative and postoperative radiographs of 117 knees that underwent MOWHTO were investigated to assess radiographic limb alignment 12-months postoperatively. The desired correction was defined as a weight bearing line (Mikulicz point {MP}) 58% of the width of the tibial plateau from the medial tibial margin. Sixty-five knees were corrected using a conventional technique and 52 knees were corrected using computer navigation. The mean MP percentage was 59% in the navigated group, compared with 56% in the fluoroscopic group (p=0.183). 51.9% of the navigation knees were corrected to within five percent of the desired correction, in contrast to 38.5% of the fluoroscopically corrected knees (p=0.15). 71.2% of the navigated knees were corrected to within 10% of the desired correction, compared with 63.1% of the fluoroscopically corrected knees (p=0.36). Large preoperative deformities were more accurately corrected with navigation assistance (57% vs 49%, p=0.049). No statistically significant difference was found in the radiographic correction of varus alignment twelve months postoperatively between navigated and fluoroscopic techniques of MOWHTO. However, a subgroup analysis demonstrated that larger preoperative varus deformities may be more accurately corrected using computer navigation. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads and metadata visualization: an example with the Pezizomycotina tree of life.

    PubMed

    Carbone, Ignazio; White, James B; Miadlikowska, Jolanta; Arnold, A Elizabeth; Miller, Mark A; Kauff, Frank; U'Ren, Jana M; May, Georgiana; Lutzoni, François

    2017-04-15

    High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades. In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families and 496 genera) representing all 13 classes of largest subphylum of Fungi-Pezizomycotina (Ascomycota)-based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2 ). T-BAS v1.0 has three main uses: (i) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (ii) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (iii) User-customizable metadata can be visualized on the tree. T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu . Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources. icarbon@ncsu.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  19. 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

  20. A Polar Initial Alignment Algorithm for Unmanned Underwater Vehicles

    PubMed Central

    Yan, Zheping; Wang, Lu; Wang, Tongda; Zhang, Honghan; Zhang, Xun; Liu, Xiangling

    2017-01-01

    Due to its highly autonomy, the strapdown inertial navigation system (SINS) is widely used in unmanned underwater vehicles (UUV) navigation. Initial alignment is crucial because the initial alignment results will be used as the initial SINS value, which might affect the subsequent SINS results. Due to the rapid convergence of Earth meridians, there is a calculation overflow in conventional initial alignment algorithms, making conventional initial algorithms are invalid for polar UUV navigation. To overcome these problems, a polar initial alignment algorithm for UUV is proposed in this paper, which consists of coarse and fine alignment algorithms. Based on the principle of the conical slow drift of gravity, the coarse alignment algorithm is derived under the grid frame. By choosing the velocity and attitude as the measurement, the fine alignment with the Kalman filter (KF) is derived under the grid frame. Simulation and experiment are realized among polar, conventional and transversal initial alignment algorithms for polar UUV navigation. Results demonstrate that the proposed polar initial alignment algorithm can complete the initial alignment of UUV in the polar region rapidly and accurately. PMID:29168735

  1. A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS

    PubMed Central

    Jiao, Xiaoli; Zheng, Xin; Ma, Liang; Kutty, Geetha; Gogineni, Emile; Sun, Qiang; Sherman, Brad T.; Hu, Xiaojun; Jones, Kristine; Raley, Castle; Tran, Bao; Munroe, David J.; Stephens, Robert; Liang, Dun; Imamichi, Tomozumi; Kovacs, Joseph A.; Lempicki, Richard A.; Huang, Da Wei

    2013-01-01

    PacBio RS, a newly emerging third-generation DNA sequencing platform, is based on a real-time, single-molecule, nano-nitch sequencing technology that can generate very long reads (up to 20-kb) in contrast to the shorter reads produced by the first and second generation sequencing technologies. As a new platform, it is important to assess the sequencing error rate, as well as the quality control (QC) parameters associated with the PacBio sequence data. In this study, a mixture of 10 prior known, closely related DNA amplicons were sequenced using the PacBio RS sequencing platform. After aligning Circular Consensus Sequence (CCS) reads derived from the above sequencing experiment to the known reference sequences, we found that the median error rate was 2.5% without read QC, and improved to 1.3% with an SVM based multi-parameter QC method. In addition, a De Novo assembly was used as a downstream application to evaluate the effects of different QC approaches. This benchmark study indicates that even though CCS reads are post error-corrected it is still necessary to perform appropriate QC on CCS reads in order to produce successful downstream bioinformatics analytical results. PMID:24179701

  2. A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS.

    PubMed

    Jiao, Xiaoli; Zheng, Xin; Ma, Liang; Kutty, Geetha; Gogineni, Emile; Sun, Qiang; Sherman, Brad T; Hu, Xiaojun; Jones, Kristine; Raley, Castle; Tran, Bao; Munroe, David J; Stephens, Robert; Liang, Dun; Imamichi, Tomozumi; Kovacs, Joseph A; Lempicki, Richard A; Huang, Da Wei

    2013-07-31

    PacBio RS, a newly emerging third-generation DNA sequencing platform, is based on a real-time, single-molecule, nano-nitch sequencing technology that can generate very long reads (up to 20-kb) in contrast to the shorter reads produced by the first and second generation sequencing technologies. As a new platform, it is important to assess the sequencing error rate, as well as the quality control (QC) parameters associated with the PacBio sequence data. In this study, a mixture of 10 prior known, closely related DNA amplicons were sequenced using the PacBio RS sequencing platform. After aligning Circular Consensus Sequence (CCS) reads derived from the above sequencing experiment to the known reference sequences, we found that the median error rate was 2.5% without read QC, and improved to 1.3% with an SVM based multi-parameter QC method. In addition, a De Novo assembly was used as a downstream application to evaluate the effects of different QC approaches. This benchmark study indicates that even though CCS reads are post error-corrected it is still necessary to perform appropriate QC on CCS reads in order to produce successful downstream bioinformatics analytical results.

  3. Self-Aligning Sensor-Mounting Fixture

    NASA Technical Reports Server (NTRS)

    Gilbert, Jeffrey L.; Mills, Rhonda J.

    1991-01-01

    Optical welding sensors replaced without realignment. Mounting fixture for optical weld-penetration sensor enables accurate and repeatable alignment. Simple and easy to use. Assembled on welding torch, it holds sensor securely and keeps it pointed toward weld pool. Designed for use on gas/tungsten arc-welding torch, fixture replaces multipiece bracket.

  4. The Development of the easyCBM CCSS Reading Assessments: Grade 3. Technical Report #1221

    ERIC Educational Resources Information Center

    Alonzo, Julie; Park, Bitnara Jasmine; Tindal, Gerald

    2012-01-01

    In this technical report, we document the development and piloting of easyCBM reading measures aligned to the Common Core State Standards, designed for use in screening students at risk for reading difficulty and monitoring their progress as they develop reading skills. The measures, which assess students' ability to respond to…

  5. Teachers' Basic Knowledge of Reading Instruction: Insights from a Teacher Preparation Program

    ERIC Educational Resources Information Center

    Berkeley, Sheri; Regan, Kelley; Dimitrov, Dimiter; Guckert, Mary; Ray, Sharon

    2016-01-01

    Effective reading instruction is essential for all students, and especially students with disabilities; however, studies have indicated that both pre-service and in-service teachers lack an adequate knowledge of reading. To ensure adequate teacher knowledge, teacher preparation reform advocates suggest purposeful alignment of teacher preparation…

  6. Design of practical alignment device in KSTAR Thomson diagnostic.

    PubMed

    Lee, J H; Lee, S H; Yamada, I

    2016-11-01

    The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak's Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broad wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR's Thomson scattering diagnostics.

  7. Long-read sequencing of chicken transcripts and identification of new transcript isoforms.

    PubMed

    Thomas, Sean; Underwood, Jason G; Tseng, Elizabeth; Holloway, Alisha K

    2014-01-01

    The chicken has long served as an important model organism in many fields, and continues to aid our understanding of animal development. Functional genomics studies aimed at probing the mechanisms that regulate development require high-quality genomes and transcript annotations. The quality of these resources has improved dramatically over the last several years, but many isoforms and genes have yet to be identified. We hope to contribute to the process of improving these resources with the data presented here: a set of long cDNA sequencing reads, and a curated set of new genes and transcript isoforms not currently represented in the most up-to-date genome annotation currently available to the community of researchers who rely on the chicken genome.

  8. Three Planes of Practice: Examining Intersections of Reading Identity and Pedagogy

    ERIC Educational Resources Information Center

    Bernstein, Malayna

    2014-01-01

    This paper reports on a project that examined teachers' reading identities and explored ways in which those identities were manifested in reading pedagogy and were adopted by students. The paper focuses on one purposively selected teacher and his class. Tom Ziegler's personal and pedagogical practices were deeply aligned, and his…

  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. Image Alignment for Multiple Camera High Dynamic Range Microscopy.

    PubMed

    Eastwood, Brian S; Childs, Elisabeth C

    2012-01-09

    This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera.

  11. Image Alignment for Multiple Camera High Dynamic Range Microscopy

    PubMed Central

    Eastwood, Brian S.; Childs, Elisabeth C.

    2012-01-01

    This paper investigates the problem of image alignment for multiple camera high dynamic range (HDR) imaging. HDR imaging combines information from images taken with different exposure settings. Combining information from multiple cameras requires an alignment process that is robust to the intensity differences in the images. HDR applications that use a limited number of component images require an alignment technique that is robust to large exposure differences. We evaluate the suitability for HDR alignment of three exposure-robust techniques. We conclude that image alignment based on matching feature descriptors extracted from radiant power images from calibrated cameras yields the most accurate and robust solution. We demonstrate the use of this alignment technique in a high dynamic range video microscope that enables live specimen imaging with a greater level of detail than can be captured with a single camera. PMID:22545028

  12. A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

    PubMed

    Fostier, Jan; Proost, Sebastian; Dhoedt, Bart; Saeys, Yvan; Demeester, Piet; Van de Peer, Yves; Vandepoele, Klaas

    2011-03-15

    Many comparative genomics studies rely on the correct identification of homologous genomic regions using accurate alignment tools. In such case, the alphabet of the input sequences consists of complete genes, rather than nucleotides or amino acids. As optimal multiple sequence alignment is computationally impractical, a progressive alignment strategy is often employed. However, such an approach is susceptible to the propagation of alignment errors in early pairwise alignment steps, especially when dealing with strongly diverged genomic regions. In this article, we present a novel accurate and efficient greedy, graph-based algorithm for the alignment of multiple homologous genomic segments, represented as ordered gene lists. Based on provable properties of the graph structure, several heuristics are developed to resolve local alignment conflicts that occur due to gene duplication and/or rearrangement events on the different genomic segments. The performance of the algorithm is assessed by comparing the alignment results of homologous genomic segments in Arabidopsis thaliana to those obtained by using both a progressive alignment method and an earlier graph-based implementation. Especially for datasets that contain strongly diverged segments, the proposed method achieves a substantially higher alignment accuracy, and proves to be sufficiently fast for large datasets including a few dozens of eukaryotic genomes. http://bioinformatics.psb.ugent.be/software. The algorithm is implemented as a part of the i-ADHoRe 3.0 package.

  13. 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…

  14. Implementation of a parallel protein structure alignment service on cloud.

    PubMed

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.

  15. Implementation of a Parallel Protein Structure Alignment Service on Cloud

    PubMed Central

    Hung, Che-Lun; Lin, Yaw-Ling

    2013-01-01

    Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform. PMID:23671842

  16. Alignment of sensor arrays in optical instruments using a geometric approach.

    PubMed

    Sawyer, Travis W

    2018-02-01

    Alignment of sensor arrays in optical instruments is critical to maximize the instrument's performance. While many commercial systems use standardized mounting threads for alignment, custom systems require specialized equipment and alignment procedures. These alignment procedures can be time-consuming, dependent on operator experience, and have low repeatability. Furthermore, each alignment solution must be considered on a case-by-case basis, leading to additional time and resource cost. Here I present a method to align a sensor array using geometric analysis. By imaging a grid pattern of dots, I show that it is possible to calculate the misalignment for a sensor in five degrees of freedom simultaneously. I first test the approach by simulating different cases of misalignment using Zemax before applying the method to experimentally acquired data of sensor misalignment for an echelle spectrograph. The results show that the algorithm effectively quantifies misalignment in five degrees of freedom for an F/5 imaging system, accurate to within ±0.87  deg in rotation and ±0.86  μm in translation. Furthermore, the results suggest that the method can also be applied to non-imaging systems with a small penalty to precision. This general approach can potentially improve the alignment of sensor arrays in custom instruments by offering an accurate, quantitative approach to calculating misalignment in five degrees of freedom simultaneously.

  17. Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

    PubMed

    Hamada, Michiaki; Ono, Yukiteru; Asai, Kiyoshi; Frith, Martin C

    2017-03-15

    LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads. the source code is freely available at http://last.cbrc.jp/. mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  18. SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.

    PubMed

    Wala, Jeremiah; Beroukhim, Rameen

    2017-03-01

    We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. jwala@broadinstitue.org ; rameen@broadinstitute.org. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  19. Design of practical alignment device in KSTAR Thomson diagnostic

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

    Lee, J. H., E-mail: jhlee@nfri.re.kr; University of Science and Technology; Lee, S. H.

    2016-11-15

    The precise alignment of the laser path and collection optics in Thomson scattering measurements is essential for accurately determining electron temperature and density in tokamak experiments. For the last five years, during the development stage, the KSTAR tokamak’s Thomson diagnostic system has had alignment fibers installed in its optical collection modules, but these lacked a proper alignment detection system. In order to address these difficulties, an alignment verifying detection device between lasers and an object field of collection optics is developed. The alignment detection device utilizes two types of filters: a narrow laser band wavelength for laser, and a broadmore » wavelength filter for Thomson scattering signal. Four such alignment detection devices have been successfully developed for the KSTAR Thomson scattering system in this year, and these will be tested in KSTAR experiments in 2016. In this paper, we present the newly developed alignment detection device for KSTAR’s Thomson scattering diagnostics.« less

  20. Effect of stump flexion contracture with and without prosthetic alignment intervention towards postural stability among transtibial prosthesis users

    NASA Astrophysics Data System (ADS)

    Ghazali, M. F.; Razak, N. A. Abd; Abu Osman, N. A.; Gholizadeh, H.

    2017-06-01

    Knee flexion contracture on a stump side is a phenomenon in which the stump cannot move in normal range of motion (ROM) or cannot be fully extended. This study has been carried out by using Biodex Stability System (BSS) in order to investigate the effect of stump flexion contracture towards the postural stability among the transtibial prosthesis users with the intervention of alignment accommodation. The BSS provides the reading of anterior-posterior stability index (APSI), medial-lateral stability index (MLSI), and overall stability index (OSI). Higher reading of the index indicates lesser stability. Each of the subjects had been tested in three different sessions that were Visit 1 (before contracture improvement), Visit 2 (after contracture improvement without alignment readjustment), and Visit 3 (after contracture improvement with alignment readjustment). The APSI reading was significantly higher during Visit 2 compared to Visit 1 and Visit 3. The OSI during Visit 2 was also found significantly higher compared to Visit 3. In Visit 2, the degree of contracture was significantly improved with 44.1% less than Visit 1. The stability index in anterior-posterior aspect (APSI) was proven to be lower as the prosthetic alignment was adjusted according to the ROM of knee. This finding explained that the alignment set up based on the adaptation with the stump’s ROM can contribute positively in maintaining postural stability.

  1. "Passageless" Administration of the Nelson-Denny Reading Comprehension Test: Associations with IQ and Reading Skills

    ERIC Educational Resources Information Center

    Ready, Rebecca E.; Chaudhry, Maheen F.; Schatz, Kelly C.; Strazzullo, Sarah

    2013-01-01

    There are few tests that assess reading comprehension in adults, but these tests are needed for a comprehensive assessment of reading disorders (RD). "The Nelson-Denny Reading Test" (NDRT) has a long-passage reading comprehension component that can be used with adolescents and adults. A problem with the NDRT is that reading comprehension…

  2. biobambam: tools for read pair collation based algorithms on BAM files

    PubMed Central

    2014-01-01

    Background Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped data and the reference or of variants within the mapped data. In this order paired reads are usually separated in the file, which complicates some other applications like duplicate marking or conversion to the FastQ format which require to access the full information of the pairs. Results In this paper we introduce biobambam, a set of tools based on the efficient collation of alignments in BAM files by read name. The employed collation algorithm avoids time and space consuming sorting of alignments by read name where this is possible without using more than a specified amount of main memory. Using this algorithm tasks like duplicate marking in BAM files and conversion of BAM files to the FastQ format can be performed very efficiently with limited resources. We also make the collation algorithm available in the form of an API for other projects. This API is part of the libmaus package. Conclusions In comparison with previous approaches to problems involving the collation of alignments by read name like the BAM to FastQ or duplication marking utilities our approach can often perform an equivalent task more efficiently in terms of the required main memory and run-time. Our BAM to FastQ conversion is faster than all widely known alternatives including Picard and bamUtil. Our duplicate marking is about as fast as the closest competitor bamUtil for small data sets and faster than all known alternatives on large and complex data sets.

  3. 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.

  4. THE BANANA PROJECT. III. SPIN-ORBIT ALIGNMENT IN THE LONG-PERIOD ECLIPSING BINARY NY CEPHEI

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

    Albrecht, Simon; Winn, Joshua N.; Carter, Joshua A.

    Binaries are not always neatly aligned. Previous observations of the DI Her system showed that the spin axes of both stars are highly inclined with respect to one another and the orbital axis. Here, we report on a measurement of the spin-axis orientation of the primary star of the NY Cep system, which is similar to DI Her in many respects: it features two young early-type stars ({approx}6 Myr, B0.5V+B2V), in an eccentric and relatively long-period orbit (e = 0.48, P = 15fd3). The sky projections of the rotation vector and the spin vector are well aligned ({beta}{sub p} =more » 2{sup 0} {+-} 4{sup 0}), in strong contrast to DI Her. Although no convincing explanation has yet been given for the misalignment of DI Her, our results show that the phenomenon is not universal, and that a successful theory will need to account for the different outcome in the case of NY Cep.« less

  5. The Impact of Online Reading Tasks and Reading Strategies on EFL Learners' Reading Test Scores

    ERIC Educational Resources Information Center

    Altay, Ismail Firat; Altay, Ayse

    2017-01-01

    Integration of technology in foreign language classes has long been a matter of interest for researchers. Yet, studies have often yielded indecisive and conflicting results. Besides, there have been few, if any, studies exploring the relationship between learners' use of metacognitive reading strategies and their performance in reading tests. The…

  6. Wrinkled, wavelength-tunable graphene-based surface topographies for directing cell alignment and morphology

    PubMed Central

    Wang, Zhongying; Tonderys, Daniel; Leggett, Susan E.; Williams, Evelyn Kendall; Kiani, Mehrdad T.; Steinberg, Ruben Spitz; Qiu, Yang; Wong, Ian Y.; Hurt, Robert H.

    2015-01-01

    Textured surfaces with periodic topographical features and long-range order are highly attractive for directing cell-material interactions. They mimic physiological environments more accurately than planar surfaces and can fundamentally alter cell alignment, shape, gene expression, and cellular assembly into superstructures or microtissues. Here we demonstrate for the first time that wrinkled graphene-based surfaces are suitable as textured cell attachment substrates, and that engineered wrinkling can dramatically alter cell alignment and morphology. The wrinkled surfaces are fabricated by graphene oxide wet deposition onto pre-stretched elastomers followed by relaxation and mild thermal treatment to stabilize the films in cell culture medium. Multilayer graphene oxide films form periodic, delaminated buckle textures whose wavelengths and amplitudes can be systematically tuned by variation in the wet deposition process. Human and murine fibroblasts attach to these textured films and remain viable, while developing pronounced alignment and elongation relative to those on planar graphene controls. Compared to lithographic patterning of nanogratings, this method has advantages in the simplicity and scalability of fabrication, as well as the opportunity to couple the use of topographic cues with the unique conductive, adsorptive, or barrier properties of graphene materials for functional biomedical devices. PMID:25848137

  7. Rcount: simple and flexible RNA-Seq read counting.

    PubMed

    Schmid, Marc W; Grossniklaus, Ueli

    2015-02-01

    Analysis of differential gene expression by RNA sequencing (RNA-Seq) is frequently done using feature counts, i.e. the number of reads mapping to a gene. However, commonly used count algorithms (e.g. HTSeq) do not address the problem of reads aligning with multiple locations in the genome (multireads) or reads aligning with positions where two or more genes overlap (ambiguous reads). Rcount specifically addresses these issues. Furthermore, Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA-coding genes) or to add flanking regions. Rcount provides a fast and easy-to-use graphical user interface requiring no command line or programming skills. It is implemented in C++ using the SeqAn (www.seqan.de) and the Qt libraries (qt-project.org). Source code and 64 bit binaries for (Ubuntu) Linux, Windows (7) and MacOSX are released under the GPLv3 license and are freely available on github.com/MWSchmid/Rcount. marcschmid@gmx.ch Test data, genome annotation files, useful Python and R scripts and a step-by-step user guide (including run-time and memory usage tests) are available on github.com/MWSchmid/Rcount. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  8. ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

    PubMed

    Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

    2006-12-15

    We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

  9. Pediatric occipitocervical fusion: long-term radiographic changes in curvature, growth, and alignment.

    PubMed

    Martinez-Del-Campo, Eduardo; Turner, Jay D; Soriano-Baron, Hector; Newcomb, Anna G U S; Kalb, Samuel; Theodore, Nicholas

    2016-11-01

    increased diameter at the immediately inferior vertebral bodies compensating for the decreased width. No cervical deformation, malalignment, or detrimental clinical status was evident in any patient. CONCLUSIONS The craniovertebral junction and the upper cervical spine continue to present normal growth, curvature, and alignment parameters in children with OCF constructs spanning a distance as long as Oc-C4.

  10. Alignment verification procedures

    NASA Technical Reports Server (NTRS)

    Edwards, P. R.; Phillips, E. P.; Newman, J. C., Jr.

    1988-01-01

    In alignment verification procedures each laboratory is required to align its test machines and gripping fixtures to produce a nearly uniform tensile stress field on an un-notched sheet specimen. The blank specimens (50 mm w X 305 mm l X 2.3 mm th) supplied by the coordinators were strain gauged. Strain gauge readings were taken at all gauges (n = 1 through 10). The alignment verification procedures are as follows: (1) zero all strain gauges while specimen is in a free-supported condition; (2) put strain-gauged specimen in the test machine so that specimen front face (face 1) is in contact with reference jaw (standard position of specimen), tighten grips, and at zero load measure strains on all gauges. (epsilon sub nS0 is strain at gauge n, standard position, zero load); (3) with specimen in machine and at a tensile load of 10 kN measure strains (specimen in standard position). (Strain = epsilon sub nS10); (4) remove specimen from machine. Put specimen in machine so that specimen back face (face 2) is in contact with reference jaw (reverse position of specimen), tighten grips, and at zero load measure strains on all gauges. (Strain - epsilon sub nR0); and (5) with specimen in machine and at tensile load of 10 kN measure strains (specimen in reverse position). (epsilon sub nR10 is strain at gauge n, reverse position, 10 kN load).

  11. Psychophysiological Correlates of Reading Dysfunction in Junior College Students with a Long History of Reading Problems.

    ERIC Educational Resources Information Center

    Reichurdt, Konrad W.; Wilson, John A. R.

    This study was undertaken to measure emotional expression as mediated by the automatic nervous system during reading and during other tasks related to school work. Subjects for this research were eight normal readers, reading above the 46th percentile on the Davis Reading Test Form 1-A, used as a control group and sixteen abnormal readers drawn…

  12. 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…

  13. GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads

    PubMed Central

    Manconi, Andrea; Orro, Alessandro; Manca, Emanuele; Armano, Giuliano; Milanesi, Luciano

    2014-01-01

    Cytosine DNA methylation is an epigenetic mark implicated in several biological processes. Bisulfite treatment of DNA is acknowledged as the gold standard technique to study methylation. This technique introduces changes in the genomic DNA by converting cytosines to uracils while 5-methylcytosines remain nonreactive. During PCR amplification 5-methylcytosines are amplified as cytosine, whereas uracils and thymines as thymine. To detect the methylation levels, reads treated with the bisulfite must be aligned against a reference genome. Mapping these reads to a reference genome represents a significant computational challenge mainly due to the increased search space and the loss of information introduced by the treatment. To deal with this computational challenge we devised GPU-BSM, a tool based on modern Graphics Processing Units. Graphics Processing Units are hardware accelerators that are increasingly being used successfully to accelerate general-purpose scientific applications. GPU-BSM is a tool able to map bisulfite-treated reads from whole genome bisulfite sequencing and reduced representation bisulfite sequencing, and to estimate methylation levels, with the goal of detecting methylation. Due to the massive parallelization obtained by exploiting graphics cards, GPU-BSM aligns bisulfite-treated reads faster than other cutting-edge solutions, while outperforming most of them in terms of unique mapped reads. PMID:24842718

  14. Development of Accurate Structure for Mounting and Aligning Thin-Foil X-Ray Mirrors

    NASA Technical Reports Server (NTRS)

    Heilmann, Ralf K.

    2001-01-01

    The goal of this work was to improve the assembly accuracy for foil x-ray optics as produced by the high-energy astrophysics group at the NASA Goddard Space Flight Center. Two main design choices lead to an alignment concept that was shown to improve accuracy well within the requirements currently pursued by the Constellation-X Spectroscopy X-Ray Telescope (SXT).

  15. COACH: profile-profile alignment of protein families using hidden Markov models.

    PubMed

    Edgar, Robert C; Sjölander, Kimmen

    2004-05-22

    Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings. COACH is freely available from www.drive5.com/lobster

  16. Location of long-period events below Kilauea Volcano using seismic amplitudes and accurate relative relocation

    USGS Publications Warehouse

    Battaglia, J.; Got, J.-L.; Okubo, P.

    2003-01-01

    We present methods for improving the location of long-period (LP) events, deep and shallow, recorded below Kilauea Volcano by the permanent seismic network. LP events might be of particular interest to understanding eruptive processes as their source mechanism is assumed to directly involve fluid transport. However, it is usually difficult or impossible to locate their source using traditional arrival time methods because of emergent wave arrivals. At Kilauea, similar LP waveform signatures suggest the existence of LP multiplets. The waveform similarity suggests spatially close sources, while catalog solutions using arrival time estimates are widely scattered beneath Kilauea's summit caldera. In order to improve estimates of absolute LP location, we use the distribution of seismic amplitudes corrected for station site effects. The decay of the amplitude as a function of hypocentral distance is used for inferring LP location. In a second stage, we use the similarity of the events to calculate their relative positions. The analysis of the entire LP seismicity recorded between January 1997 and December 1999 suggests that a very large part of the LP event population, both deep and shallow, is generated by a small number of compact sources. Deep events are systematically composed of a weak high-frequency onset followed by a low-frequency wave train. Aligning the low-frequency wave trains does not lead to aligning the onsets indicating the two parts of the signal are dissociated. This observation favors an interpretation in terms of triggering and resonance of a magmatic conduit. Instead of defining fault planes, the precise relocation of similar LP events, based on the alignment of the high-energy low-frequency wave trains, defines limited size volumes. Copyright 2003 by the American Geophysical Union.

  17. MetAlign: interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing.

    PubMed

    Lommen, Arjen

    2009-04-15

    Hyphenated full-scan MS technology creates large amounts of data. A versatile easy to handle automation tool aiding in the data analysis is very important in handling such a data stream. MetAlign softwareas described in this manuscripthandles a broad range of accurate mass and nominal mass GC/MS and LC/MS data. It is capable of automatic format conversions, accurate mass calculations, baseline corrections, peak-picking, saturation and mass-peak artifact filtering, as well as alignment of up to 1000 data sets. A 100 to 1000-fold data reduction is achieved. MetAlign software output is compatible with most multivariate statistics programs.

  18. High-throughput sequence alignment using Graphics Processing Units

    PubMed Central

    Schatz, Michael C; Trapnell, Cole; Delcher, Arthur L; Varshney, Amitabh

    2007-01-01

    Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs) in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA) from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU. PMID:18070356

  19. Home Reading: The Key to Proficiency.

    ERIC Educational Resources Information Center

    Henderson, Bill

    2000-01-01

    A Boston principal reflects on decade-long efforts to get students and their families to read together. Initiatives ranged from reading contests and upgraded reading materials to reading contracts, literacy shows, parent/home visiting programs, pizza parties, and off-site tutors. Persistence paid off in higher reading scores. (MLH)

  20. TotalReCaller: improved accuracy and performance via integrated alignment and base-calling.

    PubMed

    Menges, Fabian; Narzisi, Giuseppe; Mishra, Bud

    2011-09-01

    Currently, re-sequencing approaches use multiple modules serially to interpret raw sequencing data from next-generation sequencing platforms, while remaining oblivious to the genomic information until the final alignment step. Such approaches fail to exploit the full information from both raw sequencing data and the reference genome that can yield better quality sequence reads, SNP-calls, variant detection, as well as an alignment at the best possible location in the reference genome. Thus, there is a need for novel reference-guided bioinformatics algorithms for interpreting analog signals representing sequences of the bases ({A, C, G, T}), while simultaneously aligning possible sequence reads to a source reference genome whenever available. Here, we propose a new base-calling algorithm, TotalReCaller, to achieve improved performance. A linear error model for the raw intensity data and Burrows-Wheeler transform (BWT) based alignment are combined utilizing a Bayesian score function, which is then globally optimized over all possible genomic locations using an efficient branch-and-bound approach. The algorithm has been implemented in soft- and hardware [field-programmable gate array (FPGA)] to achieve real-time performance. Empirical results on real high-throughput Illumina data were used to evaluate TotalReCaller's performance relative to its peers-Bustard, BayesCall, Ibis and Rolexa-based on several criteria, particularly those important in clinical and scientific applications. Namely, it was evaluated for (i) its base-calling speed and throughput, (ii) its read accuracy and (iii) its specificity and sensitivity in variant calling. A software implementation of TotalReCaller as well as additional information, is available at: http://bioinformatics.nyu.edu/wordpress/projects/totalrecaller/ fabian.menges@nyu.edu.

  1. CAFE: aCcelerated Alignment-FrEe sequence analysis

    PubMed Central

    Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A.; Waterman, Michael S.

    2017-01-01

    Abstract Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^*$\\end{document} and \\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}$d_2^S$\\end{document} are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. PMID:28472388

  2. FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.

    PubMed

    Gatto, Alberto; Torroja-Fungairiño, Carlos; Mazzarotto, Francesco; Cook, Stuart A; Barton, Paul J R; Sánchez-Cabo, Fátima; Lara-Pezzi, Enrique

    2014-04-01

    Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in the analysis of alternative splicing. This is particularly important for the identification of exon-exon junctions, which is a critical step in any analysis workflow. Here we performed a systematic benchmarking of alignment tools to dissect the impact of design and method on the mapping, detection and quantification of splice junctions from multi-exon reads. Accordingly, we devised a novel pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named FineSplice. FineSplice allows effective elimination of spurious junction hits arising from artefactual alignments, achieving up to 99% precision in both real and simulated data sets and yielding superior F1 scores under most tested conditions. The proposed strategy conjugates an efficient mapping solution with a semi-supervised anomaly detection scheme to filter out false positives and allows reliable estimation of expressed junctions from the alignment output. Ultimately this provides more accurate information to identify meaningful splicing patterns. FineSplice is freely available at https://sourceforge.net/p/finesplice/.

  3. STELLAR: fast and exact local alignments

    PubMed Central

    2011-01-01

    Background Large-scale comparison of genomic sequences requires reliable tools for the search of local alignments. Practical local aligners are in general fast, but heuristic, and hence sometimes miss significant matches. Results We present here the local pairwise aligner STELLAR that has full sensitivity for ε-alignments, i.e. guarantees to report all local alignments of a given minimal length and maximal error rate. The aligner is composed of two steps, filtering and verification. We apply the SWIFT algorithm for lossless filtering, and have developed a new verification strategy that we prove to be exact. Our results on simulated and real genomic data confirm and quantify the conjecture that heuristic tools like BLAST or BLAT miss a large percentage of significant local alignments. Conclusions STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X at http://www.seqan.de/projects/stellar. The source code is freely distributed with the SeqAn C++ library version 1.3 and later at http://www.seqan.de. PMID:22151882

  4. Robust temporal alignment of multimodal cardiac sequences

    NASA Astrophysics Data System (ADS)

    Perissinotto, Andrea; Queirós, Sandro; Morais, Pedro; Baptista, Maria J.; Monaghan, Mark; Rodrigues, Nuno F.; D'hooge, Jan; Vilaça, João. L.; Barbosa, Daniel

    2015-03-01

    Given the dynamic nature of cardiac function, correct temporal alignment of pre-operative models and intraoperative images is crucial for augmented reality in cardiac image-guided interventions. As such, the current study focuses on the development of an image-based strategy for temporal alignment of multimodal cardiac imaging sequences, such as cine Magnetic Resonance Imaging (MRI) or 3D Ultrasound (US). First, we derive a robust, modality-independent signal from the image sequences, estimated by computing the normalized cross-correlation between each frame in the temporal sequence and the end-diastolic frame. This signal is a resembler for the left-ventricle (LV) volume curve over time, whose variation indicates different temporal landmarks of the cardiac cycle. We then perform the temporal alignment of these surrogate signals derived from MRI and US sequences of the same patient through Dynamic Time Warping (DTW), allowing to synchronize both sequences. The proposed framework was evaluated in 98 patients, which have undergone both 3D+t MRI and US scans. The end-systolic frame could be accurately estimated as the minimum of the image-derived surrogate signal, presenting a relative error of 1.6 +/- 1.9% and 4.0 +/- 4.2% for the MRI and US sequences, respectively, thus supporting its association with key temporal instants of the cardiac cycle. The use of DTW reduces the desynchronization of the cardiac events in MRI and US sequences, allowing to temporally align multimodal cardiac imaging sequences. Overall, a generic, fast and accurate method for temporal synchronization of MRI and US sequences of the same patient was introduced. This approach could be straightforwardly used for the correct temporal alignment of pre-operative MRI information and intra-operative US images.

  5. JavaScript DNA translator: DNA-aligned protein translations.

    PubMed

    Perry, William L

    2002-12-01

    There are many instances in molecular biology when it is necessary to identify ORFs in a DNA sequence. While programs exist for displaying protein translations in multiple ORFs in alignment with a DNA sequence, they are often expensive, exist as add-ons to software that must be purchased, or are only compatible with a particular operating system. JavaScript DNA Translator is a shareware application written in JavaScript, a scripting language interpreted by the Netscape Communicator and Internet Explorer Web browsers, which makes it compatible with several different operating systems. While the program uses a familiar Web page interface, it requires no connection to the Internet since calculations are performed on the user's own computer. The program analyzes one or multiple DNA sequences and generates translations in up to six reading frames aligned to a DNA sequence, in addition to displaying translations as separate sequences in FASTA format. ORFs within a reading frame can also be displayed as separate sequences. Flexible formatting options are provided, including the ability to hide ORFs below a minimum size specified by the user. The program is available free of charge at the BioTechniques Software Library (www.Biotechniques.com).

  6. Software for Alignment of Segments of a Telescope Mirror

    NASA Technical Reports Server (NTRS)

    Hall, Drew P.; Howard, Richard T.; Ly, William C.; Rakoczy, John M.; Weir, John M.

    2006-01-01

    The Segment Alignment Maintenance System (SAMS) software is designed to maintain the overall focus and figure of the large segmented primary mirror of the Hobby-Eberly Telescope. This software reads measurements made by sensors attached to the segments of the primary mirror and from these measurements computes optimal control values to send to actuators that move the mirror segments.

  7. Face Alignment via Regressing Local Binary Features.

    PubMed

    Ren, Shaoqing; Cao, Xudong; Wei, Yichen; Sun, Jian

    2016-03-01

    This paper presents a highly efficient and accurate regression approach for face alignment. Our approach has two novel components: 1) a set of local binary features and 2) a locality principle for learning those features. The locality principle guides us to learn a set of highly discriminative local binary features for each facial landmark independently. The obtained local binary features are used to jointly learn a linear regression for the final output. This approach achieves the state-of-the-art results when tested on the most challenging benchmarks to date. Furthermore, because extracting and regressing local binary features are computationally very cheap, our system is much faster than previous methods. It achieves over 3000 frames per second (FPS) on a desktop or 300 FPS on a mobile phone for locating a few dozens of landmarks. We also study a key issue that is important but has received little attention in the previous research, which is the face detector used to initialize alignment. We investigate several face detectors and perform quantitative evaluation on how they affect alignment accuracy. We find that an alignment friendly detector can further greatly boost the accuracy of our alignment method, reducing the error up to 16% relatively. To facilitate practical usage of face detection/alignment methods, we also propose a convenient metric to measure how good a detector is for alignment initialization.

  8. Reading Ability and Memory Span: Long-Term Memory Contributions to Span for Good and Poor Readers.

    ERIC Educational Resources Information Center

    McDougall, Sine J. P.; Donohoe, Rachael

    2002-01-01

    Investigates the extent to which differences in memory span for good and poor readers can be explained by differences in a long-term memory component to span as well as by differences in short-term memory processes. Discusses the nature of the interrelationships between memory span, reading and measures of phonological awareness. (SG)

  9. Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection.

    PubMed

    Zhang, Qi; Zeng, Xin; Younkin, Sam; Kawli, Trupti; Snyder, Michael P; Keleş, Sündüz

    2016-02-24

    Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36-50 bps), long (75-100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection. We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell lines. Systematic evaluations using in silico variations of these data as well as fully simulated data, revealed complex interplay between the sequencing parameters and analysis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment accuracy, peak resolution, and most notably, allele-specific binding detection. Our work elucidates the effect of design on the downstream analysis and provides insights to investigators in deciding sequencing parameters in ChIP-seq experiments. We present the first systematic evaluation of the impact of ChIP-seq designs on allele-specific binding detection and highlights the power of pair-end designs in such studies.

  10. Beam/seam alignment control for electron beam welding

    DOEpatents

    Burkhardt, Jr., James H.; Henry, J. James; Davenport, Clyde M.

    1980-01-01

    This invention relates to a dynamic beam/seam alignment control system for electron beam welds utilizing video apparatus. The system includes automatic control of workpiece illumination, near infrared illumination of the workpiece to limit the range of illumination and camera sensitivity adjustment, curve fitting of seam position data to obtain an accurate measure of beam/seam alignment, and automatic beam detection and calculation of the threshold beam level from the peak beam level of the preceding video line to locate the beam or seam edges.

  11. Novel Models of Visual Topographic Map Alignment in the Superior Colliculus

    PubMed Central

    El-Ghazawi, Tarek A.; Triplett, Jason W.

    2016-01-01

    The establishment of precise neuronal connectivity during development is critical for sensing the external environment and informing appropriate behavioral responses. In the visual system, many connections are organized topographically, which preserves the spatial order of the visual scene. The superior colliculus (SC) is a midbrain nucleus that integrates visual inputs from the retina and primary visual cortex (V1) to regulate goal-directed eye movements. In the SC, topographically organized inputs from the retina and V1 must be aligned to facilitate integration. Previously, we showed that retinal input instructs the alignment of V1 inputs in the SC in a manner dependent on spontaneous neuronal activity; however, the mechanism of activity-dependent instruction remains unclear. To begin to address this gap, we developed two novel computational models of visual map alignment in the SC that incorporate distinct activity-dependent components. First, a Correlational Model assumes that V1 inputs achieve alignment with established retinal inputs through simple correlative firing mechanisms. A second Integrational Model assumes that V1 inputs contribute to the firing of SC neurons during alignment. Both models accurately replicate in vivo findings in wild type, transgenic and combination mutant mouse models, suggesting either activity-dependent mechanism is plausible. In silico experiments reveal distinct behaviors in response to weakening retinal drive, providing insight into the nature of the system governing map alignment depending on the activity-dependent strategy utilized. Overall, we describe novel computational frameworks of visual map alignment that accurately model many aspects of the in vivo process and propose experiments to test them. PMID:28027309

  12. 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.

  13. ReadXplorer—visualization and analysis of mapped sequences

    PubMed Central

    Hilker, Rolf; Stadermann, Kai Bernd; Doppmeier, Daniel; Kalinowski, Jörn; Stoye, Jens; Straube, Jasmin; Winnebald, Jörn; Goesmann, Alexander

    2014-01-01

    Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data. Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion–insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets. Availability and implementation: ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual. Contact: rhilker@mikrobio.med.uni-giessen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24790157

  14. Ultra-fast microwave-assisted hydrothermal synthesis of long vertically aligned ZnO nanowires for dye-sensitized solar cell application.

    PubMed

    Mahpeykar, S M; Koohsorkhi, J; Ghafoori-Fard, H

    2012-04-27

    Long vertically aligned ZnO nanowire arrays were synthesized using an ultra-fast microwave-assisted hydrothermal process. Using this method, we were able to grow ZnO nanowire arrays at an average growth rate as high as 200 nm min(-1) for maximum microwave power level. This method does not suffer from the growth stoppage problem at long growth times that, according to our investigations, a normal microwave-assisted hydrothermal method suffers from. Longitudinal growth of the nanowire arrays was investigated as a function of microwave power level and growth time using cross-sectional FESEM images of the grown arrays. Effect of seed layer on the alignment of nanowires was also studied. X-ray diffraction analysis confirmed c-axis orientation and single-phase wurtzite structure of the nanowires. J-V curves of the fabricated ZnO nanowire-based mercurochrome-sensitized solar cells indicated that the short-circuit current density is increased with increasing the length of the nanowire array. According to the UV-vis spectra of the dyes detached from the cells, these increments were mainly attributed to the enlarged internal surface area and therefore dye loading enhancement in the lengthened nanowire arrays.

  15. Designing robust watermark barcodes for multiplex long-read sequencing.

    PubMed

    Ezpeleta, Joaquín; Krsticevic, Flavia J; Bulacio, Pilar; Tapia, Elizabeth

    2017-03-15

    To attain acceptable sample misassignment rates, current approaches to multiplex single-molecule real-time sequencing require upstream quality improvement, which is obtained from multiple passes over the sequenced insert and significantly reduces the effective read length. In order to fully exploit the raw read length on multiplex applications, robust barcodes capable of dealing with the full single-pass error rates are needed. We present a method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing. The manuscript focuses on the design of barcodes for full-length single-pass reads, impaired by challenging error rates in the order of 11%. The proposed barcodes can multiplex hundreds or thousands of samples while achieving sample misassignment probabilities as low as 10-7 under the above conditions, and are designed to be compatible with chemical constraints imposed by the sequencing process. Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads, are freely available at www.cifasis-conicet.gov.ar/ezpeleta/NS-watermark . ezpeleta@cifasis-conicet.gov.ar. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  16. Aligning Metabolic Pathways Exploiting Binary Relation of Reactions.

    PubMed

    Huang, Yiran; Zhong, Cheng; Lin, Hai Xiang; Huang, Jing

    2016-01-01

    Metabolic pathway alignment has been widely used to find one-to-one and/or one-to-many reaction mappings to identify the alternative pathways that have similar functions through different sets of reactions, which has important applications in reconstructing phylogeny and understanding metabolic functions. The existing alignment methods exhaustively search reaction sets, which may become infeasible for large pathways. To address this problem, we present an effective alignment method for accurately extracting reaction mappings between two metabolic pathways. We show that connected relation between reactions can be formalized as binary relation of reactions in metabolic pathways, and the multiplications of zero-one matrices for binary relations of reactions can be accomplished in finite steps. By utilizing the multiplications of zero-one matrices for binary relation of reactions, we efficiently obtain reaction sets in a small number of steps without exhaustive search, and accurately uncover biologically relevant reaction mappings. Furthermore, we introduce a measure of topological similarity of nodes (reactions) by comparing the structural similarity of the k-neighborhood subgraphs of the nodes in aligning metabolic pathways. We employ this similarity metric to improve the accuracy of the alignments. The experimental results on the KEGG database show that when compared with other state-of-the-art methods, in most cases, our method obtains better performance in the node correctness and edge correctness, and the number of the edges of the largest common connected subgraph for one-to-one reaction mappings, and the number of correct one-to-many reaction mappings. Our method is scalable in finding more reaction mappings with better biological relevance in large metabolic pathways.

  17. 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…

  18. MANGO: a new approach to multiple sequence alignment.

    PubMed

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2007-01-01

    Multiple sequence alignment is a classical and challenging task for biological sequence analysis. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state of the art multiple sequence alignment programs suffer from the 'once a gap, always a gap' phenomenon. Is there a radically new way to do multiple sequence alignment? This paper introduces a novel and orthogonal multiple sequence alignment method, using multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds are provably significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks showing that MANGO compares favorably, in both accuracy and speed, against state-of-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, Prob-ConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0 and Kalign 2.0.

  19. Automated and Adaptable Quantification of Cellular Alignment from Microscopic Images for Tissue Engineering Applications

    PubMed Central

    Xu, Feng; Beyazoglu, Turker; Hefner, Evan; Gurkan, Umut Atakan

    2011-01-01

    Cellular alignment plays a critical role in functional, physical, and biological characteristics of many tissue types, such as muscle, tendon, nerve, and cornea. Current efforts toward regeneration of these tissues include replicating the cellular microenvironment by developing biomaterials that facilitate cellular alignment. To assess the functional effectiveness of the engineered microenvironments, one essential criterion is quantification of cellular alignment. Therefore, there is a need for rapid, accurate, and adaptable methodologies to quantify cellular alignment for tissue engineering applications. To address this need, we developed an automated method, binarization-based extraction of alignment score (BEAS), to determine cell orientation distribution in a wide variety of microscopic images. This method combines a sequenced application of median and band-pass filters, locally adaptive thresholding approaches and image processing techniques. Cellular alignment score is obtained by applying a robust scoring algorithm to the orientation distribution. We validated the BEAS method by comparing the results with the existing approaches reported in literature (i.e., manual, radial fast Fourier transform-radial sum, and gradient based approaches). Validation results indicated that the BEAS method resulted in statistically comparable alignment scores with the manual method (coefficient of determination R2=0.92). Therefore, the BEAS method introduced in this study could enable accurate, convenient, and adaptable evaluation of engineered tissue constructs and biomaterials in terms of cellular alignment and organization. PMID:21370940

  20. 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.

  1. 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…

  2. PROPER: global protein interaction network alignment through percolation matching.

    PubMed

    Kazemi, Ehsan; Hassani, Hamed; Grossglauser, Matthias; Pezeshgi Modarres, Hassan

    2016-12-12

    The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PPI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch .

  3. The long reads ahead: de novo genome assembly using the MinION

    PubMed Central

    de Lannoy, Carlos; de Ridder, Dick; Risse, Judith

    2017-01-01

    Nanopore technology provides a novel approach to DNA sequencing that yields long, label-free reads of constant quality. The first commercial implementation of this approach, the MinION, has shown promise in various sequencing applications. This review gives an up-to-date overview of the MinION's utility as a de novo sequencing device. It is argued that the MinION may allow for portable and affordable de novo sequencing of even complex genomes in the near future, despite the currently error-prone nature of its reads. Through continuous updates to the MinION hardware and the development of new assembly pipelines, both sequencing accuracy and assembly quality have already risen rapidly. However, this fast pace of development has also lead to a lack of overview of the expanding landscape of analysis tools, as performance evaluations are outdated quickly. As the MinION is approaching a state of maturity, its user community would benefit from a thorough comparative benchmarking effort of de novo assembly pipelines in the near future. An earlier version of this article can be found on  bioRxiv. PMID:29375809

  4. Assessment of Cognitive Abilities and Reading Comprehension across School-Age Development: A Meta-Analysis

    ERIC Educational Resources Information Center

    Finn, Diana Baker

    2014-01-01

    The purpose of this study was to examine the relationship of specific cognitive abilities and reading comprehension across a variety of norm referenced tests that align with Cattell-Horn-Carroll (CHC) theory of cognitive abilities and integrative models of reading. Data from existing studies was analyzed by comparing the relationships of four…

  5. Fast alignment-free sequence comparison using spaced-word frequencies.

    PubMed

    Leimeister, Chris-Andre; Boden, Marcus; Horwege, Sebastian; Lindner, Sebastian; Morgenstern, Burkhard

    2014-07-15

    Alignment-free methods for sequence comparison are increasingly used for genome analysis and phylogeny reconstruction; they circumvent various difficulties of traditional alignment-based approaches. In particular, alignment-free methods are much faster than pairwise or multiple alignments. They are, however, less accurate than methods based on sequence alignment. Most alignment-free approaches work by comparing the word composition of sequences. A well-known problem with these methods is that neighbouring word matches are far from independent. To reduce the statistical dependency between adjacent word matches, we propose to use 'spaced words', defined by patterns of 'match' and 'don't care' positions, for alignment-free sequence comparison. We describe a fast implementation of this approach using recursive hashing and bit operations, and we show that further improvements can be achieved by using multiple patterns instead of single patterns. To evaluate our approach, we use spaced-word frequencies as a basis for fast phylogeny reconstruction. Using real-world and simulated sequence data, we demonstrate that our multiple-pattern approach produces better phylogenies than approaches relying on contiguous words. Our program is freely available at http://spaced.gobics.de/. © The Author 2014. Published by Oxford University Press.

  6. svviz: a read viewer for validating structural variants.

    PubMed

    Spies, Noah; Zook, Justin M; Salit, Marc; Sidow, Arend

    2015-12-15

    Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data. We present svviz, a sequencing read visualizer for SVs that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele and identifying reads that match one allele better than the other. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared with the single reference genome-based view common to most current read browsers. The browser view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations and manual refinement of breakpoints. svviz supports data from most modern sequencing platforms. svviz is implemented in python and freely available from http://svviz.github.io/. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

  7. 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…

  8. Reading Acceleration Program: The Effect of Concentrated Practice on Reading Skills

    ERIC Educational Resources Information Center

    Pilotti, Maura; Martinez, Edward; Broderick, Tyler; Caballero, Sharon; LaGrange, Linda

    2012-01-01

    A well-established principle in the literature on learning, which maintains that variability of practice enhances long-term retention, served as the foundation of a summer program intended to ameliorate reading skills in incoming freshmen. During a 4-week period, students received reading instruction in the context of four areas: humanities,…

  9. Intervention Program for Long-Term English Learners: A Study of Long-Term English Learners' Literacy Performance in a Reading Intervention Program at Falcon School District

    ERIC Educational Resources Information Center

    Ayala, Erika

    2016-01-01

    The purpose of this sequential explanatory embedded mixed methods study was to: (a) investigate and describe the academic performance of eighth grade students in the Falcon School District (FSD) who were designated as Long Term English Learners (LTELs) and participants in FSD's reading intervention program during their fourth through eighth grade…

  10. Energy-level alignment at organic heterointerfaces

    PubMed Central

    Oehzelt, Martin; Akaike, Kouki; Koch, Norbert; Heimel, Georg

    2015-01-01

    Today’s champion organic (opto-)electronic devices comprise an ever-increasing number of different organic-semiconductor layers. The functionality of these complex heterostructures largely derives from the relative alignment of the frontier molecular-orbital energies in each layer with respect to those in all others. Despite the technological relevance of the energy-level alignment at organic heterointerfaces, and despite continued scientific interest, a reliable model that can quantitatively predict the full range of phenomena observed at such interfaces is notably absent. We identify the limitations of previous attempts to formulate such a model and highlight inconsistencies in the interpretation of the experimental data they were based on. We then develop a theoretical framework, which we demonstrate to accurately reproduce experiment. Applying this theory, a comprehensive overview of all possible energy-level alignment scenarios that can be encountered at organic heterojunctions is finally given. These results will help focus future efforts on developing functional organic interfaces for superior device performance. PMID:26702447

  11. Mango: multiple alignment with N gapped oligos.

    PubMed

    Zhang, Zefeng; Lin, Hao; Li, Ming

    2008-06-01

    Multiple sequence alignment is a classical and challenging task. The problem is NP-hard. The full dynamic programming takes too much time. The progressive alignment heuristics adopted by most state-of-the-art works suffer from the "once a gap, always a gap" phenomenon. Is there a radically new way to do multiple sequence alignment? In this paper, we introduce a novel and orthogonal multiple sequence alignment method, using both multiple optimized spaced seeds and new algorithms to handle these seeds efficiently. Our new algorithm processes information of all sequences as a whole and tries to build the alignment vertically, avoiding problems caused by the popular progressive approaches. Because the optimized spaced seeds have proved significantly more sensitive than the consecutive k-mers, the new approach promises to be more accurate and reliable. To validate our new approach, we have implemented MANGO: Multiple Alignment with N Gapped Oligos. Experiments were carried out on large 16S RNA benchmarks, showing that MANGO compares favorably, in both accuracy and speed, against state-of-the-art multiple sequence alignment methods, including ClustalW 1.83, MUSCLE 3.6, MAFFT 5.861, ProbConsRNA 1.11, Dialign 2.2.1, DIALIGN-T 0.2.1, T-Coffee 4.85, POA 2.0, and Kalign 2.0. We have further demonstrated the scalability of MANGO on very large datasets of repeat elements. MANGO can be downloaded at http://www.bioinfo.org.cn/mango/ and is free for academic usage.

  12. Robust image alignment for cryogenic transmission electron microscopy.

    PubMed

    McLeod, Robert A; Kowal, Julia; Ringler, Philippe; Stahlberg, Henning

    2017-03-01

    Cryo-electron microscopy recently experienced great improvements in structure resolution due to direct electron detectors with improved contrast and fast read-out leading to single electron counting. High frames rates enabled dose fractionation, where a long exposure is broken into a movie, permitting specimen drift to be registered and corrected. The typical approach for image registration, with high shot noise and low contrast, is multi-reference (MR) cross-correlation. Here we present the software package Zorro, which provides robust drift correction for dose fractionation by use of an intensity-normalized cross-correlation and logistic noise model to weight each cross-correlation in the MR model and filter each cross-correlation optimally. Frames are reliably registered by Zorro with low dose and defocus. Methods to evaluate performance are presented, by use of independently-evaluated even- and odd-frame stacks by trajectory comparison and Fourier ring correlation. Alignment of tiled sub-frames is also introduced, and demonstrated on an example dataset. Zorro source code is available at github.com/CINA/zorro. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2013-01-01

    Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using global structure alignment (GSA), there is a room to improve the performance by properly incorporating local structure alignment (LSA) because BS are local structures and often similar for proteins with dissimilar global folds. We present a template-based ligand BS prediction method using G-LoSA, our LSA tool. A large benchmark set validation shows that G-LoSA predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, a GSA-based method, while the overall success rate of TM-align is better. G-LoSA is particularly efficient for accurate detection of local structures conserved across proteins with diverse global topologies. Recognizing the performance complementarity of G-LoSA to TM-align and a non-template geometry-based method, fpocket, a robust consensus scoring method, CMCS-BSP (Complementary Methods and Consensus Scoring for ligand Binding Site Prediction), is developed and shows improvement on prediction accuracy. The G-LoSA source code is freely available at http://im.bioinformatics.ku.edu/GLoSA. PMID:23957286

  14. 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…

  15. Read-only high accuracy volume holographic optical correlator

    NASA Astrophysics Data System (ADS)

    Zhao, Tian; Li, Jingming; Cao, Liangcai; He, Qingsheng; Jin, Guofan

    2011-10-01

    A read-only volume holographic correlator (VHC) is proposed. After the recording of all of the correlation database pages by angular multiplexing, a stand-alone read-only high accuracy VHC will be separated from the VHC recording facilities which include the high-power laser and the angular multiplexing system. The stand-alone VHC has its own low power readout laser and very compact and simple structure. Since there are two lasers that are employed for recording and readout, respectively, the optical alignment tolerance of the laser illumination on the SLM is very sensitive. The twodimensional angular tolerance is analyzed based on the theoretical model of the volume holographic correlator. The experimental demonstration of the proposed read-only VHC is introduced and discussed.

  16. 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.

  17. Mask aligner for ultrahigh vacuum with capacitive distance control

    NASA Astrophysics Data System (ADS)

    Bhaskar, Priyamvada; Mathioudakis, Simon; Olschewski, Tim; Muckel, Florian; Bindel, Jan Raphael; Pratzer, Marco; Liebmann, Marcus; Morgenstern, Markus

    2018-04-01

    We present a mask aligner driven by three piezomotors which guides and aligns a SiN shadow mask under capacitive control towards a sample surface. The three capacitors for read out are located at the backside of the thin mask such that the mask can be placed at a μm distance from the sample surface, while keeping it parallel to the surface, without touching the sample by the mask a priori. Samples and masks can be exchanged in-situ and the mask can additionally be displaced parallel to the surface. We demonstrate an edge sharpness of the deposited structures below 100 nm, which is likely limited by the diffusion of the deposited Au on Si(111).

  18. Fidelity of Implementation and Instructional Alignment in Response to Intervention Research

    ERIC Educational Resources Information Center

    Hill, David R.; King, Seth A.; Lemons, Christopher J.; Partanen, Jane N.

    2012-01-01

    In this review, we explore the extent to which researchers evaluating the efficacy of Tier 2 elementary reading interventions within the framework of Response to Intervention reported on fidelity of implementation and alignment of instruction between tiers. A literature search identified 22 empirical studies from which conclusions were drawn.…

  19. 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…

  20. Compact laser transmitter delivering a long-range infrared beam aligned with a monitoring visible beam.

    PubMed

    Lee, Hong-Shik; Kim, Haeng-In; Lee, Sang-Shin

    2012-06-10

    A compact laser transmitter, which takes advantage of an optical subassembly module, was proposed and demonstrated, providing precisely aligned collinear IR and visible beams. The collimated IR beam acts as a long-range projectile for simulated combat, carrying an optical pulsed signal, whereas the visible beam plays the role of tracking the IR beam. The proposed laser transmitter utilizes IR (λ(1)=905 nm) and visible (λ(2)=660 nm) light sources, a fiber-optic collimator, and a beam combiner, which includes a wavelength division multiplexing (WDM) filter in conjunction with optical fiber. The device was built via the laser welding technique and then evaluated by investigating the characteristics of the generated light beams. The IR collimated beam produced had a Gaussian profile and a divergence angle of ~1.3 mrad, and the visible monitoring beam was appropriately collimated to be readily discernible in the vicinity of the transmitter. The two beams were highly aligned within an angle of 0.004 deg as anticipated. Finally, we performed a practical outdoor field test to assess the IR beam with the help of a receiver. An effective trajectory was observed ranging up to 660 m with an overall detectable beam width of ~60 cm.

  1. Constructing Reading: Building Conceptions of Literacy in a Volunteer Read-Aloud Program

    ERIC Educational Resources Information Center

    Dawes, Erika Thulin

    2007-01-01

    This study describes the interactions of three adult-child reading partnerships in a program that matches corporate volunteers with "at risk" students for weekly hour-long story reading sessions. Using discourse analysis within a sociocultural framework, the researcher identified variation in the way these partners were constructing the act and…

  2. 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

  3. Computational design and engineering of polymeric orthodontic aligners.

    PubMed

    Barone, S; Paoli, A; Razionale, A V; Savignano, R

    2016-10-05

    Transparent and removable aligners represent an effective solution to correct various orthodontic malocclusions through minimally invasive procedures. An aligner-based treatment requires patients to sequentially wear dentition-mating shells obtained by thermoforming polymeric disks on reference dental models. An aligner is shaped introducing a geometrical mismatch with respect to the actual tooth positions to induce a loading system, which moves the target teeth toward the correct positions. The common practice is based on selecting the aligner features (material, thickness, and auxiliary elements) by only considering clinician's subjective assessments. In this article, a computational design and engineering methodology has been developed to reconstruct anatomical tissues, to model parametric aligner shapes, to simulate orthodontic movements, and to enhance the aligner design. The proposed approach integrates computer-aided technologies, from tomographic imaging to optical scanning, from parametric modeling to finite element analyses, within a 3-dimensional digital framework. The anatomical modeling provides anatomies, including teeth (roots and crowns), jaw bones, and periodontal ligaments, which are the references for the down streaming parametric aligner shaping. The biomechanical interactions between anatomical models and aligner geometries are virtually reproduced using a finite element analysis software. The methodology allows numerical simulations of patient-specific conditions and the comparative analyses of different aligner configurations. In this article, the digital framework has been used to study the influence of various auxiliary elements on the loading system delivered to a maxillary and a mandibular central incisor during an orthodontic tipping movement. Numerical simulations have shown a high dependency of the orthodontic tooth movement on the auxiliary element configuration, which should then be accurately selected to maximize the aligner

  4. Sequence harmony: detecting functional specificity from alignments

    PubMed Central

    Feenstra, K. Anton; Pirovano, Walter; Krab, Klaas; Heringa, Jaap

    2007-01-01

    Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The SH web server allows a quick selection of subtype specific sites from a multiple alignment given a subfamily grouping. In addition, it allows the predicted sites to be directly mapped onto a protein structure and displayed. We demonstrate the use of the SH server using the family of plant mitochondrial alternative oxidases (AOX). In addition, we illustrate the usefulness of combining sequence and structural information by showing that the predicted sites are clustered into a few distinct regions in an AOX homology model. The SH web server can be accessed at www.ibi.vu.nl/programs/seqharmwww. PMID:17584793

  5. Precise Synaptic Efficacy Alignment Suggests Potentiation Dominated Learning.

    PubMed

    Hartmann, Christoph; Miner, Daniel C; Triesch, Jochen

    2015-01-01

    Recent evidence suggests that parallel synapses from the same axonal branch onto the same dendritic branch have almost identical strength. It has been proposed that this alignment is only possible through learning rules that integrate activity over long time spans. However, learning mechanisms such as spike-timing-dependent plasticity (STDP) are commonly assumed to be temporally local. Here, we propose that the combination of temporally local STDP and a multiplicative synaptic normalization mechanism is sufficient to explain the alignment of parallel synapses. To address this issue, we introduce three increasingly complex models: First, we model the idealized interaction of STDP and synaptic normalization in a single neuron as a simple stochastic process and derive analytically that the alignment effect can be described by a so-called Kesten process. From this we can derive that synaptic efficacy alignment requires potentiation-dominated learning regimes. We verify these conditions in a single-neuron model with independent spiking activities but more realistic synapses. As expected, we only observe synaptic efficacy alignment for long-term potentiation-biased STDP. Finally, we explore how well the findings transfer to recurrent neural networks where the learning mechanisms interact with the correlated activity of the network. We find that due to the self-reinforcing correlations in recurrent circuits under STDP, alignment occurs for both long-term potentiation- and depression-biased STDP, because the learning will be potentiation dominated in both cases due to the potentiating events induced by correlated activity. This is in line with recent results demonstrating a dominance of potentiation over depression during waking and normalization during sleep. This leads us to predict that individual spine pairs will be more similar after sleep compared to after sleep deprivation. In conclusion, we show that synaptic normalization in conjunction with coordinated

  6. A Meta-Analysis of the Long-Term Effects of Phonemic Awareness, Phonics, Fluency, and Reading Comprehension Interventions

    ERIC Educational Resources Information Center

    Suggate, Sebastian P.

    2016-01-01

    Much is known about short-term--but very little about the long-term--effects of reading interventions. To rectify this, a detailed analysis of follow-up effects as a function of intervention, sample, and methodological variables was conducted. A total of 71 intervention-control groups were selected (N = 8,161 at posttest) from studies reporting…

  7. OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

    PubMed

    Verzotto, Davide; M Teo, Audrey S; Hillmer, Axel M; Nagarajan, Niranjan

    2016-01-01

    Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA fragments (150 kilo base pairs (kbp) to 2 Mbp) and thus provide a unique source of information for disambiguating complex rearrangements in cancer genomes. Despite their utility, combining high-throughput sequencing and mapping technologies has been challenging because of the lack of efficient and sensitive map-alignment algorithms for robustly aligning error-prone maps to sequences. We introduce a novel seed-and-extend glocal (short for global-local) alignment method, OPTIMA (and a sliding-window extension for overlap alignment, OPTIMA-Overlap), which is the first to create indexes for continuous-valued mapping data while accounting for mapping errors. We also present a novel statistical model, agnostic with respect to technology-dependent error rates, for conservatively evaluating the significance of alignments without relying on expensive permutation-based tests. We show that OPTIMA and OPTIMA-Overlap outperform other state-of-the-art approaches (1.6-2 times more sensitive) and are more efficient (170-200 %) and precise in their alignments (nearly 99 % precision). These advantages are independent of the quality of the data, suggesting that our indexing approach and statistical evaluation are robust, provide improved sensitivity and guarantee high precision.

  8. Long-Term Effectiveness of the Reading Recovery Early Reading Intervention Program in a Rural School District

    ERIC Educational Resources Information Center

    Vaughan, Adam Warren

    2011-01-01

    There are many programs that specialize in teaching students the necessary strategies for reading. But which ones will have the greatest impact and provide lasting skills to struggling students? The purpose of this study was to assess the effectiveness of the Reading Recovery early intervention program on the lowest performing first grade students…

  9. 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.

  10. Early Intervention for Reading Difficulties: The Interactive Strategies Approach

    ERIC Educational Resources Information Center

    Scanlon, Donna M.; Anderson, Kimberly L.; Sweeney, Joan M.

    2010-01-01

    This book presents a research-supported framework for early literacy instruction that aligns with multi-tiered response-to-intervention (RTI) models. The book focuses on giving teachers a better understanding of literacy development and how to effectively support children as they begin to read and write. The authors' interactive strategies…

  11. A distributed system for fast alignment of next-generation sequencing data.

    PubMed

    Srimani, Jaydeep K; Wu, Po-Yen; Phan, John H; Wang, May D

    2010-12-01

    We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.

  12. Open Reading Frame Phylogenetic Analysis on the Cloud

    PubMed Central

    2013-01-01

    Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

  13. pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment.

    PubMed

    Warris, Sven; Timal, N Roshan N; Kempenaar, Marcel; Poortinga, Arne M; van de Geest, Henri; Varbanescu, Ana L; Nap, Jan-Peter

    2018-01-01

    Our previously published CUDA-only application PaSWAS for Smith-Waterman (SW) sequence alignment of any type of sequence on NVIDIA-based GPUs is platform-specific and therefore adopted less than could be. The OpenCL language is supported more widely and allows use on a variety of hardware platforms. Moreover, there is a need to promote the adoption of parallel computing in bioinformatics by making its use and extension more simple through more and better application of high-level languages commonly used in bioinformatics, such as Python. The novel application pyPaSWAS presents the parallel SW sequence alignment code fully packed in Python. It is a generic SW implementation running on several hardware platforms with multi-core systems and/or GPUs that provides accurate sequence alignments that also can be inspected for alignment details. Additionally, pyPaSWAS support the affine gap penalty. Python libraries are used for automated system configuration, I/O and logging. This way, the Python environment will stimulate further extension and use of pyPaSWAS. pyPaSWAS presents an easy Python-based environment for accurate and retrievable parallel SW sequence alignments on GPUs and multi-core systems. The strategy of integrating Python with high-performance parallel compute languages to create a developer- and user-friendly environment should be considered for other computationally intensive bioinformatics algorithms.

  14. MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.

    PubMed

    Tyakht, Alexander V; Popenko, Anna S; Belenikin, Maxim S; Altukhov, Ilya A; Pavlenko, Alexander V; Kostryukova, Elena S; Selezneva, Oksana V; Larin, Andrei K; Karpova, Irina Y; Alexeev, Dmitry G

    2012-12-07

    MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors' knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from http://hmpdacc.org). MALINA is made freely available on the web at http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.

  15. Technology Alignment and Portfolio Prioritization (TAPP)

    NASA Technical Reports Server (NTRS)

    Funaro, Gregory V.; Alexander, Reginald A.

    2015-01-01

    Technology Alignment and Portfolio Prioritization (TAPP) is a method being developed by the Advanced Concepts Office, at NASA Marshall Space Flight Center. The TAPP method expands on current technology assessment methods by incorporating the technological structure underlying technology development, e.g., organizational structures and resources, institutional policy and strategy, and the factors that motivate technological change. This paper discusses the methods ACO is currently developing to better perform technology assessments while taking into consideration Strategic Alignment, Technology Forecasting, and Long Term Planning.

  16. The Impact of Read Right: Semester-Only versus Year-Long Inplementation

    ERIC Educational Resources Information Center

    Sell, John B.

    2013-01-01

    Faced with meeting the requirements of the No Child Left Behind Act of 2001, schools are under pressure to have 100% of their students meet national standards in reading by 2014. For the 2010-2011 and 2011-2012 school years, Sussex Technical High School (STHS) in Georgetown, Delaware chose to adopt Read Right, a reading comprehension improvement…

  17. Expanding the catalog of binary black-hole simulations: aligned-spin configurations

    NASA Astrophysics Data System (ADS)

    Chu, Tony; Pfeiffer, Harald; Scheel, Mark; Szilagyi, Bela; SXS Collaboration

    2015-04-01

    A major goal of numerical relativity is to model the inspiral and merger of binary black holes through sufficiently accurate and long simulations, to enable the successful detection of gravitational waves. However, covering the full parameter space of binary configurations is a computationally daunting task. The SXS Collaboration has made important progress in this direction recently, with a catalog of 174 publicly available binary black-hole simulations [black-holes.org/waveforms]. Nevertheless, the parameter-space coverage remains sparse, even for non-precessing binaries. In this talk, I will describe an addition to the SXS catalog to improve its coverage, consisting of 95 new simulations of aligned-spin binaries with moderate mass ratios and dimensionless spins as high as 0.9. Some applications of these new simulations will also be mentioned.

  18. A Novel Partial Sequence Alignment Tool for Finding Large Deletions

    PubMed Central

    Aruk, Taner; Ustek, Duran; Kursun, Olcay

    2012-01-01

    Finding large deletions in genome sequences has become increasingly more useful in bioinformatics, such as in clinical research and diagnosis. Although there are a number of publically available next generation sequencing mapping and sequence alignment programs, these software packages do not correctly align fragments containing deletions larger than one kb. We present a fast alignment software package, BinaryPartialAlign, that can be used by wet lab scientists to find long structural variations in their experiments. For BinaryPartialAlign, we make use of the Smith-Waterman (SW) algorithm with a binary-search-based approach for alignment with large gaps that we called partial alignment. BinaryPartialAlign implementation is compared with other straight-forward applications of SW. Simulation results on mtDNA fragments demonstrate the effectiveness (runtime and accuracy) of the proposed method. PMID:22566777

  19. A short note on dynamic programming in a band.

    PubMed

    Gibrat, Jean-François

    2018-06-15

    Third generation sequencing technologies generate long reads that exhibit high error rates, in particular for insertions and deletions which are usually the most difficult errors to cope with. The only exact algorithm capable of aligning sequences with insertions and deletions is a dynamic programming algorithm. In this note, for the sake of efficiency, we consider dynamic programming in a band. We show how to choose the band width in function of the long reads' error rates, thus obtaining an [Formula: see text] algorithm in space and time. We also propose a procedure to decide whether this algorithm, when applied to semi-global alignments, provides the optimal score. We suggest that dynamic programming in a band is well suited to the problem of aligning long reads between themselves and can be used as a core component of methods for obtaining a consensus sequence from the long reads alone. The function implementing the dynamic programming algorithm in a band is available, as a standalone program, at: https://forgemia.inra.fr/jean-francois.gibrat/BAND_DYN_PROG.git.

  20. 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…

  1. Component alignment in revision total knee arthroplasty using diaphyseal engaging modular offset press-fit stems.

    PubMed

    Nakasone, Cass K; Abdeen, Ayesha; Khachatourians, Armond G; Sugimori, Tanzo; Vince, Kelly G

    2008-12-01

    We performed a retrospective study of the radiographic position of femoral and tibial components in a series of revision total knee arthroplasties using diaphyseal-engaging, press fit, modular stems. Fifty-two consecutive revision cases were performed. Femoral and tibial component alignment was measured preoperatively and postoperatively. The canal-filling ratio was measured and correlated with anatomic alignment. There was a trend toward improved alignment with increasing canal fill, suggesting that uncemented diaphyseal engaging press-fit modular stems facilitate accurate alignment for both femoral and tibial components in revision surgery.

  2. 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…

  3. Spacecraft alignment estimation. [for onboard sensors

    NASA Technical Reports Server (NTRS)

    Shuster, Malcolm D.; Bierman, Gerald J.

    1988-01-01

    A numerically well-behaved factorized methodology is developed for estimating spacecraft sensor alignments from prelaunch and inflight data without the need to compute the spacecraft attitude or angular velocity. Such a methodology permits the estimation of sensor alignments (or other biases) in a framework free of unknown dynamical variables. In actual mission implementation such an algorithm is usually better behaved than one that must compute sensor alignments simultaneously with the spacecraft attitude, for example by means of a Kalman filter. In particular, such a methodology is less sensitive to data dropouts of long duration, and the derived measurement used in the attitude-independent algorithm usually makes data checking and editing of outliers much simpler than would be the case in the filter.

  4. Haplotype-Based Genotyping in Polyploids.

    PubMed

    Clevenger, Josh P; Korani, Walid; Ozias-Akins, Peggy; Jackson, Scott

    2018-01-01

    Accurate identification of polymorphisms from sequence data is crucial to unlocking the potential of high throughput sequencing for genomics. Single nucleotide polymorphisms (SNPs) are difficult to accurately identify in polyploid crops due to the duplicative nature of polyploid genomes leading to low confidence in the true alignment of short reads. Implementing a haplotype-based method in contrasting subgenome-specific sequences leads to higher accuracy of SNP identification in polyploids. To test this method, a large-scale 48K SNP array (Axiom Arachis2) was developed for Arachis hypogaea (peanut), an allotetraploid, in which 1,674 haplotype-based SNPs were included. Results of the array show that 74% of the haplotype-based SNP markers could be validated, which is considerably higher than previous methods used for peanut. The haplotype method has been implemented in a standalone program, HAPLOSWEEP, which takes as input bam files and a vcf file and identifies haplotype-based markers. Haplotype discovery can be made within single reads or span paired reads, and can leverage long read technology by targeting any length of haplotype. Haplotype-based genotyping is applicable in all allopolyploid genomes and provides confidence in marker identification and in silico-based genotyping for polyploid genomics.

  5. A Long Road to Recovery: Healing an Ailing Reading Program

    ERIC Educational Resources Information Center

    Welsh, Kimberly

    2014-01-01

    This one-year exploratory case study attempted to discern which adjustments in culture, physical classroom environment, and instruction were needed to improve reading instruction in ailing K-2 classrooms at Lion Elementary School. A holistic approach was created to diagnose the problem surrounding poor early reading achievement. After proper…

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

    PubMed

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

    2017-08-09

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

  7. Note: long range and accurate measurement of deep trench microstructures by a specialized scanning tunneling microscope.

    PubMed

    Ju, Bing-Feng; Chen, Yuan-Liu; Zhang, Wei; Zhu, Wule; Jin, Chao; Fang, F Z

    2012-05-01

    A compact but practical scanning tunneling microscope (STM) with high aspect ratio and high depth capability has been specially developed. Long range scanning mechanism with tilt-adjustment stage is adopted for the purpose of adjusting the probe-sample relative angle to compensate the non-parallel effects. A periodical trench microstructure with a pitch of 10 μm has been successfully imaged with a long scanning range up to 2.0 mm. More innovatively, a deep trench with depth and step height of 23.0 μm has also been successfully measured, and slope angle of the sidewall can approximately achieve 67°. The probe can continuously climb the high step and exploring the trench bottom without tip crashing. The new STM could perform long range measurement for the deep trench and high step surfaces without image distortion. It enables accurate measurement and quality control of periodical trench microstructures.

  8. Learning to Read in Arabic: The Long and Winding Road

    ERIC Educational Resources Information Center

    Asaad, Hanan; Eviatar, Zohar

    2014-01-01

    We examined the relative contribution of visual abilities, accessibility of letter names, and phonological awareness, to text reading speed and accuracy of Arabic in first, third, and fifth grades. The results revealed that for all levels of skill, phonological awareness contributes significantly to reading accuracy, to the same degree. For…

  9. 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.…

  10. 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…

  11. Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi.

    PubMed

    Batty, Elizabeth M; Chaemchuen, Suwittra; Blacksell, Stuart; Richards, Allen L; Paris, Daniel; Bowden, Rory; Chan, Caroline; Lachumanan, Ramkumar; Day, Nicholas; Donnelly, Peter; Chen, Swaine; Salje, Jeanne

    2018-06-01

    Orientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies of Orientia have revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using short read sequencing methodologies, and consequently there have been few studies of the comparative genomics of this neglected species. We report new high-quality genomes of O. tsutsugamushi, generated using PacBio single molecule long read sequencing, for six strains: Karp, Kato, Gilliam, TA686, UT76 and UT176. In comparative genomics analyses of these strains together with existing reference genomes from Ikeda and Boryong strains, we identify a relatively small core genome of 657 genes, grouped into core gene islands and separated by repeat regions, and use the core genes to infer the first whole-genome phylogeny of Orientia. Complete assemblies of multiple Orientia genomes verify initial suggestions that these are remarkable organisms. They have larger genomes compared with most other Rickettsiaceae, with widespread amplification of repeat elements and massive chromosomal rearrangements between strains. At the gene level, Orientia has a relatively small set of universally conserved genes, similar to other obligate intracellular bacteria, and the relative expansion in genome size can be accounted for by gene duplication and repeat amplification. Our study demonstrates the utility of long read sequencing to investigate complex bacterial genomes and characterise genomic variation.

  12. 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.

  13. Global Network Alignment in the Context of Aging.

    PubMed

    Faisal, Fazle Elahi; Zhao, Han; Milenkovic, Tijana

    2015-01-01

    Analogous to sequence alignment, network alignment (NA) can be used to transfer biological knowledge across species between conserved network regions. NA faces two algorithmic challenges: 1) Which cost function to use to capture "similarities" between nodes in different networks? 2) Which alignment strategy to use to rapidly identify "high-scoring" alignments from all possible alignments? We "break down" existing state-of-the-art methods that use both different cost functions and different alignment strategies to evaluate each combination of their cost functions and alignment strategies. We find that a combination of the cost function of one method and the alignment strategy of another method beats the existing methods. Hence, we propose this combination as a novel superior NA method. Then, since human aging is hard to study experimentally due to long lifespan, we use NA to transfer aging-related knowledge from well annotated model species to poorly annotated human. By doing so, we produce novel human aging-related knowledge, which complements currently available knowledge about aging that has been obtained mainly by sequence alignment. We demonstrate significant similarity between topological and functional properties of our novel predictions and those of known aging-related genes. We are the first to use NA to learn more about aging.

  14. Direct numerical simulation of particle alignment in viscoelastic fluids

    NASA Astrophysics Data System (ADS)

    Hulsen, Martien; Jaensson, Nick; Anderson, Patrick

    2016-11-01

    Rigid particles suspended in viscoelastic fluids under shear can align in string-like structures in flow direction. To unravel this phenomenon, we present 3D direct numerical simulations of the alignment of two and three rigid, non-Brownian particles in a shear flow of a viscoelastic fluid. The equations are solved on moving, boundary-fitted meshes, which are locally refined to accurately describe the polymer stresses around and in between the particles. A small minimal gap size between the particles is introduced. The Giesekus model is used and the effect of the Weissenberg number, shear thinning and solvent viscosity is investigated. Alignment of two and three particles is observed. Morphology plots have been created for various combinations of fluid parameters. Alignment is mainly governed by the value of the elasticity parameter S, defined as half of the ratio between the first normal stress difference and shear stress of the suspending fluid. Alignment appears to occur above a critical value of S, which decreases with increasing shear thinning. This result, together with simulations of a shear-thinning Carreau fluid, leads us to the conclusion that normal stress differences are essential for particle alignment to occur, but it is also strongly promoted by shear thinning.

  15. Beam alignment based on two-dimensional power spectral density of a near-field image.

    PubMed

    Wang, Shenzhen; Yuan, Qiang; Zeng, Fa; Zhang, Xin; Zhao, Junpu; Li, Kehong; Zhang, Xiaolu; Xue, Qiao; Yang, Ying; Dai, Wanjun; Zhou, Wei; Wang, Yuanchen; Zheng, Kuixing; Su, Jingqin; Hu, Dongxia; Zhu, Qihua

    2017-10-30

    Beam alignment is crucial to high-power laser facilities and is used to adjust the laser beams quickly and accurately to meet stringent requirements of pointing and centering. In this paper, a novel alignment method is presented, which employs data processing of the two-dimensional power spectral density (2D-PSD) for a near-field image and resolves the beam pointing error relative to the spatial filter pinhole directly. Combining this with a near-field fiducial mark, the operation of beam alignment is achieved. It is experimentally demonstrated that this scheme realizes a far-field alignment precision of approximately 3% of the pinhole size. This scheme adopts only one near-field camera to construct the alignment system, which provides a simple, efficient, and low-cost way to align lasers.

  16. The Effect of Pitch Peak Alignment on Sentence Type Identification in Russian

    ERIC Educational Resources Information Center

    Makarova, Veronika

    2007-01-01

    This paper reports the results of an experimental phonetic study examining pitch peak alignment in production and perception of three-syllable one-word sentences with phonetic rising-falling pitch movement by speakers of Russian. The first part of the study (Experiment 1) utilizes 22 one-word three-syllable utterances read by five female speakers…

  17. Automatic readout micrometer

    DOEpatents

    Lauritzen, Ted

    1982-01-01

    A measuring system is disclosed for surveying and very accurately positioning objects with respect to a reference line. A principal use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a particle accelerator. Prior art surveying systems require highly skilled surveyors. Prior art systems include, for example, optical surveying systems which are susceptible to operator reading errors, and celestial navigation-type surveying systems, with their inherent complexities. The present invention provides an automatic readout micrometer which can very accurately measure distances. The invention has a simplicity of operation which practically eliminates the possibilities of operator optical reading error, owning to the elimination of traditional optical alignments for making measurements. The invention has an extendable arm which carries a laser surveying target. The extendable arm can be continuously positioned over its entire length of travel by either a coarse or fine adjustment without having the fine adjustment outrun the coarse adjustment until a reference laser beam is centered on the target as indicated by a digital readout. The length of the micrometer can then be accurately and automatically read by a computer and compared with a standardized set of alignment measurements. Due to its construction, the micrometer eliminates any errors due to temperature changes when the system is operated within a standard operating temperature range.

  18. Automatic readout micrometer

    DOEpatents

    Lauritzen, T.

    A measuring system is described for surveying and very accurately positioning objects with respect to a reference line. A principle use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a particle accelerator. Prior art surveying systems require highly skilled surveyors. Prior art systems include, for example, optical surveying systems which are susceptible to operator reading errors, and celestial navigation-type surveying systems, with their inherent complexities. The present invention provides an automatic readout micrometer which can very accurately measure distances. The invention has a simplicity of operation which practically eliminates the possibilities of operator optical reading error, owning to the elimination of traditional optical alignments for making measurements. The invention has an extendable arm which carries a laser surveying target. The extendable arm can be continuously positioned over its entire length of travel by either a coarse of fine adjustment without having the fine adjustment outrun the coarse adjustment until a reference laser beam is centered on the target as indicated by a digital readout. The length of the micrometer can then be accurately and automatically read by a computer and compared with a standardized set of alignment measurements. Due to its construction, the micrometer eliminates any errors due to temperature changes when the system is operated within a standard operating temperature range.

  19. Aligning the unalignable: bacteriophage whole genome alignments.

    PubMed

    Bérard, Sèverine; Chateau, Annie; Pompidor, Nicolas; Guertin, Paul; Bergeron, Anne; Swenson, Krister M

    2016-01-13

    In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for comparing whole genomes exist: dot plots diagrams give a mostly qualitative assessment of the similarity/dissimilarity between two or more genomes, and clustering techniques are used to classify genomes. Multiple alignments are conspicuously absent from this scene. Indeed, whole genome aligners interpret lack of similarity between sequences as an indication of rearrangements, insertions, or losses. This behavior makes them ill-prepared to align bacteriophage genomes, where even closely related strains can accomplish the same biological function with highly dissimilar sequences. In this paper, we propose a multiple alignment strategy that exploits functional collinearity shared by related strains of bacteriophages, and uses partial orders to capture mosaicism of sets of genomes. As classical alignments do, the computed alignments can be used to predict that genes have the same biological function, even in the absence of detectable similarity. The Alpha aligner implements these ideas in visual interactive displays, and is used to compute several examples of alignments of Staphylococcus aureus and Mycobacterium bacteriophages, involving up to 29 genomes. Using these datasets, we prove that Alpha alignments are at least as good as those computed by standard aligners. Comparison with the progressive Mauve aligner - which implements a partial order strategy, but whose alignments are linearized - shows a greatly improved interactive graphic display, while avoiding misalignments. Multiple alignments of whole bacteriophage genomes work, and will become an important conceptual and visual tool in comparative genomics of sets of related strains. A python implementation of Alpha, along with installation instructions for Ubuntu and OSX, is available on bitbucket (https://bitbucket.org/thekswenson/alpha).

  20. A machine-learning approach reveals that alignment properties alone can accurately predict inference of lateral gene transfer from discordant phylogenies.

    PubMed

    Roettger, Mayo; Martin, William; Dagan, Tal

    2009-09-01

    Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80% accuracy from alignment properties alone.

  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. A Workflow to Improve the Alignment of Prostate Imaging with Whole-mount Histopathology.

    PubMed

    Yamamoto, Hidekazu; Nir, Dror; Vyas, Lona; Chang, Richard T; Popert, Rick; Cahill, Declan; Challacombe, Ben; Dasgupta, Prokar; Chandra, Ashish

    2014-08-01

    Evaluation of prostate imaging tests against whole-mount histology specimens requires accurate alignment between radiologic and histologic data sets. Misalignment results in false-positive and -negative zones as assessed by imaging. We describe a workflow for three-dimensional alignment of prostate imaging data against whole-mount prostatectomy reference specimens and assess its performance against a standard workflow. Ethical approval was granted. Patients underwent motorized transrectal ultrasound (Prostate Histoscanning) to generate a three-dimensional image of the prostate before radical prostatectomy. The test workflow incorporated steps for axial alignment between imaging and histology, size adjustments following formalin fixation, and use of custom-made parallel cutters and digital caliper instruments. The control workflow comprised freehand cutting and assumed homogeneous block thicknesses at the same relative angles between pathology and imaging sections. Thirty radical prostatectomy specimens were histologically and radiologically processed, either by an alignment-optimized workflow (n = 20) or a control workflow (n = 10). The optimized workflow generated tissue blocks of heterogeneous thicknesses but with no significant drifting in the cutting plane. The control workflow resulted in significantly nonparallel blocks, accurately matching only one out of four histology blocks to their respective imaging data. The image-to-histology alignment accuracy was 20% greater in the optimized workflow (P < .0001), with higher sensitivity (85% vs. 69%) and specificity (94% vs. 73%) for margin prediction in a 5 × 5-mm grid analysis. A significantly better alignment was observed in the optimized workflow. Evaluation of prostate imaging biomarkers using whole-mount histology references should include a test-to-reference spatial alignment workflow. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

  3. Patterned Cell Alignment in Response to Macroscale Curvature

    NASA Astrophysics Data System (ADS)

    Bade, Nathan; Kamien, Randall; Assoian, Richard; Stebe, Kathleen

    The formation of spatial behavior patterns in tissues is a long-standing problem in biology. Decades of research have focused on understanding how biochemical signaling and morphogen gradients establish cell patterns during development and tissue morphogenesis. Here, we show that geometry and physical cues can drive organization and pattern formation. We find that mouse embryonic fibroblasts and human vascular smooth muscle cells sense curvature differently when in monolayers than when isolated on surfaces with various amounts of Gaussian curvature. While the long, apical stress fibers within these cells align in the direction of minimum curvature on cylindrical substrates, a subpopulation of stress fibers beneath the nucleus aligns in the circumferential direction and is bent maximally. We find dramatic reorganization of the actin cytoskeleton upon activation of RhoA, which is associated with increased contractility of the fibers. Thus, stress fiber alignment is likely a result of a complex balance between energy penalties associated with stress fiber bending, contractility, and the dynamics of F-actin assembly.

  4. Galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation

    NASA Astrophysics Data System (ADS)

    Chisari, N. E.; Koukoufilippas, N.; Jindal, A.; Peirani, S.; Beckmann, R. S.; Codis, S.; Devriendt, J.; Miller, L.; Dubois, Y.; Laigle, C.; Slyz, A.; Pichon, C.

    2017-11-01

    Intrinsic alignments of galaxies are a significant astrophysical systematic affecting cosmological constraints from weak gravitational lensing. Obtaining numerical predictions from hydrodynamical simulations of expected survey volumes is expensive, and a cheaper alternative relies on populating large dark matter-only simulations with accurate models of alignments calibrated on smaller hydrodynamical runs. This requires connecting the shapes and orientations of galaxies to those of dark matter haloes and to the large-scale structure. In this paper, we characterize galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation. We compare the shapes and orientations of galaxies in the redshift range of 0 < z < 3 to those of their embedding dark matter haloes, and to the matching haloes of a twin dark-matter only run with identical initial conditions. We find that galaxy ellipticities, in general, cannot be predicted directly from halo ellipticities. The mean misalignment angle between the minor axis of a galaxy and its embedding halo is a function of halo mass, with residuals arising from the dependence of alignment on galaxy type, but not on environment. Haloes are much more strongly aligned among themselves than galaxies, and they decrease their alignment towards low redshift. Galaxy alignments compete with this effect, as galaxies tend to increase their alignment with haloes towards low redshift. We discuss the implications of these results for current halo models of intrinsic alignments and suggest several avenues for improvement.

  5. An accurate registration technique for distorted images

    NASA Technical Reports Server (NTRS)

    Delapena, Michele; Shaw, Richard A.; Linde, Peter; Dravins, Dainis

    1990-01-01

    Accurate registration of International Ultraviolet Explorer (IUE) images is crucial because the variability of the geometrical distortions that are introduced by the SEC-Vidicon cameras ensures that raw science images are never perfectly aligned with the Intensity Transfer Functions (ITFs) (i.e., graded floodlamp exposures that are used to linearize and normalize the camera response). A technique for precisely registering IUE images which uses a cross correlation of the fixed pattern that exists in all raw IUE images is described.

  6. MaxAlign: maximizing usable data in an alignment.

    PubMed

    Gouveia-Oliveira, Rodrigo; Sackett, Peter W; Pedersen, Anders G

    2007-08-28

    The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. MaxAlign is a program that optimizes the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign. In this paper we also introduce a new simple measure of tree similarity, Normalized Symmetric Similarity (NSS) that we consider useful for comparing tree topologies. We demonstrate how MaxAlign is helpful in detecting misaligned or defective sequences without requiring manual inspection. We also show that it is not advisable to exclude gapped columns from phylogenetic analyses unless MaxAlign is used first. Finally, we find that the sequences removed by MaxAlign from an alignment tend to be those that would otherwise be associated with low phylogenetic accuracy, and that the presence of gaps in any given sequence does not seem to disturb the phylogenetic estimates of other sequences. The MaxAlign web-server is freely available online at http://www.cbs.dtu.dk/services/MaxAlign where supplementary information can also be found. The program is also freely available as a Perl stand-alone package.

  7. Reading Sacred Texts in the Classroom: The Alignment between Students and Their Teacher's Interpretive Stances When Reading the Hebrew Bible

    ERIC Educational Resources Information Center

    Hassenfeld, Ziva R.

    2016-01-01

    This study investigated the voices of students interpreting Hebrew Bible texts in one fourth-grade classroom. Through think-alouds on the Biblical text with each student, exit interviews, teacher interviews, and classroom observations, this study found that those students whose interpretive stances were more aligned with the teacher's were given…

  8. Quasiparticle Level Alignment for Photocatalytic Interfaces.

    PubMed

    Migani, Annapaoala; Mowbray, Duncan J; Zhao, Jin; Petek, Hrvoje; Rubio, Angel

    2014-05-13

    Electronic level alignment at the interface between an adsorbed molecular layer and a semiconducting substrate determines the activity and efficiency of many photocatalytic materials. Standard density functional theory (DFT)-based methods have proven unable to provide a quantitative description of this level alignment. This requires a proper treatment of the anisotropic screening, necessitating the use of quasiparticle (QP) techniques. However, the computational complexity of QP algorithms has meant a quantitative description of interfacial levels has remained elusive. We provide a systematic study of a prototypical interface, bare and methanol-covered rutile TiO2(110) surfaces, to determine the type of many-body theory required to obtain an accurate description of the level alignment. This is accomplished via a direct comparison with metastable impact electron spectroscopy (MIES), ultraviolet photoelectron spectroscopy (UPS), and two-photon photoemission (2PP) spectroscopy. We consider GGA DFT, hybrid DFT, and G0W0, scQPGW1, scQPGW0, and scQPGW QP calculations. Our results demonstrate that G0W0, or our recently introduced scQPGW1 approach, are required to obtain the correct alignment of both the highest occupied and lowest unoccupied interfacial molecular levels (HOMO/LUMO). These calculations set a new standard in the interpretation of electronic structure probe experiments of complex organic molecule/semiconductor interfaces.

  9. A Novel Center Star Multiple Sequence Alignment Algorithm Based on Affine Gap Penalty and K-Band

    NASA Astrophysics Data System (ADS)

    Zou, Quan; Shan, Xiao; Jiang, Yi

    Multiple sequence alignment is one of the most important topics in computational biology, but it cannot deal with the large data so far. As the development of copy-number variant(CNV) and Single Nucleotide Polymorphisms(SNP) research, many researchers want to align numbers of similar sequences for detecting CNV and SNP. In this paper, we propose a novel multiple sequence alignment algorithm based on affine gap penalty and k-band. It can align more quickly and accurately, that will be helpful for mining CNV and SNP. Experiments prove the performance of our algorithm.

  10. 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…

  11. Impact of spine alignment on the rotator cuff in long-term wheelchair users.

    PubMed

    Kentar, Yasser; Brunner, Manuela; Bruckner, Thomas; Hug, Andreas; Raiss, Patric; Zeifang, Felix; Loew, Markus; Almansour, Haidara; Akbar, Michael

    2018-06-01

    We investigated the impact of poor seated posture on the prevalence of rotator cuff tears (RCTs) among wheelchair-dependent individuals with long-standing paraplegia. The study included 319 patients. Lateral radiographs of the spine were collected from a database and analyzed to assess the global spinopelvic alignment (SPA). Magnetic resonance images of both shoulders were obtained to detect the presence of cuff tears. Patients were divided into 2 groups: Group RCT-I included all patients with cuff tears (right, left, or bilateral), whereas group RCT-II consisted exclusively of patients with bilateral cuff tears. We used the classification systems developed by Kendall et al and Roussouly et al to assess the sagittal spine alignment and SPA, respectively. Univariate and multivariate analyses were performed. To fit both models (groups RCT-I and RCT-II) to the data, the 4 spine curves according to Roussouly et al were subdivided into 2 groups: Group SPA-I included both type 1 and type 2, whereas group SPA-II included both type 3 and type 4. Magnetic resonance images showed a cuff tear in 192 patients (60.19%) (group RCT-I). Among those, 37 patients (11.60%) had tears in both shoulders (group RCT-II). In group RCT-I, 70.31% of the patients had a kyphotic-lordotic posture. The kyphotic-lordotic posture, a longer duration, and a more rostral neurologic level of injury were highly associated with cuff tear prevalence. In group RCT-II, the multivariate analysis showed that only the duration of spinal cord injury was significantly associated with RCTs. Thoracic hyperkyphosis was associated with a markedly high rate of RCTs. The data from this study may provide support for developing preventive strategies. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

  12. 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…

  13. The Long-Term Effectiveness of Reading Recovery and the Cost-Efficiency of Reading Recovery Relative to the Learning Disabled Classification Rate

    ERIC Educational Resources Information Center

    Galluzzo, Charles A.

    2010-01-01

    There is a great deal of research supporting Reading Recovery as a successful reading intervention program that assists below level first graders readers in closing the gap in reading at the same level of their average peers. There is a lack of research that analyses the cost-effectiveness of the Reading Recovery program compared to the cost in…

  14. Pair aligning improved motility of Quincke rollers.

    PubMed

    Lu, Shi Qing; Zhang, Bing Yue; Zhang, Zhi Chao; Shi, Yan; Zhang, Tian Hui

    2018-06-06

    Density-dependent speed is studied in a two-dimensional active colloid in which the colloidal particles are propelled by an external electric field via a Quincke rotation. Above the critcal electric field, dense dynamic clusters form spotaneously, in which the particles are highly aligned in velocity and move much faster than isolated units. Detailed observations on pair collision reveal that the alignment of velocity is induced by the long-ranged hydrodynamic interactions and the improvement of speed in the clusters arises from pair aligning in which two particles are closely paired and rotate synchronically. In the aligning state, the short-range in-plane dipole-dipole attraction enhances the rotation torque and gives rises to a larger rolling speed. The pair aligning becomes difficult and unstable at high electric field where the normal dipole-dipole repulsion becomes dominant. As a consequence, the dependence of speed on density becomes weak increasingly upon the increase of the electric field. This result offers an interpretation for the discrepancy between our and previous observations on Quincke rollers.

  15. L-GRAAL: Lagrangian graphlet-based network aligner.

    PubMed

    Malod-Dognin, Noël; Pržulj, Nataša

    2015-07-01

    Discovering and understanding patterns in networks of protein-protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge. We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions. L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/. n.malod-dognin@imperial.ac.uk Supplementary data are available at

  16. 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.

  17. 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…

  18. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

    PubMed

    Chung, Dongjun; Kuan, Pei Fen; Li, Bo; Sanalkumar, Rajendran; Liang, Kun; Bresnick, Emery H; Dewey, Colin; Keleş, Sündüz

    2011-07-01

    Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.

  19. [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.

  20. Best Practices for Achieving High, Rapid Reading Gains

    ERIC Educational Resources Information Center

    Carbo, Marie

    2008-01-01

    The percentage of students who read at the proficient level on the National Assessment of Educational Progress (NAEP) has not improved, and is appallingly low. In order for students to achieve high reading gains and become life-long readers, reading comprehension and reading enjoyment must be the top two goals. This article presents several…

  1. Fine-tuning structural RNA alignments in the twilight zone

    PubMed Central

    2010-01-01

    Background A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Results Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Conclusions Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index. PMID:20433706

  2. Fine-tuning structural RNA alignments in the twilight zone.

    PubMed

    Bremges, Andreas; Schirmer, Stefanie; Giegerich, Robert

    2010-04-30

    A widely used method to find conserved secondary structure in RNA is to first construct a multiple sequence alignment, and then fold the alignment, optimizing a score based on thermodynamics and covariance. This method works best around 75% sequence similarity. However, in a "twilight zone" below 55% similarity, the sequence alignment tends to obscure the covariance signal used in the second phase. Therefore, while the overall shape of the consensus structure may still be found, the degree of conservation cannot be estimated reliably. Based on a combination of available methods, we present a method named planACstar for improving structure conservation in structural alignments in the twilight zone. After constructing a consensus structure by alignment folding, planACstar abandons the original sequence alignment, refolds the sequences individually, but consistent with the consensus, aligns the structures, irrespective of sequence, by a pure structure alignment method, and derives an improved sequence alignment from the alignment of structures, to be re-submitted to alignment folding, etc.. This circle may be iterated as long as structural conservation improves, but normally, one step suffices. Employing the tools ClustalW, RNAalifold, and RNAforester, we find that for sequences with 30-55% sequence identity, structural conservation can be improved by 10% on average, with a large variation, measured in terms of RNAalifold's own criterion, the structure conservation index.

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

    ERIC Educational Resources Information Center

    Thomas, Lisa B.

    2012-01-01

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

  4. National Year of Reading: A Year-Long Celebration and a Lasting Legacy

    ERIC Educational Resources Information Center

    Ellard, Robyn; Kelly, Paula; McKerracher, Sue

    2012-01-01

    The alarming statistic that just under half (46%) of adult Australians cannot read confidently was a stimulus for Australian libraries to found the National Year of Reading (NYR). The idea for this campaign was based on the success of the United Kingdom's National Year of Reading (National Literacy Trust 2008), a campaign that aimed to build a…

  5. A Python Script for Aligning the STIS Echelle Blaze Function

    NASA Astrophysics Data System (ADS)

    Baer, Malinda; Proffitt, Charles R.; Lockwood, Sean A.

    2018-01-01

    Accurate flux calibration for the STIS echelle modes is heavily dependent on the proper alignment of the blaze function for each spectral order. However, due to changes in the instrument alignment over time and between exposures, the blaze function can shift in wavelength. This may result in flux calibration inconsistencies of up to 10%. We present the stisblazefix Python module as a tool for STIS users to correct their echelle spectra. The stisblazefix module assumes that the error in the blaze alignment is a linear function of spectral order, and finds the set of shifts that minimizes the flux inconsistencies in the overlap between spectral orders. We discuss the uses and limitations of this tool, and show that its use can provide significant improvements to the default pipeline flux calibration for many observations.

  6. 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.

  7. Near-Field Chipless Radio-Frequency Identification (RFID) Sensing and Identification System with Switching Reading.

    PubMed

    Paredes, Ferran; Herrojo, Cristian; Mata-Contreras, Javier; Moras, Miquel; Núñez, Alba; Ramon, Eloi; Martín, Ferran

    2018-04-09

    A chipless radio-frequency identification (chipless-RFID) and sensing system, where tags are read by proximity (near-field) through a switch, is presented. The tags consist of a set of identical resonant elements (split-ring resonators or SRRs), printed or etched at predefined and equidistant positions, forming a linear chain, each SRR providing a bit of information. The logic state ('1' or '0') associated with each resonator depends on whether it is present or not in the predefined position. The reader is an array of power splitters used to feed a set of SRR-loaded transmission lines (in equal number to the number of resonant elements, or bits, of the tag). The feeding (interrogation) signal is a harmonic (single-tone) signal tuned to a frequency in the vicinity of the fundamental resonance of the SRRs. The set of SRR-loaded lines must be designed so that the corresponding SRRs are in perfect alignment with the SRRs of the tag, provided the tag is positioned on top of the reader. Thus, in a reading operation, as long as the tag is very close to the reader, the SRRs of the tag modify (decrease) the transmission coefficient of the corresponding reader line (through electromagnetic coupling between both SRRs), and the amplitude of the output signal is severely reduced. Therefore, the identification (ID) code of the tag is contained in the amplitudes of the output signals of the SRR-loaded lines, which can be inferred sequentially by means of a switching system. Unlike previous chipless-RFID systems based on near-field and sequential bit reading, the tags in the proposed system can be merely positioned on top of the reader, conveniently aligned, without the need to mechanically place them across the reader. Since tag reading is only possible if the tag is very close to the reader, this system can be also used as a proximity sensor with applications such as target identification. The proposed chipless-RFID and sensing approach is validated by reading a designed 4-bit

  8. Near-Field Chipless Radio-Frequency Identification (RFID) Sensing and Identification System with Switching Reading

    PubMed Central

    Mata-Contreras, Javier; Moras, Miquel; Ramon, Eloi; Martín, Ferran

    2018-01-01

    A chipless radio-frequency identification (chipless-RFID) and sensing system, where tags are read by proximity (near-field) through a switch, is presented. The tags consist of a set of identical resonant elements (split-ring resonators or SRRs), printed or etched at predefined and equidistant positions, forming a linear chain, each SRR providing a bit of information. The logic state (‘1’ or ‘0’) associated with each resonator depends on whether it is present or not in the predefined position. The reader is an array of power splitters used to feed a set of SRR-loaded transmission lines (in equal number to the number of resonant elements, or bits, of the tag). The feeding (interrogation) signal is a harmonic (single-tone) signal tuned to a frequency in the vicinity of the fundamental resonance of the SRRs. The set of SRR-loaded lines must be designed so that the corresponding SRRs are in perfect alignment with the SRRs of the tag, provided the tag is positioned on top of the reader. Thus, in a reading operation, as long as the tag is very close to the reader, the SRRs of the tag modify (decrease) the transmission coefficient of the corresponding reader line (through electromagnetic coupling between both SRRs), and the amplitude of the output signal is severely reduced. Therefore, the identification (ID) code of the tag is contained in the amplitudes of the output signals of the SRR-loaded lines, which can be inferred sequentially by means of a switching system. Unlike previous chipless-RFID systems based on near-field and sequential bit reading, the tags in the proposed system can be merely positioned on top of the reader, conveniently aligned, without the need to mechanically place them across the reader. Since tag reading is only possible if the tag is very close to the reader, this system can be also used as a proximity sensor with applications such as target identification. The proposed chipless-RFID and sensing approach is validated by reading a designed

  9. An Examination of the Efficacy of a Multitiered Intervention on Early Reading Outcomes for First Grade Students at Risk for Reading Difficulties.

    PubMed

    Fien, Hank; Smith, Jean Louise M; Smolkowski, Keith; Baker, Scott K; Nelson, Nancy J; Chaparro, Erin

    2015-01-01

    This article presents findings of an efficacy trial examining the effect of a multitiered instruction and intervention model on first grade at-risk students' reading outcomes. Schools (N = 16) were randomly assigned to the treatment or control condition. In the fall of Grade 1, students were assigned to an instructional tier on the basis of Stanford Achievement Test-10th Edition scores (31st percentile and above = Tier 1; from the 10th to the 30th percentile = Tier 2). In both conditions, students identified as at risk (i.e., Tier 2; n = 267) received 90 min of whole group instruction (Tier 1) and an additional 30 min of daily small group intervention (Tier 2). In the treatment condition, teachers were trained to enhance core reading instruction by making instruction more explicit and increasing practice opportunities for students in Tier 1. In addition, at-risk readers were provided an additional 30-min daily small group intervention with content that was highly aligned with the Tier 1 core reading program. Results indicate significant, positive effects of the intervention on students' decoding and first semester fluent reading and potentially positive effects on reading comprehension and total reading achievement. © Hammill Institute on Disabilities 2014.

  10. Cryo-EM image alignment based on nonuniform fast Fourier transform.

    PubMed

    Yang, Zhengfan; Penczek, Pawel A

    2008-08-01

    In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform fast Fourier transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis.

  11. Cryo-EM Image Alignment Based on Nonuniform Fast Fourier Transform

    PubMed Central

    Yang, Zhengfan; Penczek, Pawel A.

    2008-01-01

    In single particle analysis, two-dimensional (2-D) alignment is a fundamental step intended to put into register various particle projections of biological macromolecules collected at the electron microscope. The efficiency and quality of three-dimensional (3-D) structure reconstruction largely depends on the computational speed and alignment accuracy of this crucial step. In order to improve the performance of alignment, we introduce a new method that takes advantage of the highly accurate interpolation scheme based on the gridding method, a version of the nonuniform Fast Fourier Transform, and utilizes a multi-dimensional optimization algorithm for the refinement of the orientation parameters. Using simulated data, we demonstrate that by using less than half of the sample points and taking twice the runtime, our new 2-D alignment method achieves dramatically better alignment accuracy than that based on quadratic interpolation. We also apply our method to image to volume registration, the key step in the single particle EM structure refinement protocol. We find that in this case the accuracy of the method not only surpasses the accuracy of the commonly used real-space implementation, but results are achieved in much shorter time, making gridding-based alignment a perfect candidate for efficient structure determination in single particle analysis. PMID:18499351

  12. Rod-Shaped Neural Units for Aligned 3D Neural Network Connection.

    PubMed

    Kato-Negishi, Midori; Onoe, Hiroaki; Ito, Akane; Takeuchi, Shoji

    2017-08-01

    This paper proposes neural tissue units with aligned nerve fibers (called rod-shaped neural units) that connect neural networks with aligned neurons. To make the proposed units, 3D fiber-shaped neural tissues covered with a calcium alginate hydrogel layer are prepared with a microfluidic system and are cut in an accurate and reproducible manner. These units have aligned nerve fibers inside the hydrogel layer and connectable points on both ends. By connecting the units with a poly(dimethylsiloxane) guide, 3D neural tissues can be constructed and maintained for more than two weeks of culture. In addition, neural networks can be formed between the different neural units via synaptic connections. Experimental results indicate that the proposed rod-shaped neural units are effective tools for the construction of spatially complex connections with aligned nerve fibers in vitro. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Does Student Proficiency on Local Reading Assessment Measures Align with State Mandated Reading Proficiency Standards? An Investigation of the Relationship between the Developmental Reading Assessment, Reading Curriculum Based Measurement, and Maze, with the New York State English Language Arts Exam

    ERIC Educational Resources Information Center

    Weschler, Michael J.

    2016-01-01

    Data from three reading assessment tools--the Developmental Reading Assessment (DRA), Reading Curriculum Based Measurement (R-CBM), and Maze--were compiled from 61 fourth grade and 59 fifth grade students across Fall and Spring administrations in order to determine how proficiency on these measures was associated with proficiency on the New York…

  14. Integrated crystal mounting and alignment system for high-throughput biological crystallography

    DOEpatents

    Nordmeyer, Robert A.; Snell, Gyorgy P.; Cornell, Earl W.; Kolbe, William F.; Yegian, Derek T.; Earnest, Thomas N.; Jaklevich, Joseph M.; Cork, Carl W.; Santarsiero, Bernard D.; Stevens, Raymond C.

    2007-09-25

    A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following removal. The samples must additionally be stably aligned to within a few microns at a point in space. The ability to accurately perform these tasks remotely and automatically leads to a significant increase in sample throughput and reliability for high-volume protein characterization efforts. Since the protein samples are placed in a shipping-compatible layered stack of sample cassettes each holding many samples, a large number of samples can be shipped in a single cryogenic shipping container.

  15. Integrated crystal mounting and alignment system for high-throughput biological crystallography

    DOEpatents

    Nordmeyer, Robert A.; Snell, Gyorgy P.; Cornell, Earl W.; Kolbe, William; Yegian, Derek; Earnest, Thomas N.; Jaklevic, Joseph M.; Cork, Carl W.; Santarsiero, Bernard D.; Stevens, Raymond C.

    2005-07-19

    A method and apparatus for the transportation, remote and unattended mounting, and visual alignment and monitoring of protein crystals for synchrotron generated x-ray diffraction analysis. The protein samples are maintained at liquid nitrogen temperatures at all times: during shipment, before mounting, mounting, alignment, data acquisition and following removal. The samples must additionally be stably aligned to within a few microns at a point in space. The ability to accurately perform these tasks remotely and automatically leads to a significant increase in sample throughput and reliability for high-volume protein characterization efforts. Since the protein samples are placed in a shipping-compatible layered stack of sample cassettes each holding many samples, a large number of samples can be shipped in a single cryogenic shipping container.

  16. AlignMe—a membrane protein sequence alignment web server

    PubMed Central

    Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

    2014-01-01

    We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

  17. The National Ignition Facility: alignment from construction to shot operations

    NASA Astrophysics Data System (ADS)

    Burkhart, S. C.; Bliss, E.; Di Nicola, P.; Kalantar, D.; Lowe-Webb, R.; McCarville, T.; Nelson, D.; Salmon, T.; Schindler, T.; Villanueva, J.; Wilhelmsen, K.

    2010-08-01

    The National Ignition Facility in Livermore, California, completed it's commissioning milestone on March 10, 2009 when it fired all 192 beams at a combined energy of 1.1 MJ at 351nm. Subsequently, a target shot series from August through December of 2009 culminated in scale ignition target design experiments up to 1.2 MJ in the National Ignition Campaign. Preparations are underway through the first half of of 2010 leading to DT ignition and gain experiments in the fall of 2010 into 2011. The top level requirement for beam pointing to target of 50μm rms is the culmination of 15 years of engineering design of a stable facility, commissioning of precision alignment, and precise shot operations controls. Key design documents which guided this project were published in the mid 1990's, driving systems designs. Precision Survey methods were used throughout construction, commissioning and operations for precision placement. Rigorous commissioning processes were used to ensure and validate placement and alignment throughout commissioning and in present day operations. Accurate and rapid system alignment during operations is accomplished by an impressive controls system to align and validate alignment readiness, assuring machine safety and productive experiments.

  18. A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

    PubMed

    Han, Renmin; Wang, Liansan; Liu, Zhiyong; Sun, Fei; Zhang, Fa

    2015-12-01

    Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. A statistical physics perspective on alignment-independent protein sequence comparison.

    PubMed

    Chattopadhyay, Amit K; Nasiev, Diar; Flower, Darren R

    2015-08-01

    Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from 'first passage probability distribution' to summarize statistics of ensemble averaged amino acid propensity values. In this article, we introduce and elaborate this approach. © The Author 2015. Published by Oxford University Press.

  20. Sequence verification of synthetic DNA by assembly of sequencing reads

    PubMed Central

    Wilson, Mandy L.; Cai, Yizhi; Hanlon, Regina; Taylor, Samantha; Chevreux, Bastien; Setubal, João C.; Tyler, Brett M.; Peccoud, Jean

    2013-01-01

    Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that the physical sequence of a clone matches its published sequence is a common quality control step performed at least once over the course of a research project. GenoREAD is a web-based application that breaks the sequence verification process into two steps: the assembly of sequencing reads and the alignment of the resulting contig with a reference sequence. GenoREAD can determine if a clone matches its reference sequence. Its sophisticated reporting features help identify and troubleshoot problems that arise during the sequence verification process. GenoREAD has been experimentally validated on thousands of gene-sized constructs from an ORFeome project, and on longer sequences including whole plasmids and synthetic chromosomes. Comparing GenoREAD results with those from manual analysis of the sequencing data demonstrates that GenoREAD tends to be conservative in its diagnostic. GenoREAD is available at www.genoread.org. PMID:23042248

  1. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

    PubMed Central

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-01-01

    Background Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles. Results The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR), we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. Conclusion The SMM-align method was

  2. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method.

    PubMed

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-07-04

    Antigen presenting cells (APCs) sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II) molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC) and three mouse H2-IA alleles. The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR), we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. The SMM-align method was shown to outperform other

  3. A convenient alignment approach for x-ray imaging experiments based on laser positioning devices

    PubMed Central

    Zhang, Da; Donovan, Molly; Wu, Xizeng; Liu, Hong

    2008-01-01

    This study presents a two-laser alignment approach for facilitating the precise alignment of various imaging and measuring components with respect to the x-ray beam. The first laser constantly pointed to the output window of the source, in a direction parallel to the path along which the components are placed. The second laser beam, originating from the opposite direction, was calibrated to coincide with the first laser beam. Thus, a visible indicator of the direction of the incident x-ray beam was established, and the various components could then be aligned conveniently and accurately with its help. PMID:19070224

  4. Interactional Scaffolding for Reading Comprehension: A Systematic Review

    ERIC Educational Resources Information Center

    Reynolds, Dan

    2017-01-01

    Understanding how to support student reading comprehension has long been a goal for education research. Yet no existing literature review links interactional scaffolding, defined as the responsive in-person support an expert reader offers to a novice, and reading comprehension. This review employed theories of scaffolding and reading comprehension…

  5. Alignment-Based Prediction of Sites of Metabolism.

    PubMed

    de Bruyn Kops, Christina; Friedrich, Nils-Ole; Kirchmair, Johannes

    2017-06-26

    Prediction of metabolically labile atom positions in a molecule (sites of metabolism) is a key component of the simulation of xenobiotic metabolism as a whole, providing crucial information for the development of safe and effective drugs. In 2008, an exploratory study was published in which sites of metabolism were derived based on molecular shape- and chemical feature-based alignment to a molecule whose site of metabolism (SoM) had been determined by experiments. We present a detailed analysis of the breadth of applicability of alignment-based SoM prediction, including transfer of the approach from a structure- to ligand-based method and extension of the applicability of the models from cytochrome P450 2C9 to all cytochrome P450 isozymes involved in drug metabolism. We evaluate the effect of molecular similarity of the query and reference molecules on the ability of this approach to accurately predict SoMs. In addition, we combine the alignment-based method with a leading chemical reactivity model to take reactivity into account. The combined model yielded superior performance in comparison to the alignment-based approach and the reactivity models with an average area under the receiver operating characteristic curve of 0.85 in cross-validation experiments. In particular, early enrichment was improved, as evidenced by higher BEDROC scores (mean BEDROC = 0.59 for α = 20.0, mean BEDROC = 0.73 for α = 80.5).

  6. 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…

  7. FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately.

    PubMed

    Budowski-Tal, Inbal; Nov, Yuval; Kolodny, Rachel

    2010-02-23

    Fast identification of protein structures that are similar to a specified query structure in the entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We present FragBag: An ultrafast and accurate method for comparing protein structures. We describe a protein structure by the collection of its overlapping short contiguous backbone segments, and discretize this set using a library of fragments. Then, we succinctly represent the protein as a "bags-of-fragments"-a vector that counts the number of occurrences of each fragment-and measure the similarity between two structures by the similarity between their vectors. Our representation has two additional benefits: (i) it can be used to construct an inverted index, for implementing a fast structural search engine of the entire PDB, and (ii) one can specify a structure as a collection of substructures, without combining them into a single structure; this is valuable for structure prediction, when there are reliable predictions only of parts of the protein. We use receiver operating characteristic curve analysis to quantify the success of FragBag in identifying neighbor candidate sets in a dataset of over 2,900 structures. The gold standard is the set of neighbors found by six state of the art structural aligners. Our best FragBag library finds more accurate candidate sets than the three other filter methods: The SGM, PRIDE, and a method by Zotenko et al. More interestingly, FragBag performs on a par with the computationally expensive, yet highly trusted structural aligners STRUCTAL and CE.

  8. 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.

  9. A Meta-Analysis of the Long-Term Effects of Phonemic Awareness, Phonics, Fluency, and Reading Comprehension Interventions.

    PubMed

    Suggate, Sebastian P

    2016-01-01

    Much is known about short-term--but very little about the long-term--effects of reading interventions. To rectify this, a detailed analysis of follow-up effects as a function of intervention, sample, and methodological variables was conducted. A total of 71 intervention-control groups were selected (N = 8,161 at posttest) from studies reporting posttest and follow-up data (M = 11.17 months) for previously established reading interventions. The posttest effect sizes indicated effects (dw = 0.37) that decreased to follow-up (dw = 0.22). Overall, comprehension and phonemic awareness interventions showed good maintenance of effect that transferred to nontargeted skills, whereas phonics and fluency interventions, and those for preschool and kindergarten children, tended not to. Several methodological features also related to effect sizes at follow-up, namely experimental design and dosage, and sample attrition, risk status, and gender balance. © Hammill Institute on Disabilities 2014.

  10. 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),…

  11. Markov random field based automatic image alignment for electron tomography.

    PubMed

    Amat, Fernando; Moussavi, Farshid; Comolli, Luis R; Elidan, Gal; Downing, Kenneth H; Horowitz, Mark

    2008-03-01

    We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.

  12. 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…

  13. Automatic laser beam alignment using blob detection for an environment monitoring spectroscopy

    NASA Astrophysics Data System (ADS)

    Khidir, Jarjees; Chen, Youhua; Anderson, Gary

    2013-05-01

    This paper describes a fully automated system to align an infra-red laser beam with a small retro-reflector over a wide range of distances. The component development and test were especially used for an open-path spectrometer gas detection system. Using blob detection under OpenCV library, an automatic alignment algorithm was designed to achieve fast and accurate target detection in a complex background environment. Test results are presented to show that the proposed algorithm has been successfully applied to various target distances and environment conditions.

  14. Rapid Quantification of 3D Collagen Fiber Alignment and Fiber Intersection Correlations with High Sensitivity

    PubMed Central

    Sun, Meng; Bloom, Alexander B.; Zaman, Muhammad H.

    2015-01-01

    Metastatic cancers aggressively reorganize collagen in their microenvironment. For example, radially orientated collagen fibers have been observed surrounding tumor cell clusters in vivo. The degree of fiber alignment, as a consequence of this remodeling, has often been difficult to quantify. In this paper, we present an easy to implement algorithm for accurate detection of collagen fiber orientation in a rapid pixel-wise manner. This algorithm quantifies the alignment of both computer generated and actual collagen fiber networks of varying degrees of alignment within 5°°. We also present an alternative easy method to calculate the alignment index directly from the standard deviation of fiber orientation. Using this quantitative method for determining collagen alignment, we demonstrate that the number of collagen fiber intersections has a negative correlation with the degree of fiber alignment. This decrease in intersections of aligned fibers could explain why cells move more rapidly along aligned fibers than unaligned fibers, as previously reported. Overall, our paper provides an easier, more quantitative and quicker way to quantify fiber orientation and alignment, and presents a platform in studying effects of matrix and cellular properties on fiber alignment in complex 3D environments. PMID:26158674

  15. Automated assembly of camera modules using active alignment with up to six degrees of freedom

    NASA Astrophysics Data System (ADS)

    Bräuniger, K.; Stickler, D.; Winters, D.; Volmer, C.; Jahn, M.; Krey, S.

    2014-03-01

    With the upcoming Ultra High Definition (UHD) cameras, the accurate alignment of optical systems with respect to the UHD image sensor becomes increasingly important. Even with a perfect objective lens, the image quality will deteriorate when it is poorly aligned to the sensor. For evaluating the imaging quality the Modulation Transfer Function (MTF) is used as the most accepted test. In the first part it is described how the alignment errors that lead to a low imaging quality can be measured. Collimators with crosshair at defined field positions or a test chart are used as object generators for infinite-finite or respectively finite-finite conjugation. The process how to align the image sensor accurately to the optical system will be described. The focus position, shift, tilt and rotation of the image sensor are automatically corrected to obtain an optimized MTF for all field positions including the center. The software algorithm to grab images, calculate the MTF and adjust the image sensor in six degrees of freedom within less than 30 seconds per UHD camera module is described. The resulting accuracy of the image sensor rotation is better than 2 arcmin and the accuracy position alignment in x,y,z is better 2 μm. Finally, the process of gluing and UV-curing is described and how it is managed in the integrated process.

  16. ARE TIDAL EFFECTS RESPONSIBLE FOR EXOPLANETARY SPIN–ORBIT ALIGNMENT?

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

    Li, Gongjie; Winn, Joshua N., E-mail: gli@cfa.harvard.edu

    The obliquities of planet-hosting stars are clues about the formation of planetary systems. Previous observations led to the hypothesis that for close-in giant planets, spin–orbit alignment is enforced by tidal interactions. Here, we examine two problems with this hypothesis. First, Mazeh and coworkers recently used a new technique—based on the amplitude of starspot-induced photometric variability—to conclude that spin–orbit alignment is common even for relatively long-period planets, which would not be expected if tides were responsible. We re-examine the data and find a statistically significant correlation between photometric variability and planetary orbital period that is qualitatively consistent with tidal interactions. Howevermore » it is still difficult to explain quantitatively, as it would require tides to be effective for periods as long as tens of days. Second, Rogers and Lin argued against a particular theory for tidal re-alignment by showing that initially retrograde systems would fail to be re-aligned, in contradiction with the observed prevalence of prograde systems. We investigate a simple model that overcomes this problem by taking into account the dissipation of inertial waves and the equilibrium tide, as well as magnetic braking. We identify a region of parameter space where re-alignment can be achieved, but it only works for close-in giant planets, and requires some fine tuning. Thus, while we find both problems to be more nuanced than they first appeared, the tidal model still has serious shortcomings.« less

  17. AntiClustal: Multiple Sequence Alignment by antipole clustering and linear approximate 1-median computation.

    PubMed

    Di Pietro, C; Di Pietro, V; Emmanuele, G; Ferro, A; Maugeri, T; Modica, E; Pigola, G; Pulvirenti, A; Purrello, M; Ragusa, M; Scalia, M; Shasha, D; Travali, S; Zimmitti, V

    2003-01-01

    In this paper we present a new Multiple Sequence Alignment (MSA) algorithm called AntiClusAl. The method makes use of the commonly use idea of aligning homologous sequences belonging to classes generated by some clustering algorithm, and then continue the alignment process ina bottom-up way along a suitable tree structure. The final result is then read at the root of the tree. Multiple sequence alignment in each cluster makes use of the progressive alignment with the 1-median (center) of the cluster. The 1-median of set S of sequences is the element of S which minimizes the average distance from any other sequence in S. Its exact computation requires quadratic time. The basic idea of our proposed algorithm is to make use of a simple and natural algorithmic technique based on randomized tournaments which has been successfully applied to large size search problems in general metric spaces. In particular a clustering algorithm called Antipole tree and an approximate linear 1-median computation are used. Our algorithm compared with Clustal W, a widely used tool to MSA, shows a better running time results with fully comparable alignment quality. A successful biological application showing high aminoacid conservation during evolution of Xenopus laevis SOD2 is also cited.

  18. 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.

  19. Application of long sequence reads to improve genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7

    DOE PAGES

    Utturkar, Sagar M.; Bayer, Edward A.; Borovok, Ilya; ...

    2016-09-29

    Here, we and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.

  20. CCD Camera Lens Interface for Real-Time Theodolite Alignment

    NASA Technical Reports Server (NTRS)

    Wake, Shane; Scott, V. Stanley, III

    2012-01-01

    Theodolites are a common instrument in the testing, alignment, and building of various systems ranging from a single optical component to an entire instrument. They provide a precise way to measure horizontal and vertical angles. They can be used to align multiple objects in a desired way at specific angles. They can also be used to reference a specific location or orientation of an object that has moved. Some systems may require a small margin of error in position of components. A theodolite can assist with accurately measuring and/or minimizing that error. The technology is an adapter for a CCD camera with lens to attach to a Leica Wild T3000 Theodolite eyepiece that enables viewing on a connected monitor, and thus can be utilized with multiple theodolites simultaneously. This technology removes a substantial part of human error by relying on the CCD camera and monitors. It also allows image recording of the alignment, and therefore provides a quantitative means to measure such error.

  1. 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,…

  2. Xylem vulnerability to cavitation can be accurately characterised in species with long vessels using a centrifuge method.

    PubMed

    Tobin, M F; Pratt, R B; Jacobsen, A L; De Guzman, M E

    2013-05-01

    Vulnerability to cavitation curves describe the decrease in xylem hydraulic conductivity as xylem pressure declines. Several techniques for constructing vulnerability curves use centrifugal force to induce negative xylem pressure in stem or root segments. Centrifuge vulnerability curves constructed for long-vesselled species have been hypothesised to overestimate xylem vulnerability to cavitation due to increased vulnerability of vessels cut open at stem ends that extend to the middle or entirely through segments. We tested two key predictions of this hypothesis: (i) centrifugation induces greater embolism than dehydration in long-vesselled species, and (ii) the proportion of open vessels changes centrifuge vulnerability curves. Centrifuge and dehydration vulnerability curves were compared for a long- and short-vesselled species. The effect of open vessels was tested in four species by comparing centrifuge vulnerability curves for stems of two lengths. Centrifuge and dehydration vulnerability curves agreed well for the long- and short-vesselled species. Centrifuge vulnerability curves constructed using two stem lengths were similar. Also, the distribution of embolism along the length of centrifuged stems matched the theoretical pressure profile induced by centrifugation. We conclude that vulnerability to cavitation can be accurately characterised with vulnerability curves constructed using a centrifuge technique, even in long-vesselled species. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  3. Evaluation of Eight Methods for Aligning Orientation of Two Coordinate Systems.

    PubMed

    Mecheri, Hakim; Robert-Lachaine, Xavier; Larue, Christian; Plamondon, André

    2016-08-01

    The aim of this study was to evaluate eight methods for aligning the orientation of two different local coordinate systems. Alignment is very important when combining two different systems of motion analysis. Two of the methods were developed specifically for biomechanical studies, and because there have been at least three decades of algorithm development in robotics, it was decided to include six methods from this field. To compare these methods, an Xsens sensor and two Optotrak clusters were attached to a Plexiglas plate. The first optical marker cluster was fixed on the sensor and 20 trials were recorded. The error of alignment was calculated for each trial, and the mean, the standard deviation, and the maximum values of this error over all trials were reported. One-way repeated measures analysis of variance revealed that the alignment error differed significantly across the eight methods. Post-hoc tests showed that the alignment error from the methods based on angular velocities was significantly lower than for the other methods. The method using angular velocities performed the best, with an average error of 0.17 ± 0.08 deg. We therefore recommend this method, which is easy to perform and provides accurate alignment.

  4. Alignment of high-throughput sequencing data inside in-memory databases.

    PubMed

    Firnkorn, Daniel; Knaup-Gregori, Petra; Lorenzo Bermejo, Justo; Ganzinger, Matthias

    2014-01-01

    In times of high-throughput DNA sequencing techniques, performance-capable analysis of DNA sequences is of high importance. Computer supported DNA analysis is still an intensive time-consuming task. In this paper we explore the potential of a new In-Memory database technology by using SAP's High Performance Analytic Appliance (HANA). We focus on read alignment as one of the first steps in DNA sequence analysis. In particular, we examined the widely used Burrows-Wheeler Aligner (BWA) and implemented stored procedures in both, HANA and the free database system MySQL, to compare execution time and memory management. To ensure that the results are comparable, MySQL has been running in memory as well, utilizing its integrated memory engine for database table creation. We implemented stored procedures, containing exact and inexact searching of DNA reads within the reference genome GRCh37. Due to technical restrictions in SAP HANA concerning recursion, the inexact matching problem could not be implemented on this platform. Hence, performance analysis between HANA and MySQL was made by comparing the execution time of the exact search procedures. Here, HANA was approximately 27 times faster than MySQL which means, that there is a high potential within the new In-Memory concepts, leading to further developments of DNA analysis procedures in the future.

  5. Functionalization of vertically aligned carbon nanotubes.

    PubMed

    Van Hooijdonk, Eloise; Bittencourt, Carla; Snyders, Rony; Colomer, Jean-François

    2013-01-01

    This review focuses and summarizes recent studies on the functionalization of carbon nanotubes oriented perpendicularly to their substrate, so-called vertically aligned carbon nanotubes (VA-CNTs). The intrinsic properties of individual nanotubes make the VA-CNTs ideal candidates for integration in a wide range of devices, and many potential applications have been envisaged. These applications can benefit from the unidirectional alignment of the nanotubes, the large surface area, the high carbon purity, the outstanding electrical conductivity, and the uniformly long length. However, practical uses of VA-CNTs are limited by their surface characteristics, which must be often modified in order to meet the specificity of each particular application. The proposed approaches are based on the chemical modifications of the surface by functionalization (grafting of functional chemical groups, decoration with metal particles or wrapping of polymers) to bring new properties or to improve the interactions between the VA-CNTs and their environment while maintaining the alignment of CNTs.

  6. Functionalization of vertically aligned carbon nanotubes

    PubMed Central

    Snyders, Rony; Colomer, Jean-François

    2013-01-01

    Summary This review focuses and summarizes recent studies on the functionalization of carbon nanotubes oriented perpendicularly to their substrate, so-called vertically aligned carbon nanotubes (VA-CNTs). The intrinsic properties of individual nanotubes make the VA-CNTs ideal candidates for integration in a wide range of devices, and many potential applications have been envisaged. These applications can benefit from the unidirectional alignment of the nanotubes, the large surface area, the high carbon purity, the outstanding electrical conductivity, and the uniformly long length. However, practical uses of VA-CNTs are limited by their surface characteristics, which must be often modified in order to meet the specificity of each particular application. The proposed approaches are based on the chemical modifications of the surface by functionalization (grafting of functional chemical groups, decoration with metal particles or wrapping of polymers) to bring new properties or to improve the interactions between the VA-CNTs and their environment while maintaining the alignment of CNTs. PMID:23504581

  7. Spatiotemporal alignment of in utero BOLD-MRI series.

    PubMed

    Turk, Esra Abaci; Luo, Jie; Gagoski, Borjan; Pascau, Javier; Bibbo, Carolina; Robinson, Julian N; Grant, P Ellen; Adalsteinsson, Elfar; Golland, Polina; Malpica, Norberto

    2017-08-01

    To present a method for spatiotemporal alignment of in-utero magnetic resonance imaging (MRI) time series acquired during maternal hyperoxia for enabling improved quantitative tracking of blood oxygen level-dependent (BOLD) signal changes that characterize oxygen transport through the placenta to fetal organs. The proposed pipeline for spatiotemporal alignment of images acquired with a single-shot gradient echo echo-planar imaging includes 1) signal nonuniformity correction, 2) intravolume motion correction based on nonrigid registration, 3) correction of motion and nonrigid deformations across volumes, and 4) detection of the outlier volumes to be discarded from subsequent analysis. BOLD MRI time series collected from 10 pregnant women during 3T scans were analyzed using this pipeline. To assess pipeline performance, signal fluctuations between consecutive timepoints were examined. In addition, volume overlap and distance between manual region of interest (ROI) delineations in a subset of frames and the delineations obtained through propagation of the ROIs from the reference frame were used to quantify alignment accuracy. A previously demonstrated rigid registration approach was used for comparison. The proposed pipeline improved anatomical alignment of placenta and fetal organs over the state-of-the-art rigid motion correction methods. In particular, unexpected temporal signal fluctuations during the first normoxia period were significantly decreased (P < 0.01) and volume overlap and distance between region boundaries measures were significantly improved (P < 0.01). The proposed approach to align MRI time series enables more accurate quantitative studies of placental function by improving spatiotemporal alignment across placenta and fetal organs. 1 Technical Efficacy: Stage 1 J. MAGN. RESON. IMAGING 2017;46:403-412. © 2017 International Society for Magnetic Resonance in Medicine.

  8. Geometry calibration for x-ray equipment in radiation treatment devices and estimation of remaining patient alignment errors

    NASA Astrophysics Data System (ADS)

    Selby, Boris P.; Sakas, Georgios; Walter, Stefan; Stilla, Uwe

    2008-03-01

    Positioning a patient accurately in treatment devices is crucial for radiological treatment, especially if accuracy vantages of particle beam treatment are exploited. To avoid sub-millimeter misalignments, X-ray images acquired from within the device are compared to a CT to compute respective alignment corrections. Unfortunately, deviations of the underlying geometry model for the imaging system degrade the achievable accuracy. We propose an automatic calibration routine, which bases on the geometry of a phantom and its automatic detection in digital radiographs acquired for various geometric device settings during the calibration. The results from the registration of the phantom's X-ray projections and its known geometry are used to update the model of the respective beamlines, which is used to compute the patient alignment correction. The geometric calibration of a beamline takes all nine relevant degrees of freedom into account, including detector translations in three directions, detector tilt by three axes and three possible translations for the X-ray tube. Introducing a stochastic model for the calibration we are able to predict the patient alignment deviations resulting from inaccuracies inherent to the phantom design and the calibration. Comparisons of the alignment results for a treatment device without calibrated imaging systems and a calibrated device show that an accurate calibration can enhance alignment accuracy.

  9. The influence of atomic alignment on absorption and emission spectroscopy

    NASA Astrophysics Data System (ADS)

    Zhang, Heshou; Yan, Huirong; Richter, Philipp

    2018-06-01

    Spectroscopic observations play essential roles in astrophysics. They are crucial for determining physical parameters in the universe, providing information about the chemistry of various astronomical environments. The proper execution of the spectroscopic analysis requires accounting for all the physical effects that are compatible to the signal-to-noise ratio. We find in this paper the influence on spectroscopy from the atomic/ground state alignment owing to anisotropic radiation and modulated by interstellar magnetic field, has significant impact on the study of interstellar gas. In different observational scenarios, we comprehensively demonstrate how atomic alignment influences the spectral analysis and provide the expressions for correcting the effect. The variations are even more pronounced for multiplets and line ratios. We show the variation of the deduced physical parameters caused by the atomic alignment effect, including alpha-to-iron ratio ([X/Fe]) and ionisation fraction. Synthetic observations are performed to illustrate the visibility of such effect with current facilities. A study of PDRs in ρ Ophiuchi cloud is presented to demonstrate how to account for atomic alignment in practice. Our work has shown that due to its potential impact, atomic alignment has to be included in an accurate spectroscopic analysis of the interstellar gas with current observational capability.

  10. 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…

  11. IUS prerelease alignment

    NASA Technical Reports Server (NTRS)

    Evans, F. A.

    1978-01-01

    Space shuttle orbiter/IUS alignment transfer was evaluated. Although the orbiter alignment accuracy was originally believed to be the major contributor to the overall alignment transfer error, it was shown that orbiter alignment accuracy is not a factor affecting IUS alignment accuracy, if certain procedures are followed. Results are reported of alignment transfer accuracy analysis.

  12. Optimal Parameter Design of Coarse Alignment for Fiber Optic Gyro Inertial Navigation System.

    PubMed

    Lu, Baofeng; Wang, Qiuying; Yu, Chunmei; Gao, Wei

    2015-06-25

    Two different coarse alignment algorithms for Fiber Optic Gyro (FOG) Inertial Navigation System (INS) based on inertial reference frame are discussed in this paper. Both of them are based on gravity vector integration, therefore, the performance of these algorithms is determined by integration time. In previous works, integration time is selected by experience. In order to give a criterion for the selection process, and make the selection of the integration time more accurate, optimal parameter design of these algorithms for FOG INS is performed in this paper. The design process is accomplished based on the analysis of the error characteristics of these two coarse alignment algorithms. Moreover, this analysis and optimal parameter design allow us to make an adequate selection of the most accurate algorithm for FOG INS according to the actual operational conditions. The analysis and simulation results show that the parameter provided by this work is the optimal value, and indicate that in different operational conditions, the coarse alignment algorithms adopted for FOG INS are different in order to achieve better performance. Lastly, the experiment results validate the effectiveness of the proposed algorithm.

  13. 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

  14. 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.

  15. Reading, Writing & Rings: Science Literacy for K-4 Students

    NASA Astrophysics Data System (ADS)

    McConnell, S.; Spilker, L.; Zimmerman-Brachman, R.

    2007-12-01

    Scientific discovery is the impetus for the K-4 Education program, "Reading, Writing & Rings." This program is unique because its focus is to engage elementary students in reading and writing to strengthen these basic academic skills through scientific content. As science has been increasingly overtaken by the language arts in elementary classrooms, the Cassini Education Program has taken advantage of a new cross-disciplinary approach to use language arts as a vehicle for increasing scientific content in the classroom. By utilizing the planet Saturn and the Cassini-Huygens mission as a model in both primary reading and writing students in these grade levels, young students can explore science material while at the same time learning these basic academic skills. Content includes reading, thinking, and hands-on activities. Developed in partnership with the Cassini-Huygens Education and Public Outreach Program, the Bay Area Writing Project/California Writing Project, Foundations in Reading Through Science & Technology (FIRST), and the Caltech Pre-College Science Initiative (CAPSI), and classroom educators, "Reading, Writing & Rings" blends the excitement of space exploration with reading and writing. All materials are teacher developed, aligned with national science and language education standards, and are available from the Cassini-Huygens website: http://saturn.jpl.nasa.gov/education/edu-k4.cfm Materials are divided into two grade level units. One unit is designed for students in grades 1 and 2 while the other unit focuses on students in grades 3 and 4. Each includes a series of lessons that take students on a path of exploration of Saturn using reading and writing prompts.

  16. 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.

  17. AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

    PubMed Central

    Aniba, Mohamed Radhouene; Poch, Olivier; Marchler-Bauer, Aron; Thompson, Julie Dawn

    2010-01-01

    Multiple sequence alignment (MSA) is a cornerstone of modern molecular biology and represents a unique means of investigating the patterns of conservation and diversity in complex biological systems. Many different algorithms have been developed to construct MSAs, but previous studies have shown that no single aligner consistently outperforms the rest. This has led to the development of a number of ‘meta-methods’ that systematically run several aligners and merge the output into one single solution. Although these methods generally produce more accurate alignments, they are inefficient because all the aligners need to be run first and the choice of the best solution is made a posteriori. Here, we describe the development of a new expert system, AlexSys, for the multiple alignment of protein sequences. AlexSys incorporates an intelligent inference engine to automatically select an appropriate aligner a priori, depending only on the nature of the input sequences. The inference engine was trained on a large set of reference multiple alignments, using a novel machine learning approach. Applying AlexSys to a test set of 178 alignments, we show that the expert system represents a good compromise between alignment quality and running time, making it suitable for high throughput projects. AlexSys is freely available from http://alnitak.u-strasbg.fr/∼aniba/alexsys. PMID:20530533

  18. SU-F-I-59: Quality Assurance Phantom for PET/CT Alignment and Attenuation Correction

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

    Lin, T; Hamacher, K

    2016-06-15

    Purpose: This study utilizes a commercial PET/CT phantom to investigate two specific properties of a PET/CT system: the alignment accuracy of PET images with those from CT used for attenuation correction and the accuracy of this correction in PET images. Methods: A commercial PET/CT phantom consisting of three aluminum rods, two long central cylinders containing uniform activity, and attenuating materials such as air, water, bone and iodine contrast was scanned using a standard PET/CT protocol. Images reconstructed with 2 mm slice thickness and a 512 by 512 matrix were obtained. The center of each aluminum rod in the PET andmore » CT images was compared to evaluate alignment accuracy. ROIs were drawn on transaxial images of the central rods at each section of attenuating material to determine the corrected activity (in BQML). BQML values were graphed as a function of slice number to provide a visual representation of the attenuation-correction throughout the whole phantom. Results: Alignment accuracy is high between the PET and CT images. The maximum deviation between the two in the axial plane is less than 1.5 mm, which is less than the width of a single pixel. BQML values measured along different sections of the large central rods are similar among the different attenuating materials except iodine contrast. Deviation of BQML values in the air and bone sections from the water section is less than 1%. Conclusion: Accurate alignment of PET and CT images is critical to ensure proper calculation and application of CT-based attenuation correction. This study presents a simple and quick method to evaluate the two with a single acquisition. As the phantom also includes spheres of increasing diameter, this could serve as a straightforward means to annually evaluate the status of a modern PET/CT system.« less

  19. Evaluation of GMI and PMI diffeomorphic-based demons algorithms for aligning PET and CT Images.

    PubMed

    Yang, Juan; Wang, Hongjun; Zhang, You; Yin, Yong

    2015-07-08

    Fusion of anatomic information in computed tomography (CT) and functional information in 18F-FDG positron emission tomography (PET) is crucial for accurate differentiation of tumor from benign masses, designing radiotherapy treatment plan and staging of cancer. Although current PET and CT images can be acquired from combined 18F-FDG PET/CT scanner, the two acquisitions are scanned separately and take a long time, which may induce potential positional errors in global and local caused by respiratory motion or organ peristalsis. So registration (alignment) of whole-body PET and CT images is a prerequisite for their meaningful fusion. The purpose of this study was to assess the performance of two multimodal registration algorithms for aligning PET and CT images. The proposed gradient of mutual information (GMI)-based demons algorithm, which incorporated the GMI between two images as an external force to facilitate the alignment, was compared with the point-wise mutual information (PMI) diffeomorphic-based demons algorithm whose external force was modified by replacing the image intensity difference in diffeomorphic demons algorithm with the PMI to make it appropriate for multimodal image registration. Eight patients with esophageal cancer(s) were enrolled in this IRB-approved study. Whole-body PET and CT images were acquired from a combined 18F-FDG PET/CT scanner for each patient. The modified Hausdorff distance (d(MH)) was used to evaluate the registration accuracy of the two algorithms. Of all patients, the mean values and standard deviations (SDs) of d(MH) were 6.65 (± 1.90) voxels and 6.01 (± 1.90) after the GMI-based demons and the PMI diffeomorphic-based demons registration algorithms respectively. Preliminary results on oncological patients showed that the respiratory motion and organ peristalsis in PET/CT esophageal images could not be neglected, although a combined 18F-FDG PET/CT scanner was used for image acquisition. The PMI diffeomorphic-based demons

  20. Long-read sequencing of nascent RNA reveals coupling among RNA processing events.

    PubMed

    Herzel, Lydia; Straube, Korinna; Neugebauer, Karla M

    2018-06-14

    Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates. Here, we overcome this obstacle through long-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe Most multi-intron transcripts were fully spliced, consistent with rapid cotranscriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced, suggesting that splicing of any given intron is dependent on the splicing status of other introns in the transcript. Supporting this, mild inhibition of splicing by a temperature-sensitive mutation in prp2 , the homolog of vertebrate U2AF65, increased the frequency of fully unspliced transcripts. Importantly, fully unspliced transcripts displayed transcriptional read-through at the polyA site and were degraded cotranscriptionally by the nuclear exosome. Finally, we show that cellular mRNA levels were reduced in genes with a high number of unspliced nascent transcripts during caffeine treatment, showing regulatory significance of cotranscriptional splicing. Therefore, overall splicing of individual nascent transcripts, 3' end formation, and mRNA half-life depend on the splicing status of neighboring introns, suggesting crosstalk among spliceosomes and the polyA cleavage machinery during transcription elongation. © 2018 Herzel et al.; Published by Cold Spring Harbor Laboratory Press.

  1. Kinematically aligned TKA can align knee joint line to horizontal.

    PubMed

    Ji, Hyung-Min; Han, Jun; Jin, Dong San; Seo, Hyunseok; Won, Ye-Yeon

    2016-08-01

    The joint line of the native knee is horizontal to the floor and perpendicular to the vertical weight-bearing axis of the patient in a bipedal stance. The purposes of this study were as follows: (1) to find out the distribution of the native joint line in a population of normal patients with normal knees; (2) to compare the native joint line orientation between patients receiving conventional mechanically aligned total knee arthroplasty (TKA), navigated mechanically aligned TKA, and kinematically aligned TKA; and (3) to determine which of the three TKA methods aligns the postoperative knee joint perpendicular to the weight-bearing axis of the limb in bipedal stance. To determine the joint line orientation of a native knee, 50 full-length standing hip-to-ankle digital radiographs were obtained in 50 young, healthy individuals. The angle between knee joint line and the line parallel to the floor was measured and defined as joint line orientation angle (JLOA). JLOA was also measured prior to and after conventional mechanically aligned TKA (65 knees), mechanically aligned TKA using imageless navigation (65 knees), and kinematically aligned TKA (65 knees). The proportion of the knees similar to the native joint line was calculated for each group. The mean JLOA in healthy individuals was parallel to the floor (0.2° ± 1.1°). The pre-operative JLOA of all treatment groups slanted down to the lateral side. Postoperative JLOA slanted down to the lateral side in conventional mechanically aligned TKA (-3.3° ± 2.2°) and in navigation mechanically aligned TKA (-2.6° ± 1.8°), while it was horizontal to the floor in kinematically aligned TKA (0.6° ± 1.7°). Only 6.9 % of the conventional mechanically aligned TKA and 16.9 % of the navigation mechanically aligned TKA were within one SD of the mean JLOA of the native knee, while the proportion was significantly higher (50.8 %) in kinematically aligned TKA. The portion was statistically greater in mechanically

  2. Foreign Language Reading and Spelling in Gifted Students with Dyslexia in Secondary Education

    ERIC Educational Resources Information Center

    van Viersen, Sietske; de Bree, Elise H.; Kalee, Lilian; Kroesbergen, Evelyn H.; de Jong, Peter F.

    2017-01-01

    A few studies suggest that gifted children with dyslexia have better literacy skills than averagely intelligent children with dyslexia. This finding aligns with the hypothesis that giftedness-related factors provide compensation for poor reading. The present study investigated whether, as in the native language (NL), the level of foreign language…

  3. 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.

  4. Studying long 16S rDNA sequences with ultrafast-metagenomic sequence classification using exact alignments (Kraken).

    PubMed

    Valenzuela-González, Fabiola; Martínez-Porchas, Marcel; Villalpando-Canchola, Enrique; Vargas-Albores, Francisco

    2016-03-01

    Ultrafast-metagenomic sequence classification using exact alignments (Kraken) is a novel approach to classify 16S rDNA sequences. The classifier is based on mapping short sequences to the lowest ancestor and performing alignments to form subtrees with specific weights in each taxon node. This study aimed to evaluate the classification performance of Kraken with long 16S rDNA random environmental sequences produced by cloning and then Sanger sequenced. A total of 480 clones were isolated and expanded, and 264 of these clones formed contigs (1352 ± 153 bp). The same sequences were analyzed using the Ribosomal Database Project (RDP) classifier. Deeper classification performance was achieved by Kraken than by the RDP: 73% of the contigs were classified up to the species or variety levels, whereas 67% of these contigs were classified no further than the genus level by the RDP. The results also demonstrated that unassembled sequences analyzed by Kraken provide similar or inclusively deeper information. Moreover, sequences that did not form contigs, which are usually discarded by other programs, provided meaningful information when analyzed by Kraken. Finally, it appears that the assembly step for Sanger sequences can be eliminated when using Kraken. Kraken cumulates the information of both sequence senses, providing additional elements for the classification. In conclusion, the results demonstrate that Kraken is an excellent choice for use in the taxonomic assignment of sequences obtained by Sanger sequencing or based on third generation sequencing, of which the main goal is to generate larger sequences. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Self-Noise of the STS-2 and sensitivity of its computation to errors in alignment of sensors

    NASA Astrophysics Data System (ADS)

    Gerner, Andreas; Sleeman, Reinoud; Grasemann, Bernhard; Lenhardt, Wolfgang

    2016-04-01

    The assessment of a seismometer's self-noise is an important part of establishing its health, quality, and suitability. A spectral coherence technique proposed by Sleeman et al. (2006) using synchronously recorded data of triples of collocated and co-aligned seismometers has shown to be a very robust and reliable way to estimate the self-noise of modern broadband seismic sensors. It has been demonstrated in previous works that the resulting self-noise spectra, primarily in the frequency range of Earth's microseisms, are considerably affected by small errors in the alignment of sensors. Further, due to the sensitivity of the 3-channel correlation technique to misalignment, numerical rotation of the recorded traces prior to self-noise computation can be performed to find best possible alignment by searching for minimum self-noise values. In this study we focus on the sensitivity of the 3-channel correlation technique to misalignment, and investigate the possibility of complete removal of the microseism signal from self-noise estimates for the sensors' three components separately. Data from a long-term installation of four STS-2 sensors, specifically intended for self-noise studies, at the Conrad Observatory (Austria) in a collaboration between the KNMI (Netherlands) and the ZAMG (Austria) provides a reliable basis for an accurate sensitivity analysis and self-noise assessment. Our work resulted in undisturbed self-noise estimates for the vertical components, and our current focus is on improving alignment of horizontal axes, and verification of the manufacturer's specification regarding orthogonality of all three components. The tools and methods developed within this research can help to quickly establish consistent self-noise models, including estimates of orthogonality and alignment, which facilitates comparison of different models and provides us with a means to test quality and accuracy of a seismic sensor over its life span.

  6. 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…

  7. Global Alignment of Pairwise Protein Interaction Networks for Maximal Common Conserved Patterns

    DOE PAGES

    Tian, Wenhong; Samatova, Nagiza F.

    2013-01-01

    A number of tools for the alignment of protein-protein interaction (PPI) networks have laid the foundation for PPI network analysis. Most of alignment tools focus on finding conserved interaction regions across the PPI networks through either local or global mapping of similar sequences. Researchers are still trying to improve the speed, scalability, and accuracy of network alignment. In view of this, we introduce a connected-components based fast algorithm, HopeMap, for network alignment. Observing that the size of true orthologs across species is small comparing to the total number of proteins in all species, we take a different approach based onmore » a precompiled list of homologs identified by KO terms. Applying this approach to S. cerevisiae (yeast) and D. melanogaster (fly), E. coli K12 and S. typhimurium , E. coli K12 and C. crescenttus , we analyze all clusters identified in the alignment. The results are evaluated through up-to-date known gene annotations, gene ontology (GO), and KEGG ortholog groups (KO). Comparing to existing tools, our approach is fast with linear computational cost, highly accurate in terms of KO and GO terms specificity and sensitivity, and can be extended to multiple alignments easily.« less

  8. 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.

  9. How To Read Faster. Power of the Printed Word.

    ERIC Educational Resources Information Center

    Cosby, Bill

    Three practical ways to get the meaning from printed words quickly and efficiently are: (1) previewing; (2) skimming; and (3) clustering. Previewing and skimming are ways of getting through a lot of reading material without reading every word. Previewing is especially helpful for heavy reading like long articles, business reports, and nonfiction…

  10. Interruptions disrupt reading comprehension.

    PubMed

    Foroughi, Cyrus K; Werner, Nicole E; Barragán, Daniela; Boehm-Davis, Deborah A

    2015-06-01

    Previous research suggests that being interrupted while reading a text does not disrupt the later recognition or recall of information from that text. This research is used as support for Ericsson and Kintsch's (1995) long-term working memory (LT-WM) theory, which posits that disruptions while reading (e.g., interruptions) do not impair subsequent text comprehension. However, to fully comprehend a text, individuals may need to do more than recognize or recall information that has been presented in the text at a later time. Reading comprehension often requires individuals to connect and synthesize information across a text (e.g., successfully identifying complex topics such as themes and tones) and not just make a familiarity-based decision (i.e., recognition). The goal for this study was to determine whether interruptions while reading disrupt reading comprehension when the questions assessing comprehension require participants to connect and synthesize information across the passage. In Experiment 1, interruptions disrupted reading comprehension. In Experiment 2, interruptions disrupted reading comprehension but not recognition of information from the text. In Experiment 3, the addition of a 15-s time-out prior to the interruption successfully removed these negative effects. These data suggest that the time it takes to process the information needed to successfully comprehend text when reading is greater than that required for recognition. Any interference (e.g., an interruption) that occurs during the comprehension process may disrupt reading comprehension. This evidence supports the need for transient activation of information in working memory for successful text comprehension and does not support LT-WM theory. (c) 2015 APA, all rights reserved).

  11. A Python object-oriented framework for the CMS alignment and calibration data

    NASA Astrophysics Data System (ADS)

    Dawes, Joshua H.; CMS Collaboration

    2017-10-01

    The Alignment, Calibrations and Databases group at the CMS Experiment delivers Alignment and Calibration Conditions Data to a large set of workflows which process recorded event data and produce simulated events. The current infrastructure for releasing and consuming Conditions Data was designed in the two years of the first LHC long shutdown to respond to use cases from the preceding data-taking period. During the second run of the LHC, new use cases were defined. For the consumption of Conditions Metadata, no common interface existed for the detector experts to use in Python-based custom scripts, resulting in many different querying and transaction management patterns. A new framework has been built to address such use cases: a simple object-oriented tool that detector experts can use to read and write Conditions Metadata when using Oracle and SQLite databases, that provides a homogeneous method of querying across all services. The tool provides mechanisms for segmenting large sets of conditions while releasing them to the production database, allows for uniform error reporting to the client-side from the server-side and optimizes the data transfer to the server. The architecture of the new service has been developed exploiting many of the features made available by the metadata consumption framework to implement the required improvements. This paper presents the details of the design and implementation of the new metadata consumption and data upload framework, as well as analyses of the new upload service’s performance as the server-side state varies.

  12. 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…

  13. Modeling of Field-Aligned Guided Echoes in the Plasmasphere

    NASA Technical Reports Server (NTRS)

    Fung, Shing F.; Green, James L.

    2004-01-01

    The conditions under which high frequency (f>>f(sub uh)) long-range extraordinary-mode discrete field-aligned echoes observed by the Radio Plasma Imager (RPI) on board the Imager for Magnetopause-to-Aurora Global Exploration (IMAGE) satellite in the plasmasphere are investigated by ray tracing modeling. Field-aligned discrete echoes are most commonly observed by RPI in the plasmasphere although they are also observed over the polar cap region. The plasmasphere field-aligned echoes appearing as multiple echo traces at different virtual ranges are attributed to signals reflected successively between conjugate hemispheres that propagate along or nearly along closed geomagnetic field lines. The ray tracing simulations show that field-aligned ducts with as little as 1% density perturbations (depletions) and less than 10 wavelengths wide can guide nearly field-aligned propagating high frequency X mode waves. Effective guidance of wave at a given frequency and wave normal angle (Psi) depends on the cross-field density scale of the duct, such that ducts with stronger density depletions need to be wider in order to maintain the same gradient of refractive index across the magnetic field. While signal guidance by field aligned density gradient without ducting is possible only over the polar region, conjugate field-aligned echoes that have traversed through the equatorial region are most likely guided by ducting.

  14. Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment

    PubMed Central

    Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L.; Yao, Xuebiao

    2015-01-01

    The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C–MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression. PMID:26240331

  15. Dynamic localization of Mps1 kinase to kinetochores is essential for accurate spindle microtubule attachment.

    PubMed

    Dou, Zhen; Liu, Xing; Wang, Wenwen; Zhu, Tongge; Wang, Xinghui; Xu, Leilei; Abrieu, Ariane; Fu, Chuanhai; Hill, Donald L; Yao, Xuebiao

    2015-08-18

    The spindle assembly checkpoint (SAC) is a conserved signaling pathway that monitors faithful chromosome segregation during mitosis. As a core component of SAC, the evolutionarily conserved kinase monopolar spindle 1 (Mps1) has been implicated in regulating chromosome alignment, but the underlying molecular mechanism remains unclear. Our molecular delineation of Mps1 activity in SAC led to discovery of a previously unidentified structural determinant underlying Mps1 function at the kinetochores. Here, we show that Mps1 contains an internal region for kinetochore localization (IRK) adjacent to the tetratricopeptide repeat domain. Importantly, the IRK region determines the kinetochore localization of inactive Mps1, and an accumulation of inactive Mps1 perturbs accurate chromosome alignment and mitotic progression. Mechanistically, the IRK region binds to the nuclear division cycle 80 complex (Ndc80C), and accumulation of inactive Mps1 at the kinetochores prevents a dynamic interaction between Ndc80C and spindle microtubules (MTs), resulting in an aberrant kinetochore attachment. Thus, our results present a previously undefined mechanism by which Mps1 functions in chromosome alignment by orchestrating Ndc80C-MT interactions and highlight the importance of the precise spatiotemporal regulation of Mps1 kinase activity and kinetochore localization in accurate mitotic progression.

  16. Ultraaccurate genome sequencing and haplotyping of single human cells.

    PubMed

    Chu, Wai Keung; Edge, Peter; Lee, Ho Suk; Bansal, Vikas; Bafna, Vineet; Huang, Xiaohua; Zhang, Kun

    2017-11-21

    Accurate detection of variants and long-range haplotypes in genomes of single human cells remains very challenging. Common approaches require extensive in vitro amplification of genomes of individual cells using DNA polymerases and high-throughput short-read DNA sequencing. These approaches have two notable drawbacks. First, polymerase replication errors could generate tens of thousands of false-positive calls per genome. Second, relatively short sequence reads contain little to no haplotype information. Here we report a method, which is dubbed SISSOR (single-stranded sequencing using microfluidic reactors), for accurate single-cell genome sequencing and haplotyping. A microfluidic processor is used to separate the Watson and Crick strands of the double-stranded chromosomal DNA in a single cell and to randomly partition megabase-size DNA strands into multiple nanoliter compartments for amplification and construction of barcoded libraries for sequencing. The separation and partitioning of large single-stranded DNA fragments of the homologous chromosome pairs allows for the independent sequencing of each of the complementary and homologous strands. This enables the assembly of long haplotypes and reduction of sequence errors by using the redundant sequence information and haplotype-based error removal. We demonstrated the ability to sequence single-cell genomes with error rates as low as 10 -8 and average 500-kb-long DNA fragments that can be assembled into haplotype contigs with N50 greater than 7 Mb. The performance could be further improved with more uniform amplification and more accurate sequence alignment. The ability to obtain accurate genome sequences and haplotype information from single cells will enable applications of genome sequencing for diverse clinical needs. Copyright © 2017 the Author(s). Published by PNAS.

  17. Cost-Effectiveness of Double Reading versus Single Reading of Mammograms in a Breast Cancer Screening Programme

    PubMed Central

    Posso, Margarita; Carles, Misericòrdia; Rué, Montserrat; Puig, Teresa; Bonfill, Xavier

    2016-01-01

    Objectives The usual practice in breast cancer screening programmes for mammogram interpretation is to perform double reading. However, little is known about its cost-effectiveness in the context of digital mammography. Our purpose was to evaluate the cost-effectiveness of double reading versus single reading of digital mammograms in a population-based breast cancer screening programme. Methods Data from 28,636 screened women was used to establish a decision-tree model and to compare three strategies: 1) double reading; 2) double reading for women in their first participation and single reading for women in their subsequent participations; and 3) single reading. We calculated the incremental cost-effectiveness ratio (ICER), which was defined as the expected cost per one additionally detected cancer. We performed a deterministic sensitivity analysis to test the robustness of the ICER. Results The detection rate of double reading (5.17‰) was similar to that of single reading (4.78‰; P = .768). The mean cost of each detected cancer was €8,912 for double reading and €8,287 for single reading. The ICER of double reading versus single reading was €16,684. The sensitivity analysis showed variations in the ICER according to the sensitivity of reading strategies. The strategy that combines double reading in first participation with single reading in subsequent participations was ruled out due to extended dominance. Conclusions From our results, double reading appears not to be a cost-effective strategy in the context of digital mammography. Double reading would eventually be challenged in screening programmes, as single reading might entail important net savings without significantly changing the cancer detection rate. These results are not conclusive and should be confirmed in prospective studies that investigate long-term outcomes like quality adjusted life years (QALYs). PMID:27459663

  18. Integrated Flexible Electronic Devices Based on Passive Alignment for Physiological Measurement

    PubMed Central

    Ryu, Jin Hwa; Byun, Sangwon; Baek, In-Bok; Lee, Bong Kuk; Jang, Won Ick; Jang, Eun-Hye; Kim, Ah-Yung; Yu, Han Yung

    2017-01-01

    This study proposes a simple method of fabricating flexible electronic devices using a metal template for passive alignment between chip components and an interconnect layer, which enabled efficient alignment with high accuracy. An electrocardiogram (ECG) sensor was fabricated using 20 µm thick polyimide (PI) film as a flexible substrate to demonstrate the feasibility of the proposed method. The interconnect layer was fabricated by a two-step photolithography process and evaporation. After applying solder paste, the metal template was placed on top of the interconnect layer. The metal template had rectangular holes at the same position as the chip components on the interconnect layer. Rectangular hole sizes were designed to account for alignment tolerance of the chips. Passive alignment was performed by simply inserting the components in the holes of the template, which resulted in accurate alignment with positional tolerance of less than 10 µm based on the structural design, suggesting that our method can efficiently perform chip mounting with precision. Furthermore, a fabricated flexible ECG sensor was easily attachable to the curved skin surface and able to measure ECG signals from a human subject. These results suggest that the proposed method can be used to fabricate epidermal sensors, which are mounted on the skin to measure various physiological signals. PMID:28420219

  19. HAL: a hierarchical format for storing and analyzing multiple genome alignments.

    PubMed

    Hickey, Glenn; Paten, Benedict; Earl, Dent; Zerbino, Daniel; Haussler, David

    2013-05-15

    Large multiple genome alignments and inferred ancestral genomes are ideal resources for comparative studies of molecular evolution, and advances in sequencing and computing technology are making them increasingly obtainable. These structures can provide a rich understanding of the genetic relationships between all subsets of species they contain. Current formats for storing genomic alignments, such as XMFA and MAF, are all indexed or ordered using a single reference genome, however, which limits the information that can be queried with respect to other species and clades. This loss of information grows with the number of species under comparison, as well as their phylogenetic distance. We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover). All documentation and source code for the HAL API and tools are freely available at http://github.com/glennhickey/hal. hickey@soe.ucsc.edu or haussler@soe.ucsc.edu Supplementary data are available at Bioinformatics online.

  20. Model-based estimation and control for off-axis parabolic mirror alignment

    NASA Astrophysics Data System (ADS)

    Fang, Joyce; Savransky, Dmitry

    2018-02-01

    This paper propose an model-based estimation and control method for an off-axis parabolic mirror (OAP) alignment. Current studies in automated optical alignment systems typically require additional wavefront sensors. We propose a self-aligning method using only focal plane images captured by the existing camera. Image processing methods and Karhunen-Loève (K-L) decomposition are used to extract measurements for the observer in closed-loop control system. Our system has linear dynamic in state transition, and a nonlinear mapping from the state to the measurement. An iterative extended Kalman filter (IEKF) is shown to accurately predict the unknown states, and nonlinear observability is discussed. Linear-quadratic regulator (LQR) is applied to correct the misalignments. The method is validated experimentally on the optical bench with a commercial OAP. We conduct 100 tests in the experiment to demonstrate the consistency in between runs.

  1. Long-Term Effects of Strategic Reading Instruction in the Intermediate Elementary Grades

    ERIC Educational Resources Information Center

    Droop, Mienke; van Elsäcker, Willy; Voeten, Marinus J. M.; Verhoeven, Ludo

    2016-01-01

    The purpose of the present study was to examine the effects of a program that offered sustained strategic reading instruction on reading abilities of third and fourth graders. The study was conducted among 1,469 children from 40 schools in the Netherlands. Schools were randomly assigned to either the experimental or control group. Multilevel…

  2. An Exploratory Study of Reading Comprehension in College Students After Acquired Brain Injury.

    PubMed

    Sohlberg, McKay Moore; Griffiths, Gina G; Fickas, Stephen

    2015-08-01

    This exploratory study builds on the small body of existing research investigating reading comprehension deficits in college students with acquired brain injury (ABI). Twenty-four community college students with ABI completed a battery of questionnaires and standardized tests to characterize self-perceptions of academic reading ability, performance on a standardized reading comprehension measure, and a variety of cognitive functions of this population. Half of the participants in the sample reported traumatic brain injury (n = 12) and half reported nontraumatic ABI (n = 12). College students with both traumatic and nontraumatic ABI cite problems with reading comprehension and academic performance postinjury. Mean performance on a standardized reading measure, the Nelson-Denny Reading Test (Brown, Fischo, & Hanna, 1993), was low to below average and was significantly correlated with performance on the Speed and Capacity of Language Processing Test (Baddeley, Emslie, & Nimmo-Smith, 1992). Injury status of traumatic versus nontraumatic ABI did not differentiate results. Regression analysis showed that measures of verbal attention and suppression obtained from the California Verbal Language Test-II (Delis, Kramer, Kaplan, & Ober, 2000) predicted total scores on the Nelson-Denny Reading Test. College students with ABI are vulnerable to reading comprehension problems. Results align with other research suggesting that verbal attention and suppression problems may be contributing factors.

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

    PubMed

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

    2017-07-01

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

  4. High School Students and "Read Across America"?

    ERIC Educational Resources Information Center

    Fisher, Julieta Dias; Hill, Ann

    2004-01-01

    Although more commonly associated with elementary school rather than high school students, "Read Across America" celebrations can cater to any age group and generate enthusiasm for reading long after the festivities have ended. In this article, the authors, library media specialists at Washington Township High School in Sewell, New Jersey, share …

  5. 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

  6. 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.

  7. Accurate Structural Correlations from Maximum Likelihood Superpositions

    PubMed Central

    Theobald, Douglas L; Wuttke, Deborah S

    2008-01-01

    The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology. PMID:18282091

  8. Integrating Fiction and Nonfiction Reading into the Business Classroom

    ERIC Educational Resources Information Center

    Fiene, Judy; Pedersen, Erin

    2013-01-01

    One goal of high school teachers is to help students appreciate that reading does not end when they leave the classroom. When students find reading meaningful, they are more likely to see themselves as readers and choose to read long after they leave the classroom setting (Hinchman, Alvermann, Boyd, Brozo, & Vacca, 2003-2004; Wilhelm, 2001).…

  9. The need for accurate long-term measurements of water vapor in the upper troposphere and lower stratosphere with global coverage.

    PubMed

    Müller, Rolf; Kunz, Anne; Hurst, Dale F; Rolf, Christian; Krämer, Martina; Riese, Martin

    2016-02-01

    Water vapor is the most important greenhouse gas in the atmosphere although changes in carbon dioxide constitute the "control knob" for surface temperatures. While the latter fact is well recognized, resulting in extensive space-borne and ground-based measurement programs for carbon dioxide as detailed in the studies by Keeling et al. (1996), Kuze et al. (2009), and Liu et al. (2014), the need for an accurate characterization of the long-term changes in upper tropospheric and lower stratospheric (UTLS) water vapor has not yet resulted in sufficiently extensive long-term international measurement programs (although first steps have been taken). Here, we argue for the implementation of a long-term balloon-borne measurement program for UTLS water vapor covering the entire globe that will likely have to be sustained for hundreds of years.

  10. Long-Term Outcome of the Early Identification and Intervention of Reading Disabilities

    ERIC Educational Resources Information Center

    Partanen, Marita; Siegel, Linda S.

    2014-01-01

    This study examined the longitudinal effects of an early literacy intervention in Kindergarten. A group of children completed reading and cognitive measures between Kindergarten (5-6 years old) and Grade 7 (12-13 years old). Our results showed that 22% of children were identified as at-risk for reading deficits in Kindergarten, but only 6% of…

  11. The Impact of Intensive Reading Intervention on Level of Attention in Middle School Students.

    PubMed

    Roberts, Greg; Rane, Shruti; Fall, Anna-Mária; Denton, Carolyn A; Fletcher, Jack M; Vaughn, Sharon

    2015-01-01

    The purpose of the study was to estimate the impact of reading intervention on ratings of student attention over time. We used extant data from a longitudinal randomized study of a response-based reading intervention to fit a multiple-indicator, multilevel growth model. The sample at randomization was 54% male, 18% limited English proficient, 85% eligible for free or reduced-price lunch, 58% African American, and 32% Hispanic. Reading ability was measured by using the Woodcock-Johnson III Tests of Achievement. Attention was measured by using the Strengths and Weaknesses of ADHD Symptoms and Normal Behavior Scale. Findings indicate that intensive, response-based reading intervention over 3 years improved reading achievement and behavioral attention in middle school struggling readers, with treatment directly affecting reading, which in turn influenced attention. In the business-as-usual condition, there was no relation between improved reading and attention. The results are consistent with a correlated liabilities model of comorbidity. The results do not align with the inattention-as-cause hypothesis, which predicts that reading intervention should not affect attention. The findings do not support, but do not necessarily preclude, the phenocopy hypothesis. The results are especially pertinent for older students who may be inattentive partly because of years of struggling with reading.

  12. The Impact of Intensive Reading Intervention on Level of Attention in Middle School Students

    PubMed Central

    Roberts, Greg; Rane, Shruti; Fall, Anna-Mária; Denton, Carolyn A.; Fletcher, Jack M.; Vaughn, Sharon

    2014-01-01

    Objective The purpose of the study was to estimate the impact of reading intervention on ratings of student attention over time. Method We used extant data from a longitudinal randomized study of a response-based reading intervention to fit a multiple-indicator, multilevel growth model. The sample at randomization was 54% male, 18% limited English proficient, 85% eligible for free or reduced-price lunch, 58% African American, and 32% Hispanic. Reading ability was measured by using the Woodcock-Johnson III Tests of Achievement. Attention was measured by using the Strengths and Weaknesses of ADHD Symptoms and Normal Behavior Scale. Results Findings indicate that intensive, response-based reading intervention over 3 years improved reading achievement and behavioral attention in middle school struggling readers, with treatment directly affecting reading, which in turn influenced attention. In the business-as-usual condition, there was no relation between improved reading and attention. Conclusions The results are consistent with a correlated liabilities model of comorbidity. The results do not align with the inattention-as-cause hypothesis, which predicts that reading intervention should not affect attention. The findings do not support, but do not necessarily preclude, the phenocopy hypothesis. The results are especially pertinent for older students who may be inattentive partly because of years of struggling with reading. PMID:24885289

  13. How tibiofemoral alignment and contact locations affect predictions of medial and lateral tibiofemoral contact forces.

    PubMed

    Lerner, Zachary F; DeMers, Matthew S; Delp, Scott L; Browning, Raymond C

    2015-02-26

    Understanding degeneration of biological and prosthetic knee joints requires knowledge of the in-vivo loading environment during activities of daily living. Musculoskeletal models can estimate medial/lateral tibiofemoral compartment contact forces, yet anthropometric differences between individuals make accurate predictions challenging. We developed a full-body OpenSim musculoskeletal model with a knee joint that incorporates subject-specific tibiofemoral alignment (i.e. knee varus-valgus) and geometry (i.e. contact locations). We tested the accuracy of our model and determined the importance of these subject-specific parameters by comparing estimated to measured medial and lateral contact forces during walking in an individual with an instrumented knee replacement and post-operative genu valgum (6°). The errors in the predictions of the first peak medial and lateral contact force were 12.4% and 11.9%, respectively, for a model with subject-specific tibiofemoral alignment and contact locations determined through radiographic analysis, vs. 63.1% and 42.0%, respectively, for a model with generic parameters. We found that each degree of tibiofemoral alignment deviation altered the first peak medial compartment contact force by 51N (r(2)=0.99), while each millimeter of medial-lateral translation of the compartment contact point locations altered the first peak medial compartment contact force by 41N (r(2)=0.99). The model, available at www.simtk.org/home/med-lat-knee/, enables the specification of subject-specific joint alignment and compartment contact locations to more accurately estimate medial and lateral tibiofemoral contact forces in individuals with non-neutral alignment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. How Tibiofemoral Alignment and Contact Locations Affect Predictions of Medial and Lateral Tibiofemoral Contact Forces

    PubMed Central

    Lerner, Zachary F.; DeMers, Matthew S.; Delp, Scott L.; Browning, Raymond C.

    2015-01-01

    Understanding degeneration of biological and prosthetic knee joints requires knowledge of the in-vivo loading environment during activities of daily living. Musculoskeletal models can estimate medial/lateral tibiofemoral compartment contact forces, yet anthropometric differences between individuals make accurate predictions challenging. We developed a full-body OpenSim musculoskeletal model with a knee joint that incorporates subject-specific tibiofemoral alignment (i.e. knee varus-valgus) and geometry (i.e. contact locations). We tested the accuracy of our model and determined the importance of these subject-specific parameters by comparing estimated to measured medial and lateral contact forces during walking in an individual with an instrumented knee replacement and post-operative genu valgum (6°). The errors in the predictions of the first peak medial and lateral contact force were 12.4% and 11.9%, respectively, for a model with subject-specific tibiofemoral alignment and contact locations determined via radiographic analysis, vs. 63.1% and 42.0%, respectively, for a model with generic parameters. We found that each degree of tibiofemoral alignment deviation altered the first peak medial compartment contact force by 51N (r2=0.99), while each millimeter of medial-lateral translation of the compartment contact point locations altered the first peak medial compartment contact force by 41N (r2=0.99). The model, available at www.simtk.org/home/med-lat-knee/, enables the specification of subject-specific joint alignment and compartment contact locations to more accurately estimate medial and lateral tibiofemoral contact forces in individuals with non-neutral alignment. PMID:25595425

  15. 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

  16. (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

  17. (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

  18. 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…

  19. QuickProbs—A Fast Multiple Sequence Alignment Algorithm Designed for Graphics Processors

    PubMed Central

    Gudyś, Adam; Deorowicz, Sebastian

    2014-01-01

    Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain searching, phylogeny, etc. MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational time. In the paper we present QuickProbs, the variant of MSAProbs customised for graphics processors. We selected the two most time consuming stages of MSAProbs to be redesigned for GPU execution: the posterior matrices calculation and the consistency transformation. Experiments on three popular benchmarks (BAliBASE, PREFAB, OXBench-X) on quad-core PC equipped with high-end graphics card show QuickProbs to be 5.7 to 9.7 times faster than original CPU-parallel MSAProbs. Additional tests performed on several protein families from Pfam database give overall speed-up of 6.7. Compared to other algorithms like MAFFT, MUSCLE, or ClustalW, QuickProbs proved to be much more accurate at similar speed. Additionally we introduce a tuned variant of QuickProbs which is significantly more accurate on sets of distantly related sequences than MSAProbs without exceeding its computation time. The GPU part of QuickProbs was implemented in OpenCL, thus the package is suitable for graphics processors produced by all major vendors. PMID:24586435

  20. Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

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

    Mohammadi, Shahin; Gleich, David F.; Kolda, Tamara G.

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangularmore » AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.« less